Input buildinfo: https://buildinfos.debian.net/buildinfo-pool/f/falcon/falcon_1.8.8-1_amd64.buildinfo Use metasnap for getting required timestamps New buildinfo file: /tmp/falcon-1.8.8-12256qcfx/falcon_1.8.8-1_amd64.buildinfo Get source package info: falcon=1.8.8-1 Source URL: http://snapshot.notset.fr/mr/package/falcon/1.8.8-1/srcfiles?fileinfo=1 env -i PATH=/usr/sbin:/usr/bin:/sbin:/bin TMPDIR=/tmp mmdebstrap --arch=amd64 --include=autoconf=2.69-11 automake=1:1.15.1-3 autopoint=0.19.8.1-4 autotools-dev=20161112.1+nmu1 base-files=10 base-passwd=3.5.44 bash=4.4-5 binutils=2.29.1-12 binutils-common=2.29.1-12 binutils-x86-64-linux-gnu=2.29.1-12 bsdmainutils=9.0.14 bsdutils=1:2.30.2-0.1 build-essential=12.4 bzip2=1.0.6-8.1 coreutils=8.28-1 cpp=4:7.2.0-1d1 cpp-7=7.2.0-17 dash=0.5.8-2.5 debconf=1.5.65 debhelper=10.10.9 debianutils=4.8.3 dh-autoreconf=15 dh-python=2.20170125 dh-strip-nondeterminism=0.040-1 diffutils=1:3.6-1 dpkg=1.19.0.4 dpkg-dev=1.19.0.4 e2fslibs=1.43.7-1 e2fsprogs=1.43.7-1 fdisk=2.30.2-0.1 file=1:5.32-1 findutils=4.6.0+git+20170828-2 g++=4:7.2.0-1d1 g++-7=7.2.0-17 gcc=4:7.2.0-1d1 gcc-7=7.2.0-17 gcc-7-base=7.2.0-17 gettext=0.19.8.1-4 gettext-base=0.19.8.1-4 grep=3.1-2 groff-base=1.22.3-9 gzip=1.6-5+b1 hostname=3.18+b1 init-system-helpers=1.51 intltool-debian=0.35.0+20060710.4 libacl1=2.2.52-3+b1 libarchive-zip-perl=1.59-1 libasan4=7.2.0-17 libatomic1=7.2.0-17 libattr1=1:2.4.47-2+b2 libaudit-common=1:2.8.1-2 libaudit1=1:2.8.1-2 libbinutils=2.29.1-12 libblkid1=2.30.2-0.1 libbsd0=0.8.6-3 libbz2-1.0=1.0.6-8.1 libc-bin=2.25-4 libc-dev-bin=2.25-4 libc6=2.25-4 libc6-dev=2.25-4 libcap-ng0=0.7.7-3.1+b1 libcc1-0=7.2.0-17 libcilkrts5=7.2.0-17 libcomerr2=1.43.7-1 libcroco3=0.6.12-1 libdb5.3=5.3.28-13.1+b1 libdebconfclient0=0.236 libdpkg-perl=1.19.0.4 libexpat1=2.2.3-2 libexpat1-dev=2.2.3-2 libfdisk1=2.30.2-0.1 libffi6=3.2.1-7 libfile-stripnondeterminism-perl=0.040-1 libgcc-7-dev=7.2.0-17 libgcc1=1:7.2.0-17 libgcrypt20=1.8.1-4 libgdbm3=1.8.3-14 libglib2.0-0=2.54.2-1 libgmp10=2:6.1.2+dfsg-1.1 libgomp1=7.2.0-17 libgpg-error0=1.27-5 libicu57=57.1-8 libisl15=0.18-1 libitm1=7.2.0-17 liblsan0=7.2.0-17 liblz4-1=0.0~r131-2+b1 liblzma5=5.2.2-1.3 libmagic-mgc=1:5.32-1 libmagic1=1:5.32-1 libmount1=2.30.2-0.1 libmpc3=1.0.3-2 libmpdec2=2.4.2-1 libmpfr4=3.1.6-1 libmpx2=7.2.0-17 libncurses5=6.0+20171125-1 libncursesw5=6.0+20171125-1 libpam-modules=1.1.8-3.6 libpam-modules-bin=1.1.8-3.6 libpam-runtime=1.1.8-3.6 libpam0g=1.1.8-3.6 libpcre3=2:8.39-8 libperl5.26=5.26.1-3 libpipeline1=1.5.0-1 libpopt0=1.16-10+b2 libpython-all-dev=2.7.14-4 libpython-dev=2.7.14-4 libpython-stdlib=2.7.14-4 libpython2.7=2.7.14-4 libpython2.7-dev=2.7.14-4 libpython2.7-minimal=2.7.14-4 libpython2.7-stdlib=2.7.14-4 libpython3-stdlib=3.6.4~rc1-2 libpython3.6-minimal=3.6.4~rc1-2 libpython3.6-stdlib=3.6.4~rc1-2 libquadmath0=7.2.0-17 libreadline7=7.0-3 libselinux1=2.7-2 libsigsegv2=2.11-1 libsmartcols1=2.30.2-0.1 libsqlite3-0=3.21.0-1 libss2=1.43.7-1 libssl1.1=1.1.0g-2 libstdc++-7-dev=7.2.0-17 libstdc++6=7.2.0-17 libsystemd0=235-3 libtimedate-perl=2.3000-2 libtinfo5=6.0+20171125-1 libtool=2.4.6-2 libtsan0=7.2.0-17 libubsan0=7.2.0-17 libudev1=235-3 libunistring2=0.9.8-1 libuuid1=2.30.2-0.1 libxml2=2.9.4+dfsg1-5.2 linux-libc-dev=4.14.2-1 login=1:4.5-1 lsb-base=9.20170808 m4=1.4.18-1 make=4.1-9.1 man-db=2.7.6.1-4 mawk=1.3.3-17+b3 mime-support=3.60 ncurses-base=6.0+20171125-1 ncurses-bin=6.0+20171125-1 patch=2.7.5-1+b2 perl=5.26.1-3 perl-base=5.26.1-3 perl-modules-5.26=5.26.1-3 po-debconf=1.0.20 python=2.7.14-4 python-all=2.7.14-4 python-all-dev=2.7.14-4 python-decorator=4.1.2-1 python-dev=2.7.14-4 python-minimal=2.7.14-4 python-networkx=1.11-2 python-nose=1.3.7-3 python-pkg-resources=38.2.4-2 python-py=1.4.34-3 python-pytest=3.2.1-2 python-setuptools=38.2.4-2 python2.7=2.7.14-4 python2.7-dev=2.7.14-4 python2.7-minimal=2.7.14-4 python3=3.6.4~rc1-2 python3-distutils=3.6.4~rc1-6 python3-minimal=3.6.4~rc1-2 python3.6=3.6.4~rc1-2 python3.6-2to3=3.6.4~rc1-2 python3.6-minimal=3.6.4~rc1-2 readline-common=7.0-3 rsync=3.1.2-2.1 sed=4.4-1 sysvinit-utils=2.88dsf-59.10 tar=1.29b-2 util-linux=2.30.2-0.1 xz-utils=5.2.2-1.3 zlib1g=1:1.2.8.dfsg-5 --variant=apt --aptopt=Acquire::Check-Valid-Until "false" --aptopt=Acquire::http::Dl-Limit "1000"; --aptopt=Acquire::https::Dl-Limit "1000"; --aptopt=Acquire::Retries "5"; --aptopt=APT::Get::allow-downgrades "true"; --keyring=/usr/share/keyrings/ --essential-hook=chroot "$1" sh -c "apt-get --yes install fakeroot util-linux" --essential-hook=copy-in /usr/share/keyrings/debian-archive-bullseye-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-security-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-stable.gpg /usr/share/keyrings/debian-archive-buster-automatic.gpg /usr/share/keyrings/debian-archive-buster-security-automatic.gpg /usr/share/keyrings/debian-archive-buster-stable.gpg /usr/share/keyrings/debian-archive-keyring.gpg /usr/share/keyrings/debian-archive-removed-keys.gpg /usr/share/keyrings/debian-archive-stretch-automatic.gpg /usr/share/keyrings/debian-archive-stretch-security-automatic.gpg /usr/share/keyrings/debian-archive-stretch-stable.gpg /usr/share/keyrings/debian-ports-archive-keyring-removed.gpg /usr/share/keyrings/debian-ports-archive-keyring.gpg /usr/share/keyrings/debian-keyring.gpg /etc/apt/trusted.gpg.d/ --essential-hook=chroot "$1" sh -c "rm /etc/apt/sources.list && echo 'deb http://snapshot.notset.fr/archive/debian/20171221T033629Z/ buster main deb-src http://snapshot.notset.fr/archive/debian/20171221T033629Z/ buster main deb http://snapshot.notset.fr/archive/debian/20171216T092525Z/ unstable main' >> /etc/apt/sources.list && apt-get update" --customize-hook=chroot "$1" useradd --no-create-home -d /nonexistent -p "" builduser -s /bin/bash --customize-hook=chroot "$1" env sh -c "apt-get source --only-source -d falcon=1.8.8-1 && mkdir -p /build/falcon-LwwdoQ && dpkg-source --no-check -x /*.dsc /build/falcon-LwwdoQ/falcon-1.8.8 && chown -R builduser:builduser /build/falcon-LwwdoQ" --customize-hook=chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/falcon-LwwdoQ/falcon-1.8.8 && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="POSIX" SOURCE_DATE_EPOCH="1513411047" DEB_BUILD_OPTIONS=nocheck dpkg-buildpackage -uc -a amd64 --build=any" --customize-hook=sync-out /build/falcon-LwwdoQ /tmp/falcon-1.8.8-12256qcfx buster /dev/null deb http://snapshot.notset.fr/archive/debian/20171216T092525Z unstable main I: automatically chosen mode: root I: chroot architecture amd64 is equal to the host's architecture I: automatically chosen format: tar I: using /tmp/mmdebstrap.SAG5NvxJ_M as tempdir I: running apt-get update... I: downloading packages with apt... I: extracting archives... I: installing essential packages... I: running --essential-hook in shell: sh -c 'chroot "$1" sh -c "apt-get --yes install fakeroot util-linux"' exec /tmp/mmdebstrap.SAG5NvxJ_M Reading package lists... Building dependency tree... util-linux is already the newest version (2.30.2-0.1). The following NEW packages will be installed: fakeroot libfakeroot 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 132 kB of archives. After this operation, 373 kB of additional disk space will be used. Get:1 http://snapshot.notset.fr/archive/debian/20171216T092525Z unstable/main amd64 libfakeroot amd64 1.22-2 [45.9 kB] Get:2 http://snapshot.notset.fr/archive/debian/20171216T092525Z unstable/main amd64 fakeroot amd64 1.22-2 [85.7 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 132 kB in 0s (845 kB/s) Selecting previously unselected package libfakeroot:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 4409 files and directories currently installed.) Preparing to unpack .../libfakeroot_1.22-2_amd64.deb ... Unpacking libfakeroot:amd64 (1.22-2) ... Selecting previously unselected package fakeroot. Preparing to unpack .../fakeroot_1.22-2_amd64.deb ... Unpacking fakeroot (1.22-2) ... Processing triggers for libc-bin (2.25-4) ... Setting up libfakeroot:amd64 (1.22-2) ... Setting up fakeroot (1.22-2) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Processing triggers for libc-bin (2.25-4) ... I: running special hook: copy-in /usr/share/keyrings/debian-archive-bullseye-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-security-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-stable.gpg /usr/share/keyrings/debian-archive-buster-automatic.gpg /usr/share/keyrings/debian-archive-buster-security-automatic.gpg /usr/share/keyrings/debian-archive-buster-stable.gpg /usr/share/keyrings/debian-archive-keyring.gpg /usr/share/keyrings/debian-archive-removed-keys.gpg /usr/share/keyrings/debian-archive-stretch-automatic.gpg /usr/share/keyrings/debian-archive-stretch-security-automatic.gpg /usr/share/keyrings/debian-archive-stretch-stable.gpg /usr/share/keyrings/debian-ports-archive-keyring-removed.gpg /usr/share/keyrings/debian-ports-archive-keyring.gpg /usr/share/keyrings/debian-keyring.gpg /etc/apt/trusted.gpg.d/ I: running --essential-hook in shell: sh -c 'chroot "$1" sh -c "rm /etc/apt/sources.list && echo 'deb http://snapshot.notset.fr/archive/debian/20171221T033629Z/ buster main deb-src http://snapshot.notset.fr/archive/debian/20171221T033629Z/ buster main deb http://snapshot.notset.fr/archive/debian/20171216T092525Z/ unstable main' >> /etc/apt/sources.list && apt-get update"' exec /tmp/mmdebstrap.SAG5NvxJ_M Get:1 http://snapshot.notset.fr/archive/debian/20171221T033629Z buster InRelease [142 kB] Hit:2 http://snapshot.notset.fr/archive/debian/20171216T092525Z unstable InRelease Ign:3 http://snapshot.notset.fr/archive/debian/20171221T033629Z buster/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20171221T033629Z buster/main amd64 Packages Ign:3 http://snapshot.notset.fr/archive/debian/20171221T033629Z buster/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20171221T033629Z buster/main amd64 Packages Get:3 http://snapshot.notset.fr/archive/debian/20171221T033629Z buster/main Sources [9478 kB] Get:4 http://snapshot.notset.fr/archive/debian/20171221T033629Z buster/main amd64 Packages [9786 kB] Fetched 19.4 MB in 16s (1145 kB/s) Reading package lists... W: Problem unlinking the file auxfiles - pkgAcquire::Clean (21: Is a directory) I: installing remaining packages inside the chroot... I: running --customize-hook in shell: sh -c 'chroot "$1" useradd --no-create-home -d /nonexistent -p "" builduser -s /bin/bash' exec /tmp/mmdebstrap.SAG5NvxJ_M I: running --customize-hook in shell: sh -c 'chroot "$1" env sh -c "apt-get source --only-source -d falcon=1.8.8-1 && mkdir -p /build/falcon-LwwdoQ && dpkg-source --no-check -x /*.dsc /build/falcon-LwwdoQ/falcon-1.8.8 && chown -R builduser:builduser /build/falcon-LwwdoQ"' exec /tmp/mmdebstrap.SAG5NvxJ_M Reading package lists... NOTICE: 'falcon' packaging is maintained in the 'Git' version control system at: https://anonscm.debian.org/git/debian-med/falcon.git Please use: git clone https://anonscm.debian.org/git/debian-med/falcon.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 3705 kB of source archives. Get:1 http://snapshot.notset.fr/archive/debian/20171221T033629Z buster/main falcon 1.8.8-1 (dsc) [2266 B] Get:2 http://snapshot.notset.fr/archive/debian/20171221T033629Z buster/main falcon 1.8.8-1 (tar) [3695 kB] Get:3 http://snapshot.notset.fr/archive/debian/20171221T033629Z buster/main falcon 1.8.8-1 (diff) [8132 B] Fetched 3705 kB in 3s (1205 kB/s) Download complete and in download only mode W: Download is performed unsandboxed as root as file 'falcon_1.8.8-1.dsc' couldn't be accessed by user '_apt'. - pkgAcquire::Run (13: Permission denied) dpkg-source: info: extracting falcon in /build/falcon-LwwdoQ/falcon-1.8.8 dpkg-source: info: unpacking falcon_1.8.8.orig.tar.xz dpkg-source: info: unpacking falcon_1.8.8-1.debian.tar.xz dpkg-source: info: applying build-system.patch dpkg-source: info: applying versioned-deps.patch I: running --customize-hook in shell: sh -c 'chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/falcon-LwwdoQ/falcon-1.8.8 && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="POSIX" SOURCE_DATE_EPOCH="1513411047" DEB_BUILD_OPTIONS=nocheck dpkg-buildpackage -uc -a amd64 --build=any"' exec /tmp/mmdebstrap.SAG5NvxJ_M dpkg-buildpackage: info: source package falcon dpkg-buildpackage: info: source version 1.8.8-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Afif Elghraoui dpkg-source --before-build falcon-1.8.8 dpkg-buildpackage: info: host architecture amd64 fakeroot debian/rules clean dh clean --with python2 debian/rules override_dh_auto_clean make[1]: Entering directory '/build/falcon-LwwdoQ/falcon-1.8.8' dh_auto_clean rm -f -r /build/falcon-LwwdoQ/falcon-1.8.8/inst make[1]: Leaving directory '/build/falcon-LwwdoQ/falcon-1.8.8' dh_clean debian/rules build-arch dh build-arch --with python2 dh_update_autotools_config -a dh_auto_configure -a debian/rules override_dh_auto_build make[1]: Entering directory '/build/falcon-LwwdoQ/falcon-1.8.8' mkdir -p \ /build/falcon-LwwdoQ/falcon-1.8.8/inst/bin \ /build/falcon-LwwdoQ/falcon-1.8.8/inst/include \ /build/falcon-LwwdoQ/falcon-1.8.8/inst/lib \ /build/falcon-LwwdoQ/falcon-1.8.8/inst/pylib /usr/bin/make all make[2]: Entering directory '/build/falcon-LwwdoQ/falcon-1.8.8' /usr/bin/make -C ./FALCON-make/ all make[3]: Entering directory '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-make' /usr/bin/make show make[4]: Entering directory '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-make' mkdir -p /build/falcon-LwwdoQ/falcon-1.8.8/inst/bin which python /usr/bin/python echo "PYTHONUSERBASE=" PYTHONUSERBASE= python -c 'import site; print site.USER_BASE' /nonexistent/.local echo "FALCON_PIP_EDIT=--edit" FALCON_PIP_EDIT=--edit echo "FALCON_PIP_USER=" FALCON_PIP_USER= make[4]: Leaving directory '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-make' /usr/bin/make install make[4]: Entering directory '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-make' /usr/bin/make -C /build/falcon-LwwdoQ/falcon-1.8.8/DAZZ_DB all make[5]: Entering directory '/build/falcon-LwwdoQ/falcon-1.8.8/DAZZ_DB' gcc -g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wextra -fno-strict-aliasing -Wno-unused-result -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -c -o DB.o DB.c gcc -g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wextra -fno-strict-aliasing -Wno-unused-result -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -c -o QV.o QV.c ar -rcv libdazzdb.a DB.o QV.o a - DB.o a - QV.o gcc -g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wextra -fno-strict-aliasing -Wno-unused-result -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -Wl,-z,relro fasta2DB.c libdazzdb.a -lm -o fasta2DB gcc -g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wextra -fno-strict-aliasing -Wno-unused-result -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -Wl,-z,relro DB2fasta.c libdazzdb.a -lm -o DB2fasta gcc -g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wextra -fno-strict-aliasing -Wno-unused-result -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -Wl,-z,relro DBsplit.c libdazzdb.a -lm -o DBsplit gcc -g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wextra -fno-strict-aliasing -Wno-unused-result -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -Wl,-z,relro DBdust.c libdazzdb.a -lm -o DBdust gcc -g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wextra -fno-strict-aliasing -Wno-unused-result -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -Wl,-z,relro Catrack.c libdazzdb.a -lm -o Catrack gcc -g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wextra -fno-strict-aliasing -Wno-unused-result -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -Wl,-z,relro DBshow.c libdazzdb.a -lm -o DBshow gcc -g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wextra -fno-strict-aliasing -Wno-unused-result -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -Wl,-z,relro DBstats.c libdazzdb.a -lm -o DBstats gcc -g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wextra -fno-strict-aliasing -Wno-unused-result -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -Wl,-z,relro DBrm.c libdazzdb.a -lm -o DBrm gcc -g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wextra -fno-strict-aliasing -Wno-unused-result -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -Wl,-z,relro simulator.c libdazzdb.a -lm -o simulator gcc -g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wextra -fno-strict-aliasing -Wno-unused-result -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -Wl,-z,relro fasta2DAM.c libdazzdb.a -lm -o fasta2DAM gcc -g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wextra -fno-strict-aliasing -Wno-unused-result -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -Wl,-z,relro DAM2fasta.c libdazzdb.a -lm -o DAM2fasta gcc -g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wextra -fno-strict-aliasing -Wno-unused-result -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -Wl,-z,relro DBdump.c libdazzdb.a -lm -o DBdump gcc -g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wextra -fno-strict-aliasing -Wno-unused-result -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -Wl,-z,relro rangen.c libdazzdb.a -lm -o rangen make[5]: Leaving directory '/build/falcon-LwwdoQ/falcon-1.8.8/DAZZ_DB' PREFIX=/build/falcon-LwwdoQ/falcon-1.8.8/inst /usr/bin/make -C /build/falcon-LwwdoQ/falcon-1.8.8/DAZZ_DB install make[5]: Entering directory '/build/falcon-LwwdoQ/falcon-1.8.8/DAZZ_DB' rsync -av fasta2DB DB2fasta DBsplit DBdust Catrack DBshow DBstats DBrm simulator fasta2DAM DAM2fasta DBdump rangen /build/falcon-LwwdoQ/falcon-1.8.8/inst/bin sending incremental file list Catrack DAM2fasta DB2fasta DBdump DBdust DBrm DBshow DBsplit DBstats fasta2DAM fasta2DB rangen simulator sent 3,207,511 bytes received 263 bytes 6,415,548.00 bytes/sec total size is 3,205,928 speedup is 1.00 rsync -av libdazzdb.* /build/falcon-LwwdoQ/falcon-1.8.8/inst/lib sending incremental file list libdazzdb.a sent 359,815 bytes received 35 bytes 719,700.00 bytes/sec total size is 359,620 speedup is 1.00 rsync -av /build/falcon-LwwdoQ/falcon-1.8.8/DAZZ_DB/DB.h /build/falcon-LwwdoQ/falcon-1.8.8/DAZZ_DB/QV.h /build/falcon-LwwdoQ/falcon-1.8.8/inst/include sending incremental file list DB.h QV.h sent 25,544 bytes received 54 bytes 51,196.00 bytes/sec total size is 25,385 speedup is 0.99 make[5]: Leaving directory '/build/falcon-LwwdoQ/falcon-1.8.8/DAZZ_DB' /usr/bin/make -C /build/falcon-LwwdoQ/falcon-1.8.8/DALIGNER all make[5]: Entering directory '/build/falcon-LwwdoQ/falcon-1.8.8/DALIGNER' gcc -g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wextra -fno-strict-aliasing -Wno-unused-result -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/falcon-LwwdoQ/falcon-1.8.8/DALIGNER/../DAZZ_DB -I/include -c -o filter.o filter.c gcc -g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wextra -fno-strict-aliasing -Wno-unused-result -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/falcon-LwwdoQ/falcon-1.8.8/DALIGNER/../DAZZ_DB -I/include -c -o align.o align.c gcc -g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wextra -fno-strict-aliasing -Wno-unused-result -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/falcon-LwwdoQ/falcon-1.8.8/DALIGNER/../DAZZ_DB -I/include -c -o daligner.o daligner.c gcc -Wl,-z,relro -L/build/falcon-LwwdoQ/falcon-1.8.8/DALIGNER/../DAZZ_DB daligner.o filter.o align.o -ldazzdb -lm -lpthread -o daligner gcc -g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wextra -fno-strict-aliasing -Wno-unused-result -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/falcon-LwwdoQ/falcon-1.8.8/DALIGNER/../DAZZ_DB -I/include -c -o HPC.daligner.o HPC.daligner.c gcc -Wl,-z,relro -L/build/falcon-LwwdoQ/falcon-1.8.8/DALIGNER/../DAZZ_DB HPC.daligner.o align.o -ldazzdb -lm -lpthread -o HPC.daligner gcc -g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wextra -fno-strict-aliasing -Wno-unused-result -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/falcon-LwwdoQ/falcon-1.8.8/DALIGNER/../DAZZ_DB -I/include -c -o LAsort.o LAsort.c gcc -Wl,-z,relro -L/build/falcon-LwwdoQ/falcon-1.8.8/DALIGNER/../DAZZ_DB LAsort.o align.o -ldazzdb -lm -lpthread -o LAsort gcc -g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wextra -fno-strict-aliasing -Wno-unused-result -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/falcon-LwwdoQ/falcon-1.8.8/DALIGNER/../DAZZ_DB -I/include -c -o LAmerge.o LAmerge.c gcc -Wl,-z,relro -L/build/falcon-LwwdoQ/falcon-1.8.8/DALIGNER/../DAZZ_DB LAmerge.o align.o -ldazzdb -lm -lpthread -o LAmerge gcc -g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wextra -fno-strict-aliasing -Wno-unused-result -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/falcon-LwwdoQ/falcon-1.8.8/DALIGNER/../DAZZ_DB -I/include -c -o LAsplit.o LAsplit.c gcc -Wl,-z,relro -L/build/falcon-LwwdoQ/falcon-1.8.8/DALIGNER/../DAZZ_DB LAsplit.o align.o -ldazzdb -lm -lpthread -o LAsplit gcc -g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wextra -fno-strict-aliasing -Wno-unused-result -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/falcon-LwwdoQ/falcon-1.8.8/DALIGNER/../DAZZ_DB -I/include -c -o LAcat.o LAcat.c gcc -Wl,-z,relro -L/build/falcon-LwwdoQ/falcon-1.8.8/DALIGNER/../DAZZ_DB LAcat.o align.o -ldazzdb -lm -lpthread -o LAcat gcc -g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wextra -fno-strict-aliasing -Wno-unused-result -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/falcon-LwwdoQ/falcon-1.8.8/DALIGNER/../DAZZ_DB -I/include -c -o LAshow.o LAshow.c gcc -Wl,-z,relro -L/build/falcon-LwwdoQ/falcon-1.8.8/DALIGNER/../DAZZ_DB LAshow.o align.o -ldazzdb -lm -lpthread -o LAshow gcc -g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wextra -fno-strict-aliasing -Wno-unused-result -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/falcon-LwwdoQ/falcon-1.8.8/DALIGNER/../DAZZ_DB -I/include -c -o LAdump.o LAdump.c gcc -Wl,-z,relro -L/build/falcon-LwwdoQ/falcon-1.8.8/DALIGNER/../DAZZ_DB LAdump.o align.o -ldazzdb -lm -lpthread -o LAdump gcc -g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wextra -fno-strict-aliasing -Wno-unused-result -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/falcon-LwwdoQ/falcon-1.8.8/DALIGNER/../DAZZ_DB -I/include -c -o LAcheck.o LAcheck.c gcc -Wl,-z,relro -L/build/falcon-LwwdoQ/falcon-1.8.8/DALIGNER/../DAZZ_DB LAcheck.o align.o -ldazzdb -lm -lpthread -o LAcheck gcc -g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wextra -fno-strict-aliasing -Wno-unused-result -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/falcon-LwwdoQ/falcon-1.8.8/DALIGNER/../DAZZ_DB -I/include -c -o LAindex.o LAindex.c gcc -Wl,-z,relro -L/build/falcon-LwwdoQ/falcon-1.8.8/DALIGNER/../DAZZ_DB LAindex.o align.o -ldazzdb -lm -lpthread -o LAindex gcc -g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wextra -fno-strict-aliasing -Wno-unused-result -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/falcon-LwwdoQ/falcon-1.8.8/DALIGNER/../DAZZ_DB -I/include -c -o filter_p.o filter_p.c gcc -g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wextra -fno-strict-aliasing -Wno-unused-result -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/falcon-LwwdoQ/falcon-1.8.8/DALIGNER/../DAZZ_DB -I/include -c -o daligner_p.o daligner_p.c gcc -Wl,-z,relro -L/build/falcon-LwwdoQ/falcon-1.8.8/DALIGNER/../DAZZ_DB daligner_p.o filter_p.o align.o -ldazzdb -lm -lpthread -o daligner_p gcc -g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wextra -fno-strict-aliasing -Wno-unused-result -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/falcon-LwwdoQ/falcon-1.8.8/DALIGNER/../DAZZ_DB -I/include -c -o DBX.o DBX.c gcc -g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wextra -fno-strict-aliasing -Wno-unused-result -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/falcon-LwwdoQ/falcon-1.8.8/DALIGNER/../DAZZ_DB -I/include -c -o LA4Falcon.o LA4Falcon.c gcc -Wl,-z,relro -L/build/falcon-LwwdoQ/falcon-1.8.8/DALIGNER/../DAZZ_DB LA4Falcon.o DBX.o align.o -ldazzdb -lm -lpthread -o LA4Falcon gcc -g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wextra -fno-strict-aliasing -Wno-unused-result -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/falcon-LwwdoQ/falcon-1.8.8/DALIGNER/../DAZZ_DB -I/include -c -o LA4Ice.o LA4Ice.c gcc -Wl,-z,relro -L/build/falcon-LwwdoQ/falcon-1.8.8/DALIGNER/../DAZZ_DB LA4Ice.o align.o -ldazzdb -lm -lpthread -o LA4Ice gcc -g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wextra -fno-strict-aliasing -Wno-unused-result -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/falcon-LwwdoQ/falcon-1.8.8/DALIGNER/../DAZZ_DB -I/include -c -o DB2Falcon.o DB2Falcon.c gcc -Wl,-z,relro -L/build/falcon-LwwdoQ/falcon-1.8.8/DALIGNER/../DAZZ_DB DB2Falcon.o align.o -ldazzdb -lm -lpthread -o DB2Falcon rm daligner_p.o LAshow.o LAcat.o LA4Falcon.o LAdump.o LAsplit.o LAmerge.o LAcheck.o daligner.o HPC.daligner.o LAindex.o DB2Falcon.o LA4Ice.o LAsort.o make[5]: Leaving directory '/build/falcon-LwwdoQ/falcon-1.8.8/DALIGNER' PREFIX=/build/falcon-LwwdoQ/falcon-1.8.8/inst /usr/bin/make -C /build/falcon-LwwdoQ/falcon-1.8.8/DALIGNER install make[5]: Entering directory '/build/falcon-LwwdoQ/falcon-1.8.8/DALIGNER' rsync -av daligner HPC.daligner LAsort LAmerge LAsplit LAcat LAshow LAdump LAcheck LAindex daligner_p LA4Falcon LA4Ice DB2Falcon /build/falcon-LwwdoQ/falcon-1.8.8/inst/bin sending incremental file list DB2Falcon HPC.daligner LA4Falcon LA4Ice LAcat LAcheck LAdump LAindex LAmerge LAshow LAsort LAsplit daligner daligner_p sent 10,002,515 bytes received 282 bytes 20,005,594.00 bytes/sec total size is 9,999,208 speedup is 1.00 make[5]: Leaving directory '/build/falcon-LwwdoQ/falcon-1.8.8/DALIGNER' /usr/bin/make -C /build/falcon-LwwdoQ/falcon-1.8.8/DAMASKER all make[5]: Entering directory '/build/falcon-LwwdoQ/falcon-1.8.8/DAMASKER' gcc -O3 -Wall -Wextra -Wno-unused-result -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tandem.o tandem.c gcc -O3 -Wall -Wextra -Wno-unused-result -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -c -o align.o align.c gcc -O3 -Wall -Wextra -Wno-unused-result -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -c -o DB.o DB.c gcc -O3 -Wall -Wextra -Wno-unused-result -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -c -o QV.o QV.c gcc -O3 -Wall -Wextra -Wno-unused-result -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -c -o datander.o datander.c gcc -Wl,-z,relro datander.o tandem.o align.o DB.o QV.o -lm -lpthread -o datander gcc -O3 -Wall -Wextra -Wno-unused-result -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -c -o TANmask.o TANmask.c gcc -Wl,-z,relro TANmask.o align.o DB.o QV.o -lm -lpthread -o TANmask gcc -O3 -Wall -Wextra -Wno-unused-result -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -c -o REPmask.o REPmask.c gcc -Wl,-z,relro REPmask.o align.o DB.o QV.o -lm -lpthread -o REPmask gcc -O3 -Wall -Wextra -Wno-unused-result -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -c -o HPC.TANmask.o HPC.TANmask.c HPC.TANmask.c: In function ‘main’: HPC.TANmask.c:296:9: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] for (k = i; k < j; k++) ^~~ HPC.TANmask.c:308:11: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ if (DON) ^~ HPC.TANmask.c:433:9: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] for (k = 0; k < NTHREADS; k++) ^~~ HPC.TANmask.c:438:11: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ fprintf(out,"\n"); ^~~~~~~ gcc -Wl,-z,relro HPC.TANmask.o align.o DB.o QV.o -lm -lpthread -o HPC.TANmask gcc -O3 -Wall -Wextra -Wno-unused-result -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -c -o HPC.REPmask.o HPC.REPmask.c gcc -Wl,-z,relro HPC.REPmask.o align.o DB.o QV.o -lm -lpthread -o HPC.REPmask rm TANmask.o datander.o HPC.REPmask.o HPC.TANmask.o REPmask.o make[5]: Leaving directory '/build/falcon-LwwdoQ/falcon-1.8.8/DAMASKER' PREFIX=/build/falcon-LwwdoQ/falcon-1.8.8/inst /usr/bin/make -C /build/falcon-LwwdoQ/falcon-1.8.8/DAMASKER install make[5]: Entering directory '/build/falcon-LwwdoQ/falcon-1.8.8/DAMASKER' rsync -av datander TANmask REPmask HPC.TANmask HPC.REPmask /build/falcon-LwwdoQ/falcon-1.8.8/inst/bin sending incremental file list HPC.REPmask HPC.TANmask REPmask TANmask datander sent 767,199 bytes received 111 bytes 1,534,620.00 bytes/sec total size is 766,672 speedup is 1.00 make[5]: Leaving directory '/build/falcon-LwwdoQ/falcon-1.8.8/DAMASKER' /usr/bin/make -C /build/falcon-LwwdoQ/falcon-1.8.8/DEXTRACTOR all make[5]: Entering directory '/build/falcon-LwwdoQ/falcon-1.8.8/DEXTRACTOR' gcc -O3 -Wall -Wextra -Wno-unused-result -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -c -o dexta.o dexta.c gcc -O3 -Wall -Wextra -Wno-unused-result -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -c -o DB.o DB.c gcc -O3 -Wall -Wextra -Wno-unused-result -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -c -o QV.o QV.c gcc -Wl,-z,relro dexta.o DB.o QV.o -lm -lpthread -o dexta gcc -O3 -Wall -Wextra -Wno-unused-result -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -c -o undexta.o undexta.c gcc -Wl,-z,relro undexta.o DB.o QV.o -lm -lpthread -o undexta make[5]: Leaving directory '/build/falcon-LwwdoQ/falcon-1.8.8/DEXTRACTOR' PREFIX=/build/falcon-LwwdoQ/falcon-1.8.8/inst /usr/bin/make -C /build/falcon-LwwdoQ/falcon-1.8.8/DEXTRACTOR install make[5]: Entering directory '/build/falcon-LwwdoQ/falcon-1.8.8/DEXTRACTOR' rsync -av dexta undexta /build/falcon-LwwdoQ/falcon-1.8.8/inst/bin sending incremental file list dexta undexta sent 137,561 bytes received 54 bytes 275,230.00 bytes/sec total size is 137,360 speedup is 1.00 make[5]: Leaving directory '/build/falcon-LwwdoQ/falcon-1.8.8/DEXTRACTOR' cd /build/falcon-LwwdoQ/falcon-1.8.8/pypeFLOW; python setup.py install --install-lib=/build/falcon-LwwdoQ/falcon-1.8.8/inst/pylib --install-scripts=/build/falcon-LwwdoQ/falcon-1.8.8/inst/bin running install running bdist_egg running egg_info creating pypeflow.egg-info writing requirements to pypeflow.egg-info/requires.txt writing pypeflow.egg-info/PKG-INFO writing top-level names to pypeflow.egg-info/top_level.txt writing dependency_links to pypeflow.egg-info/dependency_links.txt writing entry points to pypeflow.egg-info/entry_points.txt writing manifest file 'pypeflow.egg-info/SOURCES.txt' reading manifest file 'pypeflow.egg-info/SOURCES.txt' writing manifest file 'pypeflow.egg-info/SOURCES.txt' installing library code to build/bdist.linux-x86_64/egg running install_lib running build_py creating build creating build/lib.linux-x86_64-2.7 creating build/lib.linux-x86_64-2.7/pypeflow copying ./pypeflow/simple_pwatcher_bridge.py -> build/lib.linux-x86_64-2.7/pypeflow copying ./pypeflow/pwatcher_workflow.py -> build/lib.linux-x86_64-2.7/pypeflow copying ./pypeflow/util.py -> build/lib.linux-x86_64-2.7/pypeflow copying ./pypeflow/__init__.py -> build/lib.linux-x86_64-2.7/pypeflow copying ./pypeflow/do_support.py -> build/lib.linux-x86_64-2.7/pypeflow copying ./pypeflow/do_task.py -> build/lib.linux-x86_64-2.7/pypeflow creating build/lib.linux-x86_64-2.7/pwatcher copying ./pwatcher/network_based.py -> build/lib.linux-x86_64-2.7/pwatcher copying ./pwatcher/__init__.py -> build/lib.linux-x86_64-2.7/pwatcher copying ./pwatcher/fs_based.py -> build/lib.linux-x86_64-2.7/pwatcher copying ./pwatcher/blocking.py -> build/lib.linux-x86_64-2.7/pwatcher creating build/lib.linux-x86_64-2.7/pwatcher/mains copying ./pwatcher/mains/query_server.py -> build/lib.linux-x86_64-2.7/pwatcher/mains copying ./pwatcher/mains/fs_heartbeat.py -> build/lib.linux-x86_64-2.7/pwatcher/mains copying ./pwatcher/mains/network_heartbeat.py -> build/lib.linux-x86_64-2.7/pwatcher/mains copying ./pwatcher/mains/__init__.py -> build/lib.linux-x86_64-2.7/pwatcher/mains copying ./pwatcher/mains/pypeflow_example.py -> build/lib.linux-x86_64-2.7/pwatcher/mains copying ./pwatcher/mains/pwatcher.py -> build/lib.linux-x86_64-2.7/pwatcher/mains copying ./pwatcher/mains/job_start.sh -> build/lib.linux-x86_64-2.7/pwatcher/mains creating build/bdist.linux-x86_64 creating build/bdist.linux-x86_64/egg creating build/bdist.linux-x86_64/egg/pypeflow copying build/lib.linux-x86_64-2.7/pypeflow/simple_pwatcher_bridge.py -> build/bdist.linux-x86_64/egg/pypeflow copying build/lib.linux-x86_64-2.7/pypeflow/pwatcher_workflow.py -> build/bdist.linux-x86_64/egg/pypeflow copying build/lib.linux-x86_64-2.7/pypeflow/util.py -> build/bdist.linux-x86_64/egg/pypeflow copying build/lib.linux-x86_64-2.7/pypeflow/__init__.py -> build/bdist.linux-x86_64/egg/pypeflow copying build/lib.linux-x86_64-2.7/pypeflow/do_support.py -> build/bdist.linux-x86_64/egg/pypeflow copying build/lib.linux-x86_64-2.7/pypeflow/do_task.py -> build/bdist.linux-x86_64/egg/pypeflow creating build/bdist.linux-x86_64/egg/pwatcher copying build/lib.linux-x86_64-2.7/pwatcher/network_based.py -> build/bdist.linux-x86_64/egg/pwatcher copying build/lib.linux-x86_64-2.7/pwatcher/__init__.py -> build/bdist.linux-x86_64/egg/pwatcher copying build/lib.linux-x86_64-2.7/pwatcher/fs_based.py -> build/bdist.linux-x86_64/egg/pwatcher copying build/lib.linux-x86_64-2.7/pwatcher/blocking.py -> build/bdist.linux-x86_64/egg/pwatcher creating build/bdist.linux-x86_64/egg/pwatcher/mains copying build/lib.linux-x86_64-2.7/pwatcher/mains/query_server.py -> build/bdist.linux-x86_64/egg/pwatcher/mains copying build/lib.linux-x86_64-2.7/pwatcher/mains/fs_heartbeat.py -> build/bdist.linux-x86_64/egg/pwatcher/mains copying build/lib.linux-x86_64-2.7/pwatcher/mains/network_heartbeat.py -> build/bdist.linux-x86_64/egg/pwatcher/mains copying build/lib.linux-x86_64-2.7/pwatcher/mains/__init__.py -> build/bdist.linux-x86_64/egg/pwatcher/mains copying build/lib.linux-x86_64-2.7/pwatcher/mains/pypeflow_example.py -> build/bdist.linux-x86_64/egg/pwatcher/mains copying build/lib.linux-x86_64-2.7/pwatcher/mains/pwatcher.py -> build/bdist.linux-x86_64/egg/pwatcher/mains copying build/lib.linux-x86_64-2.7/pwatcher/mains/job_start.sh -> build/bdist.linux-x86_64/egg/pwatcher/mains byte-compiling build/bdist.linux-x86_64/egg/pypeflow/simple_pwatcher_bridge.py to simple_pwatcher_bridge.pyc byte-compiling build/bdist.linux-x86_64/egg/pypeflow/pwatcher_workflow.py to pwatcher_workflow.pyc byte-compiling build/bdist.linux-x86_64/egg/pypeflow/util.py to util.pyc byte-compiling build/bdist.linux-x86_64/egg/pypeflow/__init__.py to __init__.pyc byte-compiling build/bdist.linux-x86_64/egg/pypeflow/do_support.py to do_support.pyc byte-compiling build/bdist.linux-x86_64/egg/pypeflow/do_task.py to do_task.pyc byte-compiling build/bdist.linux-x86_64/egg/pwatcher/network_based.py to network_based.pyc byte-compiling build/bdist.linux-x86_64/egg/pwatcher/__init__.py to __init__.pyc byte-compiling build/bdist.linux-x86_64/egg/pwatcher/fs_based.py to fs_based.pyc byte-compiling build/bdist.linux-x86_64/egg/pwatcher/blocking.py to blocking.pyc byte-compiling build/bdist.linux-x86_64/egg/pwatcher/mains/query_server.py to query_server.pyc byte-compiling build/bdist.linux-x86_64/egg/pwatcher/mains/fs_heartbeat.py to fs_heartbeat.pyc byte-compiling build/bdist.linux-x86_64/egg/pwatcher/mains/network_heartbeat.py to network_heartbeat.pyc byte-compiling build/bdist.linux-x86_64/egg/pwatcher/mains/__init__.py to __init__.pyc byte-compiling build/bdist.linux-x86_64/egg/pwatcher/mains/pypeflow_example.py to pypeflow_example.pyc byte-compiling build/bdist.linux-x86_64/egg/pwatcher/mains/pwatcher.py to pwatcher.pyc creating build/bdist.linux-x86_64/egg/EGG-INFO copying pypeflow.egg-info/PKG-INFO -> build/bdist.linux-x86_64/egg/EGG-INFO copying pypeflow.egg-info/SOURCES.txt -> build/bdist.linux-x86_64/egg/EGG-INFO copying pypeflow.egg-info/dependency_links.txt -> build/bdist.linux-x86_64/egg/EGG-INFO copying pypeflow.egg-info/entry_points.txt -> build/bdist.linux-x86_64/egg/EGG-INFO copying pypeflow.egg-info/not-zip-safe -> build/bdist.linux-x86_64/egg/EGG-INFO copying pypeflow.egg-info/requires.txt -> build/bdist.linux-x86_64/egg/EGG-INFO copying pypeflow.egg-info/top_level.txt -> build/bdist.linux-x86_64/egg/EGG-INFO creating dist creating 'dist/pypeflow-1.0.0-py2.7.egg' and adding 'build/bdist.linux-x86_64/egg' to it removing 'build/bdist.linux-x86_64/egg' (and everything under it) Creating /build/falcon-LwwdoQ/falcon-1.8.8/inst/pylib/site.py Processing pypeflow-1.0.0-py2.7.egg creating /build/falcon-LwwdoQ/falcon-1.8.8/inst/pylib/pypeflow-1.0.0-py2.7.egg Extracting pypeflow-1.0.0-py2.7.egg to /build/falcon-LwwdoQ/falcon-1.8.8/inst/pylib Adding pypeflow 1.0.0 to easy-install.pth file Installing pwatcher-pypeflow-example script to /build/falcon-LwwdoQ/falcon-1.8.8/inst/bin Installing heartbeat-wrapper script to /build/falcon-LwwdoQ/falcon-1.8.8/inst/bin Installing pwatcher-main script to /build/falcon-LwwdoQ/falcon-1.8.8/inst/bin Installed /build/falcon-LwwdoQ/falcon-1.8.8/inst/pylib/pypeflow-1.0.0-py2.7.egg Processing dependencies for pypeflow==1.0.0 Searching for networkx==1.11 Best match: networkx 1.11 Adding networkx 1.11 to easy-install.pth file Using /usr/lib/python2.7/dist-packages Finished processing dependencies for pypeflow==1.0.0 cd /build/falcon-LwwdoQ/falcon-1.8.8/FALCON; python setup.py install --install-lib=/build/falcon-LwwdoQ/falcon-1.8.8/inst/pylib --install-scripts=/build/falcon-LwwdoQ/falcon-1.8.8/inst/bin /bin/sh: 1: git: not found running install running bdist_egg running egg_info creating falcon_kit.egg-info writing requirements to falcon_kit.egg-info/requires.txt writing falcon_kit.egg-info/PKG-INFO writing top-level names to falcon_kit.egg-info/top_level.txt writing dependency_links to falcon_kit.egg-info/dependency_links.txt writing entry points to falcon_kit.egg-info/entry_points.txt writing manifest file 'falcon_kit.egg-info/SOURCES.txt' reading manifest file 'falcon_kit.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' writing manifest file 'falcon_kit.egg-info/SOURCES.txt' installing library code to build/bdist.linux-x86_64/egg running install_lib running build_py creating build creating build/lib.linux-x86_64-2.7 creating build/lib.linux-x86_64-2.7/falcon_kit copying falcon_kit/multiproc.py -> build/lib.linux-x86_64-2.7/falcon_kit copying falcon_kit/stats_preassembly.py -> build/lib.linux-x86_64-2.7/falcon_kit copying falcon_kit/pype_tasks.py -> build/lib.linux-x86_64-2.7/falcon_kit copying falcon_kit/__init__.py -> build/lib.linux-x86_64-2.7/falcon_kit copying falcon_kit/FastaReader.py -> build/lib.linux-x86_64-2.7/falcon_kit copying falcon_kit/bash.py -> build/lib.linux-x86_64-2.7/falcon_kit copying falcon_kit/functional.py -> build/lib.linux-x86_64-2.7/falcon_kit copying falcon_kit/run_support.py -> build/lib.linux-x86_64-2.7/falcon_kit copying falcon_kit/falcon_kit.py -> build/lib.linux-x86_64-2.7/falcon_kit copying falcon_kit/fc_asm_graph.py -> build/lib.linux-x86_64-2.7/falcon_kit creating build/lib.linux-x86_64-2.7/falcon_kit/mains copying falcon_kit/mains/ovlp_filter.py -> build/lib.linux-x86_64-2.7/falcon_kit/mains copying falcon_kit/mains/actg_coordinate.py -> build/lib.linux-x86_64-2.7/falcon_kit/mains copying falcon_kit/mains/ovlp_to_graph.py -> build/lib.linux-x86_64-2.7/falcon_kit/mains copying falcon_kit/mains/ctg_link_analysis.py -> build/lib.linux-x86_64-2.7/falcon_kit/mains copying falcon_kit/mains/rr_ctg_track.py -> build/lib.linux-x86_64-2.7/falcon_kit/mains copying falcon_kit/mains/tasks.py -> build/lib.linux-x86_64-2.7/falcon_kit/mains copying falcon_kit/mains/run1.py -> build/lib.linux-x86_64-2.7/falcon_kit/mains copying falcon_kit/mains/graph_to_utgs.py -> build/lib.linux-x86_64-2.7/falcon_kit/mains copying falcon_kit/mains/dedup_a_tigs.py -> build/lib.linux-x86_64-2.7/falcon_kit/mains copying falcon_kit/mains/fasta2fasta.py -> build/lib.linux-x86_64-2.7/falcon_kit/mains copying falcon_kit/mains/contig_annotate.py -> build/lib.linux-x86_64-2.7/falcon_kit/mains copying falcon_kit/mains/pr_ctg_track.py -> build/lib.linux-x86_64-2.7/falcon_kit/mains copying falcon_kit/mains/fetch_reads.py -> build/lib.linux-x86_64-2.7/falcon_kit/mains copying falcon_kit/mains/calc_cutoff.py -> build/lib.linux-x86_64-2.7/falcon_kit/mains copying falcon_kit/mains/LAmerge.py -> build/lib.linux-x86_64-2.7/falcon_kit/mains copying falcon_kit/mains/__init__.py -> build/lib.linux-x86_64-2.7/falcon_kit/mains copying falcon_kit/mains/ovlp_stats.py -> build/lib.linux-x86_64-2.7/falcon_kit/mains copying falcon_kit/mains/graph_to_contig.py -> build/lib.linux-x86_64-2.7/falcon_kit/mains copying falcon_kit/mains/report_pre_assembly.py -> build/lib.linux-x86_64-2.7/falcon_kit/mains copying falcon_kit/mains/get_read_ctg_map.py -> build/lib.linux-x86_64-2.7/falcon_kit/mains copying falcon_kit/mains/LAsort.py -> build/lib.linux-x86_64-2.7/falcon_kit/mains copying falcon_kit/mains/consensus.py -> build/lib.linux-x86_64-2.7/falcon_kit/mains creating build/lib.linux-x86_64-2.7/falcon_kit/util copying falcon_kit/util/system.py -> build/lib.linux-x86_64-2.7/falcon_kit/util copying falcon_kit/util/__init__.py -> build/lib.linux-x86_64-2.7/falcon_kit/util copying falcon_kit/util/io.py -> build/lib.linux-x86_64-2.7/falcon_kit/util running build_ext building 'ext_falcon' extension creating build/temp.linux-x86_64-2.7 creating build/temp.linux-x86_64-2.7/src creating build/temp.linux-x86_64-2.7/src/c gcc -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python2.7 -c src/c/ext_falcon.c -o build/temp.linux-x86_64-2.7/src/c/ext_falcon.o -fPIC -O3 -fno-omit-frame-pointer gcc -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python2.7 -c src/c/DW_banded.c -o build/temp.linux-x86_64-2.7/src/c/DW_banded.o -fPIC -O3 -fno-omit-frame-pointer gcc -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python2.7 -c src/c/kmer_lookup.c -o build/temp.linux-x86_64-2.7/src/c/kmer_lookup.o -fPIC -O3 -fno-omit-frame-pointer gcc -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python2.7 -c src/c/falcon.c -o build/temp.linux-x86_64-2.7/src/c/falcon.o -fPIC -O3 -fno-omit-frame-pointer x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-j9xj4T/python2.7-2.7.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-2.7/src/c/ext_falcon.o build/temp.linux-x86_64-2.7/src/c/DW_banded.o build/temp.linux-x86_64-2.7/src/c/kmer_lookup.o build/temp.linux-x86_64-2.7/src/c/falcon.o -o build/lib.linux-x86_64-2.7/ext_falcon.so creating build/bdist.linux-x86_64 creating build/bdist.linux-x86_64/egg creating build/bdist.linux-x86_64/egg/falcon_kit copying build/lib.linux-x86_64-2.7/falcon_kit/multiproc.py -> build/bdist.linux-x86_64/egg/falcon_kit copying build/lib.linux-x86_64-2.7/falcon_kit/stats_preassembly.py -> build/bdist.linux-x86_64/egg/falcon_kit copying build/lib.linux-x86_64-2.7/falcon_kit/pype_tasks.py -> build/bdist.linux-x86_64/egg/falcon_kit copying build/lib.linux-x86_64-2.7/falcon_kit/__init__.py -> build/bdist.linux-x86_64/egg/falcon_kit copying build/lib.linux-x86_64-2.7/falcon_kit/FastaReader.py -> build/bdist.linux-x86_64/egg/falcon_kit copying build/lib.linux-x86_64-2.7/falcon_kit/bash.py -> build/bdist.linux-x86_64/egg/falcon_kit copying build/lib.linux-x86_64-2.7/falcon_kit/functional.py -> build/bdist.linux-x86_64/egg/falcon_kit copying build/lib.linux-x86_64-2.7/falcon_kit/run_support.py -> build/bdist.linux-x86_64/egg/falcon_kit copying build/lib.linux-x86_64-2.7/falcon_kit/falcon_kit.py -> build/bdist.linux-x86_64/egg/falcon_kit copying build/lib.linux-x86_64-2.7/falcon_kit/fc_asm_graph.py -> build/bdist.linux-x86_64/egg/falcon_kit creating build/bdist.linux-x86_64/egg/falcon_kit/mains copying build/lib.linux-x86_64-2.7/falcon_kit/mains/ovlp_filter.py -> build/bdist.linux-x86_64/egg/falcon_kit/mains copying build/lib.linux-x86_64-2.7/falcon_kit/mains/actg_coordinate.py -> build/bdist.linux-x86_64/egg/falcon_kit/mains copying build/lib.linux-x86_64-2.7/falcon_kit/mains/ovlp_to_graph.py -> build/bdist.linux-x86_64/egg/falcon_kit/mains copying build/lib.linux-x86_64-2.7/falcon_kit/mains/ctg_link_analysis.py -> build/bdist.linux-x86_64/egg/falcon_kit/mains copying build/lib.linux-x86_64-2.7/falcon_kit/mains/rr_ctg_track.py -> build/bdist.linux-x86_64/egg/falcon_kit/mains copying build/lib.linux-x86_64-2.7/falcon_kit/mains/tasks.py -> build/bdist.linux-x86_64/egg/falcon_kit/mains copying build/lib.linux-x86_64-2.7/falcon_kit/mains/run1.py -> build/bdist.linux-x86_64/egg/falcon_kit/mains copying build/lib.linux-x86_64-2.7/falcon_kit/mains/graph_to_utgs.py -> build/bdist.linux-x86_64/egg/falcon_kit/mains copying build/lib.linux-x86_64-2.7/falcon_kit/mains/dedup_a_tigs.py -> build/bdist.linux-x86_64/egg/falcon_kit/mains copying build/lib.linux-x86_64-2.7/falcon_kit/mains/fasta2fasta.py -> build/bdist.linux-x86_64/egg/falcon_kit/mains copying build/lib.linux-x86_64-2.7/falcon_kit/mains/contig_annotate.py -> build/bdist.linux-x86_64/egg/falcon_kit/mains copying build/lib.linux-x86_64-2.7/falcon_kit/mains/pr_ctg_track.py -> build/bdist.linux-x86_64/egg/falcon_kit/mains copying build/lib.linux-x86_64-2.7/falcon_kit/mains/fetch_reads.py -> build/bdist.linux-x86_64/egg/falcon_kit/mains copying build/lib.linux-x86_64-2.7/falcon_kit/mains/calc_cutoff.py -> build/bdist.linux-x86_64/egg/falcon_kit/mains copying build/lib.linux-x86_64-2.7/falcon_kit/mains/LAmerge.py -> build/bdist.linux-x86_64/egg/falcon_kit/mains copying build/lib.linux-x86_64-2.7/falcon_kit/mains/__init__.py -> build/bdist.linux-x86_64/egg/falcon_kit/mains copying build/lib.linux-x86_64-2.7/falcon_kit/mains/ovlp_stats.py -> build/bdist.linux-x86_64/egg/falcon_kit/mains copying build/lib.linux-x86_64-2.7/falcon_kit/mains/graph_to_contig.py -> build/bdist.linux-x86_64/egg/falcon_kit/mains copying build/lib.linux-x86_64-2.7/falcon_kit/mains/report_pre_assembly.py -> build/bdist.linux-x86_64/egg/falcon_kit/mains copying build/lib.linux-x86_64-2.7/falcon_kit/mains/get_read_ctg_map.py -> build/bdist.linux-x86_64/egg/falcon_kit/mains copying build/lib.linux-x86_64-2.7/falcon_kit/mains/LAsort.py -> build/bdist.linux-x86_64/egg/falcon_kit/mains copying build/lib.linux-x86_64-2.7/falcon_kit/mains/consensus.py -> build/bdist.linux-x86_64/egg/falcon_kit/mains creating build/bdist.linux-x86_64/egg/falcon_kit/util copying build/lib.linux-x86_64-2.7/falcon_kit/util/system.py -> build/bdist.linux-x86_64/egg/falcon_kit/util copying build/lib.linux-x86_64-2.7/falcon_kit/util/__init__.py -> build/bdist.linux-x86_64/egg/falcon_kit/util copying build/lib.linux-x86_64-2.7/falcon_kit/util/io.py -> build/bdist.linux-x86_64/egg/falcon_kit/util copying build/lib.linux-x86_64-2.7/ext_falcon.so -> build/bdist.linux-x86_64/egg byte-compiling build/bdist.linux-x86_64/egg/falcon_kit/multiproc.py to multiproc.pyc byte-compiling build/bdist.linux-x86_64/egg/falcon_kit/stats_preassembly.py to stats_preassembly.pyc byte-compiling build/bdist.linux-x86_64/egg/falcon_kit/pype_tasks.py to pype_tasks.pyc byte-compiling build/bdist.linux-x86_64/egg/falcon_kit/__init__.py to __init__.pyc byte-compiling build/bdist.linux-x86_64/egg/falcon_kit/FastaReader.py to FastaReader.pyc byte-compiling build/bdist.linux-x86_64/egg/falcon_kit/bash.py to bash.pyc byte-compiling build/bdist.linux-x86_64/egg/falcon_kit/functional.py to functional.pyc byte-compiling build/bdist.linux-x86_64/egg/falcon_kit/run_support.py to run_support.pyc byte-compiling build/bdist.linux-x86_64/egg/falcon_kit/falcon_kit.py to falcon_kit.pyc byte-compiling build/bdist.linux-x86_64/egg/falcon_kit/fc_asm_graph.py to fc_asm_graph.pyc byte-compiling build/bdist.linux-x86_64/egg/falcon_kit/mains/ovlp_filter.py to ovlp_filter.pyc byte-compiling build/bdist.linux-x86_64/egg/falcon_kit/mains/actg_coordinate.py to actg_coordinate.pyc byte-compiling build/bdist.linux-x86_64/egg/falcon_kit/mains/ovlp_to_graph.py to ovlp_to_graph.pyc byte-compiling build/bdist.linux-x86_64/egg/falcon_kit/mains/ctg_link_analysis.py to ctg_link_analysis.pyc byte-compiling build/bdist.linux-x86_64/egg/falcon_kit/mains/rr_ctg_track.py to rr_ctg_track.pyc byte-compiling build/bdist.linux-x86_64/egg/falcon_kit/mains/tasks.py to tasks.pyc byte-compiling build/bdist.linux-x86_64/egg/falcon_kit/mains/run1.py to run1.pyc byte-compiling build/bdist.linux-x86_64/egg/falcon_kit/mains/graph_to_utgs.py to graph_to_utgs.pyc byte-compiling build/bdist.linux-x86_64/egg/falcon_kit/mains/dedup_a_tigs.py to dedup_a_tigs.pyc byte-compiling build/bdist.linux-x86_64/egg/falcon_kit/mains/fasta2fasta.py to fasta2fasta.pyc byte-compiling build/bdist.linux-x86_64/egg/falcon_kit/mains/contig_annotate.py to contig_annotate.pyc byte-compiling build/bdist.linux-x86_64/egg/falcon_kit/mains/pr_ctg_track.py to pr_ctg_track.pyc byte-compiling build/bdist.linux-x86_64/egg/falcon_kit/mains/fetch_reads.py to fetch_reads.pyc byte-compiling build/bdist.linux-x86_64/egg/falcon_kit/mains/calc_cutoff.py to calc_cutoff.pyc byte-compiling build/bdist.linux-x86_64/egg/falcon_kit/mains/LAmerge.py to LAmerge.pyc byte-compiling build/bdist.linux-x86_64/egg/falcon_kit/mains/__init__.py to __init__.pyc byte-compiling build/bdist.linux-x86_64/egg/falcon_kit/mains/ovlp_stats.py to ovlp_stats.pyc byte-compiling build/bdist.linux-x86_64/egg/falcon_kit/mains/graph_to_contig.py to graph_to_contig.pyc byte-compiling build/bdist.linux-x86_64/egg/falcon_kit/mains/report_pre_assembly.py to report_pre_assembly.pyc byte-compiling build/bdist.linux-x86_64/egg/falcon_kit/mains/get_read_ctg_map.py to get_read_ctg_map.pyc byte-compiling build/bdist.linux-x86_64/egg/falcon_kit/mains/LAsort.py to LAsort.pyc byte-compiling build/bdist.linux-x86_64/egg/falcon_kit/mains/consensus.py to consensus.pyc byte-compiling build/bdist.linux-x86_64/egg/falcon_kit/util/system.py to system.pyc byte-compiling build/bdist.linux-x86_64/egg/falcon_kit/util/__init__.py to __init__.pyc byte-compiling build/bdist.linux-x86_64/egg/falcon_kit/util/io.py to io.pyc creating stub loader for ext_falcon.so byte-compiling build/bdist.linux-x86_64/egg/ext_falcon.py to ext_falcon.pyc creating build/bdist.linux-x86_64/egg/EGG-INFO installing scripts to build/bdist.linux-x86_64/egg/EGG-INFO/scripts running install_scripts running build_scripts creating build/scripts-2.7 copying src/py_scripts/fc_graph_to_utgs.py -> build/scripts-2.7 copying src/py_scripts/fc_graph_to_contig.py -> build/scripts-2.7 copying src/py_scripts/fc_ctg_link_analysis.py -> build/scripts-2.7 copying src/py_scripts/fc_consensus.py -> build/scripts-2.7 copying src/py_scripts/fc_contig_annotate.py -> build/scripts-2.7 copying src/py_scripts/fc_ovlp_stats.py -> build/scripts-2.7 copying src/py_scripts/fc_dedup_a_tigs.py -> build/scripts-2.7 copying src/py_scripts/fc_ovlp_to_graph.py -> build/scripts-2.7 copying src/py_scripts/fc_run.py -> build/scripts-2.7 copying src/py_scripts/fc_actg_coordinate.py -> build/scripts-2.7 copying src/py_scripts/fc_ovlp_filter.py -> build/scripts-2.7 changing mode of build/scripts-2.7/fc_graph_to_utgs.py from 644 to 755 changing mode of build/scripts-2.7/fc_graph_to_contig.py from 644 to 755 changing mode of build/scripts-2.7/fc_ctg_link_analysis.py from 644 to 755 changing mode of build/scripts-2.7/fc_consensus.py from 644 to 755 changing mode of build/scripts-2.7/fc_contig_annotate.py from 644 to 755 changing mode of build/scripts-2.7/fc_ovlp_stats.py from 644 to 755 changing mode of build/scripts-2.7/fc_dedup_a_tigs.py from 644 to 755 changing mode of build/scripts-2.7/fc_ovlp_to_graph.py from 644 to 755 changing mode of build/scripts-2.7/fc_run.py from 644 to 755 changing mode of build/scripts-2.7/fc_actg_coordinate.py from 644 to 755 changing mode of build/scripts-2.7/fc_ovlp_filter.py from 644 to 755 creating build/bdist.linux-x86_64/egg/EGG-INFO/scripts copying build/scripts-2.7/fc_graph_to_utgs.py -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts copying build/scripts-2.7/fc_graph_to_contig.py -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts copying build/scripts-2.7/fc_ctg_link_analysis.py -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts copying build/scripts-2.7/fc_consensus.py -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts copying build/scripts-2.7/fc_contig_annotate.py -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts copying build/scripts-2.7/fc_ovlp_stats.py -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts copying build/scripts-2.7/fc_dedup_a_tigs.py -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts copying build/scripts-2.7/fc_ovlp_to_graph.py -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts copying build/scripts-2.7/fc_run.py -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts copying build/scripts-2.7/fc_actg_coordinate.py -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts copying build/scripts-2.7/fc_ovlp_filter.py -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/fc_graph_to_utgs.py to 755 changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/fc_graph_to_contig.py to 755 changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/fc_ctg_link_analysis.py to 755 changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/fc_consensus.py to 755 changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/fc_contig_annotate.py to 755 changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/fc_ovlp_stats.py to 755 changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/fc_dedup_a_tigs.py to 755 changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/fc_ovlp_to_graph.py to 755 changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/fc_run.py to 755 changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/fc_actg_coordinate.py to 755 changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/fc_ovlp_filter.py to 755 copying falcon_kit.egg-info/PKG-INFO -> build/bdist.linux-x86_64/egg/EGG-INFO copying falcon_kit.egg-info/SOURCES.txt -> build/bdist.linux-x86_64/egg/EGG-INFO copying falcon_kit.egg-info/dependency_links.txt -> build/bdist.linux-x86_64/egg/EGG-INFO copying falcon_kit.egg-info/entry_points.txt -> build/bdist.linux-x86_64/egg/EGG-INFO copying falcon_kit.egg-info/not-zip-safe -> build/bdist.linux-x86_64/egg/EGG-INFO copying falcon_kit.egg-info/requires.txt -> build/bdist.linux-x86_64/egg/EGG-INFO copying falcon_kit.egg-info/top_level.txt -> build/bdist.linux-x86_64/egg/EGG-INFO writing build/bdist.linux-x86_64/egg/EGG-INFO/native_libs.txt creating dist creating 'dist/falcon_kit-0.7-py2.7-linux-x86_64.egg' and adding 'build/bdist.linux-x86_64/egg' to it removing 'build/bdist.linux-x86_64/egg' (and everything under it) Processing falcon_kit-0.7-py2.7-linux-x86_64.egg creating /build/falcon-LwwdoQ/falcon-1.8.8/inst/pylib/falcon_kit-0.7-py2.7-linux-x86_64.egg Extracting falcon_kit-0.7-py2.7-linux-x86_64.egg to /build/falcon-LwwdoQ/falcon-1.8.8/inst/pylib Adding falcon-kit 0.7 to easy-install.pth file Installing fc_actg_coordinate.py script to /build/falcon-LwwdoQ/falcon-1.8.8/inst/bin Installing fc_consensus.py script to /build/falcon-LwwdoQ/falcon-1.8.8/inst/bin Installing fc_contig_annotate.py script to /build/falcon-LwwdoQ/falcon-1.8.8/inst/bin Installing fc_ctg_link_analysis.py script to /build/falcon-LwwdoQ/falcon-1.8.8/inst/bin Installing fc_dedup_a_tigs.py script to /build/falcon-LwwdoQ/falcon-1.8.8/inst/bin Installing fc_graph_to_contig.py script to /build/falcon-LwwdoQ/falcon-1.8.8/inst/bin Installing fc_graph_to_utgs.py script to /build/falcon-LwwdoQ/falcon-1.8.8/inst/bin Installing fc_ovlp_filter.py script to /build/falcon-LwwdoQ/falcon-1.8.8/inst/bin Installing fc_ovlp_stats.py script to /build/falcon-LwwdoQ/falcon-1.8.8/inst/bin Installing fc_ovlp_to_graph.py script to /build/falcon-LwwdoQ/falcon-1.8.8/inst/bin Installing fc_run.py script to /build/falcon-LwwdoQ/falcon-1.8.8/inst/bin Installing fc_fetch_reads script to /build/falcon-LwwdoQ/falcon-1.8.8/inst/bin Installing fc_pr_ctg_track script to /build/falcon-LwwdoQ/falcon-1.8.8/inst/bin Installing fc_actg_coordinate script to /build/falcon-LwwdoQ/falcon-1.8.8/inst/bin Installing fc_fasta2fasta script to /build/falcon-LwwdoQ/falcon-1.8.8/inst/bin Installing fc_ctg_link_analysis script to /build/falcon-LwwdoQ/falcon-1.8.8/inst/bin Installing fc_ovlp_to_graph script to /build/falcon-LwwdoQ/falcon-1.8.8/inst/bin Installing fc_ovlp_filter script to /build/falcon-LwwdoQ/falcon-1.8.8/inst/bin Installing fc_get_read_ctg_map script to /build/falcon-LwwdoQ/falcon-1.8.8/inst/bin Installing fc_run script to /build/falcon-LwwdoQ/falcon-1.8.8/inst/bin Installing fc_contig_annotate script to /build/falcon-LwwdoQ/falcon-1.8.8/inst/bin Installing fc_graph_to_utgs script to /build/falcon-LwwdoQ/falcon-1.8.8/inst/bin Installing fc_run1 script to /build/falcon-LwwdoQ/falcon-1.8.8/inst/bin Installing fc_ovlp_stats script to /build/falcon-LwwdoQ/falcon-1.8.8/inst/bin Installing fc_consensus script to /build/falcon-LwwdoQ/falcon-1.8.8/inst/bin Installing fc_rr_ctg_track script to /build/falcon-LwwdoQ/falcon-1.8.8/inst/bin Installing fc_calc_cutoff script to /build/falcon-LwwdoQ/falcon-1.8.8/inst/bin Installing falcon-task script to /build/falcon-LwwdoQ/falcon-1.8.8/inst/bin Installing fc_graph_to_contig script to /build/falcon-LwwdoQ/falcon-1.8.8/inst/bin Installing fc_dedup_a_tigs script to /build/falcon-LwwdoQ/falcon-1.8.8/inst/bin Installed /build/falcon-LwwdoQ/falcon-1.8.8/inst/pylib/falcon_kit-0.7-py2.7-linux-x86_64.egg Processing dependencies for falcon-kit==0.7 Searching for networkx==1.11 Best match: networkx 1.11 Adding networkx 1.11 to easy-install.pth file Using /usr/lib/python2.7/dist-packages Finished processing dependencies for falcon-kit==0.7 make[4]: Leaving directory '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-make' /usr/bin/make check make[4]: Entering directory '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-make' python -c 'import pypeflow.simple_pwatcher_bridge; print pypeflow.simple_pwatcher_bridge' python -c 'import falcon_kit; print falcon_kit.falcon' make[4]: Leaving directory '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-make' make[3]: Leaving directory '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-make' make[2]: Leaving directory '/build/falcon-LwwdoQ/falcon-1.8.8' make[1]: Leaving directory '/build/falcon-LwwdoQ/falcon-1.8.8' debian/rules override_dh_auto_test make[1]: Entering directory '/build/falcon-LwwdoQ/falcon-1.8.8' /usr/bin/make -C FALCON test make[2]: Entering directory '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON' python -c 'import falcon_kit; print falcon_kit.falcon' #pip install --user pytest py.test -v -s --junit-xml=test.basic.xml test/ ============================= test session starts ============================== platform linux2 -- Python 2.7.14+, pytest-3.2.1, py-1.4.34, pluggy-0.4.0 -- /usr/bin/python cachedir: .cache rootdir: /build/falcon-LwwdoQ/falcon-1.8.8/FALCON, inifile: collecting ... collected 39 items test/test_calc_cutoff.py::test_help usage: py.test [-h] [--coverage COVERAGE] genome_size capture Given the result of 'DBstats -u -b1' on stdin, print the lowest read-length required for sufficient coverage of the genome (i.e. 'length_cutoff'). positional arguments: genome_size Estimated number of bases in genome. (haploid?) capture File with captured output of DBstats. (Otherwise, stdin.) optional arguments: -h, --help show this help message and exit --coverage COVERAGE Desired coverage ratio (i.e. over-sampling) (default: 20) This is useful when length_cutoff is not provided but the genome-size can be estimated. The purpose is to *reduce* the amount of data seen by DALIGNER, since otherwise it will miss many alignments when it encounters resource limits. Note: If PBFALCON_ERRFILE is defined (and its directory is writable), we will write errors there in addition to stderr. PASSED test/test_calc_cutoff.py::test_calc_cutoff PASSED test/test_calc_cutoff.py::test_calc_cutoff_err PASSED test/test_calc_cutoff.py::test_calc_cutoff_errfile PASSED test/test_consensus.py::test_help usage: py.test [-h] [--n_core N_CORE] [--min_cov MIN_COV] [--min_cov_aln MIN_COV_ALN] [--max_cov_aln MAX_COV_ALN] [--min_len_aln MIN_LEN_ALN] [--min_n_read MIN_N_READ] [--max_n_read MAX_N_READ] [--trim] [--output_full] [--output_multi] [--min_idt MIN_IDT] [--edge_tolerance EDGE_TOLERANCE] [--trim_size TRIM_SIZE] a simple multi-processor consensus sequence generator optional arguments: -h, --help show this help message and exit --n_core N_CORE number of processes used for generating consensus; 0 for main process only (default: 24) --min_cov MIN_COV minimum coverage to break the consensus (default: 6) --min_cov_aln MIN_COV_ALN minimum coverage of alignment data; a seed read with less than MIN_COV_ALN average depth of coverage will be completely ignored (default: 10) --max_cov_aln MAX_COV_ALN maximum coverage of alignment data; a seed read with more than MAX_COV_ALN average depth of coverage of the longest alignments will be capped, excess shorter alignments will be ignored (default: 0) --min_len_aln MIN_LEN_ALN minimum length of a sequence in an alignment to be used in consensus; any shorter sequence will be completely ignored (default: 0) --min_n_read MIN_N_READ 1 + minimum number of reads used in generating the consensus; a seed read with fewer alignments will be completely ignored (default: 10) --max_n_read MAX_N_READ 1 + maximum number of reads used in generating the consensus (default: 500) --trim trim the input sequence with k-mer spare dynamic programming to find the mapped range (default: False) --output_full output uncorrected regions too (default: False) --output_multi output multi correct regions (default: False) --min_idt MIN_IDT minimum identity of the alignments used for correction (default: 0.7) --edge_tolerance EDGE_TOLERANCE for trimming, the there is unaligned edge leng > edge_tolerance, ignore the read (default: 1000) --trim_size TRIM_SIZE the size for triming both ends from initial sparse aligned region (default: 50) PASSED test/test_functional.py::test_get_daligner_job_descriptions PASSED test/test_functional.py::test_get_daligner_job_descriptions_with_bad_arg PASSED test/test_functional.py::test_get_daligner_job_descriptions_small PASSED test/test_functional.py::test_get_daligner_job_descriptions_se161 PASSED test/test_functional.py::test_get_mjob_data PASSED test/test_functional.py::test_skip_LAcheck PASSED test/test_functional.py::test_first_block_las PASSED test/test_functional.py::test_xform_script_for_preads PASSED test/test_functional.py::test_calc_cutoff_from_reverse_sorted_readlength_counts::[0] PASSED test/test_functional.py::test_calc_cutoff_from_reverse_sorted_readlength_counts::[1] PASSED test/test_functional.py::test_calc_cutoff_from_reverse_sorted_readlength_counts::[2] PASSED test/test_functional.py::test_calc_cutoff_from_reverse_sorted_readlength_counts::[3] PASSED test/test_functional.py::test_calc_cutoff_from_reverse_sorted_readlength_counts::[4] PASSED test/test_functional.py::test_calc_cutoff_from_reverse_sorted_readlength_counts::[5] PASSED test/test_functional.py::test_get_reverse_sorted_readlength_counts_from_DBstats PASSED test/test_functional.py::test_num2int PASSED test/test_functional.py::test_calc_cutoff PASSED test/test_functional.py::test_calc_cutoff_bad_coverage PASSED test/test_functional.py::test_parsed_readlengths_from_dbdump_output PASSED test/test_functional.py::test_mapped_readlengths_from_dbdump_output PASSED test/test_functional.py::test_average_difference PASSED test/test_functional.py::test_calc_metric_truncation PASSED test/test_functional.py::test_calc_metric_fragmentation PASSED test/test_functional.py::test_args_from_line PASSED test/test_ovlp_filter.py::test_help usage: py.test [-h] [--n_core N_CORE] [--fofn FOFN] [--db DB_FN] [--max_diff MAX_DIFF] [--max_cov MAX_COV] [--min_cov MIN_COV] [--min_len MIN_LEN] [--bestn BESTN] [--stream] [--debug] [--silent] a simple multi-processes LAS ovelap data filter optional arguments: -h, --help show this help message and exit --n_core N_CORE number of processes used for generating consensus; 0 for main process only (default: 4) --fofn FOFN file contains the path of all LAS file to be processed in parallel (default: None) --db DB_FN read db file path (default: None) --max_diff MAX_DIFF max difference of 5' and 3' coverage (default: None) --max_cov MAX_COV max coverage of 5' or 3' coverage (default: None) --min_cov MIN_COV min coverage of 5' or 3' coverage (default: None) --min_len MIN_LEN min length of the reads (default: 2500) --bestn BESTN output at least best n overlaps on 5' or 3' ends if possible (default: 10) --stream stream from LA4Falcon, instead of slurping all at once; can save memory for large data (default: False) --debug, -g single-threaded, plus other aids to debugging (default: False) --silent suppress cmd reporting on stderr (default: False) PASSED test/test_ovlp_filter.py::test_several PASSED test/test_ovlp_filter.py::test_one_not_ignored PASSED test/test_ovlp_filter.py::test_one_line_ignored PASSED test/test_ovlp_filter.py::test_empty PASSED test/test_ovlp_stats.py::test_help usage: py.test [-h] [--n_core N_CORE] --fofn FOFN [--min_len MIN_LEN] [--stream] [--debug] [--silent] a simple multi-processes LAS ovelap data filter optional arguments: -h, --help show this help message and exit --n_core N_CORE number of processes used for generating consensus; 0 for main process only (default: 4) --fofn FOFN file contains the path of all LAS file to be processed in parallel (default: None) --min_len MIN_LEN min length of the reads (default: 2500) --stream stream from LA4Falcon, instead of slurping all at once; can save memory for large data (default: False) --debug, -g single-threaded, plus other aids to debugging (default: False) --silent suppress cmd reporting on stderr (default: False) PASSED test/test_ovlp_stats.py::test PASSED test/test_ovlp_to_graph.py::test_help usage: py.test [-h] [--min_len MIN_LEN] [--min_idt MIN_IDT] [--lfc] [--disable_chimer_bridge_removal] overlap_file a example string graph assembler that is desinged for handling diploid genomes positional arguments: overlap_file a file that contains the overlap information. optional arguments: -h, --help show this help message and exit --min_len MIN_LEN minimum length of the reads to be considered for assembling (default: 4000) --min_idt MIN_IDT minimum alignment identity of the reads to be considered for assembling (default: 96) --lfc use local flow constraint method rather than best overlap method to resolve knots in string graph (default: False) --disable_chimer_bridge_removal disable chimer induced bridge removal (default: False) PASSED test/test_stats_preassembly.py::test_stats_from_sorted_readlengths PASSED test/test_stats_preassembly.py::test_stats_dict PASSED - generated xml file: /build/falcon-LwwdoQ/falcon-1.8.8/FALCON/test.basic.xml -- =============================== warnings summary =============================== test/test_functional.py::test_calc_cutoff_from_reverse_sorted_readlength_counts yield tests are deprecated, and scheduled to be removed in pytest 4.0 -- Docs: http://doc.pytest.org/en/latest/warnings.html ==================== 39 passed, 1 warnings in 0.47 seconds ===================== py.test -v -s --junit-xml=test.doctest.xml --doctest-modules falcon_kit/functional.py ============================= test session starts ============================== platform linux2 -- Python 2.7.14+, pytest-3.2.1, py-1.4.34, pluggy-0.4.0 -- /usr/bin/python cachedir: .cache rootdir: /build/falcon-LwwdoQ/falcon-1.8.8/FALCON, inifile: collecting ... collected 5 items falcon_kit/functional.py::falcon_kit.functional.choose_cat_fasta PASSED falcon_kit/functional.py::falcon_kit.functional.first_block_las PASSED falcon_kit/functional.py::falcon_kit.functional.num2int PASSED falcon_kit/functional.py::falcon_kit.functional.parse_2columns_of_ints PASSED falcon_kit/functional.py::falcon_kit.functional.weighted_average PASSED generated xml file: /build/falcon-LwwdoQ/falcon-1.8.8/FALCON/test.doctest.xml - =========================== 5 passed in 0.08 seconds =========================== cp -f test.basic.xml nose.basic.xml cp -f test.doctest.xml nose.doctest.xml make[2]: Leaving directory '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON' PATH=/build/falcon-LwwdoQ/falcon-1.8.8/inst/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/sbin:/usr/bin:/sbin:/bin /usr/bin/make test make[2]: Entering directory '/build/falcon-LwwdoQ/falcon-1.8.8' /usr/bin/make -C ./FALCON-make/ test make[3]: Entering directory '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-make' /usr/bin/make -C /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples test make[4]: Entering directory '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples' /usr/bin/make run-synth0 make[5]: Entering directory '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples' cd run/synth0; rm -rf 0-rawreads/ 1-preads_ovl/ 2-asm-falcon/; ls -l; fc_run.py fc_run.cfg logging.ini total 36 -rwxr-xr-x 1 builduser builduser 1067 Dec 16 2017 check.py drwxr-xr-x 3 builduser builduser 21 Dec 16 2017 data -rw-r--r-- 1 builduser builduser 1611 Dec 16 2017 fc_preads.cfg -rw-r--r-- 1 builduser builduser 1631 Dec 16 2017 fc_run.cfg -rw-r--r-- 1 builduser builduser 28 Dec 16 2017 input.fofn -rw-r--r-- 1 builduser builduser 461 Dec 16 2017 logging.ini -rw-r--r-- 1 builduser builduser 770 Dec 16 2017 logging.json -rw-r--r-- 1 builduser builduser 1026 Dec 16 2017 logging.many.ini -rw-r--r-- 1 builduser builduser 332 Dec 16 2017 makefile -rw-r--r-- 1 builduser builduser 56 Dec 16 2017 preads.fofn [1731051]$('lfs setstripe -c 12 /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0') sh: 1: lfs: not found [1731051]WARNING: Call 'lfs setstripe -c 12 /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0' returned 32512. 2022-01-06 16:56:54,699[INFO] Setup logging from file "logging.ini". 2022-01-06 16:56:54,700[INFO] fc_run started with configuration fc_run.cfg /build/falcon-LwwdoQ/falcon-1.8.8/inst/pylib/falcon_kit-0.7-py2.7-linux-x86_64.egg/falcon_kit/run_support.py:172: UserWarning: Deprecated setting in config: 'pa_concurrent_jobs' -- Prefer da_concurrent_jobs and la_concurrent_jobs separately warnings.warn("Deprecated setting in config: 'pa_concurrent_jobs' -- Prefer da_concurrent_jobs and la_concurrent_jobs separately") /build/falcon-LwwdoQ/falcon-1.8.8/inst/pylib/falcon_kit-0.7-py2.7-linux-x86_64.egg/falcon_kit/run_support.py:176: UserWarning: Deprecated setting in config: 'ovlp_concurrent_jobs' -- Prefer pda_concurrent_jobs and pla_concurrent_jobs separately warnings.warn("Deprecated setting in config: 'ovlp_concurrent_jobs' -- Prefer pda_concurrent_jobs and pla_concurrent_jobs separately") 2022-01-06 16:56:54,702[INFO] No target specified, assuming "assembly" as target /build/falcon-LwwdoQ/falcon-1.8.8/inst/pylib/falcon_kit-0.7-py2.7-linux-x86_64.egg/falcon_kit/run_support.py:376: UserWarning: Unexpected keys in input config: set(['pa_concurrent_jobs', 'ovlp_concurrent_jobs']) warnings.warn("Unexpected keys in input config: %s" %repr(unused)) 2022-01-06 16:56:54,703[WARNING] In simple_pwatcher_bridge, pwatcher_impl= 2022-01-06 16:56:54,703[INFO] In simple_pwatcher_bridge, pwatcher_impl= 2022-01-06 16:56:54,703[INFO] job_type='string', job_queue='bash -C ${CMD}', sge_option='-pe smp 8 -q bash -C ${CMD}', use_tmpdir=False, squash=True 2022-01-06 16:56:54,706[INFO] Num unsatisfied: 1, graph: 1 2022-01-06 16:56:54,707[INFO] About to submit: Node(0-rawreads/raw-fofn-abs) 2022-01-06 16:56:54,709[INFO] !chmod +x /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/raw-fofn-abs/run-P534c3297c0e197.bash 2022-01-06 16:56:54,722[INFO] sleep 0.1s 2022-01-06 16:56:54,727[INFO] Popen: 'bash -C /build/falcon-LwwdoQ/falcon-1.8.8/inst/pylib/pypeflow-1.0.0-py2.7.egg/pwatcher/mains/job_start.sh' executable=${PYPEFLOW_JOB_START_SCRIPT} + executable=/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/raw-fofn-abs/run-P534c3297c0e197.bash timeout=${PYPEFLOW_JOB_START_TIMEOUT:-60} # wait 60s by default + timeout=60 # Wait up to timeout seconds for the executable to become "executable", # then exec. #timeleft = int(timeout) while [[ ! -x "${executable}" ]]; do if [[ "${timeout}" == "0" ]]; then echo "timed out waiting for (${executable})" exit 77 fi echo "not executable: '${executable}', waiting ${timeout}s" sleep 1 timeout=$((timeout-1)) done + [[ ! -x /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/raw-fofn-abs/run-P534c3297c0e197.bash ]] bash ${executable} + bash /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/raw-fofn-abs/run-P534c3297c0e197.bash + '[' '!' -d /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/raw-fofn-abs ']' + cd /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/raw-fofn-abs + eval '/bin/bash run.sh' ++ /bin/bash run.sh cd /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/raw-fofn-abs + cd /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/raw-fofn-abs bash task.sh + bash task.sh 30e18b9a274d CC=gcc CFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong -Wformat -Werror=format-security CPPFLAGS=-Wdate-time -D_FORTIFY_SOURCE=2 CXX=g++ CXXFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong -Wformat -Werror=format-security DEBCONF_NONINTERACTIVE_SEEN=true DEBIAN_FRONTEND=noninteractive DEB_BUILD_ARCH=amd64 DEB_BUILD_ARCH_ABI=base DEB_BUILD_ARCH_BITS=64 DEB_BUILD_ARCH_CPU=amd64 DEB_BUILD_ARCH_ENDIAN=little DEB_BUILD_ARCH_LIBC=gnu DEB_BUILD_ARCH_OS=linux DEB_BUILD_GNU_CPU=x86_64 DEB_BUILD_GNU_SYSTEM=linux-gnu DEB_BUILD_GNU_TYPE=x86_64-linux-gnu DEB_BUILD_MULTIARCH=x86_64-linux-gnu DEB_BUILD_OPTIONS=nocheck parallel=10 DEB_HOST_ARCH=amd64 DEB_HOST_ARCH_ABI=base DEB_HOST_ARCH_BITS=64 DEB_HOST_ARCH_CPU=amd64 DEB_HOST_ARCH_ENDIAN=little DEB_HOST_ARCH_LIBC=gnu DEB_HOST_ARCH_OS=linux DEB_HOST_GNU_CPU=x86_64 DEB_HOST_GNU_SYSTEM=linux-gnu DEB_HOST_GNU_TYPE=x86_64-linux-gnu DEB_HOST_MULTIARCH=x86_64-linux-gnu DEB_TARGET_ARCH=amd64 DEB_TARGET_ARCH_ABI=base DEB_TARGET_ARCH_BITS=64 DEB_TARGET_ARCH_CPU=amd64 DEB_TARGET_ARCH_ENDIAN=little DEB_TARGET_ARCH_LIBC=gnu DEB_TARGET_ARCH_OS=linux DEB_TARGET_GNU_CPU=x86_64 DEB_TARGET_GNU_SYSTEM=linux-gnu DEB_TARGET_GNU_TYPE=x86_64-linux-gnu DEB_TARGET_MULTIARCH=x86_64-linux-gnu DH_INTERNAL_BUILDFLAGS=1 DH_INTERNAL_OPTIONS=-a DH_INTERNAL_OVERRIDE=dh_auto_test FALCON_INSTALL_RULE=install FALCON_PREFIX=/build/falcon-LwwdoQ/falcon-1.8.8/inst FALCON_WORKSPACE=/build/falcon-LwwdoQ/falcon-1.8.8 FCFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong FFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong GCJFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong HOME=/nonexistent LANG=C.UTF-8 LANGUAGE=C.UTF-8 LC_ALL=C.UTF-8 LDFLAGS=-Wl,-z,relro LOGNAME=builduser MAKEFLAGS=w MAKELEVEL=6 MFLAGS=-w MMDEBSTRAP_APT_CONFIG=/tmp/mmdebstrap.SAG5NvxJ_M/tmp/mmdebstrap.apt.conf.TRj0u44dYeZl MMDEBSTRAP_HOOK=customize MMDEBSTRAP_HOOKSOCK=6 MMDEBSTRAP_MODE=root OBJCFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong -Wformat -Werror=format-security OBJCXXFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong -Wformat -Werror=format-security OLDPWD=/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/raw-fofn-abs PATH=/build/falcon-LwwdoQ/falcon-1.8.8/inst/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/sbin:/usr/bin:/sbin:/bin PERL_USE_UNSAFE_INC=1 PWD=/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/raw-fofn-abs PYPEFLOW_JOB_START_SCRIPT=/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/raw-fofn-abs/run-P534c3297c0e197.bash PYPEFLOW_JOB_START_TIMEOUT=60 PYTHONPATH=/build/falcon-LwwdoQ/falcon-1.8.8/inst/pylib:/build/falcon-LwwdoQ/falcon-1.8.8/inst/pylib: SHELL=/bin/bash SHLVL=5 SOURCE_DATE_EPOCH=1513411047 USER=builduser _=/usr/bin/env /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/raw-fofn-abs 2022-01-06 16:56:54,828[INFO] sleep 0.2s 2022-01-06 16:56:54,851 - root - DEBUG - Running "/build/falcon-LwwdoQ/falcon-1.8.8/inst/pylib/pypeflow-1.0.0-py2.7.egg/pypeflow/do_task.py /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/raw-fofn-abs/task.json" 2022-01-06 16:56:54,853 - root - DEBUG - Checking existence of '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/raw-fofn-abs/task.json' with timeout=60 2022-01-06 16:56:54,854 - root - DEBUG - Loading JSON from '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/raw-fofn-abs/task.json' 2022-01-06 16:56:54,854 - root - DEBUG - {u'inputs': {u'i_fofn': u'/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/input.fofn'}, u'outputs': {u'o_fofn': u'input.fofn'}, u'parameters': {}, u'python_function': u'falcon_kit.pype_tasks.task_make_fofn_abs_raw'} 2022-01-06 16:56:54,854 - root - DEBUG - CD: '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/raw-fofn-abs' <- '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/raw-fofn-abs' 2022-01-06 16:56:54,854 - root - DEBUG - Checking existence of u'/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/input.fofn' with timeout=60 2022-01-06 16:56:54,890 - root - DEBUG - CD: '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/raw-fofn-abs' <- '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/raw-fofn-abs' 2022-01-06 16:56:54,890 - falcon_kit.run_support - DEBUG - CD: u'/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0' <- '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/raw-fofn-abs' 2022-01-06 16:56:54,891 - falcon_kit.run_support - DEBUG - CD: u'/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0' -> '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/raw-fofn-abs' 2022-01-06 16:56:54,891 - pypeflow.do_support - INFO - !/bin/bash -vex noop.sh echo NOOP raw + echo NOOP raw NOOP raw 2022-01-06 16:56:54,897 - root - DEBUG - CD: '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/raw-fofn-abs' -> '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/raw-fofn-abs' 2022-01-06 16:56:54,898 - root - DEBUG - Checking existence of u'input.fofn' with timeout=60 2022-01-06 16:56:54,898 - root - DEBUG - CD: '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/raw-fofn-abs' -> '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/raw-fofn-abs' real 0m0.159s user 0m0.111s sys 0m0.040s touch /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/raw-fofn-abs/run.sh.done + touch /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/raw-fofn-abs/run.sh.done + finish + echo 'finish code: 0' finish code: 0 2022-01-06 16:56:55,029[INFO] recently_satisfied: set([Node(0-rawreads/raw-fofn-abs)]) 2022-01-06 16:56:55,029[INFO] Num satisfied in this iteration: 1 2022-01-06 16:56:55,029[INFO] Num still unsatisfied: 0 2022-01-06 16:56:55,033[INFO] Num unsatisfied: 1, graph: 2 2022-01-06 16:56:55,033[INFO] About to submit: Node(0-rawreads) 2022-01-06 16:56:55,037[INFO] !chmod +x /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/run-P98f74429484946.bash 2022-01-06 16:56:55,046[INFO] sleep 0.1s 2022-01-06 16:56:55,054[INFO] Popen: 'bash -C /build/falcon-LwwdoQ/falcon-1.8.8/inst/pylib/pypeflow-1.0.0-py2.7.egg/pwatcher/mains/job_start.sh' executable=${PYPEFLOW_JOB_START_SCRIPT} + executable=/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/run-P98f74429484946.bash timeout=${PYPEFLOW_JOB_START_TIMEOUT:-60} # wait 60s by default + timeout=60 # Wait up to timeout seconds for the executable to become "executable", # then exec. #timeleft = int(timeout) while [[ ! -x "${executable}" ]]; do if [[ "${timeout}" == "0" ]]; then echo "timed out waiting for (${executable})" exit 77 fi echo "not executable: '${executable}', waiting ${timeout}s" sleep 1 timeout=$((timeout-1)) done + [[ ! -x /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/run-P98f74429484946.bash ]] bash ${executable} + bash /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/run-P98f74429484946.bash + '[' '!' -d /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads ']' + cd /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads + eval '/bin/bash run.sh' ++ /bin/bash run.sh cd /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads + cd /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads bash task.sh + bash task.sh 30e18b9a274d CC=gcc CFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong -Wformat -Werror=format-security CPPFLAGS=-Wdate-time -D_FORTIFY_SOURCE=2 CXX=g++ CXXFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong -Wformat -Werror=format-security DEBCONF_NONINTERACTIVE_SEEN=true DEBIAN_FRONTEND=noninteractive DEB_BUILD_ARCH=amd64 DEB_BUILD_ARCH_ABI=base DEB_BUILD_ARCH_BITS=64 DEB_BUILD_ARCH_CPU=amd64 DEB_BUILD_ARCH_ENDIAN=little DEB_BUILD_ARCH_LIBC=gnu DEB_BUILD_ARCH_OS=linux DEB_BUILD_GNU_CPU=x86_64 DEB_BUILD_GNU_SYSTEM=linux-gnu DEB_BUILD_GNU_TYPE=x86_64-linux-gnu DEB_BUILD_MULTIARCH=x86_64-linux-gnu DEB_BUILD_OPTIONS=nocheck parallel=10 DEB_HOST_ARCH=amd64 DEB_HOST_ARCH_ABI=base DEB_HOST_ARCH_BITS=64 DEB_HOST_ARCH_CPU=amd64 DEB_HOST_ARCH_ENDIAN=little DEB_HOST_ARCH_LIBC=gnu DEB_HOST_ARCH_OS=linux DEB_HOST_GNU_CPU=x86_64 DEB_HOST_GNU_SYSTEM=linux-gnu DEB_HOST_GNU_TYPE=x86_64-linux-gnu DEB_HOST_MULTIARCH=x86_64-linux-gnu DEB_TARGET_ARCH=amd64 DEB_TARGET_ARCH_ABI=base DEB_TARGET_ARCH_BITS=64 DEB_TARGET_ARCH_CPU=amd64 DEB_TARGET_ARCH_ENDIAN=little DEB_TARGET_ARCH_LIBC=gnu DEB_TARGET_ARCH_OS=linux DEB_TARGET_GNU_CPU=x86_64 DEB_TARGET_GNU_SYSTEM=linux-gnu DEB_TARGET_GNU_TYPE=x86_64-linux-gnu DEB_TARGET_MULTIARCH=x86_64-linux-gnu DH_INTERNAL_BUILDFLAGS=1 DH_INTERNAL_OPTIONS=-a DH_INTERNAL_OVERRIDE=dh_auto_test FALCON_INSTALL_RULE=install FALCON_PREFIX=/build/falcon-LwwdoQ/falcon-1.8.8/inst FALCON_WORKSPACE=/build/falcon-LwwdoQ/falcon-1.8.8 FCFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong FFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong GCJFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong HOME=/nonexistent LANG=C.UTF-8 LANGUAGE=C.UTF-8 LC_ALL=C.UTF-8 LDFLAGS=-Wl,-z,relro LOGNAME=builduser MAKEFLAGS=w MAKELEVEL=6 MFLAGS=-w MMDEBSTRAP_APT_CONFIG=/tmp/mmdebstrap.SAG5NvxJ_M/tmp/mmdebstrap.apt.conf.TRj0u44dYeZl MMDEBSTRAP_HOOK=customize MMDEBSTRAP_HOOKSOCK=6 MMDEBSTRAP_MODE=root OBJCFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong -Wformat -Werror=format-security OBJCXXFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong -Wformat -Werror=format-security OLDPWD=/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads PATH=/build/falcon-LwwdoQ/falcon-1.8.8/inst/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/sbin:/usr/bin:/sbin:/bin PERL_USE_UNSAFE_INC=1 PWD=/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads PYPEFLOW_JOB_START_SCRIPT=/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/run-P98f74429484946.bash PYPEFLOW_JOB_START_TIMEOUT=60 PYTHONPATH=/build/falcon-LwwdoQ/falcon-1.8.8/inst/pylib:/build/falcon-LwwdoQ/falcon-1.8.8/inst/pylib: SHELL=/bin/bash SHLVL=5 SOURCE_DATE_EPOCH=1513411047 USER=builduser _=/usr/bin/env /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads 2022-01-06 16:56:55,154[INFO] sleep 0.2s 2022-01-06 16:56:55,181 - root - DEBUG - Running "/build/falcon-LwwdoQ/falcon-1.8.8/inst/pylib/pypeflow-1.0.0-py2.7.egg/pypeflow/do_task.py /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/task.json" 2022-01-06 16:56:55,183 - root - DEBUG - Checking existence of '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/task.json' with timeout=60 2022-01-06 16:56:55,184 - root - DEBUG - Loading JSON from '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/task.json' 2022-01-06 16:56:55,186 - root - DEBUG - {u'inputs': {u'input_fofn': u'/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/raw-fofn-abs/input.fofn'}, u'outputs': {u'length_cutoff': u'length_cutoff', u'raw_reads_db': u'raw_reads.db', u'rdb_build_done': u'rdb_build_done', u'run_jobs': u'run_jobs.sh'}, u'parameters': {u'config': {u'LA4Falcon_preload': True, u'avoid_text_file_busy': True, u'cns_concurrent_jobs': 32, u'da_concurrent_jobs': 32, u'dazcon': False, u'default_concurrent_jobs': 8, u'dust': False, u'falcon_sense_greedy': False, u'falcon_sense_option': u'--output_multi --min_idt 0.70 --min_cov 1 --max_n_read 20000 --n_core 0', u'falcon_sense_skip_contained': False, u'fc_concurrent_jobs': 8, u'fc_ovlp_to_graph_option': u' --min_len 1', u'genome_size': 5000, u'input_fofn': u'input.fofn', u'input_type': u'raw', u'install_prefix': u'/usr', u'job_queue': u'bash -C ${CMD}', u'job_type': u'string', u'la_concurrent_jobs': 32, u'length_cutoff': -1, u'length_cutoff_pr': 1, u'overlap_filtering_setting': u'--max_diff 10000 --max_cov 100000 --min_cov 1 --min_len 1 --bestn 1000 --n_core 0', u'ovlp_DBsplit_option': u'-a -x5 -s50', u'ovlp_HPCdaligner_option': u'-v -B4 -t50 -h1 -e.99 -l1 -s1000', u'pa_DBdust_option': u'-w128 -t2.5 -m20', u'pa_DBsplit_option': u'-a -x5 -s.065536', u'pa_HPCdaligner_option': u'-v -B4 -t50 -h1 -e.99 -w1 -l1 -s1000', u'pa_dazcon_option': u'-j 4 -x -l 500', u'pda_concurrent_jobs': 32, u'pla_concurrent_jobs': 32, u'pwatcher_directory': u'mypwatcher', u'pwatcher_type': u'blocking', u'seed_coverage': 20.0, u'sge_option': u'-pe smp 8 -q bash -C ${CMD}', u'sge_option_cns': u'-pe smp 8 -q bash -C ${CMD}', u'sge_option_da': u'-pe smp 8 -q bash -C ${CMD}', u'sge_option_fc': u'-pe smp 24 -q bash -C ${CMD}', u'sge_option_la': u'-pe smp 2 -q bash -C ${CMD}', u'sge_option_pda': u'-pe smp 8 -q bash -C ${CMD}', u'sge_option_pla': u'-pe smp 2 -q bash -C ${CMD}', u'skip_checks': False, u'stop_all_jobs_on_failure': True, u'target': u'assembly', u'use_tmpdir': False}, u'config_fn': u'/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/fc_run.cfg', u'sge_option': u'-pe smp 8 -q bash -C ${CMD}', u'work_dir': u'/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads'}, u'python_function': u'falcon_kit.pype_tasks.task_build_rdb'} 2022-01-06 16:56:55,186 - root - DEBUG - CD: '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads' <- '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads' 2022-01-06 16:56:55,187 - root - DEBUG - Checking existence of u'/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/raw-fofn-abs/input.fofn' with timeout=60 2022-01-06 16:56:55,218 - root - DEBUG - CD: '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads' <- '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads' 2022-01-06 16:56:55,219 - pypeflow.do_support - INFO - !/bin/bash -vex /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/prepare_rdb.sh #!/bin/bash set -vex + set -vex echo "PBFALCON_ERRFILE=$PBFALCON_ERRFILE" + echo PBFALCON_ERRFILE= PBFALCON_ERRFILE= set -o pipefail + set -o pipefail #fc_fasta2fasta < /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/raw-fofn-abs/input.fofn >| fc.fofn while read fn; do undexta -vkU -w60 -i < $fn | fasta2DB -v raw_reads -i${fn##*/}; done < /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/raw-fofn-abs/input.fofn + read fn + undexta -vkU -w60 -i + fasta2DB -v raw_reads -isubreads.dexta Processing 'Standard Input' ... Adding 'subreads.dexta.fasta' ... Done + read fn #cat fc.fofn | xargs rm -f DBsplit -a -x5 -s.065536 raw_reads + DBsplit -a -x5 -s.065536 raw_reads #DBdust -w128 -t2.5 -m20 raw_reads LB=$(cat raw_reads.db | LD_LIBRARY_PATH= awk '$1 == "blocks" {print $3}') ++ cat raw_reads.db ++ LD_LIBRARY_PATH= ++ awk '$1 == "blocks" {print $3}' 2022-01-06 16:56:55,355[INFO] sleep 0.3s + LB=2 rm -f run_jobs.sh + rm -f run_jobs.sh CUTOFF=$(python2.7 -m falcon_kit.mains.calc_cutoff --coverage 20.0 5000 <(DBstats -b1 raw_reads)) ++ python2.7 -m falcon_kit.mains.calc_cutoff --coverage 20.0 5000 /dev/fd/63 +++ DBstats -b1 raw_reads + CUTOFF=2000 echo -n $CUTOFF >| length_cutoff + echo -n 2000 HPC.daligner -v -B4 -t50 -h1 -e.99 -w1 -l1 -s1000 -H$CUTOFF raw_reads 1-$LB >| run_jobs.sh + HPC.daligner -v -B4 -t50 -h1 -e.99 -w1 -l1 -s1000 -H2000 raw_reads 1-2 touch rdb_build_done + touch rdb_build_done 2022-01-06 16:56:55,429 - root - DEBUG - CD: '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads' -> '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads' 2022-01-06 16:56:55,430 - root - DEBUG - Checking existence of u'length_cutoff' with timeout=60 2022-01-06 16:56:55,430 - root - DEBUG - Checking existence of u'run_jobs.sh' with timeout=60 2022-01-06 16:56:55,430 - root - DEBUG - Checking existence of u'rdb_build_done' with timeout=60 2022-01-06 16:56:55,430 - root - DEBUG - Checking existence of u'raw_reads.db' with timeout=60 2022-01-06 16:56:55,430 - root - DEBUG - CD: '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads' -> '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads' real 0m0.359s user 0m0.156s sys 0m0.083s touch /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/run.sh.done + touch /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/run.sh.done + finish + echo 'finish code: 0' finish code: 0 2022-01-06 16:56:55,656[INFO] recently_satisfied: set([Node(0-rawreads)]) 2022-01-06 16:56:55,656[INFO] Num satisfied in this iteration: 1 2022-01-06 16:56:55,656[INFO] Num still unsatisfied: 0 2022-01-06 16:56:55,660[INFO] Num unsatisfied: 1, graph: 3 2022-01-06 16:56:55,661[INFO] About to submit: Node(0-rawreads/daligner-scatter) 2022-01-06 16:56:55,663[INFO] !chmod +x /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/daligner-scatter/run-Pae7fc021df6abd.bash 2022-01-06 16:56:55,674[INFO] sleep 0.1s 2022-01-06 16:56:55,679[INFO] Popen: 'bash -C /build/falcon-LwwdoQ/falcon-1.8.8/inst/pylib/pypeflow-1.0.0-py2.7.egg/pwatcher/mains/job_start.sh' executable=${PYPEFLOW_JOB_START_SCRIPT} + executable=/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/daligner-scatter/run-Pae7fc021df6abd.bash timeout=${PYPEFLOW_JOB_START_TIMEOUT:-60} # wait 60s by default + timeout=60 # Wait up to timeout seconds for the executable to become "executable", # then exec. #timeleft = int(timeout) while [[ ! -x "${executable}" ]]; do if [[ "${timeout}" == "0" ]]; then echo "timed out waiting for (${executable})" exit 77 fi echo "not executable: '${executable}', waiting ${timeout}s" sleep 1 timeout=$((timeout-1)) done + [[ ! -x /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/daligner-scatter/run-Pae7fc021df6abd.bash ]] bash ${executable} + bash /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/daligner-scatter/run-Pae7fc021df6abd.bash + '[' '!' -d /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/daligner-scatter ']' + cd /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/daligner-scatter + eval '/bin/bash run.sh' ++ /bin/bash run.sh cd /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/daligner-scatter + cd /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/daligner-scatter bash task.sh + bash task.sh 30e18b9a274d CC=gcc CFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong -Wformat -Werror=format-security CPPFLAGS=-Wdate-time -D_FORTIFY_SOURCE=2 CXX=g++ CXXFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong -Wformat -Werror=format-security DEBCONF_NONINTERACTIVE_SEEN=true DEBIAN_FRONTEND=noninteractive DEB_BUILD_ARCH=amd64 DEB_BUILD_ARCH_ABI=base DEB_BUILD_ARCH_BITS=64 DEB_BUILD_ARCH_CPU=amd64 DEB_BUILD_ARCH_ENDIAN=little DEB_BUILD_ARCH_LIBC=gnu DEB_BUILD_ARCH_OS=linux DEB_BUILD_GNU_CPU=x86_64 DEB_BUILD_GNU_SYSTEM=linux-gnu DEB_BUILD_GNU_TYPE=x86_64-linux-gnu DEB_BUILD_MULTIARCH=x86_64-linux-gnu DEB_BUILD_OPTIONS=nocheck parallel=10 DEB_HOST_ARCH=amd64 DEB_HOST_ARCH_ABI=base DEB_HOST_ARCH_BITS=64 DEB_HOST_ARCH_CPU=amd64 DEB_HOST_ARCH_ENDIAN=little DEB_HOST_ARCH_LIBC=gnu DEB_HOST_ARCH_OS=linux DEB_HOST_GNU_CPU=x86_64 DEB_HOST_GNU_SYSTEM=linux-gnu DEB_HOST_GNU_TYPE=x86_64-linux-gnu DEB_HOST_MULTIARCH=x86_64-linux-gnu DEB_TARGET_ARCH=amd64 DEB_TARGET_ARCH_ABI=base DEB_TARGET_ARCH_BITS=64 DEB_TARGET_ARCH_CPU=amd64 DEB_TARGET_ARCH_ENDIAN=little DEB_TARGET_ARCH_LIBC=gnu DEB_TARGET_ARCH_OS=linux DEB_TARGET_GNU_CPU=x86_64 DEB_TARGET_GNU_SYSTEM=linux-gnu DEB_TARGET_GNU_TYPE=x86_64-linux-gnu DEB_TARGET_MULTIARCH=x86_64-linux-gnu DH_INTERNAL_BUILDFLAGS=1 DH_INTERNAL_OPTIONS=-a DH_INTERNAL_OVERRIDE=dh_auto_test FALCON_INSTALL_RULE=install FALCON_PREFIX=/build/falcon-LwwdoQ/falcon-1.8.8/inst FALCON_WORKSPACE=/build/falcon-LwwdoQ/falcon-1.8.8 FCFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong FFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong GCJFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong HOME=/nonexistent LANG=C.UTF-8 LANGUAGE=C.UTF-8 LC_ALL=C.UTF-8 LDFLAGS=-Wl,-z,relro LOGNAME=builduser MAKEFLAGS=w MAKELEVEL=6 MFLAGS=-w MMDEBSTRAP_APT_CONFIG=/tmp/mmdebstrap.SAG5NvxJ_M/tmp/mmdebstrap.apt.conf.TRj0u44dYeZl MMDEBSTRAP_HOOK=customize MMDEBSTRAP_HOOKSOCK=6 MMDEBSTRAP_MODE=root OBJCFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong -Wformat -Werror=format-security OBJCXXFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong -Wformat -Werror=format-security OLDPWD=/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/daligner-scatter PATH=/build/falcon-LwwdoQ/falcon-1.8.8/inst/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/sbin:/usr/bin:/sbin:/bin PERL_USE_UNSAFE_INC=1 PWD=/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/daligner-scatter PYPEFLOW_JOB_START_SCRIPT=/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/daligner-scatter/run-Pae7fc021df6abd.bash PYPEFLOW_JOB_START_TIMEOUT=60 PYTHONPATH=/build/falcon-LwwdoQ/falcon-1.8.8/inst/pylib:/build/falcon-LwwdoQ/falcon-1.8.8/inst/pylib: SHELL=/bin/bash SHLVL=5 SOURCE_DATE_EPOCH=1513411047 USER=builduser _=/usr/bin/env /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/daligner-scatter 2022-01-06 16:56:55,775[INFO] sleep 0.2s 2022-01-06 16:56:55,802 - root - DEBUG - Running "/build/falcon-LwwdoQ/falcon-1.8.8/inst/pylib/pypeflow-1.0.0-py2.7.egg/pypeflow/do_task.py /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/daligner-scatter/task.json" 2022-01-06 16:56:55,804 - root - DEBUG - Checking existence of '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/daligner-scatter/task.json' with timeout=60 2022-01-06 16:56:55,805 - root - DEBUG - Loading JSON from '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/daligner-scatter/task.json' 2022-01-06 16:56:55,807 - root - DEBUG - {u'inputs': {u'db_build_done': u'/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/rdb_build_done', u'run_jobs_fn': u'/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/run_jobs.sh'}, u'outputs': {u'scatter_fn': u'scattered.json'}, u'parameters': {u'config': {u'LA4Falcon_preload': True, u'avoid_text_file_busy': True, u'cns_concurrent_jobs': 32, u'da_concurrent_jobs': 32, u'dazcon': False, u'default_concurrent_jobs': 8, u'dust': False, u'falcon_sense_greedy': False, u'falcon_sense_option': u'--output_multi --min_idt 0.70 --min_cov 1 --max_n_read 20000 --n_core 0', u'falcon_sense_skip_contained': False, u'fc_concurrent_jobs': 8, u'fc_ovlp_to_graph_option': u' --min_len 1', u'genome_size': 5000, u'input_fofn': u'input.fofn', u'input_type': u'raw', u'install_prefix': u'/usr', u'job_queue': u'bash -C ${CMD}', u'job_type': u'string', u'la_concurrent_jobs': 32, u'length_cutoff': -1, u'length_cutoff_pr': 1, u'overlap_filtering_setting': u'--max_diff 10000 --max_cov 100000 --min_cov 1 --min_len 1 --bestn 1000 --n_core 0', u'ovlp_DBsplit_option': u'-a -x5 -s50', u'ovlp_HPCdaligner_option': u'-v -B4 -t50 -h1 -e.99 -l1 -s1000', u'pa_DBdust_option': u'-w128 -t2.5 -m20', u'pa_DBsplit_option': u'-a -x5 -s.065536', u'pa_HPCdaligner_option': u'-v -B4 -t50 -h1 -e.99 -w1 -l1 -s1000', u'pa_dazcon_option': u'-j 4 -x -l 500', u'pda_concurrent_jobs': 32, u'pla_concurrent_jobs': 32, u'pwatcher_directory': u'mypwatcher', u'pwatcher_type': u'blocking', u'seed_coverage': 20.0, u'sge_option': u'-pe smp 8 -q bash -C ${CMD}', u'sge_option_cns': u'-pe smp 8 -q bash -C ${CMD}', u'sge_option_da': u'-pe smp 8 -q bash -C ${CMD}', u'sge_option_fc': u'-pe smp 24 -q bash -C ${CMD}', u'sge_option_la': u'-pe smp 2 -q bash -C ${CMD}', u'sge_option_pda': u'-pe smp 8 -q bash -C ${CMD}', u'sge_option_pla': u'-pe smp 2 -q bash -C ${CMD}', u'skip_checks': False, u'stop_all_jobs_on_failure': True, u'target': u'assembly', u'use_tmpdir': False}, u'db_prefix': u'raw_reads', u'nblock': 2, u'pread_aln': False}, u'python_function': u'falcon_kit.pype_tasks.task_daligner_scatter'} 2022-01-06 16:56:55,807 - root - DEBUG - CD: '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/daligner-scatter' <- '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/daligner-scatter' 2022-01-06 16:56:55,807 - root - DEBUG - Checking existence of u'/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/run_jobs.sh' with timeout=60 2022-01-06 16:56:55,808 - root - DEBUG - Checking existence of u'/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/rdb_build_done' with timeout=60 2022-01-06 16:56:55,839 - root - DEBUG - CD: '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/daligner-scatter' <- '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/daligner-scatter' 2022-01-06 16:56:55,840 - falcon_kit.pype_tasks - INFO - Skip LAcheck after daligner? False 2022-01-06 16:56:55,842 - root - DEBUG - CD: '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/daligner-scatter' -> '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/daligner-scatter' 2022-01-06 16:56:55,842 - root - DEBUG - Checking existence of u'scattered.json' with timeout=60 2022-01-06 16:56:55,843 - root - DEBUG - CD: '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/daligner-scatter' -> '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/daligner-scatter' real 0m0.150s user 0m0.094s sys 0m0.051s touch /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/daligner-scatter/run.sh.done + touch /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/daligner-scatter/run.sh.done + finish + echo 'finish code: 0' finish code: 0 2022-01-06 16:56:55,977[INFO] recently_satisfied: set([Node(0-rawreads/daligner-scatter)]) 2022-01-06 16:56:55,977[INFO] Num satisfied in this iteration: 1 2022-01-06 16:56:55,977[INFO] Num still unsatisfied: 0 2022-01-06 16:56:55,988[INFO] Num unsatisfied: 3, graph: 6 2022-01-06 16:56:55,988[INFO] About to submit: Node(0-rawreads/job_0001) 2022-01-06 16:56:55,988[INFO] About to submit: Node(0-rawreads/job_0000) 2022-01-06 16:56:55,993[INFO] !chmod +x /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/job_0000/run-P4df58ec19da890.bash 2022-01-06 16:56:56,004[INFO] !chmod +x /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/job_0001/run-P2ed4084be16966.bash 2022-01-06 16:56:56,013[INFO] Popen: 'bash -C /build/falcon-LwwdoQ/falcon-1.8.8/inst/pylib/pypeflow-1.0.0-py2.7.egg/pwatcher/mains/job_start.sh' executable=${PYPEFLOW_JOB_START_SCRIPT} + executable=/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/job_0000/run-P4df58ec19da890.bash timeout=${PYPEFLOW_JOB_START_TIMEOUT:-60} # wait 60s by default + timeout=60 # Wait up to timeout seconds for the executable to become "executable", # then exec. #timeleft = int(timeout) while [[ ! -x "${executable}" ]]; do if [[ "${timeout}" == "0" ]]; then echo "timed out waiting for (${executable})" exit 77 fi echo "not executable: '${executable}', waiting ${timeout}s" sleep 1 timeout=$((timeout-1)) done + [[ ! -x /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/job_0000/run-P4df58ec19da890.bash ]] 2022-01-06 16:56:56,023[INFO] sleep 0.1s bash ${executable} + bash /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/job_0000/run-P4df58ec19da890.bash + '[' '!' -d /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/job_0000 ']' + cd /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/job_0000 + eval '/bin/bash run.sh' ++ /bin/bash run.sh 2022-01-06 16:56:56,028[INFO] Popen: 'bash -C /build/falcon-LwwdoQ/falcon-1.8.8/inst/pylib/pypeflow-1.0.0-py2.7.egg/pwatcher/mains/job_start.sh' cd /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/job_0000 + cd /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/job_0000 bash task.sh + bash task.sh 30e18b9a274d executable=${PYPEFLOW_JOB_START_SCRIPT} + executable=/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/job_0001/run-P2ed4084be16966.bash timeout=${PYPEFLOW_JOB_START_TIMEOUT:-60} # wait 60s by default + timeout=60 # Wait up to timeout seconds for the executable to become "executable", # then exec. #timeleft = int(timeout) while [[ ! -x "${executable}" ]]; do if [[ "${timeout}" == "0" ]]; then echo "timed out waiting for (${executable})" exit 77 fi echo "not executable: '${executable}', waiting ${timeout}s" sleep 1 timeout=$((timeout-1)) done + [[ ! -x /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/job_0001/run-P2ed4084be16966.bash ]] bash ${executable} + bash /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/job_0001/run-P2ed4084be16966.bash CC=gcc CFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong -Wformat -Werror=format-security CPPFLAGS=-Wdate-time -D_FORTIFY_SOURCE=2 CXX=g++ CXXFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong -Wformat -Werror=format-security DEBCONF_NONINTERACTIVE_SEEN=true DEBIAN_FRONTEND=noninteractive DEB_BUILD_ARCH=amd64 DEB_BUILD_ARCH_ABI=base DEB_BUILD_ARCH_BITS=64 DEB_BUILD_ARCH_CPU=amd64 DEB_BUILD_ARCH_ENDIAN=little DEB_BUILD_ARCH_LIBC=gnu DEB_BUILD_ARCH_OS=linux DEB_BUILD_GNU_CPU=x86_64 DEB_BUILD_GNU_SYSTEM=linux-gnu DEB_BUILD_GNU_TYPE=x86_64-linux-gnu DEB_BUILD_MULTIARCH=x86_64-linux-gnu DEB_BUILD_OPTIONS=nocheck parallel=10 DEB_HOST_ARCH=amd64 DEB_HOST_ARCH_ABI=base DEB_HOST_ARCH_BITS=64 DEB_HOST_ARCH_CPU=amd64 DEB_HOST_ARCH_ENDIAN=little DEB_HOST_ARCH_LIBC=gnu DEB_HOST_ARCH_OS=linux DEB_HOST_GNU_CPU=x86_64 DEB_HOST_GNU_SYSTEM=linux-gnu DEB_HOST_GNU_TYPE=x86_64-linux-gnu DEB_HOST_MULTIARCH=x86_64-linux-gnu DEB_TARGET_ARCH=amd64 DEB_TARGET_ARCH_ABI=base DEB_TARGET_ARCH_BITS=64 DEB_TARGET_ARCH_CPU=amd64 DEB_TARGET_ARCH_ENDIAN=little DEB_TARGET_ARCH_LIBC=gnu DEB_TARGET_ARCH_OS=linux DEB_TARGET_GNU_CPU=x86_64 DEB_TARGET_GNU_SYSTEM=linux-gnu DEB_TARGET_GNU_TYPE=x86_64-linux-gnu DEB_TARGET_MULTIARCH=x86_64-linux-gnu DH_INTERNAL_BUILDFLAGS=1 DH_INTERNAL_OPTIONS=-a DH_INTERNAL_OVERRIDE=dh_auto_test FALCON_INSTALL_RULE=install FALCON_PREFIX=/build/falcon-LwwdoQ/falcon-1.8.8/inst FALCON_WORKSPACE=/build/falcon-LwwdoQ/falcon-1.8.8 FCFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong FFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong GCJFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong HOME=/nonexistent LANG=C.UTF-8 LANGUAGE=C.UTF-8 LC_ALL=C.UTF-8 LDFLAGS=-Wl,-z,relro LOGNAME=builduser MAKEFLAGS=w MAKELEVEL=6 MFLAGS=-w MMDEBSTRAP_APT_CONFIG=/tmp/mmdebstrap.SAG5NvxJ_M/tmp/mmdebstrap.apt.conf.TRj0u44dYeZl MMDEBSTRAP_HOOK=customize MMDEBSTRAP_HOOKSOCK=6 MMDEBSTRAP_MODE=root OBJCFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong -Wformat -Werror=format-security OBJCXXFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong -Wformat -Werror=format-security OLDPWD=/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/job_0000 PATH=/build/falcon-LwwdoQ/falcon-1.8.8/inst/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/sbin:/usr/bin:/sbin:/bin PERL_USE_UNSAFE_INC=1 PWD=/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/job_0000 PYPEFLOW_JOB_START_SCRIPT=/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/job_0000/run-P4df58ec19da890.bash PYPEFLOW_JOB_START_TIMEOUT=60 PYTHONPATH=/build/falcon-LwwdoQ/falcon-1.8.8/inst/pylib:/build/falcon-LwwdoQ/falcon-1.8.8/inst/pylib: SHELL=/bin/bash SHLVL=5 SOURCE_DATE_EPOCH=1513411047 USER=builduser _=/usr/bin/env /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/job_0000 + '[' '!' -d /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/job_0001 ']' + cd /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/job_0001 + eval '/bin/bash run.sh' ++ /bin/bash run.sh cd /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/job_0001 + cd /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/job_0001 bash task.sh + bash task.sh 30e18b9a274d CC=gcc CFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong -Wformat -Werror=format-security CPPFLAGS=-Wdate-time -D_FORTIFY_SOURCE=2 CXX=g++ CXXFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong -Wformat -Werror=format-security DEBCONF_NONINTERACTIVE_SEEN=true DEBIAN_FRONTEND=noninteractive DEB_BUILD_ARCH=amd64 DEB_BUILD_ARCH_ABI=base DEB_BUILD_ARCH_BITS=64 DEB_BUILD_ARCH_CPU=amd64 DEB_BUILD_ARCH_ENDIAN=little DEB_BUILD_ARCH_LIBC=gnu DEB_BUILD_ARCH_OS=linux DEB_BUILD_GNU_CPU=x86_64 DEB_BUILD_GNU_SYSTEM=linux-gnu DEB_BUILD_GNU_TYPE=x86_64-linux-gnu DEB_BUILD_MULTIARCH=x86_64-linux-gnu DEB_BUILD_OPTIONS=nocheck parallel=10 DEB_HOST_ARCH=amd64 DEB_HOST_ARCH_ABI=base DEB_HOST_ARCH_BITS=64 DEB_HOST_ARCH_CPU=amd64 DEB_HOST_ARCH_ENDIAN=little DEB_HOST_ARCH_LIBC=gnu DEB_HOST_ARCH_OS=linux DEB_HOST_GNU_CPU=x86_64 DEB_HOST_GNU_SYSTEM=linux-gnu DEB_HOST_GNU_TYPE=x86_64-linux-gnu DEB_HOST_MULTIARCH=x86_64-linux-gnu DEB_TARGET_ARCH=amd64 DEB_TARGET_ARCH_ABI=base DEB_TARGET_ARCH_BITS=64 DEB_TARGET_ARCH_CPU=amd64 DEB_TARGET_ARCH_ENDIAN=little DEB_TARGET_ARCH_LIBC=gnu DEB_TARGET_ARCH_OS=linux DEB_TARGET_GNU_CPU=x86_64 DEB_TARGET_GNU_SYSTEM=linux-gnu DEB_TARGET_GNU_TYPE=x86_64-linux-gnu DEB_TARGET_MULTIARCH=x86_64-linux-gnu DH_INTERNAL_BUILDFLAGS=1 DH_INTERNAL_OPTIONS=-a DH_INTERNAL_OVERRIDE=dh_auto_test FALCON_INSTALL_RULE=install FALCON_PREFIX=/build/falcon-LwwdoQ/falcon-1.8.8/inst FALCON_WORKSPACE=/build/falcon-LwwdoQ/falcon-1.8.8 FCFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong FFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong GCJFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong HOME=/nonexistent LANG=C.UTF-8 LANGUAGE=C.UTF-8 LC_ALL=C.UTF-8 LDFLAGS=-Wl,-z,relro LOGNAME=builduser MAKEFLAGS=w MAKELEVEL=6 MFLAGS=-w MMDEBSTRAP_APT_CONFIG=/tmp/mmdebstrap.SAG5NvxJ_M/tmp/mmdebstrap.apt.conf.TRj0u44dYeZl MMDEBSTRAP_HOOK=customize MMDEBSTRAP_HOOKSOCK=6 MMDEBSTRAP_MODE=root OBJCFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong -Wformat -Werror=format-security OBJCXXFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong -Wformat -Werror=format-security OLDPWD=/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/job_0001 PATH=/build/falcon-LwwdoQ/falcon-1.8.8/inst/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/sbin:/usr/bin:/sbin:/bin PERL_USE_UNSAFE_INC=1 PWD=/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/job_0001 PYPEFLOW_JOB_START_SCRIPT=/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/job_0001/run-P2ed4084be16966.bash PYPEFLOW_JOB_START_TIMEOUT=60 PYTHONPATH=/build/falcon-LwwdoQ/falcon-1.8.8/inst/pylib:/build/falcon-LwwdoQ/falcon-1.8.8/inst/pylib: SHELL=/bin/bash SHLVL=5 SOURCE_DATE_EPOCH=1513411047 USER=builduser _=/usr/bin/env /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/job_0001 2022-01-06 16:56:56,125[INFO] sleep 0.2s 2022-01-06 16:56:56,135 - root - DEBUG - Running "/build/falcon-LwwdoQ/falcon-1.8.8/inst/pylib/pypeflow-1.0.0-py2.7.egg/pypeflow/do_task.py /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/job_0000/task.json" 2022-01-06 16:56:56,137 - root - DEBUG - Checking existence of '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/job_0000/task.json' with timeout=60 2022-01-06 16:56:56,137 - root - DEBUG - Loading JSON from '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/job_0000/task.json' 2022-01-06 16:56:56,140 - root - DEBUG - {u'inputs': {u'db_build_done': u'/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/rdb_build_done', u'scatter_fn': u'/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/daligner-scatter/scattered.json'}, u'outputs': {u'job_done': u'job_0000_done'}, u'parameters': {u'config': {u'LA4Falcon_preload': True, u'avoid_text_file_busy': True, u'cns_concurrent_jobs': 32, u'da_concurrent_jobs': 32, u'dazcon': False, u'default_concurrent_jobs': 8, u'dust': False, u'falcon_sense_greedy': False, u'falcon_sense_option': u'--output_multi --min_idt 0.70 --min_cov 1 --max_n_read 20000 --n_core 0', u'falcon_sense_skip_contained': False, u'fc_concurrent_jobs': 8, u'fc_ovlp_to_graph_option': u' --min_len 1', u'genome_size': 5000, u'input_fofn': u'input.fofn', u'input_type': u'raw', u'install_prefix': u'/usr', u'job_queue': u'bash -C ${CMD}', u'job_type': u'string', u'la_concurrent_jobs': 32, u'length_cutoff': -1, u'length_cutoff_pr': 1, u'overlap_filtering_setting': u'--max_diff 10000 --max_cov 100000 --min_cov 1 --min_len 1 --bestn 1000 --n_core 0', u'ovlp_DBsplit_option': u'-a -x5 -s50', u'ovlp_HPCdaligner_option': u'-v -B4 -t50 -h1 -e.99 -l1 -s1000', u'pa_DBdust_option': u'-w128 -t2.5 -m20', u'pa_DBsplit_option': u'-a -x5 -s.065536', u'pa_HPCdaligner_option': u'-v -B4 -t50 -h1 -e.99 -w1 -l1 -s1000', u'pa_dazcon_option': u'-j 4 -x -l 500', u'pda_concurrent_jobs': 32, u'pla_concurrent_jobs': 32, u'pwatcher_directory': u'mypwatcher', u'pwatcher_type': u'blocking', u'seed_coverage': 20.0, u'sge_option': u'-pe smp 8 -q bash -C ${CMD}', u'sge_option_cns': u'-pe smp 8 -q bash -C ${CMD}', u'sge_option_da': u'-pe smp 8 -q bash -C ${CMD}', u'sge_option_fc': u'-pe smp 24 -q bash -C ${CMD}', u'sge_option_la': u'-pe smp 2 -q bash -C ${CMD}', u'sge_option_pda': u'-pe smp 8 -q bash -C ${CMD}', u'sge_option_pla': u'-pe smp 2 -q bash -C ${CMD}', u'skip_checks': False, u'stop_all_jobs_on_failure': True, u'target': u'assembly', u'use_tmpdir': False}, u'daligner_script': u'\ndb_dir=/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads\nln -sf ${db_dir}/.raw_reads.bps .\nln -sf ${db_dir}/.raw_reads.idx .\nln -sf ${db_dir}/raw_reads.db .\nln -sf ${db_dir}/.raw_reads.dust.anno .\nln -sf ${db_dir}/.raw_reads.dust.data .\ndaligner -v -w1 -h1 -t50 -H2000 -e0.99 -l1 -s1000 raw_reads.1 raw_reads.1\nLAcheck -v raw_reads *.las\nLAsort -v raw_reads.1.raw_reads.1.C0 raw_reads.1.raw_reads.1.N0 raw_reads.1.raw_reads.1.C1 raw_reads.1.raw_reads.1.N1 raw_reads.1.raw_reads.1.C2 raw_reads.1.raw_reads.1.N2 raw_reads.1.raw_reads.1.C3 raw_reads.1.raw_reads.1.N3 && LAmerge -v L1.1.1 raw_reads.1.raw_reads.1.C0.S raw_reads.1.raw_reads.1.N0.S raw_reads.1.raw_reads.1.C1.S raw_reads.1.raw_reads.1.N1.S raw_reads.1.raw_reads.1.C2.S raw_reads.1.raw_reads.1.N2.S raw_reads.1.raw_reads.1.C3.S raw_reads.1.raw_reads.1.N3.S\nLAcheck -vS raw_reads L1.1.1\n\nrm -f *.C?.las *.C?.S.las *.C??.las *.C??.S.las *.C???.las *.C???.S.las\nrm -f *.N?.las *.N?.S.las *.N??.las *.N??.S.las *.N???.las *.N???.S.las\n', u'db_prefix': u'raw_reads', u'job_uid': u'0000', u'sge_option': u'-pe smp 8 -q bash -C ${CMD}'}, u'python_function': u'falcon_kit.pype_tasks.task_run_daligner'} 2022-01-06 16:56:56,140 - root - DEBUG - CD: '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/job_0000' <- '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/job_0000' 2022-01-06 16:56:56,140 - root - DEBUG - Checking existence of u'/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/daligner-scatter/scattered.json' with timeout=60 2022-01-06 16:56:56,140 - root - DEBUG - Checking existence of u'/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/rdb_build_done' with timeout=60 2022-01-06 16:56:56,153 - root - DEBUG - Running "/build/falcon-LwwdoQ/falcon-1.8.8/inst/pylib/pypeflow-1.0.0-py2.7.egg/pypeflow/do_task.py /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/job_0001/task.json" 2022-01-06 16:56:56,155 - root - DEBUG - Checking existence of '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/job_0001/task.json' with timeout=60 2022-01-06 16:56:56,155 - root - DEBUG - Loading JSON from '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/job_0001/task.json' 2022-01-06 16:56:56,158 - root - DEBUG - {u'inputs': {u'db_build_done': u'/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/rdb_build_done', u'scatter_fn': u'/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/daligner-scatter/scattered.json'}, u'outputs': {u'job_done': u'job_0001_done'}, u'parameters': {u'config': {u'LA4Falcon_preload': True, u'avoid_text_file_busy': True, u'cns_concurrent_jobs': 32, u'da_concurrent_jobs': 32, u'dazcon': False, u'default_concurrent_jobs': 8, u'dust': False, u'falcon_sense_greedy': False, u'falcon_sense_option': u'--output_multi --min_idt 0.70 --min_cov 1 --max_n_read 20000 --n_core 0', u'falcon_sense_skip_contained': False, u'fc_concurrent_jobs': 8, u'fc_ovlp_to_graph_option': u' --min_len 1', u'genome_size': 5000, u'input_fofn': u'input.fofn', u'input_type': u'raw', u'install_prefix': u'/usr', u'job_queue': u'bash -C ${CMD}', u'job_type': u'string', u'la_concurrent_jobs': 32, u'length_cutoff': -1, u'length_cutoff_pr': 1, u'overlap_filtering_setting': u'--max_diff 10000 --max_cov 100000 --min_cov 1 --min_len 1 --bestn 1000 --n_core 0', u'ovlp_DBsplit_option': u'-a -x5 -s50', u'ovlp_HPCdaligner_option': u'-v -B4 -t50 -h1 -e.99 -l1 -s1000', u'pa_DBdust_option': u'-w128 -t2.5 -m20', u'pa_DBsplit_option': u'-a -x5 -s.065536', u'pa_HPCdaligner_option': u'-v -B4 -t50 -h1 -e.99 -w1 -l1 -s1000', u'pa_dazcon_option': u'-j 4 -x -l 500', u'pda_concurrent_jobs': 32, u'pla_concurrent_jobs': 32, u'pwatcher_directory': u'mypwatcher', u'pwatcher_type': u'blocking', u'seed_coverage': 20.0, u'sge_option': u'-pe smp 8 -q bash -C ${CMD}', u'sge_option_cns': u'-pe smp 8 -q bash -C ${CMD}', u'sge_option_da': u'-pe smp 8 -q bash -C ${CMD}', u'sge_option_fc': u'-pe smp 24 -q bash -C ${CMD}', u'sge_option_la': u'-pe smp 2 -q bash -C ${CMD}', u'sge_option_pda': u'-pe smp 8 -q bash -C ${CMD}', u'sge_option_pla': u'-pe smp 2 -q bash -C ${CMD}', u'skip_checks': False, u'stop_all_jobs_on_failure': True, u'target': u'assembly', u'use_tmpdir': False}, u'daligner_script': u'\ndb_dir=/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads\nln -sf ${db_dir}/.raw_reads.bps .\nln -sf ${db_dir}/.raw_reads.idx .\nln -sf ${db_dir}/raw_reads.db .\nln -sf ${db_dir}/.raw_reads.dust.anno .\nln -sf ${db_dir}/.raw_reads.dust.data .\ndaligner -v -w1 -h1 -t50 -H2000 -e0.99 -l1 -s1000 raw_reads.2 raw_reads.1 raw_reads.2\nLAcheck -v raw_reads *.las\nLAsort -v raw_reads.1.raw_reads.2.C0 raw_reads.1.raw_reads.2.N0 raw_reads.1.raw_reads.2.C1 raw_reads.1.raw_reads.2.N1 raw_reads.1.raw_reads.2.C2 raw_reads.1.raw_reads.2.N2 raw_reads.1.raw_reads.2.C3 raw_reads.1.raw_reads.2.N3 && LAmerge -v L1.1.2 raw_reads.1.raw_reads.2.C0.S raw_reads.1.raw_reads.2.N0.S raw_reads.1.raw_reads.2.C1.S raw_reads.1.raw_reads.2.N1.S raw_reads.1.raw_reads.2.C2.S raw_reads.1.raw_reads.2.N2.S raw_reads.1.raw_reads.2.C3.S raw_reads.1.raw_reads.2.N3.S\nLAsort -v raw_reads.2.raw_reads.1.C0 raw_reads.2.raw_reads.1.N0 raw_reads.2.raw_reads.1.C1 raw_reads.2.raw_reads.1.N1 raw_reads.2.raw_reads.1.C2 raw_reads.2.raw_reads.1.N2 raw_reads.2.raw_reads.1.C3 raw_reads.2.raw_reads.1.N3 && LAmerge -v L1.2.1 raw_reads.2.raw_reads.1.C0.S raw_reads.2.raw_reads.1.N0.S raw_reads.2.raw_reads.1.C1.S raw_reads.2.raw_reads.1.N1.S raw_reads.2.raw_reads.1.C2.S raw_reads.2.raw_reads.1.N2.S raw_reads.2.raw_reads.1.C3.S raw_reads.2.raw_reads.1.N3.S\nLAsort -v raw_reads.2.raw_reads.2.C0 raw_reads.2.raw_reads.2.N0 raw_reads.2.raw_reads.2.C1 raw_reads.2.raw_reads.2.N1 raw_reads.2.raw_reads.2.C2 raw_reads.2.raw_reads.2.N2 raw_reads.2.raw_reads.2.C3 raw_reads.2.raw_reads.2.N3 && LAmerge -v L1.2.2 raw_reads.2.raw_reads.2.C0.S raw_reads.2.raw_reads.2.N0.S raw_reads.2.raw_reads.2.C1.S raw_reads.2.raw_reads.2.N1.S raw_reads.2.raw_reads.2.C2.S raw_reads.2.raw_reads.2.N2.S raw_reads.2.raw_reads.2.C3.S raw_reads.2.raw_reads.2.N3.S\nLAcheck -vS raw_reads L1.1.2\nLAcheck -vS raw_reads L1.2.1\nLAcheck -vS raw_reads L1.2.2\n\nrm -f *.C?.las *.C?.S.las *.C??.las *.C??.S.las *.C???.las *.C???.S.las\nrm -f *.N?.las *.N?.S.las *.N??.las *.N??.S.las *.N???.las *.N???.S.las\n', u'db_prefix': u'raw_reads', u'job_uid': u'0001', u'sge_option': u'-pe smp 8 -q bash -C ${CMD}'}, u'python_function': u'falcon_kit.pype_tasks.task_run_daligner'} 2022-01-06 16:56:56,158 - root - DEBUG - CD: '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/job_0001' <- '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/job_0001' 2022-01-06 16:56:56,158 - root - DEBUG - Checking existence of u'/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/daligner-scatter/scattered.json' with timeout=60 2022-01-06 16:56:56,158 - root - DEBUG - Checking existence of u'/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/rdb_build_done' with timeout=60 2022-01-06 16:56:56,171 - root - DEBUG - CD: '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/job_0000' <- '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/job_0000' 2022-01-06 16:56:56,172 - pypeflow.do_support - INFO - !/bin/bash -vex /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/job_0000/rj_0000.sh #!/bin/bash set -vex + set -vex db_dir=/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads + db_dir=/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads ln -sf ${db_dir}/.raw_reads.bps . + ln -sf /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/.raw_reads.bps . ln -sf ${db_dir}/.raw_reads.idx . + ln -sf /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/.raw_reads.idx . ln -sf ${db_dir}/raw_reads.db . + ln -sf /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/raw_reads.db . ln -sf ${db_dir}/.raw_reads.dust.anno . + ln -sf /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/.raw_reads.dust.anno . ln -sf ${db_dir}/.raw_reads.dust.data . + ln -sf /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/.raw_reads.dust.data . 2022-01-06 16:56:56,191 - root - DEBUG - CD: '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/job_0001' <- '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/job_0001' daligner -v -w1 -h1 -t50 -H2000 -e0.99 -l1 -s1000 raw_reads.1 raw_reads.1 + daligner -v -w1 -h1 -t50 -H2000 -e0.99 -l1 -s1000 raw_reads.1 raw_reads.1 2022-01-06 16:56:56,192 - pypeflow.do_support - INFO - !/bin/bash -vex /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/job_0001/rj_0001.sh Building index for raw_reads.1 Kshift=28 BSHIFT=8 TooFrequent=50 (Kshift-1)/BSHIFT + (TooFrequent < INT32_MAX)=4 sizeof(KmerPos)=16 nreads=33 Kmer=14 block->reads[nreads].boff=66033 kmers=65571 sizeof(KmerPos)*(kmers+1)=1049152 Allocated 65572 of 16 (1049152 bytes) at 0x7bec49ea0010 Kmer count = 65,571 Using 0.00Gb of space #!/bin/bash set -vex + set -vex db_dir=/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads + db_dir=/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads ln -sf ${db_dir}/.raw_reads.bps . + ln -sf /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/.raw_reads.bps . ln -sf ${db_dir}/.raw_reads.idx . + ln -sf /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/.raw_reads.idx . Revised kmer count = 65,571 Index occupies 0.00Gb Comparing raw_reads.1 to raw_reads.1 Capping mutual k-mer matches over 10000 (effectively -t100) Hit count = 418,741 Highwater of 0.01Gb space ln -sf ${db_dir}/raw_reads.db . + ln -sf /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/raw_reads.db . ln -sf ${db_dir}/.raw_reads.dust.anno . + ln -sf /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/.raw_reads.dust.anno . ln -sf ${db_dir}/.raw_reads.dust.data . + ln -sf /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/.raw_reads.dust.data . daligner -v -w1 -h1 -t50 -H2000 -e0.99 -l1 -s1000 raw_reads.2 raw_reads.1 raw_reads.2 + daligner -v -w1 -h1 -t50 -H2000 -e0.99 -l1 -s1000 raw_reads.2 raw_reads.1 raw_reads.2 Building index for raw_reads.2 Kshift=28 BSHIFT=8 TooFrequent=50 (Kshift-1)/BSHIFT + (TooFrequent < INT32_MAX)=4 sizeof(KmerPos)=16 nreads=17 Kmer=14 block->reads[nreads].boff=34017 kmers=33779 sizeof(KmerPos)*(kmers+1)=540480 Allocated 33780 of 16 (540480 bytes) at 0x7d0b42ffb010 Kmer count = 33,779 Using 0.00Gb of space Revised kmer count = 33,779 Index occupies 0.00Gb Building index for raw_reads.1 Kshift=28 BSHIFT=8 TooFrequent=50 (Kshift-1)/BSHIFT + (TooFrequent < INT32_MAX)=4 sizeof(KmerPos)=16 nreads=33 Kmer=14 block->reads[nreads].boff=66033 kmers=65571 sizeof(KmerPos)*(kmers+1)=1049152 Allocated 65572 of 16 (1049152 bytes) at 0x7d0b40431010 Kmer count = 65,571 Using 0.00Gb of space Revised kmer count = 65,571 Index occupies 0.00Gb Comparing raw_reads.2 to raw_reads.1 Capping mutual k-mer matches over 10000 (effectively -t100) Hit count = 441,607 Highwater of 0.01Gb space 418,741 14-mers (9.612971e-05 of matrix) 412 seed hits (9.458219e-08 of matrix) 824 confirmed hits (1.891644e-07 of matrix) Building index for c(raw_reads.1) Kshift=28 BSHIFT=8 TooFrequent=50 (Kshift-1)/BSHIFT + (TooFrequent < INT32_MAX)=4 sizeof(KmerPos)=16 nreads=33 Kmer=14 block->reads[nreads].boff=66033 kmers=65571 sizeof(KmerPos)*(kmers+1)=1049152 Allocated 65572 of 16 (1049152 bytes) at 0x556313f8c900 Kmer count = 65,571 Using 0.00Gb of space Revised kmer count = 65,571 Index occupies 0.00Gb Comparing raw_reads.1 to c(raw_reads.1) Capping mutual k-mer matches over 10000 (effectively -t100) Hit count = 0 Highwater of 0.00Gb space 0 14-mers (0.000000e+00 of matrix) 0 seed hits (0.000000e+00 of matrix) 0 confirmed hits (0.000000e+00 of matrix) LAcheck -v raw_reads *.las + LAcheck -v raw_reads raw_reads.1.raw_reads.1.C0.las raw_reads.1.raw_reads.1.C1.las raw_reads.1.raw_reads.1.C2.las raw_reads.1.raw_reads.1.C3.las raw_reads.1.raw_reads.1.N0.las raw_reads.1.raw_reads.1.N1.las raw_reads.1.raw_reads.1.N2.las raw_reads.1.raw_reads.1.N3.las raw_reads.1.raw_reads.1.C0: 0 all OK raw_reads.1.raw_reads.1.C1: 0 all OK raw_reads.1.raw_reads.1.C2: 0 all OK raw_reads.1.raw_reads.1.C3: 0 all OK raw_reads.1.raw_reads.1.N0: 226 all OK raw_reads.1.raw_reads.1.N1: 194 all OK raw_reads.1.raw_reads.1.N2: 216 all OK raw_reads.1.raw_reads.1.N3: 188 all OK LAsort -v raw_reads.1.raw_reads.1.C0 raw_reads.1.raw_reads.1.N0 raw_reads.1.raw_reads.1.C1 raw_reads.1.raw_reads.1.N1 raw_reads.1.raw_reads.1.C2 raw_reads.1.raw_reads.1.N2 raw_reads.1.raw_reads.1.C3 raw_reads.1.raw_reads.1.N3 && LAmerge -v L1.1.1 raw_reads.1.raw_reads.1.C0.S raw_reads.1.raw_reads.1.N0.S raw_reads.1.raw_reads.1.C1.S raw_reads.1.raw_reads.1.N1.S raw_reads.1.raw_reads.1.C2.S raw_reads.1.raw_reads.1.N2.S raw_reads.1.raw_reads.1.C3.S raw_reads.1.raw_reads.1.N3.S + LAsort -v raw_reads.1.raw_reads.1.C0 raw_reads.1.raw_reads.1.N0 raw_reads.1.raw_reads.1.C1 raw_reads.1.raw_reads.1.N1 raw_reads.1.raw_reads.1.C2 raw_reads.1.raw_reads.1.N2 raw_reads.1.raw_reads.1.C3 raw_reads.1.raw_reads.1.N3 raw_reads.1.raw_reads.1.C0: 0 records 12 trace bytes raw_reads.1.raw_reads.1.N0: 226 records 1,380 trace bytes raw_reads.1.raw_reads.1.C1: 0 records 12 trace bytes raw_reads.1.raw_reads.1.N1: 194 records 1,204 trace bytes raw_reads.1.raw_reads.1.C2: 0 records 12 trace bytes raw_reads.1.raw_reads.1.N2: 216 records 1,316 trace bytes raw_reads.1.raw_reads.1.C3: 0 records 12 trace bytes raw_reads.1.raw_reads.1.N3: 188 records 1,156 trace bytes + LAmerge -v L1.1.1 raw_reads.1.raw_reads.1.C0.S raw_reads.1.raw_reads.1.N0.S raw_reads.1.raw_reads.1.C1.S raw_reads.1.raw_reads.1.N1.S raw_reads.1.raw_reads.1.C2.S raw_reads.1.raw_reads.1.N2.S raw_reads.1.raw_reads.1.C3.S raw_reads.1.raw_reads.1.N3.S 441,607 14-mers (1.967946e-04 of matrix) 456 seed hits (2.032086e-07 of matrix) 912 confirmed hits (4.064171e-07 of matrix) Building index for c(raw_reads.1) Kshift=28 BSHIFT=8 TooFrequent=50 (Kshift-1)/BSHIFT + (TooFrequent < INT32_MAX)=4 sizeof(KmerPos)=16 nreads=33 Kmer=14 block->reads[nreads].boff=66033 kmers=65571 sizeof(KmerPos)*(kmers+1)=1049152 Allocated 65572 of 16 (1049152 bytes) at 0x58afa2f14270 Kmer count = 65,571 Using 0.00Gb of space In file ./raw_reads.1.raw_reads.1.C0.S.las, there are 0 records In file ./raw_reads.1.raw_reads.1.N0.S.las, there are 226 records In file ./raw_reads.1.raw_reads.1.C1.S.las, there are 0 records In file ./raw_reads.1.raw_reads.1.N1.S.las, there are 194 records In file ./raw_reads.1.raw_reads.1.C2.S.las, there are 0 records In file ./raw_reads.1.raw_reads.1.N2.S.las, there are 216 records In file ./raw_reads.1.raw_reads.1.C3.S.las, there are 0 records In file ./raw_reads.1.raw_reads.1.N3.S.las, there are 188 records Merging 8 files totalling 824 records LAcheck -vS raw_reads L1.1.1 + LAcheck -vS raw_reads L1.1.1 L1.1.1: 824 all OK rm -f *.C?.las *.C?.S.las *.C??.las *.C??.S.las *.C???.las *.C???.S.las + rm -f raw_reads.1.raw_reads.1.C0.las raw_reads.1.raw_reads.1.C1.las raw_reads.1.raw_reads.1.C2.las raw_reads.1.raw_reads.1.C3.las raw_reads.1.raw_reads.1.C0.S.las raw_reads.1.raw_reads.1.C1.S.las raw_reads.1.raw_reads.1.C2.S.las raw_reads.1.raw_reads.1.C3.S.las '*.C??.las' '*.C??.S.las' raw_reads.1.raw_reads.1.C0.S.las raw_reads.1.raw_reads.1.C1.S.las raw_reads.1.raw_reads.1.C2.S.las raw_reads.1.raw_reads.1.C3.S.las '*.C???.S.las' Revised kmer count = 65,571 Index occupies 0.00Gb Comparing raw_reads.2 to c(raw_reads.1) Capping mutual k-mer matches over 10000 (effectively -t100) Hit count = 0 Highwater of 0.00Gb space 0 14-mers (0.000000e+00 of matrix) 0 seed hits (0.000000e+00 of matrix) 0 confirmed hits (0.000000e+00 of matrix) Comparing raw_reads.2 to raw_reads.2 Capping mutual k-mer matches over 10000 (effectively -t100) Hit count = 108,861 Highwater of 0.00Gb space rm -f *.N?.las *.N?.S.las *.N??.las *.N??.S.las *.N???.las *.N???.S.las + rm -f raw_reads.1.raw_reads.1.N0.las raw_reads.1.raw_reads.1.N1.las raw_reads.1.raw_reads.1.N2.las raw_reads.1.raw_reads.1.N3.las raw_reads.1.raw_reads.1.N0.S.las raw_reads.1.raw_reads.1.N1.S.las raw_reads.1.raw_reads.1.N2.S.las raw_reads.1.raw_reads.1.N3.S.las '*.N??.las' '*.N??.S.las' raw_reads.1.raw_reads.1.N0.S.las raw_reads.1.raw_reads.1.N1.S.las raw_reads.1.raw_reads.1.N2.S.las raw_reads.1.raw_reads.1.N3.S.las '*.N???.S.las' touch job_0000_done + touch job_0000_done 108,861 14-mers (9.417042e-05 of matrix) 114 seed hits (9.861592e-08 of matrix) 228 confirmed hits (1.972318e-07 of matrix) Building index for c(raw_reads.2) Kshift=28 BSHIFT=8 TooFrequent=50 (Kshift-1)/BSHIFT + (TooFrequent < INT32_MAX)=4 sizeof(KmerPos)=16 nreads=17 Kmer=14 block->reads[nreads].boff=34017 kmers=33779 sizeof(KmerPos)*(kmers+1)=540480 Allocated 33780 of 16 (540480 bytes) at 0x58afa30144d0 Kmer count = 33,779 Using 0.00Gb of space 2022-01-06 16:56:56,264 - root - DEBUG - CD: '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/job_0000' -> '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/job_0000' 2022-01-06 16:56:56,265 - root - DEBUG - Checking existence of u'job_0000_done' with timeout=60 2022-01-06 16:56:56,265 - root - DEBUG - CD: '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/job_0000' -> '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/job_0000' Revised kmer count = 33,779 Index occupies 0.00Gb Comparing raw_reads.2 to c(raw_reads.2) Capping mutual k-mer matches over 10000 (effectively -t100) Hit count = 0 Highwater of 0.00Gb space 0 14-mers (0.000000e+00 of matrix) 0 seed hits (0.000000e+00 of matrix) 0 confirmed hits (0.000000e+00 of matrix) LAcheck -v raw_reads *.las + LAcheck -v raw_reads raw_reads.1.raw_reads.2.C0.las raw_reads.1.raw_reads.2.C1.las raw_reads.1.raw_reads.2.C2.las raw_reads.1.raw_reads.2.C3.las raw_reads.1.raw_reads.2.N0.las raw_reads.1.raw_reads.2.N1.las raw_reads.1.raw_reads.2.N2.las raw_reads.1.raw_reads.2.N3.las raw_reads.2.raw_reads.1.C0.las raw_reads.2.raw_reads.1.C1.las raw_reads.2.raw_reads.1.C2.las raw_reads.2.raw_reads.1.C3.las raw_reads.2.raw_reads.1.N0.las raw_reads.2.raw_reads.1.N1.las raw_reads.2.raw_reads.1.N2.las raw_reads.2.raw_reads.1.N3.las raw_reads.2.raw_reads.2.C0.las raw_reads.2.raw_reads.2.C1.las raw_reads.2.raw_reads.2.C2.las raw_reads.2.raw_reads.2.C3.las raw_reads.2.raw_reads.2.N0.las raw_reads.2.raw_reads.2.N1.las raw_reads.2.raw_reads.2.N2.las raw_reads.2.raw_reads.2.N3.las raw_reads.1.raw_reads.2.C0: 0 all OK raw_reads.1.raw_reads.2.C1: 0 all OK raw_reads.1.raw_reads.2.C2: 0 all OK raw_reads.1.raw_reads.2.C3: 0 all OK raw_reads.1.raw_reads.2.N0: 128 all OK raw_reads.1.raw_reads.2.N1: 107 all OK raw_reads.1.raw_reads.2.N2: 116 all OK raw_reads.1.raw_reads.2.N3: 105 all OK raw_reads.2.raw_reads.1.C0: 0 all OK raw_reads.2.raw_reads.1.C1: 0 all OK raw_reads.2.raw_reads.1.C2: 0 all OK raw_reads.2.raw_reads.1.C3: 0 all OK raw_reads.2.raw_reads.1.N0: 128 all OK raw_reads.2.raw_reads.1.N1: 107 all OK raw_reads.2.raw_reads.1.N2: 116 all OK raw_reads.2.raw_reads.1.N3: 105 all OK raw_reads.2.raw_reads.2.C0: 0 all OK raw_reads.2.raw_reads.2.C1: 0 all OK raw_reads.2.raw_reads.2.C2: 0 all OK raw_reads.2.raw_reads.2.C3: 0 all OK raw_reads.2.raw_reads.2.N0: 76 all OK raw_reads.2.raw_reads.2.N1: 40 all OK raw_reads.2.raw_reads.2.N2: 60 all OK raw_reads.2.raw_reads.2.N3: 52 all OK LAsort -v raw_reads.1.raw_reads.2.C0 raw_reads.1.raw_reads.2.N0 raw_reads.1.raw_reads.2.C1 raw_reads.1.raw_reads.2.N1 raw_reads.1.raw_reads.2.C2 raw_reads.1.raw_reads.2.N2 raw_reads.1.raw_reads.2.C3 raw_reads.1.raw_reads.2.N3 && LAmerge -v L1.1.2 raw_reads.1.raw_reads.2.C0.S raw_reads.1.raw_reads.2.N0.S raw_reads.1.raw_reads.2.C1.S raw_reads.1.raw_reads.2.N1.S raw_reads.1.raw_reads.2.C2.S raw_reads.1.raw_reads.2.N2.S raw_reads.1.raw_reads.2.C3.S raw_reads.1.raw_reads.2.N3.S + LAsort -v raw_reads.1.raw_reads.2.C0 raw_reads.1.raw_reads.2.N0 raw_reads.1.raw_reads.2.C1 raw_reads.1.raw_reads.2.N1 raw_reads.1.raw_reads.2.C2 raw_reads.1.raw_reads.2.N2 raw_reads.1.raw_reads.2.C3 raw_reads.1.raw_reads.2.N3 raw_reads.1.raw_reads.2.C0: 0 records 12 trace bytes raw_reads.1.raw_reads.2.N0: 128 records 740 trace bytes raw_reads.1.raw_reads.2.C1: 0 records 12 trace bytes raw_reads.1.raw_reads.2.N1: 107 records 656 trace bytes raw_reads.1.raw_reads.2.C2: 0 records 12 trace bytes raw_reads.1.raw_reads.2.N2: 116 records 688 trace bytes raw_reads.1.raw_reads.2.C3: 0 records 12 trace bytes raw_reads.1.raw_reads.2.N3: 105 records 632 trace bytes + LAmerge -v L1.1.2 raw_reads.1.raw_reads.2.C0.S raw_reads.1.raw_reads.2.N0.S raw_reads.1.raw_reads.2.C1.S raw_reads.1.raw_reads.2.N1.S raw_reads.1.raw_reads.2.C2.S raw_reads.1.raw_reads.2.N2.S raw_reads.1.raw_reads.2.C3.S raw_reads.1.raw_reads.2.N3.S real 0m0.239s user 0m0.184s sys 0m0.118s touch /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/job_0000/run.sh.done + touch /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/job_0000/run.sh.done In file ./raw_reads.1.raw_reads.2.C0.S.las, there are 0 records In file ./raw_reads.1.raw_reads.2.N0.S.las, there are 128 records In file ./raw_reads.1.raw_reads.2.C1.S.las, there are 0 records In file ./raw_reads.1.raw_reads.2.N1.S.las, there are 107 records In file ./raw_reads.1.raw_reads.2.C2.S.las, there are 0 records In file ./raw_reads.1.raw_reads.2.N2.S.las, there are 116 records In file ./raw_reads.1.raw_reads.2.C3.S.las, there are 0 records In file ./raw_reads.1.raw_reads.2.N3.S.las, there are 105 records Merging 8 files totalling 456 records LAsort -v raw_reads.2.raw_reads.1.C0 raw_reads.2.raw_reads.1.N0 raw_reads.2.raw_reads.1.C1 raw_reads.2.raw_reads.1.N1 raw_reads.2.raw_reads.1.C2 raw_reads.2.raw_reads.1.N2 raw_reads.2.raw_reads.1.C3 raw_reads.2.raw_reads.1.N3 && LAmerge -v L1.2.1 raw_reads.2.raw_reads.1.C0.S raw_reads.2.raw_reads.1.N0.S raw_reads.2.raw_reads.1.C1.S raw_reads.2.raw_reads.1.N1.S raw_reads.2.raw_reads.1.C2.S raw_reads.2.raw_reads.1.N2.S raw_reads.2.raw_reads.1.C3.S raw_reads.2.raw_reads.1.N3.S + LAsort -v raw_reads.2.raw_reads.1.C0 raw_reads.2.raw_reads.1.N0 raw_reads.2.raw_reads.1.C1 raw_reads.2.raw_reads.1.N1 raw_reads.2.raw_reads.1.C2 raw_reads.2.raw_reads.1.N2 raw_reads.2.raw_reads.1.C3 raw_reads.2.raw_reads.1.N3 + finish + echo 'finish code: 0' finish code: 0 raw_reads.2.raw_reads.1.C0: 0 records 12 trace bytes raw_reads.2.raw_reads.1.N0: 128 records 740 trace bytes raw_reads.2.raw_reads.1.C1: 0 records 12 trace bytes raw_reads.2.raw_reads.1.N1: 107 records 656 trace bytes raw_reads.2.raw_reads.1.C2: 0 records 12 trace bytes raw_reads.2.raw_reads.1.N2: 116 records 688 trace bytes raw_reads.2.raw_reads.1.C3: 0 records 12 trace bytes raw_reads.2.raw_reads.1.N3: 105 records 632 trace bytes + LAmerge -v L1.2.1 raw_reads.2.raw_reads.1.C0.S raw_reads.2.raw_reads.1.N0.S raw_reads.2.raw_reads.1.C1.S raw_reads.2.raw_reads.1.N1.S raw_reads.2.raw_reads.1.C2.S raw_reads.2.raw_reads.1.N2.S raw_reads.2.raw_reads.1.C3.S raw_reads.2.raw_reads.1.N3.S In file ./raw_reads.2.raw_reads.1.C0.S.las, there are 0 records In file ./raw_reads.2.raw_reads.1.N0.S.las, there are 128 records In file ./raw_reads.2.raw_reads.1.C1.S.las, there are 0 records In file ./raw_reads.2.raw_reads.1.N1.S.las, there are 107 records In file ./raw_reads.2.raw_reads.1.C2.S.las, there are 0 records In file ./raw_reads.2.raw_reads.1.N2.S.las, there are 116 records In file ./raw_reads.2.raw_reads.1.C3.S.las, there are 0 records In file ./raw_reads.2.raw_reads.1.N3.S.las, there are 105 records Merging 8 files totalling 456 records LAsort -v raw_reads.2.raw_reads.2.C0 raw_reads.2.raw_reads.2.N0 raw_reads.2.raw_reads.2.C1 raw_reads.2.raw_reads.2.N1 raw_reads.2.raw_reads.2.C2 raw_reads.2.raw_reads.2.N2 raw_reads.2.raw_reads.2.C3 raw_reads.2.raw_reads.2.N3 && LAmerge -v L1.2.2 raw_reads.2.raw_reads.2.C0.S raw_reads.2.raw_reads.2.N0.S raw_reads.2.raw_reads.2.C1.S raw_reads.2.raw_reads.2.N1.S raw_reads.2.raw_reads.2.C2.S raw_reads.2.raw_reads.2.N2.S raw_reads.2.raw_reads.2.C3.S raw_reads.2.raw_reads.2.N3.S + LAsort -v raw_reads.2.raw_reads.2.C0 raw_reads.2.raw_reads.2.N0 raw_reads.2.raw_reads.2.C1 raw_reads.2.raw_reads.2.N1 raw_reads.2.raw_reads.2.C2 raw_reads.2.raw_reads.2.N2 raw_reads.2.raw_reads.2.C3 raw_reads.2.raw_reads.2.N3 raw_reads.2.raw_reads.2.C0: 0 records 12 trace bytes raw_reads.2.raw_reads.2.N0: 76 records 468 trace bytes raw_reads.2.raw_reads.2.C1: 0 records 12 trace bytes raw_reads.2.raw_reads.2.N1: 40 records 260 trace bytes raw_reads.2.raw_reads.2.C2: 0 records 12 trace bytes raw_reads.2.raw_reads.2.N2: 60 records 380 trace bytes raw_reads.2.raw_reads.2.C3: 0 records 12 trace bytes raw_reads.2.raw_reads.2.N3: 52 records 292 trace bytes + LAmerge -v L1.2.2 raw_reads.2.raw_reads.2.C0.S raw_reads.2.raw_reads.2.N0.S raw_reads.2.raw_reads.2.C1.S raw_reads.2.raw_reads.2.N1.S raw_reads.2.raw_reads.2.C2.S raw_reads.2.raw_reads.2.N2.S raw_reads.2.raw_reads.2.C3.S raw_reads.2.raw_reads.2.N3.S In file ./raw_reads.2.raw_reads.2.C0.S.las, there are 0 records In file ./raw_reads.2.raw_reads.2.N0.S.las, there are 76 records In file ./raw_reads.2.raw_reads.2.C1.S.las, there are 0 records In file ./raw_reads.2.raw_reads.2.N1.S.las, there are 40 records In file ./raw_reads.2.raw_reads.2.C2.S.las, there are 0 records In file ./raw_reads.2.raw_reads.2.N2.S.las, there are 60 records In file ./raw_reads.2.raw_reads.2.C3.S.las, there are 0 records In file ./raw_reads.2.raw_reads.2.N3.S.las, there are 52 records Merging 8 files totalling 228 records LAcheck -vS raw_reads L1.1.2 + LAcheck -vS raw_reads L1.1.2 L1.1.2: 456 all OK LAcheck -vS raw_reads L1.2.1 + LAcheck -vS raw_reads L1.2.1 L1.2.1: 456 all OK LAcheck -vS raw_reads L1.2.2 + LAcheck -vS raw_reads L1.2.2 L1.2.2: 228 all OK rm -f *.C?.las *.C?.S.las *.C??.las *.C??.S.las *.C???.las *.C???.S.las + rm -f raw_reads.1.raw_reads.2.C0.las raw_reads.1.raw_reads.2.C1.las raw_reads.1.raw_reads.2.C2.las raw_reads.1.raw_reads.2.C3.las raw_reads.2.raw_reads.1.C0.las raw_reads.2.raw_reads.1.C1.las raw_reads.2.raw_reads.1.C2.las raw_reads.2.raw_reads.1.C3.las raw_reads.2.raw_reads.2.C0.las raw_reads.2.raw_reads.2.C1.las raw_reads.2.raw_reads.2.C2.las raw_reads.2.raw_reads.2.C3.las raw_reads.1.raw_reads.2.C0.S.las raw_reads.1.raw_reads.2.C1.S.las raw_reads.1.raw_reads.2.C2.S.las raw_reads.1.raw_reads.2.C3.S.las raw_reads.2.raw_reads.1.C0.S.las raw_reads.2.raw_reads.1.C1.S.las raw_reads.2.raw_reads.1.C2.S.las raw_reads.2.raw_reads.1.C3.S.las raw_reads.2.raw_reads.2.C0.S.las raw_reads.2.raw_reads.2.C1.S.las raw_reads.2.raw_reads.2.C2.S.las raw_reads.2.raw_reads.2.C3.S.las '*.C??.las' '*.C??.S.las' raw_reads.1.raw_reads.2.C0.S.las raw_reads.1.raw_reads.2.C1.S.las raw_reads.1.raw_reads.2.C2.S.las raw_reads.1.raw_reads.2.C3.S.las raw_reads.2.raw_reads.1.C0.S.las raw_reads.2.raw_reads.1.C1.S.las raw_reads.2.raw_reads.1.C2.S.las raw_reads.2.raw_reads.1.C3.S.las raw_reads.2.raw_reads.2.C0.S.las raw_reads.2.raw_reads.2.C1.S.las raw_reads.2.raw_reads.2.C2.S.las raw_reads.2.raw_reads.2.C3.S.las '*.C???.S.las' rm -f *.N?.las *.N?.S.las *.N??.las *.N??.S.las *.N???.las *.N???.S.las + rm -f raw_reads.1.raw_reads.2.N0.las raw_reads.1.raw_reads.2.N1.las raw_reads.1.raw_reads.2.N2.las raw_reads.1.raw_reads.2.N3.las raw_reads.2.raw_reads.1.N0.las raw_reads.2.raw_reads.1.N1.las raw_reads.2.raw_reads.1.N2.las raw_reads.2.raw_reads.1.N3.las raw_reads.2.raw_reads.2.N0.las raw_reads.2.raw_reads.2.N1.las raw_reads.2.raw_reads.2.N2.las raw_reads.2.raw_reads.2.N3.las raw_reads.1.raw_reads.2.N0.S.las raw_reads.1.raw_reads.2.N1.S.las raw_reads.1.raw_reads.2.N2.S.las raw_reads.1.raw_reads.2.N3.S.las raw_reads.2.raw_reads.1.N0.S.las raw_reads.2.raw_reads.1.N1.S.las raw_reads.2.raw_reads.1.N2.S.las raw_reads.2.raw_reads.1.N3.S.las raw_reads.2.raw_reads.2.N0.S.las raw_reads.2.raw_reads.2.N1.S.las raw_reads.2.raw_reads.2.N2.S.las raw_reads.2.raw_reads.2.N3.S.las '*.N??.las' '*.N??.S.las' raw_reads.1.raw_reads.2.N0.S.las raw_reads.1.raw_reads.2.N1.S.las raw_reads.1.raw_reads.2.N2.S.las raw_reads.1.raw_reads.2.N3.S.las raw_reads.2.raw_reads.1.N0.S.las raw_reads.2.raw_reads.1.N1.S.las raw_reads.2.raw_reads.1.N2.S.las raw_reads.2.raw_reads.1.N3.S.las raw_reads.2.raw_reads.2.N0.S.las raw_reads.2.raw_reads.2.N1.S.las raw_reads.2.raw_reads.2.N2.S.las raw_reads.2.raw_reads.2.N3.S.las '*.N???.S.las' touch job_0001_done + touch job_0001_done 2022-01-06 16:56:56,318 - root - DEBUG - CD: '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/job_0001' -> '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/job_0001' 2022-01-06 16:56:56,318 - root - DEBUG - Checking existence of u'job_0001_done' with timeout=60 2022-01-06 16:56:56,318 - root - DEBUG - CD: '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/job_0001' -> '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/job_0001' 2022-01-06 16:56:56,326[INFO] recently_satisfied: set([Node(0-rawreads/job_0000)]) 2022-01-06 16:56:56,326[INFO] Num satisfied in this iteration: 1 2022-01-06 16:56:56,326[INFO] Num still unsatisfied: 2 2022-01-06 16:56:56,327[INFO] sleep 0.1s real 0m0.279s user 0m0.227s sys 0m0.147s touch /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/job_0001/run.sh.done + touch /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/job_0001/run.sh.done + finish + echo 'finish code: 0' finish code: 0 2022-01-06 16:56:56,428[INFO] recently_satisfied: set([Node(0-rawreads/job_0001)]) 2022-01-06 16:56:56,428[INFO] Num satisfied in this iteration: 1 2022-01-06 16:56:56,428[INFO] Num still unsatisfied: 1 2022-01-06 16:56:56,428[INFO] About to submit: Node(0-rawreads/raw-gather) 2022-01-06 16:56:56,431[INFO] !chmod +x /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/raw-gather/run-P499faaef2a5248.bash 2022-01-06 16:56:56,441[INFO] sleep 0.1s 2022-01-06 16:56:56,447[INFO] Popen: 'bash -C /build/falcon-LwwdoQ/falcon-1.8.8/inst/pylib/pypeflow-1.0.0-py2.7.egg/pwatcher/mains/job_start.sh' executable=${PYPEFLOW_JOB_START_SCRIPT} + executable=/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/raw-gather/run-P499faaef2a5248.bash timeout=${PYPEFLOW_JOB_START_TIMEOUT:-60} # wait 60s by default + timeout=60 # Wait up to timeout seconds for the executable to become "executable", # then exec. #timeleft = int(timeout) while [[ ! -x "${executable}" ]]; do if [[ "${timeout}" == "0" ]]; then echo "timed out waiting for (${executable})" exit 77 fi echo "not executable: '${executable}', waiting ${timeout}s" sleep 1 timeout=$((timeout-1)) done + [[ ! -x /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/raw-gather/run-P499faaef2a5248.bash ]] bash ${executable} + bash /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/raw-gather/run-P499faaef2a5248.bash + '[' '!' -d /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/raw-gather ']' + cd /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/raw-gather + eval '/bin/bash run.sh' ++ /bin/bash run.sh cd /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/raw-gather + cd /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/raw-gather bash task.sh + bash task.sh 30e18b9a274d CC=gcc CFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong -Wformat -Werror=format-security CPPFLAGS=-Wdate-time -D_FORTIFY_SOURCE=2 CXX=g++ CXXFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong -Wformat -Werror=format-security DEBCONF_NONINTERACTIVE_SEEN=true DEBIAN_FRONTEND=noninteractive DEB_BUILD_ARCH=amd64 DEB_BUILD_ARCH_ABI=base DEB_BUILD_ARCH_BITS=64 DEB_BUILD_ARCH_CPU=amd64 DEB_BUILD_ARCH_ENDIAN=little DEB_BUILD_ARCH_LIBC=gnu DEB_BUILD_ARCH_OS=linux DEB_BUILD_GNU_CPU=x86_64 DEB_BUILD_GNU_SYSTEM=linux-gnu DEB_BUILD_GNU_TYPE=x86_64-linux-gnu DEB_BUILD_MULTIARCH=x86_64-linux-gnu DEB_BUILD_OPTIONS=nocheck parallel=10 DEB_HOST_ARCH=amd64 DEB_HOST_ARCH_ABI=base DEB_HOST_ARCH_BITS=64 DEB_HOST_ARCH_CPU=amd64 DEB_HOST_ARCH_ENDIAN=little DEB_HOST_ARCH_LIBC=gnu DEB_HOST_ARCH_OS=linux DEB_HOST_GNU_CPU=x86_64 DEB_HOST_GNU_SYSTEM=linux-gnu DEB_HOST_GNU_TYPE=x86_64-linux-gnu DEB_HOST_MULTIARCH=x86_64-linux-gnu DEB_TARGET_ARCH=amd64 DEB_TARGET_ARCH_ABI=base DEB_TARGET_ARCH_BITS=64 DEB_TARGET_ARCH_CPU=amd64 DEB_TARGET_ARCH_ENDIAN=little DEB_TARGET_ARCH_LIBC=gnu DEB_TARGET_ARCH_OS=linux DEB_TARGET_GNU_CPU=x86_64 DEB_TARGET_GNU_SYSTEM=linux-gnu DEB_TARGET_GNU_TYPE=x86_64-linux-gnu DEB_TARGET_MULTIARCH=x86_64-linux-gnu DH_INTERNAL_BUILDFLAGS=1 DH_INTERNAL_OPTIONS=-a DH_INTERNAL_OVERRIDE=dh_auto_test FALCON_INSTALL_RULE=install FALCON_PREFIX=/build/falcon-LwwdoQ/falcon-1.8.8/inst FALCON_WORKSPACE=/build/falcon-LwwdoQ/falcon-1.8.8 FCFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong FFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong GCJFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong HOME=/nonexistent LANG=C.UTF-8 LANGUAGE=C.UTF-8 LC_ALL=C.UTF-8 LDFLAGS=-Wl,-z,relro LOGNAME=builduser MAKEFLAGS=w MAKELEVEL=6 MFLAGS=-w MMDEBSTRAP_APT_CONFIG=/tmp/mmdebstrap.SAG5NvxJ_M/tmp/mmdebstrap.apt.conf.TRj0u44dYeZl MMDEBSTRAP_HOOK=customize MMDEBSTRAP_HOOKSOCK=6 MMDEBSTRAP_MODE=root OBJCFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong -Wformat -Werror=format-security OBJCXXFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong -Wformat -Werror=format-security OLDPWD=/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/raw-gather PATH=/build/falcon-LwwdoQ/falcon-1.8.8/inst/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/sbin:/usr/bin:/sbin:/bin PERL_USE_UNSAFE_INC=1 PWD=/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/raw-gather PYPEFLOW_JOB_START_SCRIPT=/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/raw-gather/run-P499faaef2a5248.bash PYPEFLOW_JOB_START_TIMEOUT=60 PYTHONPATH=/build/falcon-LwwdoQ/falcon-1.8.8/inst/pylib:/build/falcon-LwwdoQ/falcon-1.8.8/inst/pylib: SHELL=/bin/bash SHLVL=5 SOURCE_DATE_EPOCH=1513411047 USER=builduser _=/usr/bin/env /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/raw-gather 2022-01-06 16:56:56,543[INFO] sleep 0.2s 2022-01-06 16:56:56,569 - root - DEBUG - Running "/build/falcon-LwwdoQ/falcon-1.8.8/inst/pylib/pypeflow-1.0.0-py2.7.egg/pypeflow/do_task.py /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/raw-gather/task.json" 2022-01-06 16:56:56,572 - root - DEBUG - Checking existence of '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/raw-gather/task.json' with timeout=60 2022-01-06 16:56:56,572 - root - DEBUG - Loading JSON from '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/raw-gather/task.json' 2022-01-06 16:56:56,572 - root - DEBUG - {u'inputs': {u'ajob_0000': u'/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/job_0000/job_0000_done', u'ajob_0001': u'/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/job_0001/job_0001_done'}, u'outputs': {u'gathered': u'gathered_las.txt'}, u'parameters': {u'nblock': 2}, u'python_function': u'falcon_kit.pype_tasks.task_daligner_gather'} 2022-01-06 16:56:56,573 - root - DEBUG - CD: '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/raw-gather' <- '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/raw-gather' 2022-01-06 16:56:56,573 - root - DEBUG - Checking existence of u'/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/job_0000/job_0000_done' with timeout=60 2022-01-06 16:56:56,573 - root - DEBUG - Checking existence of u'/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/job_0001/job_0001_done' with timeout=60 2022-01-06 16:56:56,604 - root - DEBUG - CD: '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/raw-gather' <- '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/raw-gather' 2022-01-06 16:56:56,604 - falcon_kit.pype_tasks - DEBUG - nblock=2, out_dir: {u'ajob_0000': u'/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/job_0000/job_0000_done', u'ajob_0001': u'/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/job_0001/job_0001_done'} 2022-01-06 16:56:56,605 - root - DEBUG - CD: '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/raw-gather' -> '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/raw-gather' 2022-01-06 16:56:56,606 - root - DEBUG - Checking existence of u'gathered_las.txt' with timeout=60 2022-01-06 16:56:56,606 - root - DEBUG - CD: '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/raw-gather' -> '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/raw-gather' real 0m0.145s user 0m0.103s sys 0m0.038s touch /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/raw-gather/run.sh.done + touch /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/raw-gather/run.sh.done + finish + echo 'finish code: 0' finish code: 0 2022-01-06 16:56:56,744[INFO] recently_satisfied: set([Node(0-rawreads/raw-gather)]) 2022-01-06 16:56:56,744[INFO] Num satisfied in this iteration: 1 2022-01-06 16:56:56,744[INFO] Num still unsatisfied: 0 2022-01-06 16:56:56,748[INFO] Num unsatisfied: 1, graph: 7 2022-01-06 16:56:56,748[INFO] About to submit: Node(0-rawreads/merge-scatter) 2022-01-06 16:56:56,751[INFO] !chmod +x /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/merge-scatter/run-P8f2dc772f5aa1e.bash 2022-01-06 16:56:56,762[INFO] sleep 0.1s 2022-01-06 16:56:56,768[INFO] Popen: 'bash -C /build/falcon-LwwdoQ/falcon-1.8.8/inst/pylib/pypeflow-1.0.0-py2.7.egg/pwatcher/mains/job_start.sh' executable=${PYPEFLOW_JOB_START_SCRIPT} + executable=/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/merge-scatter/run-P8f2dc772f5aa1e.bash timeout=${PYPEFLOW_JOB_START_TIMEOUT:-60} # wait 60s by default + timeout=60 # Wait up to timeout seconds for the executable to become "executable", # then exec. #timeleft = int(timeout) while [[ ! -x "${executable}" ]]; do if [[ "${timeout}" == "0" ]]; then echo "timed out waiting for (${executable})" exit 77 fi echo "not executable: '${executable}', waiting ${timeout}s" sleep 1 timeout=$((timeout-1)) done + [[ ! -x /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/merge-scatter/run-P8f2dc772f5aa1e.bash ]] bash ${executable} + bash /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/merge-scatter/run-P8f2dc772f5aa1e.bash + '[' '!' -d /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/merge-scatter ']' + cd /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/merge-scatter + eval '/bin/bash run.sh' ++ /bin/bash run.sh cd /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/merge-scatter + cd /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/merge-scatter bash task.sh + bash task.sh 30e18b9a274d CC=gcc CFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong -Wformat -Werror=format-security CPPFLAGS=-Wdate-time -D_FORTIFY_SOURCE=2 CXX=g++ CXXFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong -Wformat -Werror=format-security DEBCONF_NONINTERACTIVE_SEEN=true DEBIAN_FRONTEND=noninteractive DEB_BUILD_ARCH=amd64 DEB_BUILD_ARCH_ABI=base DEB_BUILD_ARCH_BITS=64 DEB_BUILD_ARCH_CPU=amd64 DEB_BUILD_ARCH_ENDIAN=little DEB_BUILD_ARCH_LIBC=gnu DEB_BUILD_ARCH_OS=linux DEB_BUILD_GNU_CPU=x86_64 DEB_BUILD_GNU_SYSTEM=linux-gnu DEB_BUILD_GNU_TYPE=x86_64-linux-gnu DEB_BUILD_MULTIARCH=x86_64-linux-gnu DEB_BUILD_OPTIONS=nocheck parallel=10 DEB_HOST_ARCH=amd64 DEB_HOST_ARCH_ABI=base DEB_HOST_ARCH_BITS=64 DEB_HOST_ARCH_CPU=amd64 DEB_HOST_ARCH_ENDIAN=little DEB_HOST_ARCH_LIBC=gnu DEB_HOST_ARCH_OS=linux DEB_HOST_GNU_CPU=x86_64 DEB_HOST_GNU_SYSTEM=linux-gnu DEB_HOST_GNU_TYPE=x86_64-linux-gnu DEB_HOST_MULTIARCH=x86_64-linux-gnu DEB_TARGET_ARCH=amd64 DEB_TARGET_ARCH_ABI=base DEB_TARGET_ARCH_BITS=64 DEB_TARGET_ARCH_CPU=amd64 DEB_TARGET_ARCH_ENDIAN=little DEB_TARGET_ARCH_LIBC=gnu DEB_TARGET_ARCH_OS=linux DEB_TARGET_GNU_CPU=x86_64 DEB_TARGET_GNU_SYSTEM=linux-gnu DEB_TARGET_GNU_TYPE=x86_64-linux-gnu DEB_TARGET_MULTIARCH=x86_64-linux-gnu DH_INTERNAL_BUILDFLAGS=1 DH_INTERNAL_OPTIONS=-a DH_INTERNAL_OVERRIDE=dh_auto_test FALCON_INSTALL_RULE=install FALCON_PREFIX=/build/falcon-LwwdoQ/falcon-1.8.8/inst FALCON_WORKSPACE=/build/falcon-LwwdoQ/falcon-1.8.8 FCFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong FFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong GCJFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong HOME=/nonexistent LANG=C.UTF-8 LANGUAGE=C.UTF-8 LC_ALL=C.UTF-8 LDFLAGS=-Wl,-z,relro LOGNAME=builduser MAKEFLAGS=w MAKELEVEL=6 MFLAGS=-w MMDEBSTRAP_APT_CONFIG=/tmp/mmdebstrap.SAG5NvxJ_M/tmp/mmdebstrap.apt.conf.TRj0u44dYeZl MMDEBSTRAP_HOOK=customize MMDEBSTRAP_HOOKSOCK=6 MMDEBSTRAP_MODE=root OBJCFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong -Wformat -Werror=format-security OBJCXXFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong -Wformat -Werror=format-security OLDPWD=/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/merge-scatter PATH=/build/falcon-LwwdoQ/falcon-1.8.8/inst/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/sbin:/usr/bin:/sbin:/bin PERL_USE_UNSAFE_INC=1 PWD=/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/merge-scatter PYPEFLOW_JOB_START_SCRIPT=/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/merge-scatter/run-P8f2dc772f5aa1e.bash PYPEFLOW_JOB_START_TIMEOUT=60 PYTHONPATH=/build/falcon-LwwdoQ/falcon-1.8.8/inst/pylib:/build/falcon-LwwdoQ/falcon-1.8.8/inst/pylib: SHELL=/bin/bash SHLVL=5 SOURCE_DATE_EPOCH=1513411047 USER=builduser _=/usr/bin/env /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/merge-scatter 2022-01-06 16:56:56,865[INFO] sleep 0.2s 2022-01-06 16:56:56,897 - root - DEBUG - Running "/build/falcon-LwwdoQ/falcon-1.8.8/inst/pylib/pypeflow-1.0.0-py2.7.egg/pypeflow/do_task.py /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/merge-scatter/task.json" 2022-01-06 16:56:56,900 - root - DEBUG - Checking existence of '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/merge-scatter/task.json' with timeout=60 2022-01-06 16:56:56,900 - root - DEBUG - Loading JSON from '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/merge-scatter/task.json' 2022-01-06 16:56:56,902 - root - DEBUG - {u'inputs': {u'gathered_las': u'/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/raw-gather/gathered_las.txt', u'run_jobs': u'/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/run_jobs.sh'}, u'outputs': {u'scattered': u'scattered.json'}, u'parameters': {u'config': {u'LA4Falcon_preload': True, u'avoid_text_file_busy': True, u'cns_concurrent_jobs': 32, u'da_concurrent_jobs': 32, u'dazcon': False, u'default_concurrent_jobs': 8, u'dust': False, u'falcon_sense_greedy': False, u'falcon_sense_option': u'--output_multi --min_idt 0.70 --min_cov 1 --max_n_read 20000 --n_core 0', u'falcon_sense_skip_contained': False, u'fc_concurrent_jobs': 8, u'fc_ovlp_to_graph_option': u' --min_len 1', u'genome_size': 5000, u'input_fofn': u'input.fofn', u'input_type': u'raw', u'install_prefix': u'/usr', u'job_queue': u'bash -C ${CMD}', u'job_type': u'string', u'la_concurrent_jobs': 32, u'length_cutoff': -1, u'length_cutoff_pr': 1, u'overlap_filtering_setting': u'--max_diff 10000 --max_cov 100000 --min_cov 1 --min_len 1 --bestn 1000 --n_core 0', u'ovlp_DBsplit_option': u'-a -x5 -s50', u'ovlp_HPCdaligner_option': u'-v -B4 -t50 -h1 -e.99 -l1 -s1000', u'pa_DBdust_option': u'-w128 -t2.5 -m20', u'pa_DBsplit_option': u'-a -x5 -s.065536', u'pa_HPCdaligner_option': u'-v -B4 -t50 -h1 -e.99 -w1 -l1 -s1000', u'pa_dazcon_option': u'-j 4 -x -l 500', u'pda_concurrent_jobs': 32, u'pla_concurrent_jobs': 32, u'pwatcher_directory': u'mypwatcher', u'pwatcher_type': u'blocking', u'seed_coverage': 20.0, u'sge_option': u'-pe smp 8 -q bash -C ${CMD}', u'sge_option_cns': u'-pe smp 8 -q bash -C ${CMD}', u'sge_option_da': u'-pe smp 8 -q bash -C ${CMD}', u'sge_option_fc': u'-pe smp 24 -q bash -C ${CMD}', u'sge_option_la': u'-pe smp 2 -q bash -C ${CMD}', u'sge_option_pda': u'-pe smp 8 -q bash -C ${CMD}', u'sge_option_pla': u'-pe smp 2 -q bash -C ${CMD}', u'skip_checks': False, u'stop_all_jobs_on_failure': True, u'target': u'assembly', u'use_tmpdir': False}, u'db_prefix': u'raw_reads'}, u'python_function': u'falcon_kit.pype_tasks.task_merge_scatter'} 2022-01-06 16:56:56,903 - root - DEBUG - CD: '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/merge-scatter' <- '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/merge-scatter' 2022-01-06 16:56:56,903 - root - DEBUG - Checking existence of u'/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/run_jobs.sh' with timeout=60 2022-01-06 16:56:56,903 - root - DEBUG - Checking existence of u'/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/raw-gather/gathered_las.txt' with timeout=60 2022-01-06 16:56:56,935 - root - DEBUG - CD: '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/merge-scatter' <- '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/merge-scatter' 2022-01-06 16:56:56,937 - root - DEBUG - CD: '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/merge-scatter' -> '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/merge-scatter' 2022-01-06 16:56:56,937 - root - DEBUG - Checking existence of u'scattered.json' with timeout=60 2022-01-06 16:56:56,937 - root - DEBUG - CD: '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/merge-scatter' -> '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/merge-scatter' real 0m0.157s user 0m0.105s sys 0m0.041s touch /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/merge-scatter/run.sh.done + touch /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/merge-scatter/run.sh.done + finish + echo 'finish code: 0' finish code: 0 2022-01-06 16:56:57,067[INFO] recently_satisfied: set([Node(0-rawreads/merge-scatter)]) 2022-01-06 16:56:57,067[INFO] Num satisfied in this iteration: 1 2022-01-06 16:56:57,067[INFO] Num still unsatisfied: 0 2022-01-06 16:56:57,079[INFO] Num unsatisfied: 3, graph: 10 2022-01-06 16:56:57,079[INFO] About to submit: Node(0-rawreads/m_00002) 2022-01-06 16:56:57,079[INFO] About to submit: Node(0-rawreads/m_00001) 2022-01-06 16:56:57,084[INFO] !chmod +x /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/m_00002/run-P8f4ceb3fff300e.bash 2022-01-06 16:56:57,096[INFO] !chmod +x /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/m_00001/run-P894e2471b3e37e.bash 2022-01-06 16:56:57,102[INFO] Popen: 'bash -C /build/falcon-LwwdoQ/falcon-1.8.8/inst/pylib/pypeflow-1.0.0-py2.7.egg/pwatcher/mains/job_start.sh' 2022-01-06 16:56:57,111[INFO] sleep 0.1s executable=${PYPEFLOW_JOB_START_SCRIPT} + executable=/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/m_00002/run-P8f4ceb3fff300e.bash timeout=${PYPEFLOW_JOB_START_TIMEOUT:-60} # wait 60s by default + timeout=60 # Wait up to timeout seconds for the executable to become "executable", # then exec. #timeleft = int(timeout) while [[ ! -x "${executable}" ]]; do if [[ "${timeout}" == "0" ]]; then echo "timed out waiting for (${executable})" exit 77 fi echo "not executable: '${executable}', waiting ${timeout}s" sleep 1 timeout=$((timeout-1)) done + [[ ! -x /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/m_00002/run-P8f4ceb3fff300e.bash ]] bash ${executable} + bash /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/m_00002/run-P8f4ceb3fff300e.bash 2022-01-06 16:56:57,117[INFO] Popen: 'bash -C /build/falcon-LwwdoQ/falcon-1.8.8/inst/pylib/pypeflow-1.0.0-py2.7.egg/pwatcher/mains/job_start.sh' + '[' '!' -d /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/m_00002 ']' + cd /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/m_00002 + eval '/bin/bash run.sh' ++ /bin/bash run.sh cd /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/m_00002 + cd /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/m_00002 bash task.sh + bash task.sh executable=${PYPEFLOW_JOB_START_SCRIPT} + executable=/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/m_00001/run-P894e2471b3e37e.bash timeout=${PYPEFLOW_JOB_START_TIMEOUT:-60} # wait 60s by default + timeout=60 # Wait up to timeout seconds for the executable to become "executable", # then exec. #timeleft = int(timeout) while [[ ! -x "${executable}" ]]; do if [[ "${timeout}" == "0" ]]; then echo "timed out waiting for (${executable})" exit 77 fi echo "not executable: '${executable}', waiting ${timeout}s" sleep 1 timeout=$((timeout-1)) done + [[ ! -x /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/m_00001/run-P894e2471b3e37e.bash ]] bash ${executable} + bash /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/m_00001/run-P894e2471b3e37e.bash 30e18b9a274d + '[' '!' -d /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/m_00001 ']' + cd /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/m_00001 + eval '/bin/bash run.sh' ++ /bin/bash run.sh CC=gcc CFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong -Wformat -Werror=format-security CPPFLAGS=-Wdate-time -D_FORTIFY_SOURCE=2 CXX=g++ CXXFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong -Wformat -Werror=format-security DEBCONF_NONINTERACTIVE_SEEN=true DEBIAN_FRONTEND=noninteractive DEB_BUILD_ARCH=amd64 DEB_BUILD_ARCH_ABI=base DEB_BUILD_ARCH_BITS=64 DEB_BUILD_ARCH_CPU=amd64 DEB_BUILD_ARCH_ENDIAN=little DEB_BUILD_ARCH_LIBC=gnu DEB_BUILD_ARCH_OS=linux DEB_BUILD_GNU_CPU=x86_64 DEB_BUILD_GNU_SYSTEM=linux-gnu DEB_BUILD_GNU_TYPE=x86_64-linux-gnu DEB_BUILD_MULTIARCH=x86_64-linux-gnu DEB_BUILD_OPTIONS=nocheck parallel=10 DEB_HOST_ARCH=amd64 DEB_HOST_ARCH_ABI=base DEB_HOST_ARCH_BITS=64 DEB_HOST_ARCH_CPU=amd64 DEB_HOST_ARCH_ENDIAN=little DEB_HOST_ARCH_LIBC=gnu DEB_HOST_ARCH_OS=linux DEB_HOST_GNU_CPU=x86_64 DEB_HOST_GNU_SYSTEM=linux-gnu DEB_HOST_GNU_TYPE=x86_64-linux-gnu DEB_HOST_MULTIARCH=x86_64-linux-gnu DEB_TARGET_ARCH=amd64 DEB_TARGET_ARCH_ABI=base DEB_TARGET_ARCH_BITS=64 DEB_TARGET_ARCH_CPU=amd64 DEB_TARGET_ARCH_ENDIAN=little DEB_TARGET_ARCH_LIBC=gnu DEB_TARGET_ARCH_OS=linux DEB_TARGET_GNU_CPU=x86_64 DEB_TARGET_GNU_SYSTEM=linux-gnu DEB_TARGET_GNU_TYPE=x86_64-linux-gnu DEB_TARGET_MULTIARCH=x86_64-linux-gnu DH_INTERNAL_BUILDFLAGS=1 DH_INTERNAL_OPTIONS=-a DH_INTERNAL_OVERRIDE=dh_auto_test FALCON_INSTALL_RULE=install FALCON_PREFIX=/build/falcon-LwwdoQ/falcon-1.8.8/inst FALCON_WORKSPACE=/build/falcon-LwwdoQ/falcon-1.8.8 FCFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong FFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong GCJFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong HOME=/nonexistent LANG=C.UTF-8 LANGUAGE=C.UTF-8 LC_ALL=C.UTF-8 LDFLAGS=-Wl,-z,relro LOGNAME=builduser MAKEFLAGS=w MAKELEVEL=6 MFLAGS=-w MMDEBSTRAP_APT_CONFIG=/tmp/mmdebstrap.SAG5NvxJ_M/tmp/mmdebstrap.apt.conf.TRj0u44dYeZl MMDEBSTRAP_HOOK=customize MMDEBSTRAP_HOOKSOCK=6 MMDEBSTRAP_MODE=root OBJCFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong -Wformat -Werror=format-security OBJCXXFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong -Wformat -Werror=format-security OLDPWD=/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/m_00002 PATH=/build/falcon-LwwdoQ/falcon-1.8.8/inst/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/sbin:/usr/bin:/sbin:/bin PERL_USE_UNSAFE_INC=1 PWD=/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/m_00002 PYPEFLOW_JOB_START_SCRIPT=/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/m_00002/run-P8f4ceb3fff300e.bash PYPEFLOW_JOB_START_TIMEOUT=60 PYTHONPATH=/build/falcon-LwwdoQ/falcon-1.8.8/inst/pylib:/build/falcon-LwwdoQ/falcon-1.8.8/inst/pylib: SHELL=/bin/bash SHLVL=5 SOURCE_DATE_EPOCH=1513411047 USER=builduser _=/usr/bin/env /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/m_00002 cd /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/m_00001 + cd /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/m_00001 bash task.sh + bash task.sh 30e18b9a274d CC=gcc CFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong -Wformat -Werror=format-security CPPFLAGS=-Wdate-time -D_FORTIFY_SOURCE=2 CXX=g++ CXXFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong -Wformat -Werror=format-security DEBCONF_NONINTERACTIVE_SEEN=true DEBIAN_FRONTEND=noninteractive DEB_BUILD_ARCH=amd64 DEB_BUILD_ARCH_ABI=base DEB_BUILD_ARCH_BITS=64 DEB_BUILD_ARCH_CPU=amd64 DEB_BUILD_ARCH_ENDIAN=little DEB_BUILD_ARCH_LIBC=gnu DEB_BUILD_ARCH_OS=linux DEB_BUILD_GNU_CPU=x86_64 DEB_BUILD_GNU_SYSTEM=linux-gnu DEB_BUILD_GNU_TYPE=x86_64-linux-gnu DEB_BUILD_MULTIARCH=x86_64-linux-gnu DEB_BUILD_OPTIONS=nocheck parallel=10 DEB_HOST_ARCH=amd64 DEB_HOST_ARCH_ABI=base DEB_HOST_ARCH_BITS=64 DEB_HOST_ARCH_CPU=amd64 DEB_HOST_ARCH_ENDIAN=little DEB_HOST_ARCH_LIBC=gnu DEB_HOST_ARCH_OS=linux DEB_HOST_GNU_CPU=x86_64 DEB_HOST_GNU_SYSTEM=linux-gnu DEB_HOST_GNU_TYPE=x86_64-linux-gnu DEB_HOST_MULTIARCH=x86_64-linux-gnu DEB_TARGET_ARCH=amd64 DEB_TARGET_ARCH_ABI=base DEB_TARGET_ARCH_BITS=64 DEB_TARGET_ARCH_CPU=amd64 DEB_TARGET_ARCH_ENDIAN=little DEB_TARGET_ARCH_LIBC=gnu DEB_TARGET_ARCH_OS=linux DEB_TARGET_GNU_CPU=x86_64 DEB_TARGET_GNU_SYSTEM=linux-gnu DEB_TARGET_GNU_TYPE=x86_64-linux-gnu DEB_TARGET_MULTIARCH=x86_64-linux-gnu DH_INTERNAL_BUILDFLAGS=1 DH_INTERNAL_OPTIONS=-a DH_INTERNAL_OVERRIDE=dh_auto_test FALCON_INSTALL_RULE=install FALCON_PREFIX=/build/falcon-LwwdoQ/falcon-1.8.8/inst FALCON_WORKSPACE=/build/falcon-LwwdoQ/falcon-1.8.8 FCFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong FFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong GCJFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong HOME=/nonexistent LANG=C.UTF-8 LANGUAGE=C.UTF-8 LC_ALL=C.UTF-8 LDFLAGS=-Wl,-z,relro LOGNAME=builduser MAKEFLAGS=w MAKELEVEL=6 MFLAGS=-w MMDEBSTRAP_APT_CONFIG=/tmp/mmdebstrap.SAG5NvxJ_M/tmp/mmdebstrap.apt.conf.TRj0u44dYeZl MMDEBSTRAP_HOOK=customize MMDEBSTRAP_HOOKSOCK=6 MMDEBSTRAP_MODE=root OBJCFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong -Wformat -Werror=format-security OBJCXXFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong -Wformat -Werror=format-security OLDPWD=/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/m_00001 PATH=/build/falcon-LwwdoQ/falcon-1.8.8/inst/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/sbin:/usr/bin:/sbin:/bin PERL_USE_UNSAFE_INC=1 PWD=/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/m_00001 PYPEFLOW_JOB_START_SCRIPT=/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/m_00001/run-P894e2471b3e37e.bash PYPEFLOW_JOB_START_TIMEOUT=60 PYTHONPATH=/build/falcon-LwwdoQ/falcon-1.8.8/inst/pylib:/build/falcon-LwwdoQ/falcon-1.8.8/inst/pylib: SHELL=/bin/bash SHLVL=5 SOURCE_DATE_EPOCH=1513411047 USER=builduser _=/usr/bin/env /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/m_00001 2022-01-06 16:56:57,213[INFO] sleep 0.2s 2022-01-06 16:56:57,231 - root - DEBUG - Running "/build/falcon-LwwdoQ/falcon-1.8.8/inst/pylib/pypeflow-1.0.0-py2.7.egg/pypeflow/do_task.py /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/m_00002/task.json" 2022-01-06 16:56:57,233 - root - DEBUG - Checking existence of '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/m_00002/task.json' with timeout=60 2022-01-06 16:56:57,233 - root - DEBUG - Loading JSON from '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/m_00002/task.json' 2022-01-06 16:56:57,236 - root - DEBUG - {u'inputs': {u'gathered_las': u'/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/raw-gather/gathered_las.txt', u'scatter_fn': u'/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/merge-scatter/scattered.json'}, u'outputs': {u'job_done': u'm_00002_done', u'merged_las': u'raw_reads.2.las'}, u'parameters': {u'config': {u'LA4Falcon_preload': True, u'avoid_text_file_busy': True, u'cns_concurrent_jobs': 32, u'da_concurrent_jobs': 32, u'dazcon': False, u'default_concurrent_jobs': 8, u'dust': False, u'falcon_sense_greedy': False, u'falcon_sense_option': u'--output_multi --min_idt 0.70 --min_cov 1 --max_n_read 20000 --n_core 0', u'falcon_sense_skip_contained': False, u'fc_concurrent_jobs': 8, u'fc_ovlp_to_graph_option': u' --min_len 1', u'genome_size': 5000, u'input_fofn': u'input.fofn', u'input_type': u'raw', u'install_prefix': u'/usr', u'job_queue': u'bash -C ${CMD}', u'job_type': u'string', u'la_concurrent_jobs': 32, u'length_cutoff': -1, u'length_cutoff_pr': 1, u'overlap_filtering_setting': u'--max_diff 10000 --max_cov 100000 --min_cov 1 --min_len 1 --bestn 1000 --n_core 0', u'ovlp_DBsplit_option': u'-a -x5 -s50', u'ovlp_HPCdaligner_option': u'-v -B4 -t50 -h1 -e.99 -l1 -s1000', u'pa_DBdust_option': u'-w128 -t2.5 -m20', u'pa_DBsplit_option': u'-a -x5 -s.065536', u'pa_HPCdaligner_option': u'-v -B4 -t50 -h1 -e.99 -w1 -l1 -s1000', u'pa_dazcon_option': u'-j 4 -x -l 500', u'pda_concurrent_jobs': 32, u'pla_concurrent_jobs': 32, u'pwatcher_directory': u'mypwatcher', u'pwatcher_type': u'blocking', u'seed_coverage': 20.0, u'sge_option': u'-pe smp 8 -q bash -C ${CMD}', u'sge_option_cns': u'-pe smp 8 -q bash -C ${CMD}', u'sge_option_da': u'-pe smp 8 -q bash -C ${CMD}', u'sge_option_fc': u'-pe smp 24 -q bash -C ${CMD}', u'sge_option_la': u'-pe smp 2 -q bash -C ${CMD}', u'sge_option_pda': u'-pe smp 8 -q bash -C ${CMD}', u'sge_option_pla': u'-pe smp 2 -q bash -C ${CMD}', u'skip_checks': False, u'stop_all_jobs_on_failure': True, u'target': u'assembly', u'use_tmpdir': False}, u'job_id': 2, u'merge_script': u'\n# Get the real path of a link, following all links (since \'readlink -f\' is not on OSX).\n# http://stackoverflow.com/questions/7665/how-to-resolve-symbolic-links-in-a-shell-script/697552\nrealpath() {\n local r=$1; local t=$(readlink $r)\n while [ $t ]; do\n r=$(cd $(dirname $r) && cd $(dirname $t) && pwd -P)/$(basename $t)\n t=$(readlink $r)\n done\n echo $r\n}\nrmfollow() {\n local path=$(realpath $1)\n rm -f "${path}"\n}\nLAmerge -v raw_reads.2 L1.2.1 L1.2.2\n# rmfollow L1.2.1.las\n# rmfollow L1.2.2.las\n', u'sge_option': u'-pe smp 2 -q bash -C ${CMD}'}, u'python_function': u'falcon_kit.pype_tasks.task_run_las_merge'} 2022-01-06 16:56:57,236 - root - DEBUG - CD: '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/m_00002' <- '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/m_00002' 2022-01-06 16:56:57,236 - root - DEBUG - Checking existence of u'/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/raw-gather/gathered_las.txt' with timeout=60 2022-01-06 16:56:57,236 - root - DEBUG - Checking existence of u'/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/merge-scatter/scattered.json' with timeout=60 2022-01-06 16:56:57,241 - root - DEBUG - Running "/build/falcon-LwwdoQ/falcon-1.8.8/inst/pylib/pypeflow-1.0.0-py2.7.egg/pypeflow/do_task.py /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/m_00001/task.json" 2022-01-06 16:56:57,243 - root - DEBUG - Checking existence of '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/m_00001/task.json' with timeout=60 2022-01-06 16:56:57,243 - root - DEBUG - Loading JSON from '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/m_00001/task.json' 2022-01-06 16:56:57,246 - root - DEBUG - {u'inputs': {u'gathered_las': u'/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/raw-gather/gathered_las.txt', u'scatter_fn': u'/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/merge-scatter/scattered.json'}, u'outputs': {u'job_done': u'm_00001_done', u'merged_las': u'raw_reads.1.las'}, u'parameters': {u'config': {u'LA4Falcon_preload': True, u'avoid_text_file_busy': True, u'cns_concurrent_jobs': 32, u'da_concurrent_jobs': 32, u'dazcon': False, u'default_concurrent_jobs': 8, u'dust': False, u'falcon_sense_greedy': False, u'falcon_sense_option': u'--output_multi --min_idt 0.70 --min_cov 1 --max_n_read 20000 --n_core 0', u'falcon_sense_skip_contained': False, u'fc_concurrent_jobs': 8, u'fc_ovlp_to_graph_option': u' --min_len 1', u'genome_size': 5000, u'input_fofn': u'input.fofn', u'input_type': u'raw', u'install_prefix': u'/usr', u'job_queue': u'bash -C ${CMD}', u'job_type': u'string', u'la_concurrent_jobs': 32, u'length_cutoff': -1, u'length_cutoff_pr': 1, u'overlap_filtering_setting': u'--max_diff 10000 --max_cov 100000 --min_cov 1 --min_len 1 --bestn 1000 --n_core 0', u'ovlp_DBsplit_option': u'-a -x5 -s50', u'ovlp_HPCdaligner_option': u'-v -B4 -t50 -h1 -e.99 -l1 -s1000', u'pa_DBdust_option': u'-w128 -t2.5 -m20', u'pa_DBsplit_option': u'-a -x5 -s.065536', u'pa_HPCdaligner_option': u'-v -B4 -t50 -h1 -e.99 -w1 -l1 -s1000', u'pa_dazcon_option': u'-j 4 -x -l 500', u'pda_concurrent_jobs': 32, u'pla_concurrent_jobs': 32, u'pwatcher_directory': u'mypwatcher', u'pwatcher_type': u'blocking', u'seed_coverage': 20.0, u'sge_option': u'-pe smp 8 -q bash -C ${CMD}', u'sge_option_cns': u'-pe smp 8 -q bash -C ${CMD}', u'sge_option_da': u'-pe smp 8 -q bash -C ${CMD}', u'sge_option_fc': u'-pe smp 24 -q bash -C ${CMD}', u'sge_option_la': u'-pe smp 2 -q bash -C ${CMD}', u'sge_option_pda': u'-pe smp 8 -q bash -C ${CMD}', u'sge_option_pla': u'-pe smp 2 -q bash -C ${CMD}', u'skip_checks': False, u'stop_all_jobs_on_failure': True, u'target': u'assembly', u'use_tmpdir': False}, u'job_id': 1, u'merge_script': u'\n# Get the real path of a link, following all links (since \'readlink -f\' is not on OSX).\n# http://stackoverflow.com/questions/7665/how-to-resolve-symbolic-links-in-a-shell-script/697552\nrealpath() {\n local r=$1; local t=$(readlink $r)\n while [ $t ]; do\n r=$(cd $(dirname $r) && cd $(dirname $t) && pwd -P)/$(basename $t)\n t=$(readlink $r)\n done\n echo $r\n}\nrmfollow() {\n local path=$(realpath $1)\n rm -f "${path}"\n}\nLAmerge -v raw_reads.1 L1.1.1 L1.1.2\n# rmfollow L1.1.1.las\n# rmfollow L1.1.2.las\n', u'sge_option': u'-pe smp 2 -q bash -C ${CMD}'}, u'python_function': u'falcon_kit.pype_tasks.task_run_las_merge'} 2022-01-06 16:56:57,246 - root - DEBUG - CD: '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/m_00001' <- '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/m_00001' 2022-01-06 16:56:57,246 - root - DEBUG - Checking existence of u'/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/raw-gather/gathered_las.txt' with timeout=60 2022-01-06 16:56:57,246 - root - DEBUG - Checking existence of u'/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/merge-scatter/scattered.json' with timeout=60 2022-01-06 16:56:57,269 - root - DEBUG - CD: '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/m_00002' <- '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/m_00002' 2022-01-06 16:56:57,269 - falcon_kit.pype_tasks - DEBUG - symlink '../job_0001/L1.2.1.las' <- '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/m_00002/L1.2.1.las' 2022-01-06 16:56:57,270 - falcon_kit.pype_tasks - DEBUG - symlink '../job_0001/L1.2.2.las' <- '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/m_00002/L1.2.2.las' 2022-01-06 16:56:57,271 - pypeflow.do_support - INFO - !/bin/bash -vex /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/m_00002/rp_00002.sh #!/bin/bash set -vex + set -vex # Get the real path of a link, following all links (since 'readlink -f' is not on OSX). # http://stackoverflow.com/questions/7665/how-to-resolve-symbolic-links-in-a-shell-script/697552 realpath() { local r=$1; local t=$(readlink $r) while [ $t ]; do r=$(cd $(dirname $r) && cd $(dirname $t) && pwd -P)/$(basename $t) t=$(readlink $r) done echo $r } rmfollow() { local path=$(realpath $1) rm -f "${path}" } LAmerge -v raw_reads.2 L1.2.1 L1.2.2 + LAmerge -v raw_reads.2 L1.2.1 L1.2.2 2022-01-06 16:56:57,278 - root - DEBUG - CD: '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/m_00001' <- '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/m_00001' 2022-01-06 16:56:57,278 - falcon_kit.pype_tasks - DEBUG - symlink '../job_0000/L1.1.1.las' <- '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/m_00001/L1.1.1.las' 2022-01-06 16:56:57,279 - falcon_kit.pype_tasks - DEBUG - symlink '../job_0001/L1.1.2.las' <- '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/m_00001/L1.1.2.las' In file ./L1.2.1.las, there are 456 records In file ./L1.2.2.las, there are 228 records Merging 2 files totalling 684 records # rmfollow L1.2.1.las # rmfollow L1.2.2.las touch m_00002_done + touch m_00002_done 2022-01-06 16:56:57,280 - pypeflow.do_support - INFO - !/bin/bash -vex /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/m_00001/rp_00001.sh 2022-01-06 16:56:57,283 - root - DEBUG - CD: '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/m_00002' -> '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/m_00002' 2022-01-06 16:56:57,284 - root - DEBUG - Checking existence of u'm_00002_done' with timeout=60 2022-01-06 16:56:57,284 - root - DEBUG - Checking existence of u'raw_reads.2.las' with timeout=60 2022-01-06 16:56:57,284 - root - DEBUG - CD: '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/m_00002' -> '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/m_00002' #!/bin/bash set -vex + set -vex # Get the real path of a link, following all links (since 'readlink -f' is not on OSX). # http://stackoverflow.com/questions/7665/how-to-resolve-symbolic-links-in-a-shell-script/697552 realpath() { local r=$1; local t=$(readlink $r) while [ $t ]; do r=$(cd $(dirname $r) && cd $(dirname $t) && pwd -P)/$(basename $t) t=$(readlink $r) done echo $r } rmfollow() { local path=$(realpath $1) rm -f "${path}" } LAmerge -v raw_reads.1 L1.1.1 L1.1.2 + LAmerge -v raw_reads.1 L1.1.1 L1.1.2 In file ./L1.1.1.las, there are 824 records In file ./L1.1.2.las, there are 456 records Merging 2 files totalling 1,280 records # rmfollow L1.1.1.las # rmfollow L1.1.2.las touch m_00001_done + touch m_00001_done 2022-01-06 16:56:57,292 - root - DEBUG - CD: '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/m_00001' -> '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/m_00001' 2022-01-06 16:56:57,293 - root - DEBUG - Checking existence of u'm_00001_done' with timeout=60 2022-01-06 16:56:57,293 - root - DEBUG - Checking existence of u'raw_reads.1.las' with timeout=60 2022-01-06 16:56:57,293 - root - DEBUG - CD: '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/m_00001' -> '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/m_00001' real 0m0.167s user 0m0.114s sys 0m0.048s touch /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/m_00002/run.sh.done + touch /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/m_00002/run.sh.done + finish + echo 'finish code: 0' finish code: 0 real 0m0.163s user 0m0.109s sys 0m0.052s touch /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/m_00001/run.sh.done + touch /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/m_00001/run.sh.done + finish + echo 'finish code: 0' finish code: 0 2022-01-06 16:56:57,414[INFO] recently_satisfied: set([Node(0-rawreads/m_00002), Node(0-rawreads/m_00001)]) 2022-01-06 16:56:57,414[INFO] Num satisfied in this iteration: 2 2022-01-06 16:56:57,415[INFO] Num still unsatisfied: 1 2022-01-06 16:56:57,415[INFO] About to submit: Node(0-rawreads/merge-gather) 2022-01-06 16:56:57,418[INFO] !chmod +x /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/merge-gather/run-P7d073d25c6bf52.bash 2022-01-06 16:56:57,429[INFO] sleep 0.1s 2022-01-06 16:56:57,434[INFO] Popen: 'bash -C /build/falcon-LwwdoQ/falcon-1.8.8/inst/pylib/pypeflow-1.0.0-py2.7.egg/pwatcher/mains/job_start.sh' executable=${PYPEFLOW_JOB_START_SCRIPT} + executable=/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/merge-gather/run-P7d073d25c6bf52.bash timeout=${PYPEFLOW_JOB_START_TIMEOUT:-60} # wait 60s by default + timeout=60 # Wait up to timeout seconds for the executable to become "executable", # then exec. #timeleft = int(timeout) while [[ ! -x "${executable}" ]]; do if [[ "${timeout}" == "0" ]]; then echo "timed out waiting for (${executable})" exit 77 fi echo "not executable: '${executable}', waiting ${timeout}s" sleep 1 timeout=$((timeout-1)) done + [[ ! -x /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/merge-gather/run-P7d073d25c6bf52.bash ]] bash ${executable} + bash /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/merge-gather/run-P7d073d25c6bf52.bash + '[' '!' -d /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/merge-gather ']' + cd /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/merge-gather + eval '/bin/bash run.sh' ++ /bin/bash run.sh cd /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/merge-gather + cd /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/merge-gather bash task.sh + bash task.sh 30e18b9a274d CC=gcc CFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong -Wformat -Werror=format-security CPPFLAGS=-Wdate-time -D_FORTIFY_SOURCE=2 CXX=g++ CXXFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong -Wformat -Werror=format-security DEBCONF_NONINTERACTIVE_SEEN=true DEBIAN_FRONTEND=noninteractive DEB_BUILD_ARCH=amd64 DEB_BUILD_ARCH_ABI=base DEB_BUILD_ARCH_BITS=64 DEB_BUILD_ARCH_CPU=amd64 DEB_BUILD_ARCH_ENDIAN=little DEB_BUILD_ARCH_LIBC=gnu DEB_BUILD_ARCH_OS=linux DEB_BUILD_GNU_CPU=x86_64 DEB_BUILD_GNU_SYSTEM=linux-gnu DEB_BUILD_GNU_TYPE=x86_64-linux-gnu DEB_BUILD_MULTIARCH=x86_64-linux-gnu DEB_BUILD_OPTIONS=nocheck parallel=10 DEB_HOST_ARCH=amd64 DEB_HOST_ARCH_ABI=base DEB_HOST_ARCH_BITS=64 DEB_HOST_ARCH_CPU=amd64 DEB_HOST_ARCH_ENDIAN=little DEB_HOST_ARCH_LIBC=gnu DEB_HOST_ARCH_OS=linux DEB_HOST_GNU_CPU=x86_64 DEB_HOST_GNU_SYSTEM=linux-gnu DEB_HOST_GNU_TYPE=x86_64-linux-gnu DEB_HOST_MULTIARCH=x86_64-linux-gnu DEB_TARGET_ARCH=amd64 DEB_TARGET_ARCH_ABI=base DEB_TARGET_ARCH_BITS=64 DEB_TARGET_ARCH_CPU=amd64 DEB_TARGET_ARCH_ENDIAN=little DEB_TARGET_ARCH_LIBC=gnu DEB_TARGET_ARCH_OS=linux DEB_TARGET_GNU_CPU=x86_64 DEB_TARGET_GNU_SYSTEM=linux-gnu DEB_TARGET_GNU_TYPE=x86_64-linux-gnu DEB_TARGET_MULTIARCH=x86_64-linux-gnu DH_INTERNAL_BUILDFLAGS=1 DH_INTERNAL_OPTIONS=-a DH_INTERNAL_OVERRIDE=dh_auto_test FALCON_INSTALL_RULE=install FALCON_PREFIX=/build/falcon-LwwdoQ/falcon-1.8.8/inst FALCON_WORKSPACE=/build/falcon-LwwdoQ/falcon-1.8.8 FCFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong FFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong GCJFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong HOME=/nonexistent LANG=C.UTF-8 LANGUAGE=C.UTF-8 LC_ALL=C.UTF-8 LDFLAGS=-Wl,-z,relro LOGNAME=builduser MAKEFLAGS=w MAKELEVEL=6 MFLAGS=-w MMDEBSTRAP_APT_CONFIG=/tmp/mmdebstrap.SAG5NvxJ_M/tmp/mmdebstrap.apt.conf.TRj0u44dYeZl MMDEBSTRAP_HOOK=customize MMDEBSTRAP_HOOKSOCK=6 MMDEBSTRAP_MODE=root OBJCFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong -Wformat -Werror=format-security OBJCXXFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong -Wformat -Werror=format-security OLDPWD=/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/merge-gather PATH=/build/falcon-LwwdoQ/falcon-1.8.8/inst/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/sbin:/usr/bin:/sbin:/bin PERL_USE_UNSAFE_INC=1 PWD=/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/merge-gather PYPEFLOW_JOB_START_SCRIPT=/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/merge-gather/run-P7d073d25c6bf52.bash PYPEFLOW_JOB_START_TIMEOUT=60 PYTHONPATH=/build/falcon-LwwdoQ/falcon-1.8.8/inst/pylib:/build/falcon-LwwdoQ/falcon-1.8.8/inst/pylib: SHELL=/bin/bash SHLVL=5 SOURCE_DATE_EPOCH=1513411047 USER=builduser _=/usr/bin/env /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/merge-gather 2022-01-06 16:56:57,531[INFO] sleep 0.2s 2022-01-06 16:56:57,558 - root - DEBUG - Running "/build/falcon-LwwdoQ/falcon-1.8.8/inst/pylib/pypeflow-1.0.0-py2.7.egg/pypeflow/do_task.py /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/merge-gather/task.json" 2022-01-06 16:56:57,561 - root - DEBUG - Checking existence of '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/merge-gather/task.json' with timeout=60 2022-01-06 16:56:57,561 - root - DEBUG - Loading JSON from '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/merge-gather/task.json' 2022-01-06 16:56:57,562 - root - DEBUG - {u'inputs': {u'1': u'/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/m_00001/raw_reads.1.las', u'2': u'/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/m_00002/raw_reads.2.las'}, u'outputs': {u'las_fofn': u'las.fofn', u'las_fopfn': u'las.fopfn'}, u'parameters': {}, u'python_function': u'falcon_kit.pype_tasks.task_merge_gather'} 2022-01-06 16:56:57,562 - root - DEBUG - CD: '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/merge-gather' <- '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/merge-gather' 2022-01-06 16:56:57,562 - root - DEBUG - Checking existence of u'/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/m_00001/raw_reads.1.las' with timeout=60 2022-01-06 16:56:57,562 - root - DEBUG - Checking existence of u'/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/m_00002/raw_reads.2.las' with timeout=60 2022-01-06 16:56:57,594 - root - DEBUG - CD: '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/merge-gather' <- '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/merge-gather' 2022-01-06 16:56:57,595 - root - DEBUG - CD: '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/merge-gather' -> '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/merge-gather' 2022-01-06 16:56:57,595 - root - DEBUG - Checking existence of u'las.fopfn' with timeout=60 2022-01-06 16:56:57,596 - root - DEBUG - Checking existence of u'las.fofn' with timeout=60 2022-01-06 16:56:57,596 - root - DEBUG - CD: '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/merge-gather' -> '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/merge-gather' real 0m0.148s user 0m0.095s sys 0m0.048s touch /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/merge-gather/run.sh.done + touch /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/merge-gather/run.sh.done + finish + echo 'finish code: 0' finish code: 0 2022-01-06 16:56:57,732[INFO] recently_satisfied: set([Node(0-rawreads/merge-gather)]) 2022-01-06 16:56:57,732[INFO] Num satisfied in this iteration: 1 2022-01-06 16:56:57,733[INFO] Num still unsatisfied: 0 2022-01-06 16:56:57,737[INFO] Num unsatisfied: 1, graph: 11 2022-01-06 16:56:57,737[INFO] About to submit: Node(0-rawreads/cns-scatter) 2022-01-06 16:56:57,740[INFO] !chmod +x /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/cns-scatter/run-P9e7889661804f5.bash 2022-01-06 16:56:57,751[INFO] sleep 0.1s 2022-01-06 16:56:57,756[INFO] Popen: 'bash -C /build/falcon-LwwdoQ/falcon-1.8.8/inst/pylib/pypeflow-1.0.0-py2.7.egg/pwatcher/mains/job_start.sh' executable=${PYPEFLOW_JOB_START_SCRIPT} + executable=/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/cns-scatter/run-P9e7889661804f5.bash timeout=${PYPEFLOW_JOB_START_TIMEOUT:-60} # wait 60s by default + timeout=60 # Wait up to timeout seconds for the executable to become "executable", # then exec. #timeleft = int(timeout) while [[ ! -x "${executable}" ]]; do if [[ "${timeout}" == "0" ]]; then echo "timed out waiting for (${executable})" exit 77 fi echo "not executable: '${executable}', waiting ${timeout}s" sleep 1 timeout=$((timeout-1)) done + [[ ! -x /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/cns-scatter/run-P9e7889661804f5.bash ]] bash ${executable} + bash /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/cns-scatter/run-P9e7889661804f5.bash + '[' '!' -d /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/cns-scatter ']' + cd /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/cns-scatter + eval '/bin/bash run.sh' ++ /bin/bash run.sh cd /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/cns-scatter + cd /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/cns-scatter bash task.sh + bash task.sh 30e18b9a274d CC=gcc CFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong -Wformat -Werror=format-security CPPFLAGS=-Wdate-time -D_FORTIFY_SOURCE=2 CXX=g++ CXXFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong -Wformat -Werror=format-security DEBCONF_NONINTERACTIVE_SEEN=true DEBIAN_FRONTEND=noninteractive DEB_BUILD_ARCH=amd64 DEB_BUILD_ARCH_ABI=base DEB_BUILD_ARCH_BITS=64 DEB_BUILD_ARCH_CPU=amd64 DEB_BUILD_ARCH_ENDIAN=little DEB_BUILD_ARCH_LIBC=gnu DEB_BUILD_ARCH_OS=linux DEB_BUILD_GNU_CPU=x86_64 DEB_BUILD_GNU_SYSTEM=linux-gnu DEB_BUILD_GNU_TYPE=x86_64-linux-gnu DEB_BUILD_MULTIARCH=x86_64-linux-gnu DEB_BUILD_OPTIONS=nocheck parallel=10 DEB_HOST_ARCH=amd64 DEB_HOST_ARCH_ABI=base DEB_HOST_ARCH_BITS=64 DEB_HOST_ARCH_CPU=amd64 DEB_HOST_ARCH_ENDIAN=little DEB_HOST_ARCH_LIBC=gnu DEB_HOST_ARCH_OS=linux DEB_HOST_GNU_CPU=x86_64 DEB_HOST_GNU_SYSTEM=linux-gnu DEB_HOST_GNU_TYPE=x86_64-linux-gnu DEB_HOST_MULTIARCH=x86_64-linux-gnu DEB_TARGET_ARCH=amd64 DEB_TARGET_ARCH_ABI=base DEB_TARGET_ARCH_BITS=64 DEB_TARGET_ARCH_CPU=amd64 DEB_TARGET_ARCH_ENDIAN=little DEB_TARGET_ARCH_LIBC=gnu DEB_TARGET_ARCH_OS=linux DEB_TARGET_GNU_CPU=x86_64 DEB_TARGET_GNU_SYSTEM=linux-gnu DEB_TARGET_GNU_TYPE=x86_64-linux-gnu DEB_TARGET_MULTIARCH=x86_64-linux-gnu DH_INTERNAL_BUILDFLAGS=1 DH_INTERNAL_OPTIONS=-a DH_INTERNAL_OVERRIDE=dh_auto_test FALCON_INSTALL_RULE=install FALCON_PREFIX=/build/falcon-LwwdoQ/falcon-1.8.8/inst FALCON_WORKSPACE=/build/falcon-LwwdoQ/falcon-1.8.8 FCFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong FFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong GCJFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong HOME=/nonexistent LANG=C.UTF-8 LANGUAGE=C.UTF-8 LC_ALL=C.UTF-8 LDFLAGS=-Wl,-z,relro LOGNAME=builduser MAKEFLAGS=w MAKELEVEL=6 MFLAGS=-w MMDEBSTRAP_APT_CONFIG=/tmp/mmdebstrap.SAG5NvxJ_M/tmp/mmdebstrap.apt.conf.TRj0u44dYeZl MMDEBSTRAP_HOOK=customize MMDEBSTRAP_HOOKSOCK=6 MMDEBSTRAP_MODE=root OBJCFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong -Wformat -Werror=format-security OBJCXXFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong -Wformat -Werror=format-security OLDPWD=/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/cns-scatter PATH=/build/falcon-LwwdoQ/falcon-1.8.8/inst/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/sbin:/usr/bin:/sbin:/bin PERL_USE_UNSAFE_INC=1 PWD=/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/cns-scatter PYPEFLOW_JOB_START_SCRIPT=/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/cns-scatter/run-P9e7889661804f5.bash PYPEFLOW_JOB_START_TIMEOUT=60 PYTHONPATH=/build/falcon-LwwdoQ/falcon-1.8.8/inst/pylib:/build/falcon-LwwdoQ/falcon-1.8.8/inst/pylib: SHELL=/bin/bash SHLVL=5 SOURCE_DATE_EPOCH=1513411047 USER=builduser _=/usr/bin/env /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/cns-scatter 2022-01-06 16:56:57,852[INFO] sleep 0.2s 2022-01-06 16:56:57,875 - root - DEBUG - Running "/build/falcon-LwwdoQ/falcon-1.8.8/inst/pylib/pypeflow-1.0.0-py2.7.egg/pypeflow/do_task.py /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/cns-scatter/task.json" 2022-01-06 16:56:57,877 - root - DEBUG - Checking existence of '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/cns-scatter/task.json' with timeout=60 2022-01-06 16:56:57,877 - root - DEBUG - Loading JSON from '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/cns-scatter/task.json' 2022-01-06 16:56:57,880 - root - DEBUG - {u'inputs': {u'db': u'/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/raw_reads.db', u'gathered': u'/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/merge-gather/las.fopfn'}, u'outputs': {u'scattered': u'scattered.json'}, u'parameters': {u'config': {u'LA4Falcon_preload': True, u'avoid_text_file_busy': True, u'cns_concurrent_jobs': 32, u'da_concurrent_jobs': 32, u'dazcon': False, u'default_concurrent_jobs': 8, u'dust': False, u'falcon_sense_greedy': False, u'falcon_sense_option': u'--output_multi --min_idt 0.70 --min_cov 1 --max_n_read 20000 --n_core 0', u'falcon_sense_skip_contained': False, u'fc_concurrent_jobs': 8, u'fc_ovlp_to_graph_option': u' --min_len 1', u'genome_size': 5000, u'input_fofn': u'input.fofn', u'input_type': u'raw', u'install_prefix': u'/usr', u'job_queue': u'bash -C ${CMD}', u'job_type': u'string', u'la_concurrent_jobs': 32, u'length_cutoff': -1, u'length_cutoff_pr': 1, u'overlap_filtering_setting': u'--max_diff 10000 --max_cov 100000 --min_cov 1 --min_len 1 --bestn 1000 --n_core 0', u'ovlp_DBsplit_option': u'-a -x5 -s50', u'ovlp_HPCdaligner_option': u'-v -B4 -t50 -h1 -e.99 -l1 -s1000', u'pa_DBdust_option': u'-w128 -t2.5 -m20', u'pa_DBsplit_option': u'-a -x5 -s.065536', u'pa_HPCdaligner_option': u'-v -B4 -t50 -h1 -e.99 -w1 -l1 -s1000', u'pa_dazcon_option': u'-j 4 -x -l 500', u'pda_concurrent_jobs': 32, u'pla_concurrent_jobs': 32, u'pwatcher_directory': u'mypwatcher', u'pwatcher_type': u'blocking', u'seed_coverage': 20.0, u'sge_option': u'-pe smp 8 -q bash -C ${CMD}', u'sge_option_cns': u'-pe smp 8 -q bash -C ${CMD}', u'sge_option_da': u'-pe smp 8 -q bash -C ${CMD}', u'sge_option_fc': u'-pe smp 24 -q bash -C ${CMD}', u'sge_option_la': u'-pe smp 2 -q bash -C ${CMD}', u'sge_option_pda': u'-pe smp 8 -q bash -C ${CMD}', u'sge_option_pla': u'-pe smp 2 -q bash -C ${CMD}', u'skip_checks': False, u'stop_all_jobs_on_failure': True, u'target': u'assembly', u'use_tmpdir': False}, u'db_prefix': u'raw_reads'}, u'python_function': u'falcon_kit.pype_tasks.task_consensus_scatter'} 2022-01-06 16:56:57,880 - root - DEBUG - CD: '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/cns-scatter' <- '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/cns-scatter' 2022-01-06 16:56:57,880 - root - DEBUG - Checking existence of u'/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/merge-gather/las.fopfn' with timeout=60 2022-01-06 16:56:57,880 - root - DEBUG - Checking existence of u'/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/raw_reads.db' with timeout=60 2022-01-06 16:56:57,912 - root - DEBUG - CD: '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/cns-scatter' <- '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/cns-scatter' 2022-01-06 16:56:57,913 - root - DEBUG - CD: '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/cns-scatter' -> '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/cns-scatter' 2022-01-06 16:56:57,913 - root - DEBUG - Checking existence of u'scattered.json' with timeout=60 2022-01-06 16:56:57,914 - root - DEBUG - CD: '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/cns-scatter' -> '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/cns-scatter' real 0m0.144s user 0m0.103s sys 0m0.037s touch /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/cns-scatter/run.sh.done + touch /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/cns-scatter/run.sh.done + finish + echo 'finish code: 0' finish code: 0 2022-01-06 16:56:58,054[INFO] recently_satisfied: set([Node(0-rawreads/cns-scatter)]) 2022-01-06 16:56:58,054[INFO] Num satisfied in this iteration: 1 2022-01-06 16:56:58,054[INFO] Num still unsatisfied: 0 2022-01-06 16:56:58,063[INFO] Num unsatisfied: 2, graph: 13 2022-01-06 16:56:58,063[INFO] About to submit: Node(0-rawreads/preads/cns_00002) 2022-01-06 16:56:58,063[INFO] About to submit: Node(0-rawreads/preads/cns_00001) 2022-01-06 16:56:58,068[INFO] !chmod +x /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/preads/cns_00002/run-P99c98f7daa24bf.bash 2022-01-06 16:56:58,078[INFO] !chmod +x /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/preads/cns_00001/run-P7ae5bada2debf1.bash 2022-01-06 16:56:58,086[INFO] Popen: 'bash -C /build/falcon-LwwdoQ/falcon-1.8.8/inst/pylib/pypeflow-1.0.0-py2.7.egg/pwatcher/mains/job_start.sh' 2022-01-06 16:56:58,095[INFO] sleep 0.1s executable=${PYPEFLOW_JOB_START_SCRIPT} + executable=/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/preads/cns_00002/run-P99c98f7daa24bf.bash timeout=${PYPEFLOW_JOB_START_TIMEOUT:-60} # wait 60s by default + timeout=60 # Wait up to timeout seconds for the executable to become "executable", # then exec. #timeleft = int(timeout) while [[ ! -x "${executable}" ]]; do if [[ "${timeout}" == "0" ]]; then echo "timed out waiting for (${executable})" exit 77 fi echo "not executable: '${executable}', waiting ${timeout}s" sleep 1 timeout=$((timeout-1)) done + [[ ! -x /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/preads/cns_00002/run-P99c98f7daa24bf.bash ]] bash ${executable} + bash /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/preads/cns_00002/run-P99c98f7daa24bf.bash + '[' '!' -d /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/preads/cns_00002 ']' + cd /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/preads/cns_00002 + eval '/bin/bash run.sh' ++ /bin/bash run.sh 2022-01-06 16:56:58,101[INFO] Popen: 'bash -C /build/falcon-LwwdoQ/falcon-1.8.8/inst/pylib/pypeflow-1.0.0-py2.7.egg/pwatcher/mains/job_start.sh' cd /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/preads/cns_00002 + cd /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/preads/cns_00002 bash task.sh + bash task.sh 30e18b9a274d executable=${PYPEFLOW_JOB_START_SCRIPT} + executable=/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/preads/cns_00001/run-P7ae5bada2debf1.bash timeout=${PYPEFLOW_JOB_START_TIMEOUT:-60} # wait 60s by default + timeout=60 # Wait up to timeout seconds for the executable to become "executable", # then exec. #timeleft = int(timeout) while [[ ! -x "${executable}" ]]; do if [[ "${timeout}" == "0" ]]; then echo "timed out waiting for (${executable})" exit 77 fi echo "not executable: '${executable}', waiting ${timeout}s" sleep 1 timeout=$((timeout-1)) done + [[ ! -x /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/preads/cns_00001/run-P7ae5bada2debf1.bash ]] bash ${executable} + bash /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/preads/cns_00001/run-P7ae5bada2debf1.bash CC=gcc CFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong -Wformat -Werror=format-security CPPFLAGS=-Wdate-time -D_FORTIFY_SOURCE=2 CXX=g++ CXXFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong -Wformat -Werror=format-security DEBCONF_NONINTERACTIVE_SEEN=true DEBIAN_FRONTEND=noninteractive DEB_BUILD_ARCH=amd64 DEB_BUILD_ARCH_ABI=base DEB_BUILD_ARCH_BITS=64 DEB_BUILD_ARCH_CPU=amd64 DEB_BUILD_ARCH_ENDIAN=little DEB_BUILD_ARCH_LIBC=gnu DEB_BUILD_ARCH_OS=linux DEB_BUILD_GNU_CPU=x86_64 DEB_BUILD_GNU_SYSTEM=linux-gnu DEB_BUILD_GNU_TYPE=x86_64-linux-gnu DEB_BUILD_MULTIARCH=x86_64-linux-gnu DEB_BUILD_OPTIONS=nocheck parallel=10 DEB_HOST_ARCH=amd64 DEB_HOST_ARCH_ABI=base DEB_HOST_ARCH_BITS=64 DEB_HOST_ARCH_CPU=amd64 DEB_HOST_ARCH_ENDIAN=little DEB_HOST_ARCH_LIBC=gnu DEB_HOST_ARCH_OS=linux DEB_HOST_GNU_CPU=x86_64 DEB_HOST_GNU_SYSTEM=linux-gnu DEB_HOST_GNU_TYPE=x86_64-linux-gnu DEB_HOST_MULTIARCH=x86_64-linux-gnu DEB_TARGET_ARCH=amd64 DEB_TARGET_ARCH_ABI=base DEB_TARGET_ARCH_BITS=64 DEB_TARGET_ARCH_CPU=amd64 DEB_TARGET_ARCH_ENDIAN=little DEB_TARGET_ARCH_LIBC=gnu DEB_TARGET_ARCH_OS=linux DEB_TARGET_GNU_CPU=x86_64 DEB_TARGET_GNU_SYSTEM=linux-gnu DEB_TARGET_GNU_TYPE=x86_64-linux-gnu DEB_TARGET_MULTIARCH=x86_64-linux-gnu DH_INTERNAL_BUILDFLAGS=1 DH_INTERNAL_OPTIONS=-a DH_INTERNAL_OVERRIDE=dh_auto_test FALCON_INSTALL_RULE=install FALCON_PREFIX=/build/falcon-LwwdoQ/falcon-1.8.8/inst FALCON_WORKSPACE=/build/falcon-LwwdoQ/falcon-1.8.8 FCFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong FFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong GCJFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong HOME=/nonexistent LANG=C.UTF-8 LANGUAGE=C.UTF-8 LC_ALL=C.UTF-8 LDFLAGS=-Wl,-z,relro LOGNAME=builduser MAKEFLAGS=w MAKELEVEL=6 MFLAGS=-w MMDEBSTRAP_APT_CONFIG=/tmp/mmdebstrap.SAG5NvxJ_M/tmp/mmdebstrap.apt.conf.TRj0u44dYeZl MMDEBSTRAP_HOOK=customize MMDEBSTRAP_HOOKSOCK=6 MMDEBSTRAP_MODE=root OBJCFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong -Wformat -Werror=format-security OBJCXXFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong -Wformat -Werror=format-security OLDPWD=/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/preads/cns_00002 PATH=/build/falcon-LwwdoQ/falcon-1.8.8/inst/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/sbin:/usr/bin:/sbin:/bin PERL_USE_UNSAFE_INC=1 PWD=/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/preads/cns_00002 PYPEFLOW_JOB_START_SCRIPT=/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/preads/cns_00002/run-P99c98f7daa24bf.bash PYPEFLOW_JOB_START_TIMEOUT=60 PYTHONPATH=/build/falcon-LwwdoQ/falcon-1.8.8/inst/pylib:/build/falcon-LwwdoQ/falcon-1.8.8/inst/pylib: SHELL=/bin/bash SHLVL=5 SOURCE_DATE_EPOCH=1513411047 USER=builduser _=/usr/bin/env /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/preads/cns_00002 + '[' '!' -d /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/preads/cns_00001 ']' + cd /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/preads/cns_00001 + eval '/bin/bash run.sh' ++ /bin/bash run.sh cd /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/preads/cns_00001 + cd /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/preads/cns_00001 bash task.sh + bash task.sh 30e18b9a274d CC=gcc CFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong -Wformat -Werror=format-security CPPFLAGS=-Wdate-time -D_FORTIFY_SOURCE=2 CXX=g++ CXXFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong -Wformat -Werror=format-security DEBCONF_NONINTERACTIVE_SEEN=true DEBIAN_FRONTEND=noninteractive DEB_BUILD_ARCH=amd64 DEB_BUILD_ARCH_ABI=base DEB_BUILD_ARCH_BITS=64 DEB_BUILD_ARCH_CPU=amd64 DEB_BUILD_ARCH_ENDIAN=little DEB_BUILD_ARCH_LIBC=gnu DEB_BUILD_ARCH_OS=linux DEB_BUILD_GNU_CPU=x86_64 DEB_BUILD_GNU_SYSTEM=linux-gnu DEB_BUILD_GNU_TYPE=x86_64-linux-gnu DEB_BUILD_MULTIARCH=x86_64-linux-gnu DEB_BUILD_OPTIONS=nocheck parallel=10 DEB_HOST_ARCH=amd64 DEB_HOST_ARCH_ABI=base DEB_HOST_ARCH_BITS=64 DEB_HOST_ARCH_CPU=amd64 DEB_HOST_ARCH_ENDIAN=little DEB_HOST_ARCH_LIBC=gnu DEB_HOST_ARCH_OS=linux DEB_HOST_GNU_CPU=x86_64 DEB_HOST_GNU_SYSTEM=linux-gnu DEB_HOST_GNU_TYPE=x86_64-linux-gnu DEB_HOST_MULTIARCH=x86_64-linux-gnu DEB_TARGET_ARCH=amd64 DEB_TARGET_ARCH_ABI=base DEB_TARGET_ARCH_BITS=64 DEB_TARGET_ARCH_CPU=amd64 DEB_TARGET_ARCH_ENDIAN=little DEB_TARGET_ARCH_LIBC=gnu DEB_TARGET_ARCH_OS=linux DEB_TARGET_GNU_CPU=x86_64 DEB_TARGET_GNU_SYSTEM=linux-gnu DEB_TARGET_GNU_TYPE=x86_64-linux-gnu DEB_TARGET_MULTIARCH=x86_64-linux-gnu DH_INTERNAL_BUILDFLAGS=1 DH_INTERNAL_OPTIONS=-a DH_INTERNAL_OVERRIDE=dh_auto_test FALCON_INSTALL_RULE=install FALCON_PREFIX=/build/falcon-LwwdoQ/falcon-1.8.8/inst FALCON_WORKSPACE=/build/falcon-LwwdoQ/falcon-1.8.8 FCFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong FFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong GCJFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong HOME=/nonexistent LANG=C.UTF-8 LANGUAGE=C.UTF-8 LC_ALL=C.UTF-8 LDFLAGS=-Wl,-z,relro LOGNAME=builduser MAKEFLAGS=w MAKELEVEL=6 MFLAGS=-w MMDEBSTRAP_APT_CONFIG=/tmp/mmdebstrap.SAG5NvxJ_M/tmp/mmdebstrap.apt.conf.TRj0u44dYeZl MMDEBSTRAP_HOOK=customize MMDEBSTRAP_HOOKSOCK=6 MMDEBSTRAP_MODE=root OBJCFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong -Wformat -Werror=format-security OBJCXXFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong -Wformat -Werror=format-security OLDPWD=/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/preads/cns_00001 PATH=/build/falcon-LwwdoQ/falcon-1.8.8/inst/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/sbin:/usr/bin:/sbin:/bin PERL_USE_UNSAFE_INC=1 PWD=/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/preads/cns_00001 PYPEFLOW_JOB_START_SCRIPT=/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/preads/cns_00001/run-P7ae5bada2debf1.bash PYPEFLOW_JOB_START_TIMEOUT=60 PYTHONPATH=/build/falcon-LwwdoQ/falcon-1.8.8/inst/pylib:/build/falcon-LwwdoQ/falcon-1.8.8/inst/pylib: SHELL=/bin/bash SHLVL=5 SOURCE_DATE_EPOCH=1513411047 USER=builduser _=/usr/bin/env /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/preads/cns_00001 2022-01-06 16:56:58,198[INFO] sleep 0.2s 2022-01-06 16:56:58,213 - root - DEBUG - Running "/build/falcon-LwwdoQ/falcon-1.8.8/inst/pylib/pypeflow-1.0.0-py2.7.egg/pypeflow/do_task.py /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/preads/cns_00002/task.json" 2022-01-06 16:56:58,216 - root - DEBUG - Checking existence of '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/preads/cns_00002/task.json' with timeout=60 2022-01-06 16:56:58,216 - root - DEBUG - Loading JSON from '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/preads/cns_00002/task.json' 2022-01-06 16:56:58,218 - root - DEBUG - {u'inputs': {u'db': u'/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/raw_reads.db', u'las': u'/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/m_00002/raw_reads.2.las', u'scatter_fn': u'/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/cns-scatter/scattered.json'}, u'outputs': {u'out_file': u'cns_00002.fasta'}, u'parameters': {u'config': {u'LA4Falcon_preload': True, u'avoid_text_file_busy': True, u'cns_concurrent_jobs': 32, u'da_concurrent_jobs': 32, u'dazcon': False, u'default_concurrent_jobs': 8, u'dust': False, u'falcon_sense_greedy': False, u'falcon_sense_option': u'--output_multi --min_idt 0.70 --min_cov 1 --max_n_read 20000 --n_core 0', u'falcon_sense_skip_contained': False, u'fc_concurrent_jobs': 8, u'fc_ovlp_to_graph_option': u' --min_len 1', u'genome_size': 5000, u'input_fofn': u'input.fofn', u'input_type': u'raw', u'install_prefix': u'/usr', u'job_queue': u'bash -C ${CMD}', u'job_type': u'string', u'la_concurrent_jobs': 32, u'length_cutoff': -1, u'length_cutoff_pr': 1, u'overlap_filtering_setting': u'--max_diff 10000 --max_cov 100000 --min_cov 1 --min_len 1 --bestn 1000 --n_core 0', u'ovlp_DBsplit_option': u'-a -x5 -s50', u'ovlp_HPCdaligner_option': u'-v -B4 -t50 -h1 -e.99 -l1 -s1000', u'pa_DBdust_option': u'-w128 -t2.5 -m20', u'pa_DBsplit_option': u'-a -x5 -s.065536', u'pa_HPCdaligner_option': u'-v -B4 -t50 -h1 -e.99 -w1 -l1 -s1000', u'pa_dazcon_option': u'-j 4 -x -l 500', u'pda_concurrent_jobs': 32, u'pla_concurrent_jobs': 32, u'pwatcher_directory': u'mypwatcher', u'pwatcher_type': u'blocking', u'seed_coverage': 20.0, u'sge_option': u'-pe smp 8 -q bash -C ${CMD}', u'sge_option_cns': u'-pe smp 8 -q bash -C ${CMD}', u'sge_option_da': u'-pe smp 8 -q bash -C ${CMD}', u'sge_option_fc': u'-pe smp 24 -q bash -C ${CMD}', u'sge_option_la': u'-pe smp 2 -q bash -C ${CMD}', u'sge_option_pda': u'-pe smp 8 -q bash -C ${CMD}', u'sge_option_pla': u'-pe smp 2 -q bash -C ${CMD}', u'skip_checks': False, u'stop_all_jobs_on_failure': True, u'target': u'assembly', u'use_tmpdir': False}, u'job_id': 2, u'prefix': u'raw_reads', u'sge_option': u'-pe smp 8 -q bash -C ${CMD}'}, u'python_function': u'falcon_kit.pype_tasks.task_run_consensus'} 2022-01-06 16:56:58,219 - root - DEBUG - CD: '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/preads/cns_00002' <- '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/preads/cns_00002' 2022-01-06 16:56:58,219 - root - DEBUG - Checking existence of u'/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/cns-scatter/scattered.json' with timeout=60 2022-01-06 16:56:58,219 - root - DEBUG - Checking existence of u'/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/raw_reads.db' with timeout=60 2022-01-06 16:56:58,219 - root - DEBUG - Checking existence of u'/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/m_00002/raw_reads.2.las' with timeout=60 2022-01-06 16:56:58,225 - root - DEBUG - Running "/build/falcon-LwwdoQ/falcon-1.8.8/inst/pylib/pypeflow-1.0.0-py2.7.egg/pypeflow/do_task.py /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/preads/cns_00001/task.json" 2022-01-06 16:56:58,227 - root - DEBUG - Checking existence of '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/preads/cns_00001/task.json' with timeout=60 2022-01-06 16:56:58,227 - root - DEBUG - Loading JSON from '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/preads/cns_00001/task.json' 2022-01-06 16:56:58,230 - root - DEBUG - {u'inputs': {u'db': u'/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/raw_reads.db', u'las': u'/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/m_00001/raw_reads.1.las', u'scatter_fn': u'/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/cns-scatter/scattered.json'}, u'outputs': {u'out_file': u'cns_00001.fasta'}, u'parameters': {u'config': {u'LA4Falcon_preload': True, u'avoid_text_file_busy': True, u'cns_concurrent_jobs': 32, u'da_concurrent_jobs': 32, u'dazcon': False, u'default_concurrent_jobs': 8, u'dust': False, u'falcon_sense_greedy': False, u'falcon_sense_option': u'--output_multi --min_idt 0.70 --min_cov 1 --max_n_read 20000 --n_core 0', u'falcon_sense_skip_contained': False, u'fc_concurrent_jobs': 8, u'fc_ovlp_to_graph_option': u' --min_len 1', u'genome_size': 5000, u'input_fofn': u'input.fofn', u'input_type': u'raw', u'install_prefix': u'/usr', u'job_queue': u'bash -C ${CMD}', u'job_type': u'string', u'la_concurrent_jobs': 32, u'length_cutoff': -1, u'length_cutoff_pr': 1, u'overlap_filtering_setting': u'--max_diff 10000 --max_cov 100000 --min_cov 1 --min_len 1 --bestn 1000 --n_core 0', u'ovlp_DBsplit_option': u'-a -x5 -s50', u'ovlp_HPCdaligner_option': u'-v -B4 -t50 -h1 -e.99 -l1 -s1000', u'pa_DBdust_option': u'-w128 -t2.5 -m20', u'pa_DBsplit_option': u'-a -x5 -s.065536', u'pa_HPCdaligner_option': u'-v -B4 -t50 -h1 -e.99 -w1 -l1 -s1000', u'pa_dazcon_option': u'-j 4 -x -l 500', u'pda_concurrent_jobs': 32, u'pla_concurrent_jobs': 32, u'pwatcher_directory': u'mypwatcher', u'pwatcher_type': u'blocking', u'seed_coverage': 20.0, u'sge_option': u'-pe smp 8 -q bash -C ${CMD}', u'sge_option_cns': u'-pe smp 8 -q bash -C ${CMD}', u'sge_option_da': u'-pe smp 8 -q bash -C ${CMD}', u'sge_option_fc': u'-pe smp 24 -q bash -C ${CMD}', u'sge_option_la': u'-pe smp 2 -q bash -C ${CMD}', u'sge_option_pda': u'-pe smp 8 -q bash -C ${CMD}', u'sge_option_pla': u'-pe smp 2 -q bash -C ${CMD}', u'skip_checks': False, u'stop_all_jobs_on_failure': True, u'target': u'assembly', u'use_tmpdir': False}, u'job_id': 1, u'prefix': u'raw_reads', u'sge_option': u'-pe smp 8 -q bash -C ${CMD}'}, u'python_function': u'falcon_kit.pype_tasks.task_run_consensus'} 2022-01-06 16:56:58,230 - root - DEBUG - CD: '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/preads/cns_00001' <- '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/preads/cns_00001' 2022-01-06 16:56:58,230 - root - DEBUG - Checking existence of u'/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/cns-scatter/scattered.json' with timeout=60 2022-01-06 16:56:58,230 - root - DEBUG - Checking existence of u'/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/raw_reads.db' with timeout=60 2022-01-06 16:56:58,230 - root - DEBUG - Checking existence of u'/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/m_00001/raw_reads.1.las' with timeout=60 2022-01-06 16:56:58,252 - root - DEBUG - CD: '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/preads/cns_00002' <- '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/preads/cns_00002' 2022-01-06 16:56:58,253 - pypeflow.do_support - INFO - !/bin/bash -vex /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/preads/cns_00002/c_00002.sh #!/bin/bash set -vex + set -vex set -o pipefail + set -o pipefail CUTOFF=$(python2.7 -m falcon_kit.mains.calc_cutoff --coverage 20.0 5000 <(DBstats -b1 /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/raw_reads.db)) ++ python2.7 -m falcon_kit.mains.calc_cutoff --coverage 20.0 5000 /dev/fd/63 +++ DBstats -b1 /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/raw_reads.db 2022-01-06 16:56:58,262 - root - DEBUG - CD: '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/preads/cns_00001' <- '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/preads/cns_00001' 2022-01-06 16:56:58,263 - pypeflow.do_support - INFO - !/bin/bash -vex /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/preads/cns_00001/c_00001.sh #!/bin/bash set -vex + set -vex set -o pipefail + set -o pipefail CUTOFF=$(python2.7 -m falcon_kit.mains.calc_cutoff --coverage 20.0 5000 <(DBstats -b1 /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/raw_reads.db)) ++ python2.7 -m falcon_kit.mains.calc_cutoff --coverage 20.0 5000 /dev/fd/63 +++ DBstats -b1 /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/raw_reads.db + CUTOFF=2000 LA4Falcon -H$CUTOFF -Pof /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/raw_reads.db /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/m_00002/raw_reads.2.las | fc_consensus --output_multi --min_idt 0.70 --min_cov 1 --max_n_read 20000 --n_core 0 >| cns_00002.fasta + LA4Falcon -H2000 -Pof /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/raw_reads.db /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/m_00002/raw_reads.2.las + fc_consensus --output_multi --min_idt 0.70 --min_cov 1 --max_n_read 20000 --n_core 0 + CUTOFF=2000 LA4Falcon -H$CUTOFF -Pof /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/raw_reads.db /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/m_00001/raw_reads.1.las | fc_consensus --output_multi --min_idt 0.70 --min_cov 1 --max_n_read 20000 --n_core 0 >| cns_00001.fasta + LA4Falcon -H2000 -Pof /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/raw_reads.db /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/m_00001/raw_reads.1.las + fc_consensus --output_multi --min_idt 0.70 --min_cov 1 --max_n_read 20000 --n_core 0 2022-01-06 16:56:58,399[INFO] sleep 0.3s Started a worker in 1731571 from parent 1731564 Started a worker in 1731569 from parent 1731558 2022-01-06 16:56:58,700[INFO] sleep 0.4s 2022-01-06 16:56:59,101[INFO] sleep 0.5s 2022-01-06 16:56:59,603[INFO] sleep 0.6s 2022-01-06 16:57:00,204[INFO] sleep 0.7s touch out.done + touch out.done 2022-01-06 16:57:00,512 - root - DEBUG - CD: '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/preads/cns_00002' -> '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/preads/cns_00002' 2022-01-06 16:57:00,513 - root - DEBUG - Checking existence of u'cns_00002.fasta' with timeout=60 2022-01-06 16:57:00,513 - root - DEBUG - CD: '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/preads/cns_00002' -> '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/preads/cns_00002' real 0m2.414s user 0m1.687s sys 0m0.682s touch /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/preads/cns_00002/run.sh.done + touch /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/preads/cns_00002/run.sh.done + finish + echo 'finish code: 0' finish code: 0 2022-01-06 16:57:00,906[INFO] recently_satisfied: set([Node(0-rawreads/preads/cns_00002)]) 2022-01-06 16:57:00,906[INFO] Num satisfied in this iteration: 1 2022-01-06 16:57:00,906[INFO] Num still unsatisfied: 1 2022-01-06 16:57:00,906[INFO] sleep 0.1s 2022-01-06 16:57:01,007[INFO] sleep 0.2s touch out.done + touch out.done 2022-01-06 16:57:01,061 - root - DEBUG - CD: '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/preads/cns_00001' -> '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/preads/cns_00001' 2022-01-06 16:57:01,061 - root - DEBUG - Checking existence of u'cns_00001.fasta' with timeout=60 2022-01-06 16:57:01,062 - root - DEBUG - CD: '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/preads/cns_00001' -> '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/preads/cns_00001' real 0m2.948s user 0m2.219s sys 0m0.684s touch /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/preads/cns_00001/run.sh.done + touch /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/preads/cns_00001/run.sh.done + finish + echo 'finish code: 0' finish code: 0 2022-01-06 16:57:01,208[INFO] recently_satisfied: set([Node(0-rawreads/preads/cns_00001)]) 2022-01-06 16:57:01,208[INFO] Num satisfied in this iteration: 1 2022-01-06 16:57:01,209[INFO] Num still unsatisfied: 0 2022-01-06 16:57:01,217[INFO] Num unsatisfied: 2, graph: 15 2022-01-06 16:57:01,217[INFO] About to submit: Node(0-rawreads/preads) 2022-01-06 16:57:01,220[INFO] !chmod +x /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/preads/run-P4c19196970a3e0.bash 2022-01-06 16:57:01,230[INFO] sleep 0.1s 2022-01-06 16:57:01,236[INFO] Popen: 'bash -C /build/falcon-LwwdoQ/falcon-1.8.8/inst/pylib/pypeflow-1.0.0-py2.7.egg/pwatcher/mains/job_start.sh' executable=${PYPEFLOW_JOB_START_SCRIPT} + executable=/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/preads/run-P4c19196970a3e0.bash timeout=${PYPEFLOW_JOB_START_TIMEOUT:-60} # wait 60s by default + timeout=60 # Wait up to timeout seconds for the executable to become "executable", # then exec. #timeleft = int(timeout) while [[ ! -x "${executable}" ]]; do if [[ "${timeout}" == "0" ]]; then echo "timed out waiting for (${executable})" exit 77 fi echo "not executable: '${executable}', waiting ${timeout}s" sleep 1 timeout=$((timeout-1)) done + [[ ! -x /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/preads/run-P4c19196970a3e0.bash ]] bash ${executable} + bash /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/preads/run-P4c19196970a3e0.bash + '[' '!' -d /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/preads ']' + cd /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/preads + eval '/bin/bash run.sh' ++ /bin/bash run.sh cd /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/preads + cd /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/preads bash task.sh + bash task.sh 30e18b9a274d CC=gcc CFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong -Wformat -Werror=format-security CPPFLAGS=-Wdate-time -D_FORTIFY_SOURCE=2 CXX=g++ CXXFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong -Wformat -Werror=format-security DEBCONF_NONINTERACTIVE_SEEN=true DEBIAN_FRONTEND=noninteractive DEB_BUILD_ARCH=amd64 DEB_BUILD_ARCH_ABI=base DEB_BUILD_ARCH_BITS=64 DEB_BUILD_ARCH_CPU=amd64 DEB_BUILD_ARCH_ENDIAN=little DEB_BUILD_ARCH_LIBC=gnu DEB_BUILD_ARCH_OS=linux DEB_BUILD_GNU_CPU=x86_64 DEB_BUILD_GNU_SYSTEM=linux-gnu DEB_BUILD_GNU_TYPE=x86_64-linux-gnu DEB_BUILD_MULTIARCH=x86_64-linux-gnu DEB_BUILD_OPTIONS=nocheck parallel=10 DEB_HOST_ARCH=amd64 DEB_HOST_ARCH_ABI=base DEB_HOST_ARCH_BITS=64 DEB_HOST_ARCH_CPU=amd64 DEB_HOST_ARCH_ENDIAN=little DEB_HOST_ARCH_LIBC=gnu DEB_HOST_ARCH_OS=linux DEB_HOST_GNU_CPU=x86_64 DEB_HOST_GNU_SYSTEM=linux-gnu DEB_HOST_GNU_TYPE=x86_64-linux-gnu DEB_HOST_MULTIARCH=x86_64-linux-gnu DEB_TARGET_ARCH=amd64 DEB_TARGET_ARCH_ABI=base DEB_TARGET_ARCH_BITS=64 DEB_TARGET_ARCH_CPU=amd64 DEB_TARGET_ARCH_ENDIAN=little DEB_TARGET_ARCH_LIBC=gnu DEB_TARGET_ARCH_OS=linux DEB_TARGET_GNU_CPU=x86_64 DEB_TARGET_GNU_SYSTEM=linux-gnu DEB_TARGET_GNU_TYPE=x86_64-linux-gnu DEB_TARGET_MULTIARCH=x86_64-linux-gnu DH_INTERNAL_BUILDFLAGS=1 DH_INTERNAL_OPTIONS=-a DH_INTERNAL_OVERRIDE=dh_auto_test FALCON_INSTALL_RULE=install FALCON_PREFIX=/build/falcon-LwwdoQ/falcon-1.8.8/inst FALCON_WORKSPACE=/build/falcon-LwwdoQ/falcon-1.8.8 FCFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong FFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong GCJFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong HOME=/nonexistent LANG=C.UTF-8 LANGUAGE=C.UTF-8 LC_ALL=C.UTF-8 LDFLAGS=-Wl,-z,relro LOGNAME=builduser MAKEFLAGS=w MAKELEVEL=6 MFLAGS=-w MMDEBSTRAP_APT_CONFIG=/tmp/mmdebstrap.SAG5NvxJ_M/tmp/mmdebstrap.apt.conf.TRj0u44dYeZl MMDEBSTRAP_HOOK=customize MMDEBSTRAP_HOOKSOCK=6 MMDEBSTRAP_MODE=root OBJCFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong -Wformat -Werror=format-security OBJCXXFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong -Wformat -Werror=format-security OLDPWD=/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/preads PATH=/build/falcon-LwwdoQ/falcon-1.8.8/inst/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/sbin:/usr/bin:/sbin:/bin PERL_USE_UNSAFE_INC=1 PWD=/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/preads PYPEFLOW_JOB_START_SCRIPT=/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/preads/run-P4c19196970a3e0.bash PYPEFLOW_JOB_START_TIMEOUT=60 PYTHONPATH=/build/falcon-LwwdoQ/falcon-1.8.8/inst/pylib:/build/falcon-LwwdoQ/falcon-1.8.8/inst/pylib: SHELL=/bin/bash SHLVL=5 SOURCE_DATE_EPOCH=1513411047 USER=builduser _=/usr/bin/env /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/preads 2022-01-06 16:57:01,331[INFO] sleep 0.2s 2022-01-06 16:57:01,354 - root - DEBUG - Running "/build/falcon-LwwdoQ/falcon-1.8.8/inst/pylib/pypeflow-1.0.0-py2.7.egg/pypeflow/do_task.py /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/preads/task.json" 2022-01-06 16:57:01,356 - root - DEBUG - Checking existence of '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/preads/task.json' with timeout=60 2022-01-06 16:57:01,356 - root - DEBUG - Loading JSON from '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/preads/task.json' 2022-01-06 16:57:01,357 - root - DEBUG - {u'inputs': {u'cjob_1': u'/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/preads/cns_00001/cns_00001.fasta', u'cjob_2': u'/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/preads/cns_00002/cns_00002.fasta'}, u'outputs': {u'preads_fofn': u'input_preads.fofn'}, u'parameters': {}, u'python_function': u'falcon_kit.pype_tasks.task_cns_gather'} 2022-01-06 16:57:01,357 - root - DEBUG - CD: '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/preads' <- '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/preads' 2022-01-06 16:57:01,357 - root - DEBUG - Checking existence of u'/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/preads/cns_00002/cns_00002.fasta' with timeout=60 2022-01-06 16:57:01,357 - root - DEBUG - Checking existence of u'/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/preads/cns_00001/cns_00001.fasta' with timeout=60 2022-01-06 16:57:01,388 - root - DEBUG - CD: '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/preads' <- '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/preads' 2022-01-06 16:57:01,388 - root - DEBUG - CD: '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/preads' -> '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/preads' 2022-01-06 16:57:01,388 - root - DEBUG - Checking existence of u'input_preads.fofn' with timeout=60 2022-01-06 16:57:01,389 - root - DEBUG - CD: '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/preads' -> '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/preads' real 0m0.144s user 0m0.099s sys 0m0.042s touch /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/preads/run.sh.done + touch /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/preads/run.sh.done + finish + echo 'finish code: 0' finish code: 0 2022-01-06 16:57:01,533[INFO] recently_satisfied: set([Node(0-rawreads/preads)]) 2022-01-06 16:57:01,533[INFO] Num satisfied in this iteration: 1 2022-01-06 16:57:01,533[INFO] Num still unsatisfied: 1 2022-01-06 16:57:01,534[INFO] About to submit: Node(0-rawreads/report) 2022-01-06 16:57:01,538[INFO] !chmod +x /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/report/run-P6bf41e4869fd4d.bash 2022-01-06 16:57:01,546[INFO] sleep 0.1s 2022-01-06 16:57:01,552[INFO] Popen: 'bash -C /build/falcon-LwwdoQ/falcon-1.8.8/inst/pylib/pypeflow-1.0.0-py2.7.egg/pwatcher/mains/job_start.sh' executable=${PYPEFLOW_JOB_START_SCRIPT} + executable=/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/report/run-P6bf41e4869fd4d.bash timeout=${PYPEFLOW_JOB_START_TIMEOUT:-60} # wait 60s by default + timeout=60 # Wait up to timeout seconds for the executable to become "executable", # then exec. #timeleft = int(timeout) while [[ ! -x "${executable}" ]]; do if [[ "${timeout}" == "0" ]]; then echo "timed out waiting for (${executable})" exit 77 fi echo "not executable: '${executable}', waiting ${timeout}s" sleep 1 timeout=$((timeout-1)) done + [[ ! -x /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/report/run-P6bf41e4869fd4d.bash ]] bash ${executable} + bash /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/report/run-P6bf41e4869fd4d.bash + '[' '!' -d /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/report ']' + cd /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/report + eval '/bin/bash run.sh' ++ /bin/bash run.sh cd /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/report + cd /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/report bash task.sh + bash task.sh 30e18b9a274d CC=gcc CFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong -Wformat -Werror=format-security CPPFLAGS=-Wdate-time -D_FORTIFY_SOURCE=2 CXX=g++ CXXFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong -Wformat -Werror=format-security DEBCONF_NONINTERACTIVE_SEEN=true DEBIAN_FRONTEND=noninteractive DEB_BUILD_ARCH=amd64 DEB_BUILD_ARCH_ABI=base DEB_BUILD_ARCH_BITS=64 DEB_BUILD_ARCH_CPU=amd64 DEB_BUILD_ARCH_ENDIAN=little DEB_BUILD_ARCH_LIBC=gnu DEB_BUILD_ARCH_OS=linux DEB_BUILD_GNU_CPU=x86_64 DEB_BUILD_GNU_SYSTEM=linux-gnu DEB_BUILD_GNU_TYPE=x86_64-linux-gnu DEB_BUILD_MULTIARCH=x86_64-linux-gnu DEB_BUILD_OPTIONS=nocheck parallel=10 DEB_HOST_ARCH=amd64 DEB_HOST_ARCH_ABI=base DEB_HOST_ARCH_BITS=64 DEB_HOST_ARCH_CPU=amd64 DEB_HOST_ARCH_ENDIAN=little DEB_HOST_ARCH_LIBC=gnu DEB_HOST_ARCH_OS=linux DEB_HOST_GNU_CPU=x86_64 DEB_HOST_GNU_SYSTEM=linux-gnu DEB_HOST_GNU_TYPE=x86_64-linux-gnu DEB_HOST_MULTIARCH=x86_64-linux-gnu DEB_TARGET_ARCH=amd64 DEB_TARGET_ARCH_ABI=base DEB_TARGET_ARCH_BITS=64 DEB_TARGET_ARCH_CPU=amd64 DEB_TARGET_ARCH_ENDIAN=little DEB_TARGET_ARCH_LIBC=gnu DEB_TARGET_ARCH_OS=linux DEB_TARGET_GNU_CPU=x86_64 DEB_TARGET_GNU_SYSTEM=linux-gnu DEB_TARGET_GNU_TYPE=x86_64-linux-gnu DEB_TARGET_MULTIARCH=x86_64-linux-gnu DH_INTERNAL_BUILDFLAGS=1 DH_INTERNAL_OPTIONS=-a DH_INTERNAL_OVERRIDE=dh_auto_test FALCON_INSTALL_RULE=install FALCON_PREFIX=/build/falcon-LwwdoQ/falcon-1.8.8/inst FALCON_WORKSPACE=/build/falcon-LwwdoQ/falcon-1.8.8 FCFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong FFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong GCJFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong HOME=/nonexistent LANG=C.UTF-8 LANGUAGE=C.UTF-8 LC_ALL=C.UTF-8 LDFLAGS=-Wl,-z,relro LOGNAME=builduser MAKEFLAGS=w MAKELEVEL=6 MFLAGS=-w MMDEBSTRAP_APT_CONFIG=/tmp/mmdebstrap.SAG5NvxJ_M/tmp/mmdebstrap.apt.conf.TRj0u44dYeZl MMDEBSTRAP_HOOK=customize MMDEBSTRAP_HOOKSOCK=6 MMDEBSTRAP_MODE=root OBJCFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong -Wformat -Werror=format-security OBJCXXFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong -Wformat -Werror=format-security OLDPWD=/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/report PATH=/build/falcon-LwwdoQ/falcon-1.8.8/inst/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/sbin:/usr/bin:/sbin:/bin PERL_USE_UNSAFE_INC=1 PWD=/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/report PYPEFLOW_JOB_START_SCRIPT=/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/report/run-P6bf41e4869fd4d.bash PYPEFLOW_JOB_START_TIMEOUT=60 PYTHONPATH=/build/falcon-LwwdoQ/falcon-1.8.8/inst/pylib:/build/falcon-LwwdoQ/falcon-1.8.8/inst/pylib: SHELL=/bin/bash SHLVL=5 SOURCE_DATE_EPOCH=1513411047 USER=builduser _=/usr/bin/env /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/report 2022-01-06 16:57:01,648[INFO] sleep 0.2s 2022-01-06 16:57:01,674 - root - DEBUG - Running "/build/falcon-LwwdoQ/falcon-1.8.8/inst/pylib/pypeflow-1.0.0-py2.7.egg/pypeflow/do_task.py /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/report/task.json" 2022-01-06 16:57:01,676 - root - DEBUG - Checking existence of '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/report/task.json' with timeout=60 2022-01-06 16:57:01,677 - root - DEBUG - Loading JSON from '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/report/task.json' 2022-01-06 16:57:01,679 - root - DEBUG - {u'inputs': {u'length_cutoff_fn': u'/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/length_cutoff', u'preads_fofn': u'/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/preads/input_preads.fofn', u'raw_reads_db': u'/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/raw_reads.db'}, u'outputs': {u'pre_assembly_report': u'pre_assembly_stats.json'}, u'parameters': {u'LA4Falcon_preload': True, u'avoid_text_file_busy': True, u'cns_concurrent_jobs': 32, u'cwd': u'/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/report', u'da_concurrent_jobs': 32, u'dazcon': False, u'default_concurrent_jobs': 8, u'dust': False, u'falcon_sense_greedy': False, u'falcon_sense_option': u'--output_multi --min_idt 0.70 --min_cov 1 --max_n_read 20000 --n_core 0', u'falcon_sense_skip_contained': False, u'fc_concurrent_jobs': 8, u'fc_ovlp_to_graph_option': u' --min_len 1', u'genome_size': 5000, u'input_fofn': u'input.fofn', u'input_type': u'raw', u'install_prefix': u'/usr', u'job_queue': u'bash -C ${CMD}', u'job_type': u'string', u'la_concurrent_jobs': 32, u'length_cutoff': -1, u'length_cutoff_pr': 1, u'overlap_filtering_setting': u'--max_diff 10000 --max_cov 100000 --min_cov 1 --min_len 1 --bestn 1000 --n_core 0', u'ovlp_DBsplit_option': u'-a -x5 -s50', u'ovlp_HPCdaligner_option': u'-v -B4 -t50 -h1 -e.99 -l1 -s1000', u'pa_DBdust_option': u'-w128 -t2.5 -m20', u'pa_DBsplit_option': u'-a -x5 -s.065536', u'pa_HPCdaligner_option': u'-v -B4 -t50 -h1 -e.99 -w1 -l1 -s1000', u'pa_dazcon_option': u'-j 4 -x -l 500', u'pda_concurrent_jobs': 32, u'pla_concurrent_jobs': 32, u'pwatcher_directory': u'mypwatcher', u'pwatcher_type': u'blocking', u'seed_coverage': 20.0, u'sge_option': u'-pe smp 8 -q bash -C ${CMD}', u'sge_option_cns': u'-pe smp 8 -q bash -C ${CMD}', u'sge_option_da': u'-pe smp 8 -q bash -C ${CMD}', u'sge_option_fc': u'-pe smp 24 -q bash -C ${CMD}', u'sge_option_la': u'-pe smp 2 -q bash -C ${CMD}', u'sge_option_pda': u'-pe smp 8 -q bash -C ${CMD}', u'sge_option_pla': u'-pe smp 2 -q bash -C ${CMD}', u'skip_checks': False, u'stop_all_jobs_on_failure': True, u'target': u'assembly', u'use_tmpdir': False}, u'python_function': u'falcon_kit.pype_tasks.task_report_pre_assembly'} 2022-01-06 16:57:01,679 - root - DEBUG - CD: '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/report' <- '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/report' 2022-01-06 16:57:01,679 - root - DEBUG - Checking existence of u'/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/raw_reads.db' with timeout=60 2022-01-06 16:57:01,680 - root - DEBUG - Checking existence of u'/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/length_cutoff' with timeout=60 2022-01-06 16:57:01,680 - root - DEBUG - Checking existence of u'/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/preads/input_preads.fofn' with timeout=60 2022-01-06 16:57:01,711 - root - DEBUG - CD: '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/report' <- '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/report' 2022-01-06 16:57:01,712 - falcon_kit.run_support - INFO - length_cutoff=2000 from u'/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/length_cutoff' 2022-01-06 16:57:01,712 - falcon_kit.pype_tasks - INFO - Report inputs: {'job_done': '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/report/report_pa_done', 'length_cutoff': 2000, 'i_preads_fofn_fn': u'/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/preads/input_preads.fofn', 'genome_length': 5000, 'script_fn': '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/report/run_report_pre_assembly.sh', 'o_json_fn': u'pre_assembly_stats.json', 'i_raw_reads_db_fn': u'/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/raw_reads.db'} 2022-01-06 16:57:01,712 - pypeflow.do_support - INFO - !/bin/bash -vex /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/report/run_report_pre_assembly.sh #!/bin/bash set -vex + set -vex python2.7 -m falcon_kit.mains.report_pre_assembly --genome-length 5000 --length-cutoff 2000 --db /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/raw_reads.db --preads-fofn /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/preads/input_preads.fofn --out pre_assembly_stats.json + python2.7 -m falcon_kit.mains.report_pre_assembly --genome-length 5000 --length-cutoff 2000 --db /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/raw_reads.db --preads-fofn /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/preads/input_preads.fofn --out pre_assembly_stats.json [1731605]$ perl -e 'while (<>) { if ( m{>[^/]+/(\d+)\d/} ) { $id{$1}++; } }; while (my ($k, $v) = each %id) { $counts{$v}++; }; while (my ($k, $v) = each %counts) { print "$v $k "; };' /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/preads/cns_00001/cns_00001.fasta /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/preads/cns_00002/cns_00002.fasta > [1731605]$ perl -e 'while (<>) { if ( m{>[^/]+/0*(\d+)\d/(\d+)_(\d+)} ) { $lengths{(1 + $1)} += ($3 - $2); } }; while (my ($k, $v) = each %lengths) { print "$k $v "; };' /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/preads/cns_00001/cns_00001.fasta /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/preads/cns_00002/cns_00002.fasta > [1731605]$ DBdump -rh /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/raw_reads.db > [1731605]$ DBdump -h /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/raw_reads.db > INFO:falcon_kit.stats_preassembly:stats for raw reads: FastaStats(nreads=50, total=100000, n50=2000, p95=2000, esize=2000.0) INFO:falcon_kit.stats_preassembly:stats for seed reads: FastaStats(nreads=50, total=100000, n50=2000, p95=2000, esize=2000.0) INFO:falcon_kit.stats_preassembly:stats for corrected reads: FastaStats(nreads=50, total=99447, n50=1989, p95=1989, esize=1988.9400283568132) INFO:falcon_kit.stats_preassembly:Calculated pre-assembly stats: {'genome_length': 5000, 'length_cutoff': 2000, 'preassembled_bases': 99447, 'preassembled_coverage': 19.889, 'preassembled_esize': 1988.94, 'preassembled_mean': 1988.94, 'preassembled_n50': 1989, 'preassembled_p95': 1989, 'preassembled_reads': 50, 'preassembled_seed_fragmentation': 1.0, 'preassembled_seed_truncation': 11.06, 'preassembled_yield': 0.994, 'raw_bases': 100000, 'raw_coverage': 20.0, 'raw_esize': 2000.0, 'raw_mean': 2000.0, 'raw_n50': 2000, 'raw_p95': 2000, 'raw_reads': 50, 'seed_bases': 100000, 'seed_coverage': 20.0, 'seed_esize': 2000.0, 'seed_mean': 2000.0, 'seed_n50': 2000, 'seed_p95': 2000, 'seed_reads': 50} touch /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/report/report_pa_done + touch /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/report/report_pa_done 2022-01-06 16:57:01,847 - root - DEBUG - CD: '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/report' -> '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/report' 2022-01-06 16:57:01,848 - root - DEBUG - Checking existence of u'pre_assembly_stats.json' with timeout=60 2022-01-06 16:57:01,848 - root - DEBUG - CD: '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/report' -> '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/report' 2022-01-06 16:57:01,848[INFO] sleep 0.3s real 0m0.285s user 0m0.184s sys 0m0.099s touch /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/report/run.sh.done + touch /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/report/run.sh.done + finish + echo 'finish code: 0' finish code: 0 2022-01-06 16:57:02,150[INFO] recently_satisfied: set([Node(0-rawreads/report)]) 2022-01-06 16:57:02,150[INFO] Num satisfied in this iteration: 1 2022-01-06 16:57:02,150[INFO] Num still unsatisfied: 0 2022-01-06 16:57:02,155[INFO] Num unsatisfied: 1, graph: 16 2022-01-06 16:57:02,155[INFO] About to submit: Node(1-preads_ovl) 2022-01-06 16:57:02,158[INFO] !chmod +x /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/run-Pdb2e5581a70d88.bash 2022-01-06 16:57:02,168[INFO] sleep 0.1s 2022-01-06 16:57:02,174[INFO] Popen: 'bash -C /build/falcon-LwwdoQ/falcon-1.8.8/inst/pylib/pypeflow-1.0.0-py2.7.egg/pwatcher/mains/job_start.sh' executable=${PYPEFLOW_JOB_START_SCRIPT} + executable=/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/run-Pdb2e5581a70d88.bash timeout=${PYPEFLOW_JOB_START_TIMEOUT:-60} # wait 60s by default + timeout=60 # Wait up to timeout seconds for the executable to become "executable", # then exec. #timeleft = int(timeout) while [[ ! -x "${executable}" ]]; do if [[ "${timeout}" == "0" ]]; then echo "timed out waiting for (${executable})" exit 77 fi echo "not executable: '${executable}', waiting ${timeout}s" sleep 1 timeout=$((timeout-1)) done + [[ ! -x /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/run-Pdb2e5581a70d88.bash ]] bash ${executable} + bash /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/run-Pdb2e5581a70d88.bash + '[' '!' -d /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl ']' + cd /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl + eval '/bin/bash run.sh' ++ /bin/bash run.sh cd /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl + cd /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl bash task.sh + bash task.sh 30e18b9a274d CC=gcc CFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong -Wformat -Werror=format-security CPPFLAGS=-Wdate-time -D_FORTIFY_SOURCE=2 CXX=g++ CXXFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong -Wformat -Werror=format-security DEBCONF_NONINTERACTIVE_SEEN=true DEBIAN_FRONTEND=noninteractive DEB_BUILD_ARCH=amd64 DEB_BUILD_ARCH_ABI=base DEB_BUILD_ARCH_BITS=64 DEB_BUILD_ARCH_CPU=amd64 DEB_BUILD_ARCH_ENDIAN=little DEB_BUILD_ARCH_LIBC=gnu DEB_BUILD_ARCH_OS=linux DEB_BUILD_GNU_CPU=x86_64 DEB_BUILD_GNU_SYSTEM=linux-gnu DEB_BUILD_GNU_TYPE=x86_64-linux-gnu DEB_BUILD_MULTIARCH=x86_64-linux-gnu DEB_BUILD_OPTIONS=nocheck parallel=10 DEB_HOST_ARCH=amd64 DEB_HOST_ARCH_ABI=base DEB_HOST_ARCH_BITS=64 DEB_HOST_ARCH_CPU=amd64 DEB_HOST_ARCH_ENDIAN=little DEB_HOST_ARCH_LIBC=gnu DEB_HOST_ARCH_OS=linux DEB_HOST_GNU_CPU=x86_64 DEB_HOST_GNU_SYSTEM=linux-gnu DEB_HOST_GNU_TYPE=x86_64-linux-gnu DEB_HOST_MULTIARCH=x86_64-linux-gnu DEB_TARGET_ARCH=amd64 DEB_TARGET_ARCH_ABI=base DEB_TARGET_ARCH_BITS=64 DEB_TARGET_ARCH_CPU=amd64 DEB_TARGET_ARCH_ENDIAN=little DEB_TARGET_ARCH_LIBC=gnu DEB_TARGET_ARCH_OS=linux DEB_TARGET_GNU_CPU=x86_64 DEB_TARGET_GNU_SYSTEM=linux-gnu DEB_TARGET_GNU_TYPE=x86_64-linux-gnu DEB_TARGET_MULTIARCH=x86_64-linux-gnu DH_INTERNAL_BUILDFLAGS=1 DH_INTERNAL_OPTIONS=-a DH_INTERNAL_OVERRIDE=dh_auto_test FALCON_INSTALL_RULE=install FALCON_PREFIX=/build/falcon-LwwdoQ/falcon-1.8.8/inst FALCON_WORKSPACE=/build/falcon-LwwdoQ/falcon-1.8.8 FCFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong FFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong GCJFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong HOME=/nonexistent LANG=C.UTF-8 LANGUAGE=C.UTF-8 LC_ALL=C.UTF-8 LDFLAGS=-Wl,-z,relro LOGNAME=builduser MAKEFLAGS=w MAKELEVEL=6 MFLAGS=-w MMDEBSTRAP_APT_CONFIG=/tmp/mmdebstrap.SAG5NvxJ_M/tmp/mmdebstrap.apt.conf.TRj0u44dYeZl MMDEBSTRAP_HOOK=customize MMDEBSTRAP_HOOKSOCK=6 MMDEBSTRAP_MODE=root OBJCFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong -Wformat -Werror=format-security OBJCXXFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong -Wformat -Werror=format-security OLDPWD=/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl PATH=/build/falcon-LwwdoQ/falcon-1.8.8/inst/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/sbin:/usr/bin:/sbin:/bin PERL_USE_UNSAFE_INC=1 PWD=/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl PYPEFLOW_JOB_START_SCRIPT=/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/run-Pdb2e5581a70d88.bash PYPEFLOW_JOB_START_TIMEOUT=60 PYTHONPATH=/build/falcon-LwwdoQ/falcon-1.8.8/inst/pylib:/build/falcon-LwwdoQ/falcon-1.8.8/inst/pylib: SHELL=/bin/bash SHLVL=5 SOURCE_DATE_EPOCH=1513411047 USER=builduser _=/usr/bin/env /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl 2022-01-06 16:57:02,269[INFO] sleep 0.2s 2022-01-06 16:57:02,297 - root - DEBUG - Running "/build/falcon-LwwdoQ/falcon-1.8.8/inst/pylib/pypeflow-1.0.0-py2.7.egg/pypeflow/do_task.py /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/task.json" 2022-01-06 16:57:02,299 - root - DEBUG - Checking existence of '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/task.json' with timeout=60 2022-01-06 16:57:02,299 - root - DEBUG - Loading JSON from '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/task.json' 2022-01-06 16:57:02,302 - root - DEBUG - {u'inputs': {u'preads_fofn': u'/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/preads/input_preads.fofn'}, u'outputs': {u'pdb_build_done': u'pdb_build_done', u'preads_db': u'preads.db', u'run_jobs': u'run_jobs.sh'}, u'parameters': {u'config': {u'LA4Falcon_preload': True, u'avoid_text_file_busy': True, u'cns_concurrent_jobs': 32, u'da_concurrent_jobs': 32, u'dazcon': False, u'default_concurrent_jobs': 8, u'dust': False, u'falcon_sense_greedy': False, u'falcon_sense_option': u'--output_multi --min_idt 0.70 --min_cov 1 --max_n_read 20000 --n_core 0', u'falcon_sense_skip_contained': False, u'fc_concurrent_jobs': 8, u'fc_ovlp_to_graph_option': u' --min_len 1', u'genome_size': 5000, u'input_fofn': u'input.fofn', u'input_type': u'raw', u'install_prefix': u'/usr', u'job_queue': u'bash -C ${CMD}', u'job_type': u'string', u'la_concurrent_jobs': 32, u'length_cutoff': -1, u'length_cutoff_pr': 1, u'overlap_filtering_setting': u'--max_diff 10000 --max_cov 100000 --min_cov 1 --min_len 1 --bestn 1000 --n_core 0', u'ovlp_DBsplit_option': u'-a -x5 -s50', u'ovlp_HPCdaligner_option': u'-v -B4 -t50 -h1 -e.99 -l1 -s1000', u'pa_DBdust_option': u'-w128 -t2.5 -m20', u'pa_DBsplit_option': u'-a -x5 -s.065536', u'pa_HPCdaligner_option': u'-v -B4 -t50 -h1 -e.99 -w1 -l1 -s1000', u'pa_dazcon_option': u'-j 4 -x -l 500', u'pda_concurrent_jobs': 32, u'pla_concurrent_jobs': 32, u'pwatcher_directory': u'mypwatcher', u'pwatcher_type': u'blocking', u'seed_coverage': 20.0, u'sge_option': u'-pe smp 8 -q bash -C ${CMD}', u'sge_option_cns': u'-pe smp 8 -q bash -C ${CMD}', u'sge_option_da': u'-pe smp 8 -q bash -C ${CMD}', u'sge_option_fc': u'-pe smp 24 -q bash -C ${CMD}', u'sge_option_la': u'-pe smp 2 -q bash -C ${CMD}', u'sge_option_pda': u'-pe smp 8 -q bash -C ${CMD}', u'sge_option_pla': u'-pe smp 2 -q bash -C ${CMD}', u'skip_checks': False, u'stop_all_jobs_on_failure': True, u'target': u'assembly', u'use_tmpdir': False}, u'config_fn': u'/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/fc_run.cfg', u'sge_option': u'-pe smp 8 -q bash -C ${CMD}', u'work_dir': u'/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl'}, u'python_function': u'falcon_kit.pype_tasks.task_build_pdb'} 2022-01-06 16:57:02,302 - root - DEBUG - CD: '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl' <- '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl' 2022-01-06 16:57:02,302 - root - DEBUG - Checking existence of u'/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/preads/input_preads.fofn' with timeout=60 2022-01-06 16:57:02,334 - root - DEBUG - CD: '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl' <- '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl' 2022-01-06 16:57:02,335 - pypeflow.do_support - INFO - !/bin/bash -vex /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/prepare_pdb.sh #!/bin/bash set -vex + set -vex while read fn; do fasta2DB -v preads $fn; done < /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/preads/input_preads.fofn + read fn + fasta2DB -v preads /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/preads/cns_00001/cns_00001.fasta Adding 'cns_00001.fasta' ... + read fn + fasta2DB -v preads /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/0-rawreads/preads/cns_00002/cns_00002.fasta Adding 'cns_00002.fasta' ... + read fn DBsplit -a -x5 -s50 preads + DBsplit -a -x5 -s50 preads 2022-01-06 16:57:02,470[INFO] sleep 0.3s LB=$(cat preads.db | LD_LIBRARY_PATH= awk '$1 == "blocks" {print $3}') ++ cat preads.db ++ LD_LIBRARY_PATH= ++ awk '$1 == "blocks" {print $3}' + LB=1 HPC.daligner -v -B4 -t50 -h1 -e.99 -l1 -s1000 -H1 preads 1-$LB >| run_jobs.sh + HPC.daligner -v -B4 -t50 -h1 -e.99 -l1 -s1000 -H1 preads 1-1 touch pdb_build_done + touch pdb_build_done 2022-01-06 16:57:02,562 - root - DEBUG - CD: '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl' -> '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl' 2022-01-06 16:57:02,562 - root - DEBUG - Checking existence of u'run_jobs.sh' with timeout=60 2022-01-06 16:57:02,563 - root - DEBUG - Checking existence of u'pdb_build_done' with timeout=60 2022-01-06 16:57:02,563 - root - DEBUG - Checking existence of u'preads.db' with timeout=60 2022-01-06 16:57:02,563 - root - DEBUG - CD: '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl' -> '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl' real 0m0.377s user 0m0.108s sys 0m0.069s touch /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/run.sh.done + touch /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/run.sh.done + finish + echo 'finish code: 0' finish code: 0 2022-01-06 16:57:02,772[INFO] recently_satisfied: set([Node(1-preads_ovl)]) 2022-01-06 16:57:02,772[INFO] Num satisfied in this iteration: 1 2022-01-06 16:57:02,772[INFO] Num still unsatisfied: 0 2022-01-06 16:57:02,777[INFO] Num unsatisfied: 1, graph: 17 2022-01-06 16:57:02,777[INFO] About to submit: Node(1-preads_ovl/daligner-scatter) 2022-01-06 16:57:02,780[INFO] !chmod +x /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/daligner-scatter/run-P34eeb9e90d15bc.bash 2022-01-06 16:57:02,790[INFO] sleep 0.1s 2022-01-06 16:57:02,796[INFO] Popen: 'bash -C /build/falcon-LwwdoQ/falcon-1.8.8/inst/pylib/pypeflow-1.0.0-py2.7.egg/pwatcher/mains/job_start.sh' executable=${PYPEFLOW_JOB_START_SCRIPT} + executable=/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/daligner-scatter/run-P34eeb9e90d15bc.bash timeout=${PYPEFLOW_JOB_START_TIMEOUT:-60} # wait 60s by default + timeout=60 # Wait up to timeout seconds for the executable to become "executable", # then exec. #timeleft = int(timeout) while [[ ! -x "${executable}" ]]; do if [[ "${timeout}" == "0" ]]; then echo "timed out waiting for (${executable})" exit 77 fi echo "not executable: '${executable}', waiting ${timeout}s" sleep 1 timeout=$((timeout-1)) done + [[ ! -x /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/daligner-scatter/run-P34eeb9e90d15bc.bash ]] bash ${executable} + bash /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/daligner-scatter/run-P34eeb9e90d15bc.bash + '[' '!' -d /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/daligner-scatter ']' + cd /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/daligner-scatter + eval '/bin/bash run.sh' ++ /bin/bash run.sh cd /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/daligner-scatter + cd /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/daligner-scatter bash task.sh + bash task.sh 30e18b9a274d CC=gcc CFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong -Wformat -Werror=format-security CPPFLAGS=-Wdate-time -D_FORTIFY_SOURCE=2 CXX=g++ CXXFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong -Wformat -Werror=format-security DEBCONF_NONINTERACTIVE_SEEN=true DEBIAN_FRONTEND=noninteractive DEB_BUILD_ARCH=amd64 DEB_BUILD_ARCH_ABI=base DEB_BUILD_ARCH_BITS=64 DEB_BUILD_ARCH_CPU=amd64 DEB_BUILD_ARCH_ENDIAN=little DEB_BUILD_ARCH_LIBC=gnu DEB_BUILD_ARCH_OS=linux DEB_BUILD_GNU_CPU=x86_64 DEB_BUILD_GNU_SYSTEM=linux-gnu DEB_BUILD_GNU_TYPE=x86_64-linux-gnu DEB_BUILD_MULTIARCH=x86_64-linux-gnu DEB_BUILD_OPTIONS=nocheck parallel=10 DEB_HOST_ARCH=amd64 DEB_HOST_ARCH_ABI=base DEB_HOST_ARCH_BITS=64 DEB_HOST_ARCH_CPU=amd64 DEB_HOST_ARCH_ENDIAN=little DEB_HOST_ARCH_LIBC=gnu DEB_HOST_ARCH_OS=linux DEB_HOST_GNU_CPU=x86_64 DEB_HOST_GNU_SYSTEM=linux-gnu DEB_HOST_GNU_TYPE=x86_64-linux-gnu DEB_HOST_MULTIARCH=x86_64-linux-gnu DEB_TARGET_ARCH=amd64 DEB_TARGET_ARCH_ABI=base DEB_TARGET_ARCH_BITS=64 DEB_TARGET_ARCH_CPU=amd64 DEB_TARGET_ARCH_ENDIAN=little DEB_TARGET_ARCH_LIBC=gnu DEB_TARGET_ARCH_OS=linux DEB_TARGET_GNU_CPU=x86_64 DEB_TARGET_GNU_SYSTEM=linux-gnu DEB_TARGET_GNU_TYPE=x86_64-linux-gnu DEB_TARGET_MULTIARCH=x86_64-linux-gnu DH_INTERNAL_BUILDFLAGS=1 DH_INTERNAL_OPTIONS=-a DH_INTERNAL_OVERRIDE=dh_auto_test FALCON_INSTALL_RULE=install FALCON_PREFIX=/build/falcon-LwwdoQ/falcon-1.8.8/inst FALCON_WORKSPACE=/build/falcon-LwwdoQ/falcon-1.8.8 FCFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong FFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong GCJFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong HOME=/nonexistent LANG=C.UTF-8 LANGUAGE=C.UTF-8 LC_ALL=C.UTF-8 LDFLAGS=-Wl,-z,relro LOGNAME=builduser MAKEFLAGS=w MAKELEVEL=6 MFLAGS=-w MMDEBSTRAP_APT_CONFIG=/tmp/mmdebstrap.SAG5NvxJ_M/tmp/mmdebstrap.apt.conf.TRj0u44dYeZl MMDEBSTRAP_HOOK=customize MMDEBSTRAP_HOOKSOCK=6 MMDEBSTRAP_MODE=root OBJCFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong -Wformat -Werror=format-security OBJCXXFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong -Wformat -Werror=format-security OLDPWD=/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/daligner-scatter PATH=/build/falcon-LwwdoQ/falcon-1.8.8/inst/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/sbin:/usr/bin:/sbin:/bin PERL_USE_UNSAFE_INC=1 PWD=/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/daligner-scatter PYPEFLOW_JOB_START_SCRIPT=/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/daligner-scatter/run-P34eeb9e90d15bc.bash PYPEFLOW_JOB_START_TIMEOUT=60 PYTHONPATH=/build/falcon-LwwdoQ/falcon-1.8.8/inst/pylib:/build/falcon-LwwdoQ/falcon-1.8.8/inst/pylib: SHELL=/bin/bash SHLVL=5 SOURCE_DATE_EPOCH=1513411047 USER=builduser _=/usr/bin/env /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/daligner-scatter 2022-01-06 16:57:02,891[INFO] sleep 0.2s 2022-01-06 16:57:02,923 - root - DEBUG - Running "/build/falcon-LwwdoQ/falcon-1.8.8/inst/pylib/pypeflow-1.0.0-py2.7.egg/pypeflow/do_task.py /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/daligner-scatter/task.json" 2022-01-06 16:57:02,926 - root - DEBUG - Checking existence of '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/daligner-scatter/task.json' with timeout=60 2022-01-06 16:57:02,926 - root - DEBUG - Loading JSON from '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/daligner-scatter/task.json' 2022-01-06 16:57:02,928 - root - DEBUG - {u'inputs': {u'db_build_done': u'/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/pdb_build_done', u'run_jobs_fn': u'/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/run_jobs.sh'}, u'outputs': {u'scatter_fn': u'scattered.json'}, u'parameters': {u'config': {u'LA4Falcon_preload': True, u'avoid_text_file_busy': True, u'cns_concurrent_jobs': 32, u'da_concurrent_jobs': 32, u'dazcon': False, u'default_concurrent_jobs': 8, u'dust': False, u'falcon_sense_greedy': False, u'falcon_sense_option': u'--output_multi --min_idt 0.70 --min_cov 1 --max_n_read 20000 --n_core 0', u'falcon_sense_skip_contained': False, u'fc_concurrent_jobs': 8, u'fc_ovlp_to_graph_option': u' --min_len 1', u'genome_size': 5000, u'input_fofn': u'input.fofn', u'input_type': u'raw', u'install_prefix': u'/usr', u'job_queue': u'bash -C ${CMD}', u'job_type': u'string', u'la_concurrent_jobs': 32, u'length_cutoff': -1, u'length_cutoff_pr': 1, u'overlap_filtering_setting': u'--max_diff 10000 --max_cov 100000 --min_cov 1 --min_len 1 --bestn 1000 --n_core 0', u'ovlp_DBsplit_option': u'-a -x5 -s50', u'ovlp_HPCdaligner_option': u'-v -B4 -t50 -h1 -e.99 -l1 -s1000', u'pa_DBdust_option': u'-w128 -t2.5 -m20', u'pa_DBsplit_option': u'-a -x5 -s.065536', u'pa_HPCdaligner_option': u'-v -B4 -t50 -h1 -e.99 -w1 -l1 -s1000', u'pa_dazcon_option': u'-j 4 -x -l 500', u'pda_concurrent_jobs': 32, u'pla_concurrent_jobs': 32, u'pwatcher_directory': u'mypwatcher', u'pwatcher_type': u'blocking', u'seed_coverage': 20.0, u'sge_option': u'-pe smp 8 -q bash -C ${CMD}', u'sge_option_cns': u'-pe smp 8 -q bash -C ${CMD}', u'sge_option_da': u'-pe smp 8 -q bash -C ${CMD}', u'sge_option_fc': u'-pe smp 24 -q bash -C ${CMD}', u'sge_option_la': u'-pe smp 2 -q bash -C ${CMD}', u'sge_option_pda': u'-pe smp 8 -q bash -C ${CMD}', u'sge_option_pla': u'-pe smp 2 -q bash -C ${CMD}', u'skip_checks': False, u'stop_all_jobs_on_failure': True, u'target': u'assembly', u'use_tmpdir': False}, u'db_prefix': u'preads', u'nblock': 1, u'pread_aln': True}, u'python_function': u'falcon_kit.pype_tasks.task_daligner_scatter'} 2022-01-06 16:57:02,928 - root - DEBUG - CD: '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/daligner-scatter' <- '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/daligner-scatter' 2022-01-06 16:57:02,929 - root - DEBUG - Checking existence of u'/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/run_jobs.sh' with timeout=60 2022-01-06 16:57:02,929 - root - DEBUG - Checking existence of u'/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/pdb_build_done' with timeout=60 2022-01-06 16:57:02,960 - root - DEBUG - CD: '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/daligner-scatter' <- '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/daligner-scatter' 2022-01-06 16:57:02,960 - falcon_kit.pype_tasks - INFO - Skip LAcheck after daligner? False 2022-01-06 16:57:02,962 - root - DEBUG - CD: '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/daligner-scatter' -> '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/daligner-scatter' 2022-01-06 16:57:02,962 - root - DEBUG - Checking existence of u'scattered.json' with timeout=60 2022-01-06 16:57:02,962 - root - DEBUG - CD: '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/daligner-scatter' -> '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/daligner-scatter' real 0m0.154s user 0m0.106s sys 0m0.042s touch /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/daligner-scatter/run.sh.done + touch /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/daligner-scatter/run.sh.done + finish + echo 'finish code: 0' finish code: 0 2022-01-06 16:57:03,093[INFO] recently_satisfied: set([Node(1-preads_ovl/daligner-scatter)]) 2022-01-06 16:57:03,093[INFO] Num satisfied in this iteration: 1 2022-01-06 16:57:03,093[INFO] Num still unsatisfied: 0 2022-01-06 16:57:03,100[INFO] Num unsatisfied: 2, graph: 19 2022-01-06 16:57:03,101[INFO] About to submit: Node(1-preads_ovl/job_0000) 2022-01-06 16:57:03,104[INFO] !chmod +x /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/job_0000/run-Pa7aa533d784247.bash 2022-01-06 16:57:03,114[INFO] sleep 0.1s 2022-01-06 16:57:03,120[INFO] Popen: 'bash -C /build/falcon-LwwdoQ/falcon-1.8.8/inst/pylib/pypeflow-1.0.0-py2.7.egg/pwatcher/mains/job_start.sh' executable=${PYPEFLOW_JOB_START_SCRIPT} + executable=/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/job_0000/run-Pa7aa533d784247.bash timeout=${PYPEFLOW_JOB_START_TIMEOUT:-60} # wait 60s by default + timeout=60 # Wait up to timeout seconds for the executable to become "executable", # then exec. #timeleft = int(timeout) while [[ ! -x "${executable}" ]]; do if [[ "${timeout}" == "0" ]]; then echo "timed out waiting for (${executable})" exit 77 fi echo "not executable: '${executable}', waiting ${timeout}s" sleep 1 timeout=$((timeout-1)) done + [[ ! -x /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/job_0000/run-Pa7aa533d784247.bash ]] bash ${executable} + bash /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/job_0000/run-Pa7aa533d784247.bash + '[' '!' -d /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/job_0000 ']' + cd /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/job_0000 + eval '/bin/bash run.sh' ++ /bin/bash run.sh cd /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/job_0000 + cd /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/job_0000 bash task.sh + bash task.sh 30e18b9a274d CC=gcc CFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong -Wformat -Werror=format-security CPPFLAGS=-Wdate-time -D_FORTIFY_SOURCE=2 CXX=g++ CXXFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong -Wformat -Werror=format-security DEBCONF_NONINTERACTIVE_SEEN=true DEBIAN_FRONTEND=noninteractive DEB_BUILD_ARCH=amd64 DEB_BUILD_ARCH_ABI=base DEB_BUILD_ARCH_BITS=64 DEB_BUILD_ARCH_CPU=amd64 DEB_BUILD_ARCH_ENDIAN=little DEB_BUILD_ARCH_LIBC=gnu DEB_BUILD_ARCH_OS=linux DEB_BUILD_GNU_CPU=x86_64 DEB_BUILD_GNU_SYSTEM=linux-gnu DEB_BUILD_GNU_TYPE=x86_64-linux-gnu DEB_BUILD_MULTIARCH=x86_64-linux-gnu DEB_BUILD_OPTIONS=nocheck parallel=10 DEB_HOST_ARCH=amd64 DEB_HOST_ARCH_ABI=base DEB_HOST_ARCH_BITS=64 DEB_HOST_ARCH_CPU=amd64 DEB_HOST_ARCH_ENDIAN=little DEB_HOST_ARCH_LIBC=gnu DEB_HOST_ARCH_OS=linux DEB_HOST_GNU_CPU=x86_64 DEB_HOST_GNU_SYSTEM=linux-gnu DEB_HOST_GNU_TYPE=x86_64-linux-gnu DEB_HOST_MULTIARCH=x86_64-linux-gnu DEB_TARGET_ARCH=amd64 DEB_TARGET_ARCH_ABI=base DEB_TARGET_ARCH_BITS=64 DEB_TARGET_ARCH_CPU=amd64 DEB_TARGET_ARCH_ENDIAN=little DEB_TARGET_ARCH_LIBC=gnu DEB_TARGET_ARCH_OS=linux DEB_TARGET_GNU_CPU=x86_64 DEB_TARGET_GNU_SYSTEM=linux-gnu DEB_TARGET_GNU_TYPE=x86_64-linux-gnu DEB_TARGET_MULTIARCH=x86_64-linux-gnu DH_INTERNAL_BUILDFLAGS=1 DH_INTERNAL_OPTIONS=-a DH_INTERNAL_OVERRIDE=dh_auto_test FALCON_INSTALL_RULE=install FALCON_PREFIX=/build/falcon-LwwdoQ/falcon-1.8.8/inst FALCON_WORKSPACE=/build/falcon-LwwdoQ/falcon-1.8.8 FCFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong FFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong GCJFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong HOME=/nonexistent LANG=C.UTF-8 LANGUAGE=C.UTF-8 LC_ALL=C.UTF-8 LDFLAGS=-Wl,-z,relro LOGNAME=builduser MAKEFLAGS=w MAKELEVEL=6 MFLAGS=-w MMDEBSTRAP_APT_CONFIG=/tmp/mmdebstrap.SAG5NvxJ_M/tmp/mmdebstrap.apt.conf.TRj0u44dYeZl MMDEBSTRAP_HOOK=customize MMDEBSTRAP_HOOKSOCK=6 MMDEBSTRAP_MODE=root OBJCFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong -Wformat -Werror=format-security OBJCXXFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong -Wformat -Werror=format-security OLDPWD=/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/job_0000 PATH=/build/falcon-LwwdoQ/falcon-1.8.8/inst/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/sbin:/usr/bin:/sbin:/bin PERL_USE_UNSAFE_INC=1 PWD=/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/job_0000 PYPEFLOW_JOB_START_SCRIPT=/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/job_0000/run-Pa7aa533d784247.bash PYPEFLOW_JOB_START_TIMEOUT=60 PYTHONPATH=/build/falcon-LwwdoQ/falcon-1.8.8/inst/pylib:/build/falcon-LwwdoQ/falcon-1.8.8/inst/pylib: SHELL=/bin/bash SHLVL=5 SOURCE_DATE_EPOCH=1513411047 USER=builduser _=/usr/bin/env /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/job_0000 2022-01-06 16:57:03,215[INFO] sleep 0.2s 2022-01-06 16:57:03,238 - root - DEBUG - Running "/build/falcon-LwwdoQ/falcon-1.8.8/inst/pylib/pypeflow-1.0.0-py2.7.egg/pypeflow/do_task.py /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/job_0000/task.json" 2022-01-06 16:57:03,240 - root - DEBUG - Checking existence of '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/job_0000/task.json' with timeout=60 2022-01-06 16:57:03,240 - root - DEBUG - Loading JSON from '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/job_0000/task.json' 2022-01-06 16:57:03,243 - root - DEBUG - {u'inputs': {u'db_build_done': u'/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/pdb_build_done', u'scatter_fn': u'/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/daligner-scatter/scattered.json'}, u'outputs': {u'job_done': u'job_0000_done'}, u'parameters': {u'config': {u'LA4Falcon_preload': True, u'avoid_text_file_busy': True, u'cns_concurrent_jobs': 32, u'da_concurrent_jobs': 32, u'dazcon': False, u'default_concurrent_jobs': 8, u'dust': False, u'falcon_sense_greedy': False, u'falcon_sense_option': u'--output_multi --min_idt 0.70 --min_cov 1 --max_n_read 20000 --n_core 0', u'falcon_sense_skip_contained': False, u'fc_concurrent_jobs': 8, u'fc_ovlp_to_graph_option': u' --min_len 1', u'genome_size': 5000, u'input_fofn': u'input.fofn', u'input_type': u'raw', u'install_prefix': u'/usr', u'job_queue': u'bash -C ${CMD}', u'job_type': u'string', u'la_concurrent_jobs': 32, u'length_cutoff': -1, u'length_cutoff_pr': 1, u'overlap_filtering_setting': u'--max_diff 10000 --max_cov 100000 --min_cov 1 --min_len 1 --bestn 1000 --n_core 0', u'ovlp_DBsplit_option': u'-a -x5 -s50', u'ovlp_HPCdaligner_option': u'-v -B4 -t50 -h1 -e.99 -l1 -s1000', u'pa_DBdust_option': u'-w128 -t2.5 -m20', u'pa_DBsplit_option': u'-a -x5 -s.065536', u'pa_HPCdaligner_option': u'-v -B4 -t50 -h1 -e.99 -w1 -l1 -s1000', u'pa_dazcon_option': u'-j 4 -x -l 500', u'pda_concurrent_jobs': 32, u'pla_concurrent_jobs': 32, u'pwatcher_directory': u'mypwatcher', u'pwatcher_type': u'blocking', u'seed_coverage': 20.0, u'sge_option': u'-pe smp 8 -q bash -C ${CMD}', u'sge_option_cns': u'-pe smp 8 -q bash -C ${CMD}', u'sge_option_da': u'-pe smp 8 -q bash -C ${CMD}', u'sge_option_fc': u'-pe smp 24 -q bash -C ${CMD}', u'sge_option_la': u'-pe smp 2 -q bash -C ${CMD}', u'sge_option_pda': u'-pe smp 8 -q bash -C ${CMD}', u'sge_option_pla': u'-pe smp 2 -q bash -C ${CMD}', u'skip_checks': False, u'stop_all_jobs_on_failure': True, u'target': u'assembly', u'use_tmpdir': False}, u'daligner_script': u'\ndb_dir=/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl\nln -sf ${db_dir}/.preads.bps .\nln -sf ${db_dir}/.preads.idx .\nln -sf ${db_dir}/preads.db .\nln -sf ${db_dir}/.preads.dust.anno .\nln -sf ${db_dir}/.preads.dust.data .\ndaligner_p -v -h1 -t50 -H1 -e0.99 -l1 -s1000 preads.1 preads.1\nLAcheck -v preads *.las\nLAsort -v preads.1.preads.1.C0 preads.1.preads.1.N0 preads.1.preads.1.C1 preads.1.preads.1.N1 preads.1.preads.1.C2 preads.1.preads.1.N2 preads.1.preads.1.C3 preads.1.preads.1.N3 && LAmerge -v preads.1 preads.1.preads.1.C0.S preads.1.preads.1.N0.S preads.1.preads.1.C1.S preads.1.preads.1.N1.S preads.1.preads.1.C2.S preads.1.preads.1.N2.S preads.1.preads.1.C3.S preads.1.preads.1.N3.S\nLAcheck -vS preads preads.1\n\nrm -f *.C?.las *.C?.S.las *.C??.las *.C??.S.las *.C???.las *.C???.S.las\nrm -f *.N?.las *.N?.S.las *.N??.las *.N??.S.las *.N???.las *.N???.S.las\n', u'db_prefix': u'preads', u'job_uid': u'0000', u'sge_option': u'-pe smp 8 -q bash -C ${CMD}'}, u'python_function': u'falcon_kit.pype_tasks.task_run_daligner'} 2022-01-06 16:57:03,243 - root - DEBUG - CD: '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/job_0000' <- '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/job_0000' 2022-01-06 16:57:03,243 - root - DEBUG - Checking existence of u'/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/daligner-scatter/scattered.json' with timeout=60 2022-01-06 16:57:03,243 - root - DEBUG - Checking existence of u'/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/pdb_build_done' with timeout=60 2022-01-06 16:57:03,274 - root - DEBUG - CD: '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/job_0000' <- '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/job_0000' 2022-01-06 16:57:03,275 - pypeflow.do_support - INFO - !/bin/bash -vex /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/job_0000/rj_0000.sh #!/bin/bash set -vex + set -vex db_dir=/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl + db_dir=/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl ln -sf ${db_dir}/.preads.bps . + ln -sf /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/.preads.bps . ln -sf ${db_dir}/.preads.idx . + ln -sf /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/.preads.idx . ln -sf ${db_dir}/preads.db . + ln -sf /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/preads.db . ln -sf ${db_dir}/.preads.dust.anno . + ln -sf /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/.preads.dust.anno . ln -sf ${db_dir}/.preads.dust.data . + ln -sf /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/.preads.dust.data . daligner_p -v -h1 -t50 -H1 -e0.99 -l1 -s1000 preads.1 preads.1 + daligner_p -v -h1 -t50 -H1 -e0.99 -l1 -s1000 preads.1 preads.1 Building index for preads.1 Kshift=28 BSHIFT=8 TooFrequent=50 (Kshift-1)/BSHIFT + (TooFrequent < INT32_MAX)=4 sizeof(KmerPos)=16 nreads=50 Kmer=14 block->reads[nreads].boff=99497 kmers=98797 sizeof(KmerPos)*(kmers+1)=1580768 Allocated 98798 of 16 (1580768 bytes) at 0x7ec688abf010 Kmer count = 98,797 Using 0.00Gb of space Revised kmer count = 98,797 Index occupies 0.00Gb Comparing preads.1 to preads.1 Capping mutual k-mer matches over 10000 (effectively -t100) Hit count = 957,676 Highwater of 0.03Gb space 957,676 14-mers (9.683564e-05 of matrix) 978 seed hits (9.889071e-08 of matrix) 1,956 confirmed hits (1.977814e-07 of matrix) Building index for c(preads.1) Kshift=28 BSHIFT=8 TooFrequent=50 (Kshift-1)/BSHIFT + (TooFrequent < INT32_MAX)=4 sizeof(KmerPos)=16 nreads=50 Kmer=14 block->reads[nreads].boff=99497 kmers=98797 sizeof(KmerPos)*(kmers+1)=1580768 Allocated 98798 of 16 (1580768 bytes) at 0x560a7af854a0 Kmer count = 98,797 Using 0.00Gb of space Revised kmer count = 98,797 Index occupies 0.00Gb Comparing preads.1 to c(preads.1) Capping mutual k-mer matches over 10000 (effectively -t100) Hit count = 0 Highwater of 0.00Gb space 0 14-mers (0.000000e+00 of matrix) 0 seed hits (0.000000e+00 of matrix) 0 confirmed hits (0.000000e+00 of matrix) LAcheck -v preads *.las + LAcheck -v preads preads.1.preads.1.C0.las preads.1.preads.1.C1.las preads.1.preads.1.C2.las preads.1.preads.1.C3.las preads.1.preads.1.N0.las preads.1.preads.1.N1.las preads.1.preads.1.N2.las preads.1.preads.1.N3.las preads.1.preads.1.C0: 0 all OK preads.1.preads.1.C1: 0 all OK preads.1.preads.1.C2: 0 all OK preads.1.preads.1.C3: 0 all OK preads.1.preads.1.N0: 504 all OK preads.1.preads.1.N1: 518 all OK preads.1.preads.1.N2: 456 all OK preads.1.preads.1.N3: 478 all OK LAsort -v preads.1.preads.1.C0 preads.1.preads.1.N0 preads.1.preads.1.C1 preads.1.preads.1.N1 preads.1.preads.1.C2 preads.1.preads.1.N2 preads.1.preads.1.C3 preads.1.preads.1.N3 && LAmerge -v preads.1 preads.1.preads.1.C0.S preads.1.preads.1.N0.S preads.1.preads.1.C1.S preads.1.preads.1.N1.S preads.1.preads.1.C2.S preads.1.preads.1.N2.S preads.1.preads.1.C3.S preads.1.preads.1.N3.S + LAsort -v preads.1.preads.1.C0 preads.1.preads.1.N0 preads.1.preads.1.C1 preads.1.preads.1.N1 preads.1.preads.1.C2 preads.1.preads.1.N2 preads.1.preads.1.C3 preads.1.preads.1.N3 preads.1.preads.1.C0: 0 records 12 trace bytes preads.1.preads.1.N0: 504 records 2,988 trace bytes preads.1.preads.1.C1: 0 records 12 trace bytes preads.1.preads.1.N1: 518 records 3,120 trace bytes preads.1.preads.1.C2: 0 records 12 trace bytes preads.1.preads.1.N2: 456 records 2,740 trace bytes preads.1.preads.1.C3: 0 records 12 trace bytes preads.1.preads.1.N3: 478 records 2,840 trace bytes + LAmerge -v preads.1 preads.1.preads.1.C0.S preads.1.preads.1.N0.S preads.1.preads.1.C1.S preads.1.preads.1.N1.S preads.1.preads.1.C2.S preads.1.preads.1.N2.S preads.1.preads.1.C3.S preads.1.preads.1.N3.S In file ./preads.1.preads.1.C0.S.las, there are 0 records In file ./preads.1.preads.1.N0.S.las, there are 504 records In file ./preads.1.preads.1.C1.S.las, there are 0 records In file ./preads.1.preads.1.N1.S.las, there are 518 records In file ./preads.1.preads.1.C2.S.las, there are 0 records In file ./preads.1.preads.1.N2.S.las, there are 456 records In file ./preads.1.preads.1.C3.S.las, there are 0 records In file ./preads.1.preads.1.N3.S.las, there are 478 records Merging 8 files totalling 1,956 records LAcheck -vS preads preads.1 + LAcheck -vS preads preads.1 preads.1: 1,956 all OK rm -f *.C?.las *.C?.S.las *.C??.las *.C??.S.las *.C???.las *.C???.S.las + rm -f preads.1.preads.1.C0.las preads.1.preads.1.C1.las preads.1.preads.1.C2.las preads.1.preads.1.C3.las preads.1.preads.1.C0.S.las preads.1.preads.1.C1.S.las preads.1.preads.1.C2.S.las preads.1.preads.1.C3.S.las '*.C??.las' '*.C??.S.las' preads.1.preads.1.C0.S.las preads.1.preads.1.C1.S.las preads.1.preads.1.C2.S.las preads.1.preads.1.C3.S.las '*.C???.S.las' rm -f *.N?.las *.N?.S.las *.N??.las *.N??.S.las *.N???.las *.N???.S.las + rm -f preads.1.preads.1.N0.las preads.1.preads.1.N1.las preads.1.preads.1.N2.las preads.1.preads.1.N3.las preads.1.preads.1.N0.S.las preads.1.preads.1.N1.S.las preads.1.preads.1.N2.S.las preads.1.preads.1.N3.S.las '*.N??.las' '*.N??.S.las' preads.1.preads.1.N0.S.las preads.1.preads.1.N1.S.las preads.1.preads.1.N2.S.las preads.1.preads.1.N3.S.las '*.N???.S.las' touch job_0000_done + touch job_0000_done 2022-01-06 16:57:03,390 - root - DEBUG - CD: '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/job_0000' -> '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/job_0000' 2022-01-06 16:57:03,390 - root - DEBUG - Checking existence of u'job_0000_done' with timeout=60 2022-01-06 16:57:03,391 - root - DEBUG - CD: '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/job_0000' -> '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/job_0000' real 0m0.259s user 0m0.270s sys 0m0.130s touch /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/job_0000/run.sh.done + touch /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/job_0000/run.sh.done + finish + echo 'finish code: 0' finish code: 0 2022-01-06 16:57:03,417[INFO] recently_satisfied: set([Node(1-preads_ovl/job_0000)]) 2022-01-06 16:57:03,417[INFO] Num satisfied in this iteration: 1 2022-01-06 16:57:03,417[INFO] Num still unsatisfied: 1 2022-01-06 16:57:03,417[INFO] About to submit: Node(1-preads_ovl/gathered-las) 2022-01-06 16:57:03,420[INFO] !chmod +x /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/gathered-las/run-P8ee34045dc3445.bash 2022-01-06 16:57:03,430[INFO] sleep 0.1s 2022-01-06 16:57:03,436[INFO] Popen: 'bash -C /build/falcon-LwwdoQ/falcon-1.8.8/inst/pylib/pypeflow-1.0.0-py2.7.egg/pwatcher/mains/job_start.sh' executable=${PYPEFLOW_JOB_START_SCRIPT} + executable=/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/gathered-las/run-P8ee34045dc3445.bash timeout=${PYPEFLOW_JOB_START_TIMEOUT:-60} # wait 60s by default + timeout=60 # Wait up to timeout seconds for the executable to become "executable", # then exec. #timeleft = int(timeout) while [[ ! -x "${executable}" ]]; do if [[ "${timeout}" == "0" ]]; then echo "timed out waiting for (${executable})" exit 77 fi echo "not executable: '${executable}', waiting ${timeout}s" sleep 1 timeout=$((timeout-1)) done + [[ ! -x /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/gathered-las/run-P8ee34045dc3445.bash ]] bash ${executable} + bash /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/gathered-las/run-P8ee34045dc3445.bash + '[' '!' -d /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/gathered-las ']' + cd /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/gathered-las + eval '/bin/bash run.sh' ++ /bin/bash run.sh cd /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/gathered-las + cd /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/gathered-las bash task.sh + bash task.sh 30e18b9a274d CC=gcc CFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong -Wformat -Werror=format-security CPPFLAGS=-Wdate-time -D_FORTIFY_SOURCE=2 CXX=g++ CXXFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong -Wformat -Werror=format-security DEBCONF_NONINTERACTIVE_SEEN=true DEBIAN_FRONTEND=noninteractive DEB_BUILD_ARCH=amd64 DEB_BUILD_ARCH_ABI=base DEB_BUILD_ARCH_BITS=64 DEB_BUILD_ARCH_CPU=amd64 DEB_BUILD_ARCH_ENDIAN=little DEB_BUILD_ARCH_LIBC=gnu DEB_BUILD_ARCH_OS=linux DEB_BUILD_GNU_CPU=x86_64 DEB_BUILD_GNU_SYSTEM=linux-gnu DEB_BUILD_GNU_TYPE=x86_64-linux-gnu DEB_BUILD_MULTIARCH=x86_64-linux-gnu DEB_BUILD_OPTIONS=nocheck parallel=10 DEB_HOST_ARCH=amd64 DEB_HOST_ARCH_ABI=base DEB_HOST_ARCH_BITS=64 DEB_HOST_ARCH_CPU=amd64 DEB_HOST_ARCH_ENDIAN=little DEB_HOST_ARCH_LIBC=gnu DEB_HOST_ARCH_OS=linux DEB_HOST_GNU_CPU=x86_64 DEB_HOST_GNU_SYSTEM=linux-gnu DEB_HOST_GNU_TYPE=x86_64-linux-gnu DEB_HOST_MULTIARCH=x86_64-linux-gnu DEB_TARGET_ARCH=amd64 DEB_TARGET_ARCH_ABI=base DEB_TARGET_ARCH_BITS=64 DEB_TARGET_ARCH_CPU=amd64 DEB_TARGET_ARCH_ENDIAN=little DEB_TARGET_ARCH_LIBC=gnu DEB_TARGET_ARCH_OS=linux DEB_TARGET_GNU_CPU=x86_64 DEB_TARGET_GNU_SYSTEM=linux-gnu DEB_TARGET_GNU_TYPE=x86_64-linux-gnu DEB_TARGET_MULTIARCH=x86_64-linux-gnu DH_INTERNAL_BUILDFLAGS=1 DH_INTERNAL_OPTIONS=-a DH_INTERNAL_OVERRIDE=dh_auto_test FALCON_INSTALL_RULE=install FALCON_PREFIX=/build/falcon-LwwdoQ/falcon-1.8.8/inst FALCON_WORKSPACE=/build/falcon-LwwdoQ/falcon-1.8.8 FCFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong FFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong GCJFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong HOME=/nonexistent LANG=C.UTF-8 LANGUAGE=C.UTF-8 LC_ALL=C.UTF-8 LDFLAGS=-Wl,-z,relro LOGNAME=builduser MAKEFLAGS=w MAKELEVEL=6 MFLAGS=-w MMDEBSTRAP_APT_CONFIG=/tmp/mmdebstrap.SAG5NvxJ_M/tmp/mmdebstrap.apt.conf.TRj0u44dYeZl MMDEBSTRAP_HOOK=customize MMDEBSTRAP_HOOKSOCK=6 MMDEBSTRAP_MODE=root OBJCFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong -Wformat -Werror=format-security OBJCXXFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong -Wformat -Werror=format-security OLDPWD=/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/gathered-las PATH=/build/falcon-LwwdoQ/falcon-1.8.8/inst/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/sbin:/usr/bin:/sbin:/bin PERL_USE_UNSAFE_INC=1 PWD=/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/gathered-las PYPEFLOW_JOB_START_SCRIPT=/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/gathered-las/run-P8ee34045dc3445.bash PYPEFLOW_JOB_START_TIMEOUT=60 PYTHONPATH=/build/falcon-LwwdoQ/falcon-1.8.8/inst/pylib:/build/falcon-LwwdoQ/falcon-1.8.8/inst/pylib: SHELL=/bin/bash SHLVL=5 SOURCE_DATE_EPOCH=1513411047 USER=builduser _=/usr/bin/env /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/gathered-las 2022-01-06 16:57:03,531[INFO] sleep 0.2s 2022-01-06 16:57:03,562 - root - DEBUG - Running "/build/falcon-LwwdoQ/falcon-1.8.8/inst/pylib/pypeflow-1.0.0-py2.7.egg/pypeflow/do_task.py /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/gathered-las/task.json" 2022-01-06 16:57:03,564 - root - DEBUG - Checking existence of '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/gathered-las/task.json' with timeout=60 2022-01-06 16:57:03,564 - root - DEBUG - Loading JSON from '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/gathered-las/task.json' 2022-01-06 16:57:03,565 - root - DEBUG - {u'inputs': {u'ajob_0000': u'/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/job_0000/job_0000_done'}, u'outputs': {u'gathered': u'gathered-las.txt'}, u'parameters': {u'nblock': 1}, u'python_function': u'falcon_kit.pype_tasks.task_daligner_gather'} 2022-01-06 16:57:03,565 - root - DEBUG - CD: '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/gathered-las' <- '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/gathered-las' 2022-01-06 16:57:03,565 - root - DEBUG - Checking existence of u'/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/job_0000/job_0000_done' with timeout=60 2022-01-06 16:57:03,597 - root - DEBUG - CD: '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/gathered-las' <- '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/gathered-las' 2022-01-06 16:57:03,598 - falcon_kit.pype_tasks - DEBUG - nblock=1, out_dir: {u'ajob_0000': u'/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/job_0000/job_0000_done'} 2022-01-06 16:57:03,599 - root - DEBUG - CD: '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/gathered-las' -> '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/gathered-las' 2022-01-06 16:57:03,599 - root - DEBUG - Checking existence of u'gathered-las.txt' with timeout=60 2022-01-06 16:57:03,600 - root - DEBUG - CD: '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/gathered-las' -> '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/gathered-las' real 0m0.150s user 0m0.104s sys 0m0.040s touch /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/gathered-las/run.sh.done + touch /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/gathered-las/run.sh.done + finish + echo 'finish code: 0' finish code: 0 2022-01-06 16:57:03,733[INFO] recently_satisfied: set([Node(1-preads_ovl/gathered-las)]) 2022-01-06 16:57:03,733[INFO] Num satisfied in this iteration: 1 2022-01-06 16:57:03,733[INFO] Num still unsatisfied: 0 2022-01-06 16:57:03,738[INFO] Num unsatisfied: 1, graph: 20 2022-01-06 16:57:03,738[INFO] About to submit: Node(1-preads_ovl/merge-scatter) 2022-01-06 16:57:03,741[INFO] !chmod +x /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/merge-scatter/run-P78048291cb1766.bash 2022-01-06 16:57:03,753[INFO] sleep 0.1s 2022-01-06 16:57:03,757[INFO] Popen: 'bash -C /build/falcon-LwwdoQ/falcon-1.8.8/inst/pylib/pypeflow-1.0.0-py2.7.egg/pwatcher/mains/job_start.sh' executable=${PYPEFLOW_JOB_START_SCRIPT} + executable=/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/merge-scatter/run-P78048291cb1766.bash timeout=${PYPEFLOW_JOB_START_TIMEOUT:-60} # wait 60s by default + timeout=60 # Wait up to timeout seconds for the executable to become "executable", # then exec. #timeleft = int(timeout) while [[ ! -x "${executable}" ]]; do if [[ "${timeout}" == "0" ]]; then echo "timed out waiting for (${executable})" exit 77 fi echo "not executable: '${executable}', waiting ${timeout}s" sleep 1 timeout=$((timeout-1)) done + [[ ! -x /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/merge-scatter/run-P78048291cb1766.bash ]] bash ${executable} + bash /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/merge-scatter/run-P78048291cb1766.bash + '[' '!' -d /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/merge-scatter ']' + cd /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/merge-scatter + eval '/bin/bash run.sh' ++ /bin/bash run.sh cd /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/merge-scatter + cd /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/merge-scatter bash task.sh + bash task.sh 30e18b9a274d CC=gcc CFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong -Wformat -Werror=format-security CPPFLAGS=-Wdate-time -D_FORTIFY_SOURCE=2 CXX=g++ CXXFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong -Wformat -Werror=format-security DEBCONF_NONINTERACTIVE_SEEN=true DEBIAN_FRONTEND=noninteractive DEB_BUILD_ARCH=amd64 DEB_BUILD_ARCH_ABI=base DEB_BUILD_ARCH_BITS=64 DEB_BUILD_ARCH_CPU=amd64 DEB_BUILD_ARCH_ENDIAN=little DEB_BUILD_ARCH_LIBC=gnu DEB_BUILD_ARCH_OS=linux DEB_BUILD_GNU_CPU=x86_64 DEB_BUILD_GNU_SYSTEM=linux-gnu DEB_BUILD_GNU_TYPE=x86_64-linux-gnu DEB_BUILD_MULTIARCH=x86_64-linux-gnu DEB_BUILD_OPTIONS=nocheck parallel=10 DEB_HOST_ARCH=amd64 DEB_HOST_ARCH_ABI=base DEB_HOST_ARCH_BITS=64 DEB_HOST_ARCH_CPU=amd64 DEB_HOST_ARCH_ENDIAN=little DEB_HOST_ARCH_LIBC=gnu DEB_HOST_ARCH_OS=linux DEB_HOST_GNU_CPU=x86_64 DEB_HOST_GNU_SYSTEM=linux-gnu DEB_HOST_GNU_TYPE=x86_64-linux-gnu DEB_HOST_MULTIARCH=x86_64-linux-gnu DEB_TARGET_ARCH=amd64 DEB_TARGET_ARCH_ABI=base DEB_TARGET_ARCH_BITS=64 DEB_TARGET_ARCH_CPU=amd64 DEB_TARGET_ARCH_ENDIAN=little DEB_TARGET_ARCH_LIBC=gnu DEB_TARGET_ARCH_OS=linux DEB_TARGET_GNU_CPU=x86_64 DEB_TARGET_GNU_SYSTEM=linux-gnu DEB_TARGET_GNU_TYPE=x86_64-linux-gnu DEB_TARGET_MULTIARCH=x86_64-linux-gnu DH_INTERNAL_BUILDFLAGS=1 DH_INTERNAL_OPTIONS=-a DH_INTERNAL_OVERRIDE=dh_auto_test FALCON_INSTALL_RULE=install FALCON_PREFIX=/build/falcon-LwwdoQ/falcon-1.8.8/inst FALCON_WORKSPACE=/build/falcon-LwwdoQ/falcon-1.8.8 FCFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong FFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong GCJFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong HOME=/nonexistent LANG=C.UTF-8 LANGUAGE=C.UTF-8 LC_ALL=C.UTF-8 LDFLAGS=-Wl,-z,relro LOGNAME=builduser MAKEFLAGS=w MAKELEVEL=6 MFLAGS=-w MMDEBSTRAP_APT_CONFIG=/tmp/mmdebstrap.SAG5NvxJ_M/tmp/mmdebstrap.apt.conf.TRj0u44dYeZl MMDEBSTRAP_HOOK=customize MMDEBSTRAP_HOOKSOCK=6 MMDEBSTRAP_MODE=root OBJCFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong -Wformat -Werror=format-security OBJCXXFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong -Wformat -Werror=format-security OLDPWD=/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/merge-scatter PATH=/build/falcon-LwwdoQ/falcon-1.8.8/inst/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/sbin:/usr/bin:/sbin:/bin PERL_USE_UNSAFE_INC=1 PWD=/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/merge-scatter PYPEFLOW_JOB_START_SCRIPT=/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/merge-scatter/run-P78048291cb1766.bash PYPEFLOW_JOB_START_TIMEOUT=60 PYTHONPATH=/build/falcon-LwwdoQ/falcon-1.8.8/inst/pylib:/build/falcon-LwwdoQ/falcon-1.8.8/inst/pylib: SHELL=/bin/bash SHLVL=5 SOURCE_DATE_EPOCH=1513411047 USER=builduser _=/usr/bin/env /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/merge-scatter 2022-01-06 16:57:03,854[INFO] sleep 0.2s 2022-01-06 16:57:03,876 - root - DEBUG - Running "/build/falcon-LwwdoQ/falcon-1.8.8/inst/pylib/pypeflow-1.0.0-py2.7.egg/pypeflow/do_task.py /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/merge-scatter/task.json" 2022-01-06 16:57:03,878 - root - DEBUG - Checking existence of '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/merge-scatter/task.json' with timeout=60 2022-01-06 16:57:03,879 - root - DEBUG - Loading JSON from '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/merge-scatter/task.json' 2022-01-06 16:57:03,881 - root - DEBUG - {u'inputs': {u'gathered_las': u'/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/gathered-las/gathered-las.txt', u'run_jobs': u'/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/run_jobs.sh'}, u'outputs': {u'scattered': u'scattered.json'}, u'parameters': {u'config': {u'LA4Falcon_preload': True, u'avoid_text_file_busy': True, u'cns_concurrent_jobs': 32, u'da_concurrent_jobs': 32, u'dazcon': False, u'default_concurrent_jobs': 8, u'dust': False, u'falcon_sense_greedy': False, u'falcon_sense_option': u'--output_multi --min_idt 0.70 --min_cov 1 --max_n_read 20000 --n_core 0', u'falcon_sense_skip_contained': False, u'fc_concurrent_jobs': 8, u'fc_ovlp_to_graph_option': u' --min_len 1', u'genome_size': 5000, u'input_fofn': u'input.fofn', u'input_type': u'raw', u'install_prefix': u'/usr', u'job_queue': u'bash -C ${CMD}', u'job_type': u'string', u'la_concurrent_jobs': 32, u'length_cutoff': -1, u'length_cutoff_pr': 1, u'overlap_filtering_setting': u'--max_diff 10000 --max_cov 100000 --min_cov 1 --min_len 1 --bestn 1000 --n_core 0', u'ovlp_DBsplit_option': u'-a -x5 -s50', u'ovlp_HPCdaligner_option': u'-v -B4 -t50 -h1 -e.99 -l1 -s1000', u'pa_DBdust_option': u'-w128 -t2.5 -m20', u'pa_DBsplit_option': u'-a -x5 -s.065536', u'pa_HPCdaligner_option': u'-v -B4 -t50 -h1 -e.99 -w1 -l1 -s1000', u'pa_dazcon_option': u'-j 4 -x -l 500', u'pda_concurrent_jobs': 32, u'pla_concurrent_jobs': 32, u'pwatcher_directory': u'mypwatcher', u'pwatcher_type': u'blocking', u'seed_coverage': 20.0, u'sge_option': u'-pe smp 8 -q bash -C ${CMD}', u'sge_option_cns': u'-pe smp 8 -q bash -C ${CMD}', u'sge_option_da': u'-pe smp 8 -q bash -C ${CMD}', u'sge_option_fc': u'-pe smp 24 -q bash -C ${CMD}', u'sge_option_la': u'-pe smp 2 -q bash -C ${CMD}', u'sge_option_pda': u'-pe smp 8 -q bash -C ${CMD}', u'sge_option_pla': u'-pe smp 2 -q bash -C ${CMD}', u'skip_checks': False, u'stop_all_jobs_on_failure': True, u'target': u'assembly', u'use_tmpdir': False}, u'db_prefix': u'preads'}, u'python_function': u'falcon_kit.pype_tasks.task_merge_scatter'} 2022-01-06 16:57:03,881 - root - DEBUG - CD: '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/merge-scatter' <- '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/merge-scatter' 2022-01-06 16:57:03,881 - root - DEBUG - Checking existence of u'/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/run_jobs.sh' with timeout=60 2022-01-06 16:57:03,881 - root - DEBUG - Checking existence of u'/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/gathered-las/gathered-las.txt' with timeout=60 2022-01-06 16:57:03,912 - root - DEBUG - CD: '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/merge-scatter' <- '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/merge-scatter' 2022-01-06 16:57:03,914 - root - DEBUG - CD: '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/merge-scatter' -> '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/merge-scatter' 2022-01-06 16:57:03,914 - root - DEBUG - Checking existence of u'scattered.json' with timeout=60 2022-01-06 16:57:03,914 - root - DEBUG - CD: '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/merge-scatter' -> '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/merge-scatter' real 0m0.143s user 0m0.096s sys 0m0.045s touch /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/merge-scatter/run.sh.done + touch /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/merge-scatter/run.sh.done + finish + echo 'finish code: 0' finish code: 0 2022-01-06 16:57:04,056[INFO] recently_satisfied: set([Node(1-preads_ovl/merge-scatter)]) 2022-01-06 16:57:04,056[INFO] Num satisfied in this iteration: 1 2022-01-06 16:57:04,056[INFO] Num still unsatisfied: 0 2022-01-06 16:57:04,065[INFO] Num unsatisfied: 2, graph: 22 2022-01-06 16:57:04,066[INFO] About to submit: Node(1-preads_ovl/m_00001) 2022-01-06 16:57:04,069[INFO] !chmod +x /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/m_00001/run-P05e6b4fec990e1.bash 2022-01-06 16:57:04,080[INFO] sleep 0.1s 2022-01-06 16:57:04,085[INFO] Popen: 'bash -C /build/falcon-LwwdoQ/falcon-1.8.8/inst/pylib/pypeflow-1.0.0-py2.7.egg/pwatcher/mains/job_start.sh' executable=${PYPEFLOW_JOB_START_SCRIPT} + executable=/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/m_00001/run-P05e6b4fec990e1.bash timeout=${PYPEFLOW_JOB_START_TIMEOUT:-60} # wait 60s by default + timeout=60 # Wait up to timeout seconds for the executable to become "executable", # then exec. #timeleft = int(timeout) while [[ ! -x "${executable}" ]]; do if [[ "${timeout}" == "0" ]]; then echo "timed out waiting for (${executable})" exit 77 fi echo "not executable: '${executable}', waiting ${timeout}s" sleep 1 timeout=$((timeout-1)) done + [[ ! -x /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/m_00001/run-P05e6b4fec990e1.bash ]] bash ${executable} + bash /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/m_00001/run-P05e6b4fec990e1.bash + '[' '!' -d /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/m_00001 ']' + cd /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/m_00001 + eval '/bin/bash run.sh' ++ /bin/bash run.sh cd /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/m_00001 + cd /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/m_00001 bash task.sh + bash task.sh 30e18b9a274d CC=gcc CFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong -Wformat -Werror=format-security CPPFLAGS=-Wdate-time -D_FORTIFY_SOURCE=2 CXX=g++ CXXFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong -Wformat -Werror=format-security DEBCONF_NONINTERACTIVE_SEEN=true DEBIAN_FRONTEND=noninteractive DEB_BUILD_ARCH=amd64 DEB_BUILD_ARCH_ABI=base DEB_BUILD_ARCH_BITS=64 DEB_BUILD_ARCH_CPU=amd64 DEB_BUILD_ARCH_ENDIAN=little DEB_BUILD_ARCH_LIBC=gnu DEB_BUILD_ARCH_OS=linux DEB_BUILD_GNU_CPU=x86_64 DEB_BUILD_GNU_SYSTEM=linux-gnu DEB_BUILD_GNU_TYPE=x86_64-linux-gnu DEB_BUILD_MULTIARCH=x86_64-linux-gnu DEB_BUILD_OPTIONS=nocheck parallel=10 DEB_HOST_ARCH=amd64 DEB_HOST_ARCH_ABI=base DEB_HOST_ARCH_BITS=64 DEB_HOST_ARCH_CPU=amd64 DEB_HOST_ARCH_ENDIAN=little DEB_HOST_ARCH_LIBC=gnu DEB_HOST_ARCH_OS=linux DEB_HOST_GNU_CPU=x86_64 DEB_HOST_GNU_SYSTEM=linux-gnu DEB_HOST_GNU_TYPE=x86_64-linux-gnu DEB_HOST_MULTIARCH=x86_64-linux-gnu DEB_TARGET_ARCH=amd64 DEB_TARGET_ARCH_ABI=base DEB_TARGET_ARCH_BITS=64 DEB_TARGET_ARCH_CPU=amd64 DEB_TARGET_ARCH_ENDIAN=little DEB_TARGET_ARCH_LIBC=gnu DEB_TARGET_ARCH_OS=linux DEB_TARGET_GNU_CPU=x86_64 DEB_TARGET_GNU_SYSTEM=linux-gnu DEB_TARGET_GNU_TYPE=x86_64-linux-gnu DEB_TARGET_MULTIARCH=x86_64-linux-gnu DH_INTERNAL_BUILDFLAGS=1 DH_INTERNAL_OPTIONS=-a DH_INTERNAL_OVERRIDE=dh_auto_test FALCON_INSTALL_RULE=install FALCON_PREFIX=/build/falcon-LwwdoQ/falcon-1.8.8/inst FALCON_WORKSPACE=/build/falcon-LwwdoQ/falcon-1.8.8 FCFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong FFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong GCJFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong HOME=/nonexistent LANG=C.UTF-8 LANGUAGE=C.UTF-8 LC_ALL=C.UTF-8 LDFLAGS=-Wl,-z,relro LOGNAME=builduser MAKEFLAGS=w MAKELEVEL=6 MFLAGS=-w MMDEBSTRAP_APT_CONFIG=/tmp/mmdebstrap.SAG5NvxJ_M/tmp/mmdebstrap.apt.conf.TRj0u44dYeZl MMDEBSTRAP_HOOK=customize MMDEBSTRAP_HOOKSOCK=6 MMDEBSTRAP_MODE=root OBJCFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong -Wformat -Werror=format-security OBJCXXFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong -Wformat -Werror=format-security OLDPWD=/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/m_00001 PATH=/build/falcon-LwwdoQ/falcon-1.8.8/inst/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/sbin:/usr/bin:/sbin:/bin PERL_USE_UNSAFE_INC=1 PWD=/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/m_00001 PYPEFLOW_JOB_START_SCRIPT=/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/m_00001/run-P05e6b4fec990e1.bash PYPEFLOW_JOB_START_TIMEOUT=60 PYTHONPATH=/build/falcon-LwwdoQ/falcon-1.8.8/inst/pylib:/build/falcon-LwwdoQ/falcon-1.8.8/inst/pylib: SHELL=/bin/bash SHLVL=5 SOURCE_DATE_EPOCH=1513411047 USER=builduser _=/usr/bin/env /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/m_00001 2022-01-06 16:57:04,181[INFO] sleep 0.2s 2022-01-06 16:57:04,206 - root - DEBUG - Running "/build/falcon-LwwdoQ/falcon-1.8.8/inst/pylib/pypeflow-1.0.0-py2.7.egg/pypeflow/do_task.py /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/m_00001/task.json" 2022-01-06 16:57:04,208 - root - DEBUG - Checking existence of '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/m_00001/task.json' with timeout=60 2022-01-06 16:57:04,208 - root - DEBUG - Loading JSON from '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/m_00001/task.json' 2022-01-06 16:57:04,211 - root - DEBUG - {u'inputs': {u'gathered_las': u'/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/gathered-las/gathered-las.txt', u'scatter_fn': u'/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/merge-scatter/scattered.json'}, u'outputs': {u'job_done': u'm_00001_done', u'merged_las': u'preads.1.las'}, u'parameters': {u'config': {u'LA4Falcon_preload': True, u'avoid_text_file_busy': True, u'cns_concurrent_jobs': 32, u'da_concurrent_jobs': 32, u'dazcon': False, u'default_concurrent_jobs': 8, u'dust': False, u'falcon_sense_greedy': False, u'falcon_sense_option': u'--output_multi --min_idt 0.70 --min_cov 1 --max_n_read 20000 --n_core 0', u'falcon_sense_skip_contained': False, u'fc_concurrent_jobs': 8, u'fc_ovlp_to_graph_option': u' --min_len 1', u'genome_size': 5000, u'input_fofn': u'input.fofn', u'input_type': u'raw', u'install_prefix': u'/usr', u'job_queue': u'bash -C ${CMD}', u'job_type': u'string', u'la_concurrent_jobs': 32, u'length_cutoff': -1, u'length_cutoff_pr': 1, u'overlap_filtering_setting': u'--max_diff 10000 --max_cov 100000 --min_cov 1 --min_len 1 --bestn 1000 --n_core 0', u'ovlp_DBsplit_option': u'-a -x5 -s50', u'ovlp_HPCdaligner_option': u'-v -B4 -t50 -h1 -e.99 -l1 -s1000', u'pa_DBdust_option': u'-w128 -t2.5 -m20', u'pa_DBsplit_option': u'-a -x5 -s.065536', u'pa_HPCdaligner_option': u'-v -B4 -t50 -h1 -e.99 -w1 -l1 -s1000', u'pa_dazcon_option': u'-j 4 -x -l 500', u'pda_concurrent_jobs': 32, u'pla_concurrent_jobs': 32, u'pwatcher_directory': u'mypwatcher', u'pwatcher_type': u'blocking', u'seed_coverage': 20.0, u'sge_option': u'-pe smp 8 -q bash -C ${CMD}', u'sge_option_cns': u'-pe smp 8 -q bash -C ${CMD}', u'sge_option_da': u'-pe smp 8 -q bash -C ${CMD}', u'sge_option_fc': u'-pe smp 24 -q bash -C ${CMD}', u'sge_option_la': u'-pe smp 2 -q bash -C ${CMD}', u'sge_option_pda': u'-pe smp 8 -q bash -C ${CMD}', u'sge_option_pla': u'-pe smp 2 -q bash -C ${CMD}', u'skip_checks': False, u'stop_all_jobs_on_failure': True, u'target': u'assembly', u'use_tmpdir': False}, u'job_id': 1, u'merge_script': u'\n# Get the real path of a link, following all links (since \'readlink -f\' is not on OSX).\n# http://stackoverflow.com/questions/7665/how-to-resolve-symbolic-links-in-a-shell-script/697552\nrealpath() {\n local r=$1; local t=$(readlink $r)\n while [ $t ]; do\n r=$(cd $(dirname $r) && cd $(dirname $t) && pwd -P)/$(basename $t)\n t=$(readlink $r)\n done\n echo $r\n}\nrmfollow() {\n local path=$(realpath $1)\n rm -f "${path}"\n}\n', u'sge_option': u'-pe smp 2 -q bash -C ${CMD}'}, u'python_function': u'falcon_kit.pype_tasks.task_run_las_merge'} 2022-01-06 16:57:04,211 - root - DEBUG - CD: '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/m_00001' <- '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/m_00001' 2022-01-06 16:57:04,211 - root - DEBUG - Checking existence of u'/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/gathered-las/gathered-las.txt' with timeout=60 2022-01-06 16:57:04,211 - root - DEBUG - Checking existence of u'/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/merge-scatter/scattered.json' with timeout=60 2022-01-06 16:57:04,242 - root - DEBUG - CD: '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/m_00001' <- '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/m_00001' 2022-01-06 16:57:04,243 - falcon_kit.pype_tasks - DEBUG - symlink '../job_0000/preads.1.las' <- '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/m_00001/preads.1.las' 2022-01-06 16:57:04,244 - pypeflow.do_support - INFO - !/bin/bash -vex /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/m_00001/rp_00001.sh #!/bin/bash set -vex + set -vex # Get the real path of a link, following all links (since 'readlink -f' is not on OSX). # http://stackoverflow.com/questions/7665/how-to-resolve-symbolic-links-in-a-shell-script/697552 realpath() { local r=$1; local t=$(readlink $r) while [ $t ]; do r=$(cd $(dirname $r) && cd $(dirname $t) && pwd -P)/$(basename $t) t=$(readlink $r) done echo $r } rmfollow() { local path=$(realpath $1) rm -f "${path}" } touch m_00001_done + touch m_00001_done 2022-01-06 16:57:04,253 - root - DEBUG - CD: '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/m_00001' -> '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/m_00001' 2022-01-06 16:57:04,253 - root - DEBUG - Checking existence of u'm_00001_done' with timeout=60 2022-01-06 16:57:04,254 - root - DEBUG - Checking existence of u'preads.1.las' with timeout=60 2022-01-06 16:57:04,254 - root - DEBUG - CD: '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/m_00001' -> '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/m_00001' real 0m0.156s user 0m0.104s sys 0m0.048s touch /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/m_00001/run.sh.done + touch /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/m_00001/run.sh.done + finish + echo 'finish code: 0' finish code: 0 2022-01-06 16:57:04,383[INFO] recently_satisfied: set([Node(1-preads_ovl/m_00001)]) 2022-01-06 16:57:04,383[INFO] Num satisfied in this iteration: 1 2022-01-06 16:57:04,383[INFO] Num still unsatisfied: 1 2022-01-06 16:57:04,383[INFO] About to submit: Node(1-preads_ovl/merge-gather) 2022-01-06 16:57:04,386[INFO] !chmod +x /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/merge-gather/run-P431a2527959108.bash 2022-01-06 16:57:04,396[INFO] sleep 0.1s 2022-01-06 16:57:04,402[INFO] Popen: 'bash -C /build/falcon-LwwdoQ/falcon-1.8.8/inst/pylib/pypeflow-1.0.0-py2.7.egg/pwatcher/mains/job_start.sh' executable=${PYPEFLOW_JOB_START_SCRIPT} + executable=/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/merge-gather/run-P431a2527959108.bash timeout=${PYPEFLOW_JOB_START_TIMEOUT:-60} # wait 60s by default + timeout=60 # Wait up to timeout seconds for the executable to become "executable", # then exec. #timeleft = int(timeout) while [[ ! -x "${executable}" ]]; do if [[ "${timeout}" == "0" ]]; then echo "timed out waiting for (${executable})" exit 77 fi echo "not executable: '${executable}', waiting ${timeout}s" sleep 1 timeout=$((timeout-1)) done + [[ ! -x /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/merge-gather/run-P431a2527959108.bash ]] bash ${executable} + bash /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/merge-gather/run-P431a2527959108.bash + '[' '!' -d /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/merge-gather ']' + cd /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/merge-gather + eval '/bin/bash run.sh' ++ /bin/bash run.sh cd /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/merge-gather + cd /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/merge-gather bash task.sh + bash task.sh 30e18b9a274d CC=gcc CFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong -Wformat -Werror=format-security CPPFLAGS=-Wdate-time -D_FORTIFY_SOURCE=2 CXX=g++ CXXFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong -Wformat -Werror=format-security DEBCONF_NONINTERACTIVE_SEEN=true DEBIAN_FRONTEND=noninteractive DEB_BUILD_ARCH=amd64 DEB_BUILD_ARCH_ABI=base DEB_BUILD_ARCH_BITS=64 DEB_BUILD_ARCH_CPU=amd64 DEB_BUILD_ARCH_ENDIAN=little DEB_BUILD_ARCH_LIBC=gnu DEB_BUILD_ARCH_OS=linux DEB_BUILD_GNU_CPU=x86_64 DEB_BUILD_GNU_SYSTEM=linux-gnu DEB_BUILD_GNU_TYPE=x86_64-linux-gnu DEB_BUILD_MULTIARCH=x86_64-linux-gnu DEB_BUILD_OPTIONS=nocheck parallel=10 DEB_HOST_ARCH=amd64 DEB_HOST_ARCH_ABI=base DEB_HOST_ARCH_BITS=64 DEB_HOST_ARCH_CPU=amd64 DEB_HOST_ARCH_ENDIAN=little DEB_HOST_ARCH_LIBC=gnu DEB_HOST_ARCH_OS=linux DEB_HOST_GNU_CPU=x86_64 DEB_HOST_GNU_SYSTEM=linux-gnu DEB_HOST_GNU_TYPE=x86_64-linux-gnu DEB_HOST_MULTIARCH=x86_64-linux-gnu DEB_TARGET_ARCH=amd64 DEB_TARGET_ARCH_ABI=base DEB_TARGET_ARCH_BITS=64 DEB_TARGET_ARCH_CPU=amd64 DEB_TARGET_ARCH_ENDIAN=little DEB_TARGET_ARCH_LIBC=gnu DEB_TARGET_ARCH_OS=linux DEB_TARGET_GNU_CPU=x86_64 DEB_TARGET_GNU_SYSTEM=linux-gnu DEB_TARGET_GNU_TYPE=x86_64-linux-gnu DEB_TARGET_MULTIARCH=x86_64-linux-gnu DH_INTERNAL_BUILDFLAGS=1 DH_INTERNAL_OPTIONS=-a DH_INTERNAL_OVERRIDE=dh_auto_test FALCON_INSTALL_RULE=install FALCON_PREFIX=/build/falcon-LwwdoQ/falcon-1.8.8/inst FALCON_WORKSPACE=/build/falcon-LwwdoQ/falcon-1.8.8 FCFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong FFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong GCJFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong HOME=/nonexistent LANG=C.UTF-8 LANGUAGE=C.UTF-8 LC_ALL=C.UTF-8 LDFLAGS=-Wl,-z,relro LOGNAME=builduser MAKEFLAGS=w MAKELEVEL=6 MFLAGS=-w MMDEBSTRAP_APT_CONFIG=/tmp/mmdebstrap.SAG5NvxJ_M/tmp/mmdebstrap.apt.conf.TRj0u44dYeZl MMDEBSTRAP_HOOK=customize MMDEBSTRAP_HOOKSOCK=6 MMDEBSTRAP_MODE=root OBJCFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong -Wformat -Werror=format-security OBJCXXFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong -Wformat -Werror=format-security OLDPWD=/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/merge-gather PATH=/build/falcon-LwwdoQ/falcon-1.8.8/inst/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/sbin:/usr/bin:/sbin:/bin PERL_USE_UNSAFE_INC=1 PWD=/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/merge-gather PYPEFLOW_JOB_START_SCRIPT=/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/merge-gather/run-P431a2527959108.bash PYPEFLOW_JOB_START_TIMEOUT=60 PYTHONPATH=/build/falcon-LwwdoQ/falcon-1.8.8/inst/pylib:/build/falcon-LwwdoQ/falcon-1.8.8/inst/pylib: SHELL=/bin/bash SHLVL=5 SOURCE_DATE_EPOCH=1513411047 USER=builduser _=/usr/bin/env /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/merge-gather 2022-01-06 16:57:04,498[INFO] sleep 0.2s 2022-01-06 16:57:04,522 - root - DEBUG - Running "/build/falcon-LwwdoQ/falcon-1.8.8/inst/pylib/pypeflow-1.0.0-py2.7.egg/pypeflow/do_task.py /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/merge-gather/task.json" 2022-01-06 16:57:04,525 - root - DEBUG - Checking existence of '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/merge-gather/task.json' with timeout=60 2022-01-06 16:57:04,525 - root - DEBUG - Loading JSON from '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/merge-gather/task.json' 2022-01-06 16:57:04,525 - root - DEBUG - {u'inputs': {u'1': u'/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/m_00001/preads.1.las'}, u'outputs': {u'las_fofn': u'las.fofn', u'las_fopfn': u'las.fopfn'}, u'parameters': {}, u'python_function': u'falcon_kit.pype_tasks.task_merge_gather'} 2022-01-06 16:57:04,526 - root - DEBUG - CD: '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/merge-gather' <- '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/merge-gather' 2022-01-06 16:57:04,526 - root - DEBUG - Checking existence of u'/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/m_00001/preads.1.las' with timeout=60 2022-01-06 16:57:04,557 - root - DEBUG - CD: '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/merge-gather' <- '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/merge-gather' 2022-01-06 16:57:04,557 - root - DEBUG - CD: '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/merge-gather' -> '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/merge-gather' 2022-01-06 16:57:04,558 - root - DEBUG - Checking existence of u'las.fopfn' with timeout=60 2022-01-06 16:57:04,558 - root - DEBUG - Checking existence of u'las.fofn' with timeout=60 2022-01-06 16:57:04,558 - root - DEBUG - CD: '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/merge-gather' -> '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/merge-gather' real 0m0.145s user 0m0.104s sys 0m0.037s touch /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/merge-gather/run.sh.done + touch /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/merge-gather/run.sh.done + finish + echo 'finish code: 0' finish code: 0 2022-01-06 16:57:04,699[INFO] recently_satisfied: set([Node(1-preads_ovl/merge-gather)]) 2022-01-06 16:57:04,699[INFO] Num satisfied in this iteration: 1 2022-01-06 16:57:04,699[INFO] Num still unsatisfied: 0 2022-01-06 16:57:04,708[INFO] Num unsatisfied: 2, graph: 24 2022-01-06 16:57:04,708[INFO] About to submit: Node(1-preads_ovl/db2falcon) 2022-01-06 16:57:04,711[INFO] !chmod +x /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/db2falcon/run-Pd8c923df5d35cb.bash 2022-01-06 16:57:04,720[INFO] sleep 0.1s 2022-01-06 16:57:04,726[INFO] Popen: 'bash -C /build/falcon-LwwdoQ/falcon-1.8.8/inst/pylib/pypeflow-1.0.0-py2.7.egg/pwatcher/mains/job_start.sh' executable=${PYPEFLOW_JOB_START_SCRIPT} + executable=/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/db2falcon/run-Pd8c923df5d35cb.bash timeout=${PYPEFLOW_JOB_START_TIMEOUT:-60} # wait 60s by default + timeout=60 # Wait up to timeout seconds for the executable to become "executable", # then exec. #timeleft = int(timeout) while [[ ! -x "${executable}" ]]; do if [[ "${timeout}" == "0" ]]; then echo "timed out waiting for (${executable})" exit 77 fi echo "not executable: '${executable}', waiting ${timeout}s" sleep 1 timeout=$((timeout-1)) done + [[ ! -x /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/db2falcon/run-Pd8c923df5d35cb.bash ]] bash ${executable} + bash /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/db2falcon/run-Pd8c923df5d35cb.bash + '[' '!' -d /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/db2falcon ']' + cd /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/db2falcon + eval '/bin/bash run.sh' ++ /bin/bash run.sh cd /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/db2falcon + cd /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/db2falcon bash task.sh + bash task.sh 30e18b9a274d CC=gcc CFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong -Wformat -Werror=format-security CPPFLAGS=-Wdate-time -D_FORTIFY_SOURCE=2 CXX=g++ CXXFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong -Wformat -Werror=format-security DEBCONF_NONINTERACTIVE_SEEN=true DEBIAN_FRONTEND=noninteractive DEB_BUILD_ARCH=amd64 DEB_BUILD_ARCH_ABI=base DEB_BUILD_ARCH_BITS=64 DEB_BUILD_ARCH_CPU=amd64 DEB_BUILD_ARCH_ENDIAN=little DEB_BUILD_ARCH_LIBC=gnu DEB_BUILD_ARCH_OS=linux DEB_BUILD_GNU_CPU=x86_64 DEB_BUILD_GNU_SYSTEM=linux-gnu DEB_BUILD_GNU_TYPE=x86_64-linux-gnu DEB_BUILD_MULTIARCH=x86_64-linux-gnu DEB_BUILD_OPTIONS=nocheck parallel=10 DEB_HOST_ARCH=amd64 DEB_HOST_ARCH_ABI=base DEB_HOST_ARCH_BITS=64 DEB_HOST_ARCH_CPU=amd64 DEB_HOST_ARCH_ENDIAN=little DEB_HOST_ARCH_LIBC=gnu DEB_HOST_ARCH_OS=linux DEB_HOST_GNU_CPU=x86_64 DEB_HOST_GNU_SYSTEM=linux-gnu DEB_HOST_GNU_TYPE=x86_64-linux-gnu DEB_HOST_MULTIARCH=x86_64-linux-gnu DEB_TARGET_ARCH=amd64 DEB_TARGET_ARCH_ABI=base DEB_TARGET_ARCH_BITS=64 DEB_TARGET_ARCH_CPU=amd64 DEB_TARGET_ARCH_ENDIAN=little DEB_TARGET_ARCH_LIBC=gnu DEB_TARGET_ARCH_OS=linux DEB_TARGET_GNU_CPU=x86_64 DEB_TARGET_GNU_SYSTEM=linux-gnu DEB_TARGET_GNU_TYPE=x86_64-linux-gnu DEB_TARGET_MULTIARCH=x86_64-linux-gnu DH_INTERNAL_BUILDFLAGS=1 DH_INTERNAL_OPTIONS=-a DH_INTERNAL_OVERRIDE=dh_auto_test FALCON_INSTALL_RULE=install FALCON_PREFIX=/build/falcon-LwwdoQ/falcon-1.8.8/inst FALCON_WORKSPACE=/build/falcon-LwwdoQ/falcon-1.8.8 FCFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong FFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong GCJFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong HOME=/nonexistent LANG=C.UTF-8 LANGUAGE=C.UTF-8 LC_ALL=C.UTF-8 LDFLAGS=-Wl,-z,relro LOGNAME=builduser MAKEFLAGS=w MAKELEVEL=6 MFLAGS=-w MMDEBSTRAP_APT_CONFIG=/tmp/mmdebstrap.SAG5NvxJ_M/tmp/mmdebstrap.apt.conf.TRj0u44dYeZl MMDEBSTRAP_HOOK=customize MMDEBSTRAP_HOOKSOCK=6 MMDEBSTRAP_MODE=root OBJCFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong -Wformat -Werror=format-security OBJCXXFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong -Wformat -Werror=format-security OLDPWD=/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/db2falcon PATH=/build/falcon-LwwdoQ/falcon-1.8.8/inst/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/sbin:/usr/bin:/sbin:/bin PERL_USE_UNSAFE_INC=1 PWD=/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/db2falcon PYPEFLOW_JOB_START_SCRIPT=/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/db2falcon/run-Pd8c923df5d35cb.bash PYPEFLOW_JOB_START_TIMEOUT=60 PYTHONPATH=/build/falcon-LwwdoQ/falcon-1.8.8/inst/pylib:/build/falcon-LwwdoQ/falcon-1.8.8/inst/pylib: SHELL=/bin/bash SHLVL=5 SOURCE_DATE_EPOCH=1513411047 USER=builduser _=/usr/bin/env /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/db2falcon 2022-01-06 16:57:04,822[INFO] sleep 0.2s 2022-01-06 16:57:04,845 - root - DEBUG - Running "/build/falcon-LwwdoQ/falcon-1.8.8/inst/pylib/pypeflow-1.0.0-py2.7.egg/pypeflow/do_task.py /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/db2falcon/task.json" 2022-01-06 16:57:04,847 - root - DEBUG - Checking existence of '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/db2falcon/task.json' with timeout=60 2022-01-06 16:57:04,847 - root - DEBUG - Loading JSON from '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/db2falcon/task.json' 2022-01-06 16:57:04,850 - root - DEBUG - {u'inputs': {u'las_fofn_plf': u'/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/merge-gather/las.fofn', u'preads_db': u'/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/preads.db'}, u'outputs': {u'db2falcon_done': u'db2falcon_done', u'preads4falcon': u'preads4falcon.fasta'}, u'parameters': {u'config': {u'LA4Falcon_preload': True, u'avoid_text_file_busy': True, u'cns_concurrent_jobs': 32, u'da_concurrent_jobs': 32, u'dazcon': False, u'default_concurrent_jobs': 8, u'dust': False, u'falcon_sense_greedy': False, u'falcon_sense_option': u'--output_multi --min_idt 0.70 --min_cov 1 --max_n_read 20000 --n_core 0', u'falcon_sense_skip_contained': False, u'fc_concurrent_jobs': 8, u'fc_ovlp_to_graph_option': u' --min_len 1', u'genome_size': 5000, u'input_fofn': u'input.fofn', u'input_type': u'raw', u'install_prefix': u'/usr', u'job_queue': u'bash -C ${CMD}', u'job_type': u'string', u'la_concurrent_jobs': 32, u'length_cutoff': -1, u'length_cutoff_pr': 1, u'overlap_filtering_setting': u'--max_diff 10000 --max_cov 100000 --min_cov 1 --min_len 1 --bestn 1000 --n_core 0', u'ovlp_DBsplit_option': u'-a -x5 -s50', u'ovlp_HPCdaligner_option': u'-v -B4 -t50 -h1 -e.99 -l1 -s1000', u'pa_DBdust_option': u'-w128 -t2.5 -m20', u'pa_DBsplit_option': u'-a -x5 -s.065536', u'pa_HPCdaligner_option': u'-v -B4 -t50 -h1 -e.99 -w1 -l1 -s1000', u'pa_dazcon_option': u'-j 4 -x -l 500', u'pda_concurrent_jobs': 32, u'pla_concurrent_jobs': 32, u'pwatcher_directory': u'mypwatcher', u'pwatcher_type': u'blocking', u'seed_coverage': 20.0, u'sge_option': u'-pe smp 8 -q bash -C ${CMD}', u'sge_option_cns': u'-pe smp 8 -q bash -C ${CMD}', u'sge_option_da': u'-pe smp 8 -q bash -C ${CMD}', u'sge_option_fc': u'-pe smp 24 -q bash -C ${CMD}', u'sge_option_la': u'-pe smp 2 -q bash -C ${CMD}', u'sge_option_pda': u'-pe smp 8 -q bash -C ${CMD}', u'sge_option_pla': u'-pe smp 2 -q bash -C ${CMD}', u'skip_checks': False, u'stop_all_jobs_on_failure': True, u'target': u'assembly', u'use_tmpdir': False}, u'sge_option': u'-pe smp 24 -q bash -C ${CMD}', u'wd': u'/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/db2falcon'}, u'python_function': u'falcon_kit.pype_tasks.task_run_db2falcon'} 2022-01-06 16:57:04,850 - root - DEBUG - CD: '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/db2falcon' <- '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/db2falcon' 2022-01-06 16:57:04,850 - root - DEBUG - Checking existence of u'/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/merge-gather/las.fofn' with timeout=60 2022-01-06 16:57:04,850 - root - DEBUG - Checking existence of u'/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/preads.db' with timeout=60 2022-01-06 16:57:04,881 - root - DEBUG - CD: '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/db2falcon' <- '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/db2falcon' 2022-01-06 16:57:04,881 - pypeflow.do_support - INFO - !/bin/bash -vex /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/db2falcon/run_db2falcon.sh #!/bin/bash set -vex + set -vex # Given preads.db, # write preads4falcon.fasta (implicitly) in CWD. time DB2Falcon -U /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/preads.db + DB2Falcon -U /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/preads.db real 0m0.004s user 0m0.003s sys 0m0.000s [ -f preads4falcon.fasta ] || exit 1 + '[' -f preads4falcon.fasta ']' touch db2falcon_done + touch db2falcon_done 2022-01-06 16:57:04,893 - root - DEBUG - CD: '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/db2falcon' -> '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/db2falcon' 2022-01-06 16:57:04,893 - root - DEBUG - Checking existence of u'db2falcon_done' with timeout=60 2022-01-06 16:57:04,893 - root - DEBUG - Checking existence of u'preads4falcon.fasta' with timeout=60 2022-01-06 16:57:04,894 - root - DEBUG - CD: '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/db2falcon' -> '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/db2falcon' real 0m0.158s user 0m0.108s sys 0m0.044s touch /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/db2falcon/run.sh.done + touch /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/db2falcon/run.sh.done + finish + echo 'finish code: 0' finish code: 0 2022-01-06 16:57:05,023[INFO] recently_satisfied: set([Node(1-preads_ovl/db2falcon)]) 2022-01-06 16:57:05,023[INFO] Num satisfied in this iteration: 1 2022-01-06 16:57:05,023[INFO] Num still unsatisfied: 1 2022-01-06 16:57:05,024[INFO] About to submit: Node(2-asm-falcon) 2022-01-06 16:57:05,027[INFO] !chmod +x /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/2-asm-falcon/run-P95dc014ba3bb8e.bash 2022-01-06 16:57:05,035[INFO] sleep 0.1s 2022-01-06 16:57:05,041[INFO] Popen: 'bash -C /build/falcon-LwwdoQ/falcon-1.8.8/inst/pylib/pypeflow-1.0.0-py2.7.egg/pwatcher/mains/job_start.sh' executable=${PYPEFLOW_JOB_START_SCRIPT} + executable=/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/2-asm-falcon/run-P95dc014ba3bb8e.bash timeout=${PYPEFLOW_JOB_START_TIMEOUT:-60} # wait 60s by default + timeout=60 # Wait up to timeout seconds for the executable to become "executable", # then exec. #timeleft = int(timeout) while [[ ! -x "${executable}" ]]; do if [[ "${timeout}" == "0" ]]; then echo "timed out waiting for (${executable})" exit 77 fi echo "not executable: '${executable}', waiting ${timeout}s" sleep 1 timeout=$((timeout-1)) done + [[ ! -x /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/2-asm-falcon/run-P95dc014ba3bb8e.bash ]] bash ${executable} + bash /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/2-asm-falcon/run-P95dc014ba3bb8e.bash + '[' '!' -d /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/2-asm-falcon ']' + cd /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/2-asm-falcon + eval '/bin/bash run.sh' ++ /bin/bash run.sh cd /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/2-asm-falcon + cd /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/2-asm-falcon bash task.sh + bash task.sh 30e18b9a274d CC=gcc CFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong -Wformat -Werror=format-security CPPFLAGS=-Wdate-time -D_FORTIFY_SOURCE=2 CXX=g++ CXXFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong -Wformat -Werror=format-security DEBCONF_NONINTERACTIVE_SEEN=true DEBIAN_FRONTEND=noninteractive DEB_BUILD_ARCH=amd64 DEB_BUILD_ARCH_ABI=base DEB_BUILD_ARCH_BITS=64 DEB_BUILD_ARCH_CPU=amd64 DEB_BUILD_ARCH_ENDIAN=little DEB_BUILD_ARCH_LIBC=gnu DEB_BUILD_ARCH_OS=linux DEB_BUILD_GNU_CPU=x86_64 DEB_BUILD_GNU_SYSTEM=linux-gnu DEB_BUILD_GNU_TYPE=x86_64-linux-gnu DEB_BUILD_MULTIARCH=x86_64-linux-gnu DEB_BUILD_OPTIONS=nocheck parallel=10 DEB_HOST_ARCH=amd64 DEB_HOST_ARCH_ABI=base DEB_HOST_ARCH_BITS=64 DEB_HOST_ARCH_CPU=amd64 DEB_HOST_ARCH_ENDIAN=little DEB_HOST_ARCH_LIBC=gnu DEB_HOST_ARCH_OS=linux DEB_HOST_GNU_CPU=x86_64 DEB_HOST_GNU_SYSTEM=linux-gnu DEB_HOST_GNU_TYPE=x86_64-linux-gnu DEB_HOST_MULTIARCH=x86_64-linux-gnu DEB_TARGET_ARCH=amd64 DEB_TARGET_ARCH_ABI=base DEB_TARGET_ARCH_BITS=64 DEB_TARGET_ARCH_CPU=amd64 DEB_TARGET_ARCH_ENDIAN=little DEB_TARGET_ARCH_LIBC=gnu DEB_TARGET_ARCH_OS=linux DEB_TARGET_GNU_CPU=x86_64 DEB_TARGET_GNU_SYSTEM=linux-gnu DEB_TARGET_GNU_TYPE=x86_64-linux-gnu DEB_TARGET_MULTIARCH=x86_64-linux-gnu DH_INTERNAL_BUILDFLAGS=1 DH_INTERNAL_OPTIONS=-a DH_INTERNAL_OVERRIDE=dh_auto_test FALCON_INSTALL_RULE=install FALCON_PREFIX=/build/falcon-LwwdoQ/falcon-1.8.8/inst FALCON_WORKSPACE=/build/falcon-LwwdoQ/falcon-1.8.8 FCFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong FFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong GCJFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong HOME=/nonexistent LANG=C.UTF-8 LANGUAGE=C.UTF-8 LC_ALL=C.UTF-8 LDFLAGS=-Wl,-z,relro LOGNAME=builduser MAKEFLAGS=w MAKELEVEL=6 MFLAGS=-w MMDEBSTRAP_APT_CONFIG=/tmp/mmdebstrap.SAG5NvxJ_M/tmp/mmdebstrap.apt.conf.TRj0u44dYeZl MMDEBSTRAP_HOOK=customize MMDEBSTRAP_HOOKSOCK=6 MMDEBSTRAP_MODE=root OBJCFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong -Wformat -Werror=format-security OBJCXXFLAGS=-g -O2 -fdebug-prefix-map=/build/falcon-LwwdoQ/falcon-1.8.8=. -fstack-protector-strong -Wformat -Werror=format-security OLDPWD=/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/2-asm-falcon PATH=/build/falcon-LwwdoQ/falcon-1.8.8/inst/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/sbin:/usr/bin:/sbin:/bin PERL_USE_UNSAFE_INC=1 PWD=/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/2-asm-falcon PYPEFLOW_JOB_START_SCRIPT=/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/2-asm-falcon/run-P95dc014ba3bb8e.bash PYPEFLOW_JOB_START_TIMEOUT=60 PYTHONPATH=/build/falcon-LwwdoQ/falcon-1.8.8/inst/pylib:/build/falcon-LwwdoQ/falcon-1.8.8/inst/pylib: SHELL=/bin/bash SHLVL=5 SOURCE_DATE_EPOCH=1513411047 USER=builduser _=/usr/bin/env /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/2-asm-falcon 2022-01-06 16:57:05,137[INFO] sleep 0.2s 2022-01-06 16:57:05,164 - root - DEBUG - Running "/build/falcon-LwwdoQ/falcon-1.8.8/inst/pylib/pypeflow-1.0.0-py2.7.egg/pypeflow/do_task.py /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/2-asm-falcon/task.json" 2022-01-06 16:57:05,166 - root - DEBUG - Checking existence of '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/2-asm-falcon/task.json' with timeout=60 2022-01-06 16:57:05,167 - root - DEBUG - Loading JSON from '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/2-asm-falcon/task.json' 2022-01-06 16:57:05,169 - root - DEBUG - {u'inputs': {u'db2falcon_done': u'/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/db2falcon/db2falcon_done', u'db_file': u'/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/preads.db', u'las_fofn': u'/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/merge-gather/las.fofn', u'preads4falcon': u'/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/db2falcon/preads4falcon.fasta'}, u'outputs': {u'falcon_asm_done': u'falcon_asm_done'}, u'parameters': {u'config': {u'LA4Falcon_preload': True, u'avoid_text_file_busy': True, u'cns_concurrent_jobs': 32, u'da_concurrent_jobs': 32, u'dazcon': False, u'default_concurrent_jobs': 8, u'dust': False, u'falcon_sense_greedy': False, u'falcon_sense_option': u'--output_multi --min_idt 0.70 --min_cov 1 --max_n_read 20000 --n_core 0', u'falcon_sense_skip_contained': False, u'fc_concurrent_jobs': 8, u'fc_ovlp_to_graph_option': u' --min_len 1', u'genome_size': 5000, u'input_fofn': u'input.fofn', u'input_type': u'raw', u'install_prefix': u'/usr', u'job_queue': u'bash -C ${CMD}', u'job_type': u'string', u'la_concurrent_jobs': 32, u'length_cutoff': -1, u'length_cutoff_pr': 1, u'overlap_filtering_setting': u'--max_diff 10000 --max_cov 100000 --min_cov 1 --min_len 1 --bestn 1000 --n_core 0', u'ovlp_DBsplit_option': u'-a -x5 -s50', u'ovlp_HPCdaligner_option': u'-v -B4 -t50 -h1 -e.99 -l1 -s1000', u'pa_DBdust_option': u'-w128 -t2.5 -m20', u'pa_DBsplit_option': u'-a -x5 -s.065536', u'pa_HPCdaligner_option': u'-v -B4 -t50 -h1 -e.99 -w1 -l1 -s1000', u'pa_dazcon_option': u'-j 4 -x -l 500', u'pda_concurrent_jobs': 32, u'pla_concurrent_jobs': 32, u'pwatcher_directory': u'mypwatcher', u'pwatcher_type': u'blocking', u'seed_coverage': 20.0, u'sge_option': u'-pe smp 8 -q bash -C ${CMD}', u'sge_option_cns': u'-pe smp 8 -q bash -C ${CMD}', u'sge_option_da': u'-pe smp 8 -q bash -C ${CMD}', u'sge_option_fc': u'-pe smp 24 -q bash -C ${CMD}', u'sge_option_la': u'-pe smp 2 -q bash -C ${CMD}', u'sge_option_pda': u'-pe smp 8 -q bash -C ${CMD}', u'sge_option_pla': u'-pe smp 2 -q bash -C ${CMD}', u'skip_checks': False, u'stop_all_jobs_on_failure': True, u'target': u'assembly', u'use_tmpdir': False}, u'pread_dir': u'/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl', u'sge_option': u'-pe smp 24 -q bash -C ${CMD}', u'wd': u'/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/2-asm-falcon'}, u'python_function': u'falcon_kit.pype_tasks.task_run_falcon_asm'} 2022-01-06 16:57:05,169 - root - DEBUG - CD: '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/2-asm-falcon' <- '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/2-asm-falcon' 2022-01-06 16:57:05,170 - root - DEBUG - Checking existence of u'/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/preads.db' with timeout=60 2022-01-06 16:57:05,170 - root - DEBUG - Checking existence of u'/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/db2falcon/db2falcon_done' with timeout=60 2022-01-06 16:57:05,170 - root - DEBUG - Checking existence of u'/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/merge-gather/las.fofn' with timeout=60 2022-01-06 16:57:05,170 - root - DEBUG - Checking existence of u'/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/db2falcon/preads4falcon.fasta' with timeout=60 2022-01-06 16:57:05,200 - root - DEBUG - CD: '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/2-asm-falcon' <- '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/2-asm-falcon' 2022-01-06 16:57:05,201 - pypeflow.do_support - INFO - !/bin/bash -vex /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/2-asm-falcon/run_falcon_asm.sh #!/bin/bash set -vex + set -vex # Given, las.fofn, # write preads.ovl: time fc_ovlp_filter --db /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/preads.db --fofn /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/merge-gather/las.fofn --max_diff 10000 --max_cov 100000 --min_cov 1 --min_len 1 --bestn 1000 --n_core 0 --min_len 1 >| preads.ovl + fc_ovlp_filter --db /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/preads.db --fofn /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/merge-gather/las.fofn --max_diff 10000 --max_cov 100000 --min_cov 1 --min_len 1 --bestn 1000 --n_core 0 --min_len 1 2022-01-06 16:57:05,338[INFO] sleep 0.3s [1731859]starting ovlp_filter [1731859]fofn '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/merge-gather/las.fofn': ['/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/m_00001/preads.1.las'] [1731859]preparing filter_stage1 [1731859]maxrss: 18924 [1731859]starting run_filter_stage1('/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/preads.db', '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/m_00001/preads.1.las', 10000, 100000, 1, 1) [1731859]maxrss: 18924 [1731859]maxrss: 19352 [1731859]finished run_filter_stage1('/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/preads.db', '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/m_00001/preads.1.las', 10000, 100000, 1, 1) [1731859]preparing filter_stage2 [1731859]maxrss: 19356 [1731859]starting run_filter_stage2('/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/preads.db', '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/m_00001/preads.1.las', 10000, 100000, 1, 1, set([])) [1731859]maxrss: 19356 [1731859]maxrss: 19360 [1731859]finished run_filter_stage2('/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/preads.db', '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/m_00001/preads.1.las', 10000, 100000, 1, 1, set([])) [1731859]preparing filter_stage3 [1731859]maxrss: 19360 [1731859]starting run_filter_stage3('/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/preads.db', '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/m_00001/preads.1.las', 10000, 100000, 1, 1, set([]), set([]), 1000) [1731859]maxrss: 19360 [1731859]maxrss: 20572 [1731859]finished run_filter_stage3('/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/preads.db', '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/m_00001/preads.1.las', 10000, 100000, 1, 1, set([]), set([]), 1000) [1731859]maxrss: 20572 [1731859]finished ovlp_filter real 0m0.356s user 0m0.291s sys 0m0.062s ln -sf /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/db2falcon/preads4falcon.fasta ./preads4falcon.fasta + ln -sf /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/1-preads_ovl/db2falcon/preads4falcon.fasta ./preads4falcon.fasta # Given preads.ovl, # write sg_edges_list, c_path, utg_data, ctg_paths. time fc_ovlp_to_graph --min_len 1 preads.ovl >| fc_ovlp_to_graph.log + fc_ovlp_to_graph --min_len 1 preads.ovl 2022-01-06 16:57:05,639[INFO] sleep 0.4s real 0m0.290s user 0m0.229s sys 0m0.057s # Given sg_edges_list, utg_data, ctg_paths, preads4falcon.fasta, # write p_ctg.fa and a_ctg_all.fa, # plus a_ctg_base.fa, p_ctg_tiling_path, a_ctg_tiling_path, a_ctg_base_tiling_path: time fc_graph_to_contig + fc_graph_to_contig 2022-01-06 16:57:06,041[INFO] sleep 0.5s real 0m0.390s user 0m0.313s sys 0m0.071s rm -f ./preads4falcon.fasta + rm -f ./preads4falcon.fasta # Given a_ctg_all.fa, write a_ctg.fa: time fc_dedup_a_tigs + fc_dedup_a_tigs real 0m0.176s user 0m0.149s sys 0m0.026s touch falcon_asm_done + touch falcon_asm_done 2022-01-06 16:57:06,427 - root - DEBUG - CD: '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/2-asm-falcon' -> '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/2-asm-falcon' 2022-01-06 16:57:06,427 - root - DEBUG - Checking existence of u'falcon_asm_done' with timeout=60 2022-01-06 16:57:06,427 - root - DEBUG - CD: '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/2-asm-falcon' -> '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/2-asm-falcon' real 0m1.373s user 0m1.088s sys 0m0.261s touch /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/2-asm-falcon/run.sh.done + touch /build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0/2-asm-falcon/run.sh.done + finish + echo 'finish code: 0' finish code: 0 2022-01-06 16:57:06,542[INFO] recently_satisfied: set([Node(2-asm-falcon)]) 2022-01-06 16:57:06,542[INFO] Num satisfied in this iteration: 1 2022-01-06 16:57:06,542[INFO] Num still unsatisfied: 0 make[5]: Leaving directory '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples' /usr/bin/make -C run/synth0 test make[5]: Entering directory '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0' ./check.py shifted by 3269 (rc) make[5]: Leaving directory '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0' python -c 'import pypeflow.pwatcher_workflow; print pypeflow.pwatcher_workflow' python -c 'import falcon_kit; print falcon_kit.falcon' make[4]: Leaving directory '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples' make[3]: Leaving directory '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-make' make[2]: Leaving directory '/build/falcon-LwwdoQ/falcon-1.8.8' /usr/bin/make -C FALCON-examples clean-synth0 make[2]: Entering directory '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples' /usr/bin/make -C run/synth0 clean make[3]: Entering directory '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0' \rm -rf 0-*/ 1-*/ 2-*/ *.log mypwatcher/ make[3]: Leaving directory '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples/run/synth0' make[2]: Leaving directory '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-examples' make[1]: Leaving directory '/build/falcon-LwwdoQ/falcon-1.8.8' fakeroot debian/rules binary-arch dh binary-arch --with python2 dh_testroot -a dh_prep -a dh_auto_install -a make -j1 install DESTDIR=/build/falcon-LwwdoQ/falcon-1.8.8/debian/falcon AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/falcon-LwwdoQ/falcon-1.8.8' make -C ./FALCON-make/ install make[2]: Entering directory '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-make' make -C /build/falcon-LwwdoQ/falcon-1.8.8/DAZZ_DB all make[3]: Entering directory '/build/falcon-LwwdoQ/falcon-1.8.8/DAZZ_DB' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/falcon-LwwdoQ/falcon-1.8.8/DAZZ_DB' PREFIX=/build/falcon-LwwdoQ/falcon-1.8.8/inst make -C /build/falcon-LwwdoQ/falcon-1.8.8/DAZZ_DB install make[3]: Entering directory '/build/falcon-LwwdoQ/falcon-1.8.8/DAZZ_DB' rsync -av fasta2DB DB2fasta DBsplit DBdust Catrack DBshow DBstats DBrm simulator fasta2DAM DAM2fasta DBdump rangen /build/falcon-LwwdoQ/falcon-1.8.8/inst/bin sending incremental file list sent 274 bytes received 12 bytes 572.00 bytes/sec total size is 3,205,928 speedup is 11,209.54 rsync -av libdazzdb.* /build/falcon-LwwdoQ/falcon-1.8.8/inst/lib sending incremental file list sent 50 bytes received 12 bytes 124.00 bytes/sec total size is 359,620 speedup is 5,800.32 rsync -av /build/falcon-LwwdoQ/falcon-1.8.8/DAZZ_DB/DB.h /build/falcon-LwwdoQ/falcon-1.8.8/DAZZ_DB/QV.h /build/falcon-LwwdoQ/falcon-1.8.8/inst/include sending incremental file list sent 46 bytes received 12 bytes 116.00 bytes/sec total size is 25,385 speedup is 437.67 make[3]: Leaving directory '/build/falcon-LwwdoQ/falcon-1.8.8/DAZZ_DB' make -C /build/falcon-LwwdoQ/falcon-1.8.8/DALIGNER all make[3]: Entering directory '/build/falcon-LwwdoQ/falcon-1.8.8/DALIGNER' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/falcon-LwwdoQ/falcon-1.8.8/DALIGNER' PREFIX=/build/falcon-LwwdoQ/falcon-1.8.8/inst make -C /build/falcon-LwwdoQ/falcon-1.8.8/DALIGNER install make[3]: Entering directory '/build/falcon-LwwdoQ/falcon-1.8.8/DALIGNER' rsync -av daligner HPC.daligner LAsort LAmerge LAsplit LAcat LAshow LAdump LAcheck LAindex daligner_p LA4Falcon LA4Ice DB2Falcon /build/falcon-LwwdoQ/falcon-1.8.8/inst/bin sending incremental file list sent 299 bytes received 12 bytes 622.00 bytes/sec total size is 9,999,208 speedup is 32,151.79 make[3]: Leaving directory '/build/falcon-LwwdoQ/falcon-1.8.8/DALIGNER' make -C /build/falcon-LwwdoQ/falcon-1.8.8/DAMASKER all make[3]: Entering directory '/build/falcon-LwwdoQ/falcon-1.8.8/DAMASKER' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/falcon-LwwdoQ/falcon-1.8.8/DAMASKER' PREFIX=/build/falcon-LwwdoQ/falcon-1.8.8/inst make -C /build/falcon-LwwdoQ/falcon-1.8.8/DAMASKER install make[3]: Entering directory '/build/falcon-LwwdoQ/falcon-1.8.8/DAMASKER' rsync -av datander TANmask REPmask HPC.TANmask HPC.REPmask /build/falcon-LwwdoQ/falcon-1.8.8/inst/bin sending incremental file list sent 130 bytes received 12 bytes 284.00 bytes/sec total size is 766,672 speedup is 5,399.10 make[3]: Leaving directory '/build/falcon-LwwdoQ/falcon-1.8.8/DAMASKER' make -C /build/falcon-LwwdoQ/falcon-1.8.8/DEXTRACTOR all make[3]: Entering directory '/build/falcon-LwwdoQ/falcon-1.8.8/DEXTRACTOR' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/falcon-LwwdoQ/falcon-1.8.8/DEXTRACTOR' PREFIX=/build/falcon-LwwdoQ/falcon-1.8.8/inst make -C /build/falcon-LwwdoQ/falcon-1.8.8/DEXTRACTOR install make[3]: Entering directory '/build/falcon-LwwdoQ/falcon-1.8.8/DEXTRACTOR' rsync -av dexta undexta /build/falcon-LwwdoQ/falcon-1.8.8/inst/bin sending incremental file list sent 61 bytes received 12 bytes 146.00 bytes/sec total size is 137,360 speedup is 1,881.64 make[3]: Leaving directory '/build/falcon-LwwdoQ/falcon-1.8.8/DEXTRACTOR' cd /build/falcon-LwwdoQ/falcon-1.8.8/pypeFLOW; python setup.py install --install-lib=/build/falcon-LwwdoQ/falcon-1.8.8/inst/pylib --install-scripts=/build/falcon-LwwdoQ/falcon-1.8.8/inst/bin running install running bdist_egg running egg_info writing requirements to pypeflow.egg-info/requires.txt writing pypeflow.egg-info/PKG-INFO writing top-level names to pypeflow.egg-info/top_level.txt writing dependency_links to pypeflow.egg-info/dependency_links.txt writing entry points to pypeflow.egg-info/entry_points.txt reading manifest file 'pypeflow.egg-info/SOURCES.txt' writing manifest file 'pypeflow.egg-info/SOURCES.txt' installing library code to build/bdist.linux-x86_64/egg running install_lib running build_py creating build/bdist.linux-x86_64/egg creating build/bdist.linux-x86_64/egg/pypeflow copying build/lib.linux-x86_64-2.7/pypeflow/simple_pwatcher_bridge.py -> build/bdist.linux-x86_64/egg/pypeflow copying build/lib.linux-x86_64-2.7/pypeflow/pwatcher_workflow.py -> build/bdist.linux-x86_64/egg/pypeflow copying build/lib.linux-x86_64-2.7/pypeflow/util.py -> build/bdist.linux-x86_64/egg/pypeflow copying build/lib.linux-x86_64-2.7/pypeflow/__init__.py -> build/bdist.linux-x86_64/egg/pypeflow copying build/lib.linux-x86_64-2.7/pypeflow/do_support.py -> build/bdist.linux-x86_64/egg/pypeflow copying build/lib.linux-x86_64-2.7/pypeflow/do_task.py -> build/bdist.linux-x86_64/egg/pypeflow creating build/bdist.linux-x86_64/egg/pwatcher copying build/lib.linux-x86_64-2.7/pwatcher/network_based.py -> build/bdist.linux-x86_64/egg/pwatcher copying build/lib.linux-x86_64-2.7/pwatcher/__init__.py -> build/bdist.linux-x86_64/egg/pwatcher copying build/lib.linux-x86_64-2.7/pwatcher/fs_based.py -> build/bdist.linux-x86_64/egg/pwatcher copying build/lib.linux-x86_64-2.7/pwatcher/blocking.py -> build/bdist.linux-x86_64/egg/pwatcher creating build/bdist.linux-x86_64/egg/pwatcher/mains copying build/lib.linux-x86_64-2.7/pwatcher/mains/query_server.py -> build/bdist.linux-x86_64/egg/pwatcher/mains copying build/lib.linux-x86_64-2.7/pwatcher/mains/fs_heartbeat.py -> build/bdist.linux-x86_64/egg/pwatcher/mains copying build/lib.linux-x86_64-2.7/pwatcher/mains/network_heartbeat.py -> build/bdist.linux-x86_64/egg/pwatcher/mains copying build/lib.linux-x86_64-2.7/pwatcher/mains/__init__.py -> build/bdist.linux-x86_64/egg/pwatcher/mains copying build/lib.linux-x86_64-2.7/pwatcher/mains/pypeflow_example.py -> build/bdist.linux-x86_64/egg/pwatcher/mains copying build/lib.linux-x86_64-2.7/pwatcher/mains/pwatcher.py -> build/bdist.linux-x86_64/egg/pwatcher/mains copying build/lib.linux-x86_64-2.7/pwatcher/mains/job_start.sh -> build/bdist.linux-x86_64/egg/pwatcher/mains byte-compiling build/bdist.linux-x86_64/egg/pypeflow/simple_pwatcher_bridge.py to simple_pwatcher_bridge.pyc byte-compiling build/bdist.linux-x86_64/egg/pypeflow/pwatcher_workflow.py to pwatcher_workflow.pyc byte-compiling build/bdist.linux-x86_64/egg/pypeflow/util.py to util.pyc byte-compiling build/bdist.linux-x86_64/egg/pypeflow/__init__.py to __init__.pyc byte-compiling build/bdist.linux-x86_64/egg/pypeflow/do_support.py to do_support.pyc byte-compiling build/bdist.linux-x86_64/egg/pypeflow/do_task.py to do_task.pyc byte-compiling build/bdist.linux-x86_64/egg/pwatcher/network_based.py to network_based.pyc byte-compiling build/bdist.linux-x86_64/egg/pwatcher/__init__.py to __init__.pyc byte-compiling build/bdist.linux-x86_64/egg/pwatcher/fs_based.py to fs_based.pyc byte-compiling build/bdist.linux-x86_64/egg/pwatcher/blocking.py to blocking.pyc byte-compiling build/bdist.linux-x86_64/egg/pwatcher/mains/query_server.py to query_server.pyc byte-compiling build/bdist.linux-x86_64/egg/pwatcher/mains/fs_heartbeat.py to fs_heartbeat.pyc byte-compiling build/bdist.linux-x86_64/egg/pwatcher/mains/network_heartbeat.py to network_heartbeat.pyc byte-compiling build/bdist.linux-x86_64/egg/pwatcher/mains/__init__.py to __init__.pyc byte-compiling build/bdist.linux-x86_64/egg/pwatcher/mains/pypeflow_example.py to pypeflow_example.pyc byte-compiling build/bdist.linux-x86_64/egg/pwatcher/mains/pwatcher.py to pwatcher.pyc creating build/bdist.linux-x86_64/egg/EGG-INFO copying pypeflow.egg-info/PKG-INFO -> build/bdist.linux-x86_64/egg/EGG-INFO copying pypeflow.egg-info/SOURCES.txt -> build/bdist.linux-x86_64/egg/EGG-INFO copying pypeflow.egg-info/dependency_links.txt -> build/bdist.linux-x86_64/egg/EGG-INFO copying pypeflow.egg-info/entry_points.txt -> build/bdist.linux-x86_64/egg/EGG-INFO copying pypeflow.egg-info/not-zip-safe -> build/bdist.linux-x86_64/egg/EGG-INFO copying pypeflow.egg-info/requires.txt -> build/bdist.linux-x86_64/egg/EGG-INFO copying pypeflow.egg-info/top_level.txt -> build/bdist.linux-x86_64/egg/EGG-INFO creating 'dist/pypeflow-1.0.0-py2.7.egg' and adding 'build/bdist.linux-x86_64/egg' to it removing 'build/bdist.linux-x86_64/egg' (and everything under it) Processing pypeflow-1.0.0-py2.7.egg removing '/build/falcon-LwwdoQ/falcon-1.8.8/inst/pylib/pypeflow-1.0.0-py2.7.egg' (and everything under it) creating /build/falcon-LwwdoQ/falcon-1.8.8/inst/pylib/pypeflow-1.0.0-py2.7.egg Extracting pypeflow-1.0.0-py2.7.egg to /build/falcon-LwwdoQ/falcon-1.8.8/inst/pylib pypeflow 1.0.0 is already the active version in easy-install.pth Installing pwatcher-pypeflow-example script to /build/falcon-LwwdoQ/falcon-1.8.8/inst/bin Installing heartbeat-wrapper script to /build/falcon-LwwdoQ/falcon-1.8.8/inst/bin Installing pwatcher-main script to /build/falcon-LwwdoQ/falcon-1.8.8/inst/bin Installed /build/falcon-LwwdoQ/falcon-1.8.8/inst/pylib/pypeflow-1.0.0-py2.7.egg Processing dependencies for pypeflow==1.0.0 Searching for networkx==1.11 Best match: networkx 1.11 Adding networkx 1.11 to easy-install.pth file Using /usr/lib/python2.7/dist-packages Finished processing dependencies for pypeflow==1.0.0 cd /build/falcon-LwwdoQ/falcon-1.8.8/FALCON; python setup.py install --install-lib=/build/falcon-LwwdoQ/falcon-1.8.8/inst/pylib --install-scripts=/build/falcon-LwwdoQ/falcon-1.8.8/inst/bin /bin/sh: 1: git: not found running install running bdist_egg running egg_info writing requirements to falcon_kit.egg-info/requires.txt writing falcon_kit.egg-info/PKG-INFO writing top-level names to falcon_kit.egg-info/top_level.txt writing dependency_links to falcon_kit.egg-info/dependency_links.txt writing entry points to falcon_kit.egg-info/entry_points.txt reading manifest file 'falcon_kit.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' writing manifest file 'falcon_kit.egg-info/SOURCES.txt' installing library code to build/bdist.linux-x86_64/egg running install_lib running build_py running build_ext creating build/bdist.linux-x86_64/egg creating build/bdist.linux-x86_64/egg/falcon_kit copying build/lib.linux-x86_64-2.7/falcon_kit/multiproc.py -> build/bdist.linux-x86_64/egg/falcon_kit copying build/lib.linux-x86_64-2.7/falcon_kit/stats_preassembly.py -> build/bdist.linux-x86_64/egg/falcon_kit copying build/lib.linux-x86_64-2.7/falcon_kit/pype_tasks.py -> build/bdist.linux-x86_64/egg/falcon_kit copying build/lib.linux-x86_64-2.7/falcon_kit/__init__.py -> build/bdist.linux-x86_64/egg/falcon_kit copying build/lib.linux-x86_64-2.7/falcon_kit/FastaReader.py -> build/bdist.linux-x86_64/egg/falcon_kit copying build/lib.linux-x86_64-2.7/falcon_kit/bash.py -> build/bdist.linux-x86_64/egg/falcon_kit copying build/lib.linux-x86_64-2.7/falcon_kit/functional.py -> build/bdist.linux-x86_64/egg/falcon_kit copying build/lib.linux-x86_64-2.7/falcon_kit/run_support.py -> build/bdist.linux-x86_64/egg/falcon_kit copying build/lib.linux-x86_64-2.7/falcon_kit/falcon_kit.py -> build/bdist.linux-x86_64/egg/falcon_kit copying build/lib.linux-x86_64-2.7/falcon_kit/fc_asm_graph.py -> build/bdist.linux-x86_64/egg/falcon_kit creating build/bdist.linux-x86_64/egg/falcon_kit/mains copying build/lib.linux-x86_64-2.7/falcon_kit/mains/ovlp_filter.py -> build/bdist.linux-x86_64/egg/falcon_kit/mains copying build/lib.linux-x86_64-2.7/falcon_kit/mains/actg_coordinate.py -> build/bdist.linux-x86_64/egg/falcon_kit/mains copying build/lib.linux-x86_64-2.7/falcon_kit/mains/ovlp_to_graph.py -> build/bdist.linux-x86_64/egg/falcon_kit/mains copying build/lib.linux-x86_64-2.7/falcon_kit/mains/ctg_link_analysis.py -> build/bdist.linux-x86_64/egg/falcon_kit/mains copying build/lib.linux-x86_64-2.7/falcon_kit/mains/rr_ctg_track.py -> build/bdist.linux-x86_64/egg/falcon_kit/mains copying build/lib.linux-x86_64-2.7/falcon_kit/mains/tasks.py -> build/bdist.linux-x86_64/egg/falcon_kit/mains copying build/lib.linux-x86_64-2.7/falcon_kit/mains/run1.py -> build/bdist.linux-x86_64/egg/falcon_kit/mains copying build/lib.linux-x86_64-2.7/falcon_kit/mains/graph_to_utgs.py -> build/bdist.linux-x86_64/egg/falcon_kit/mains copying build/lib.linux-x86_64-2.7/falcon_kit/mains/dedup_a_tigs.py -> build/bdist.linux-x86_64/egg/falcon_kit/mains copying build/lib.linux-x86_64-2.7/falcon_kit/mains/fasta2fasta.py -> build/bdist.linux-x86_64/egg/falcon_kit/mains copying build/lib.linux-x86_64-2.7/falcon_kit/mains/contig_annotate.py -> build/bdist.linux-x86_64/egg/falcon_kit/mains copying build/lib.linux-x86_64-2.7/falcon_kit/mains/pr_ctg_track.py -> build/bdist.linux-x86_64/egg/falcon_kit/mains copying build/lib.linux-x86_64-2.7/falcon_kit/mains/fetch_reads.py -> build/bdist.linux-x86_64/egg/falcon_kit/mains copying build/lib.linux-x86_64-2.7/falcon_kit/mains/calc_cutoff.py -> build/bdist.linux-x86_64/egg/falcon_kit/mains copying build/lib.linux-x86_64-2.7/falcon_kit/mains/LAmerge.py -> build/bdist.linux-x86_64/egg/falcon_kit/mains copying build/lib.linux-x86_64-2.7/falcon_kit/mains/__init__.py -> build/bdist.linux-x86_64/egg/falcon_kit/mains copying build/lib.linux-x86_64-2.7/falcon_kit/mains/ovlp_stats.py -> build/bdist.linux-x86_64/egg/falcon_kit/mains copying build/lib.linux-x86_64-2.7/falcon_kit/mains/graph_to_contig.py -> build/bdist.linux-x86_64/egg/falcon_kit/mains copying build/lib.linux-x86_64-2.7/falcon_kit/mains/report_pre_assembly.py -> build/bdist.linux-x86_64/egg/falcon_kit/mains copying build/lib.linux-x86_64-2.7/falcon_kit/mains/get_read_ctg_map.py -> build/bdist.linux-x86_64/egg/falcon_kit/mains copying build/lib.linux-x86_64-2.7/falcon_kit/mains/LAsort.py -> build/bdist.linux-x86_64/egg/falcon_kit/mains copying build/lib.linux-x86_64-2.7/falcon_kit/mains/consensus.py -> build/bdist.linux-x86_64/egg/falcon_kit/mains creating build/bdist.linux-x86_64/egg/falcon_kit/util copying build/lib.linux-x86_64-2.7/falcon_kit/util/system.py -> build/bdist.linux-x86_64/egg/falcon_kit/util copying build/lib.linux-x86_64-2.7/falcon_kit/util/__init__.py -> build/bdist.linux-x86_64/egg/falcon_kit/util copying build/lib.linux-x86_64-2.7/falcon_kit/util/io.py -> build/bdist.linux-x86_64/egg/falcon_kit/util copying build/lib.linux-x86_64-2.7/ext_falcon.so -> build/bdist.linux-x86_64/egg byte-compiling build/bdist.linux-x86_64/egg/falcon_kit/multiproc.py to multiproc.pyc byte-compiling build/bdist.linux-x86_64/egg/falcon_kit/stats_preassembly.py to stats_preassembly.pyc byte-compiling build/bdist.linux-x86_64/egg/falcon_kit/pype_tasks.py to pype_tasks.pyc byte-compiling build/bdist.linux-x86_64/egg/falcon_kit/__init__.py to __init__.pyc byte-compiling build/bdist.linux-x86_64/egg/falcon_kit/FastaReader.py to FastaReader.pyc byte-compiling build/bdist.linux-x86_64/egg/falcon_kit/bash.py to bash.pyc byte-compiling build/bdist.linux-x86_64/egg/falcon_kit/functional.py to functional.pyc byte-compiling build/bdist.linux-x86_64/egg/falcon_kit/run_support.py to run_support.pyc byte-compiling build/bdist.linux-x86_64/egg/falcon_kit/falcon_kit.py to falcon_kit.pyc byte-compiling build/bdist.linux-x86_64/egg/falcon_kit/fc_asm_graph.py to fc_asm_graph.pyc byte-compiling build/bdist.linux-x86_64/egg/falcon_kit/mains/ovlp_filter.py to ovlp_filter.pyc byte-compiling build/bdist.linux-x86_64/egg/falcon_kit/mains/actg_coordinate.py to actg_coordinate.pyc byte-compiling build/bdist.linux-x86_64/egg/falcon_kit/mains/ovlp_to_graph.py to ovlp_to_graph.pyc byte-compiling build/bdist.linux-x86_64/egg/falcon_kit/mains/ctg_link_analysis.py to ctg_link_analysis.pyc byte-compiling build/bdist.linux-x86_64/egg/falcon_kit/mains/rr_ctg_track.py to rr_ctg_track.pyc byte-compiling build/bdist.linux-x86_64/egg/falcon_kit/mains/tasks.py to tasks.pyc byte-compiling build/bdist.linux-x86_64/egg/falcon_kit/mains/run1.py to run1.pyc byte-compiling build/bdist.linux-x86_64/egg/falcon_kit/mains/graph_to_utgs.py to graph_to_utgs.pyc byte-compiling build/bdist.linux-x86_64/egg/falcon_kit/mains/dedup_a_tigs.py to dedup_a_tigs.pyc byte-compiling build/bdist.linux-x86_64/egg/falcon_kit/mains/fasta2fasta.py to fasta2fasta.pyc byte-compiling build/bdist.linux-x86_64/egg/falcon_kit/mains/contig_annotate.py to contig_annotate.pyc byte-compiling build/bdist.linux-x86_64/egg/falcon_kit/mains/pr_ctg_track.py to pr_ctg_track.pyc byte-compiling build/bdist.linux-x86_64/egg/falcon_kit/mains/fetch_reads.py to fetch_reads.pyc byte-compiling build/bdist.linux-x86_64/egg/falcon_kit/mains/calc_cutoff.py to calc_cutoff.pyc byte-compiling build/bdist.linux-x86_64/egg/falcon_kit/mains/LAmerge.py to LAmerge.pyc byte-compiling build/bdist.linux-x86_64/egg/falcon_kit/mains/__init__.py to __init__.pyc byte-compiling build/bdist.linux-x86_64/egg/falcon_kit/mains/ovlp_stats.py to ovlp_stats.pyc byte-compiling build/bdist.linux-x86_64/egg/falcon_kit/mains/graph_to_contig.py to graph_to_contig.pyc byte-compiling build/bdist.linux-x86_64/egg/falcon_kit/mains/report_pre_assembly.py to report_pre_assembly.pyc byte-compiling build/bdist.linux-x86_64/egg/falcon_kit/mains/get_read_ctg_map.py to get_read_ctg_map.pyc byte-compiling build/bdist.linux-x86_64/egg/falcon_kit/mains/LAsort.py to LAsort.pyc byte-compiling build/bdist.linux-x86_64/egg/falcon_kit/mains/consensus.py to consensus.pyc byte-compiling build/bdist.linux-x86_64/egg/falcon_kit/util/system.py to system.pyc byte-compiling build/bdist.linux-x86_64/egg/falcon_kit/util/__init__.py to __init__.pyc byte-compiling build/bdist.linux-x86_64/egg/falcon_kit/util/io.py to io.pyc creating stub loader for ext_falcon.so byte-compiling build/bdist.linux-x86_64/egg/ext_falcon.py to ext_falcon.pyc creating build/bdist.linux-x86_64/egg/EGG-INFO installing scripts to build/bdist.linux-x86_64/egg/EGG-INFO/scripts running install_scripts running build_scripts creating build/bdist.linux-x86_64/egg/EGG-INFO/scripts copying build/scripts-2.7/fc_graph_to_utgs.py -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts copying build/scripts-2.7/fc_graph_to_contig.py -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts copying build/scripts-2.7/fc_ctg_link_analysis.py -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts copying build/scripts-2.7/fc_consensus.py -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts copying build/scripts-2.7/fc_contig_annotate.py -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts copying build/scripts-2.7/fc_ovlp_stats.py -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts copying build/scripts-2.7/fc_dedup_a_tigs.py -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts copying build/scripts-2.7/fc_ovlp_to_graph.py -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts copying build/scripts-2.7/fc_run.py -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts copying build/scripts-2.7/fc_actg_coordinate.py -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts copying build/scripts-2.7/fc_ovlp_filter.py -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/fc_graph_to_utgs.py to 755 changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/fc_graph_to_contig.py to 755 changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/fc_ctg_link_analysis.py to 755 changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/fc_consensus.py to 755 changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/fc_contig_annotate.py to 755 changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/fc_ovlp_stats.py to 755 changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/fc_dedup_a_tigs.py to 755 changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/fc_ovlp_to_graph.py to 755 changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/fc_run.py to 755 changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/fc_actg_coordinate.py to 755 changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/fc_ovlp_filter.py to 755 copying falcon_kit.egg-info/PKG-INFO -> build/bdist.linux-x86_64/egg/EGG-INFO copying falcon_kit.egg-info/SOURCES.txt -> build/bdist.linux-x86_64/egg/EGG-INFO copying falcon_kit.egg-info/dependency_links.txt -> build/bdist.linux-x86_64/egg/EGG-INFO copying falcon_kit.egg-info/entry_points.txt -> build/bdist.linux-x86_64/egg/EGG-INFO copying falcon_kit.egg-info/not-zip-safe -> build/bdist.linux-x86_64/egg/EGG-INFO copying falcon_kit.egg-info/requires.txt -> build/bdist.linux-x86_64/egg/EGG-INFO copying falcon_kit.egg-info/top_level.txt -> build/bdist.linux-x86_64/egg/EGG-INFO writing build/bdist.linux-x86_64/egg/EGG-INFO/native_libs.txt creating 'dist/falcon_kit-0.7-py2.7-linux-x86_64.egg' and adding 'build/bdist.linux-x86_64/egg' to it removing 'build/bdist.linux-x86_64/egg' (and everything under it) Processing falcon_kit-0.7-py2.7-linux-x86_64.egg removing '/build/falcon-LwwdoQ/falcon-1.8.8/inst/pylib/falcon_kit-0.7-py2.7-linux-x86_64.egg' (and everything under it) creating /build/falcon-LwwdoQ/falcon-1.8.8/inst/pylib/falcon_kit-0.7-py2.7-linux-x86_64.egg Extracting falcon_kit-0.7-py2.7-linux-x86_64.egg to /build/falcon-LwwdoQ/falcon-1.8.8/inst/pylib falcon-kit 0.7 is already the active version in easy-install.pth Installing fc_actg_coordinate.py script to /build/falcon-LwwdoQ/falcon-1.8.8/inst/bin Installing fc_consensus.py script to /build/falcon-LwwdoQ/falcon-1.8.8/inst/bin Installing fc_contig_annotate.py script to /build/falcon-LwwdoQ/falcon-1.8.8/inst/bin Installing fc_ctg_link_analysis.py script to /build/falcon-LwwdoQ/falcon-1.8.8/inst/bin Installing fc_dedup_a_tigs.py script to /build/falcon-LwwdoQ/falcon-1.8.8/inst/bin Installing fc_graph_to_contig.py script to /build/falcon-LwwdoQ/falcon-1.8.8/inst/bin Installing fc_graph_to_utgs.py script to /build/falcon-LwwdoQ/falcon-1.8.8/inst/bin Installing fc_ovlp_filter.py script to /build/falcon-LwwdoQ/falcon-1.8.8/inst/bin Installing fc_ovlp_stats.py script to /build/falcon-LwwdoQ/falcon-1.8.8/inst/bin Installing fc_ovlp_to_graph.py script to /build/falcon-LwwdoQ/falcon-1.8.8/inst/bin Installing fc_run.py script to /build/falcon-LwwdoQ/falcon-1.8.8/inst/bin Installing fc_fetch_reads script to /build/falcon-LwwdoQ/falcon-1.8.8/inst/bin Installing fc_pr_ctg_track script to /build/falcon-LwwdoQ/falcon-1.8.8/inst/bin Installing fc_actg_coordinate script to /build/falcon-LwwdoQ/falcon-1.8.8/inst/bin Installing fc_fasta2fasta script to /build/falcon-LwwdoQ/falcon-1.8.8/inst/bin Installing fc_ctg_link_analysis script to /build/falcon-LwwdoQ/falcon-1.8.8/inst/bin Installing fc_ovlp_to_graph script to /build/falcon-LwwdoQ/falcon-1.8.8/inst/bin Installing fc_ovlp_filter script to /build/falcon-LwwdoQ/falcon-1.8.8/inst/bin Installing fc_get_read_ctg_map script to /build/falcon-LwwdoQ/falcon-1.8.8/inst/bin Installing fc_run script to /build/falcon-LwwdoQ/falcon-1.8.8/inst/bin Installing fc_contig_annotate script to /build/falcon-LwwdoQ/falcon-1.8.8/inst/bin Installing fc_graph_to_utgs script to /build/falcon-LwwdoQ/falcon-1.8.8/inst/bin Installing fc_run1 script to /build/falcon-LwwdoQ/falcon-1.8.8/inst/bin Installing fc_ovlp_stats script to /build/falcon-LwwdoQ/falcon-1.8.8/inst/bin Installing fc_consensus script to /build/falcon-LwwdoQ/falcon-1.8.8/inst/bin Installing fc_rr_ctg_track script to /build/falcon-LwwdoQ/falcon-1.8.8/inst/bin Installing fc_calc_cutoff script to /build/falcon-LwwdoQ/falcon-1.8.8/inst/bin Installing falcon-task script to /build/falcon-LwwdoQ/falcon-1.8.8/inst/bin Installing fc_graph_to_contig script to /build/falcon-LwwdoQ/falcon-1.8.8/inst/bin Installing fc_dedup_a_tigs script to /build/falcon-LwwdoQ/falcon-1.8.8/inst/bin Installed /build/falcon-LwwdoQ/falcon-1.8.8/inst/pylib/falcon_kit-0.7-py2.7-linux-x86_64.egg Processing dependencies for falcon-kit==0.7 Searching for networkx==1.11 Best match: networkx 1.11 Adding networkx 1.11 to easy-install.pth file Using /usr/lib/python2.7/dist-packages Finished processing dependencies for falcon-kit==0.7 make[2]: Leaving directory '/build/falcon-LwwdoQ/falcon-1.8.8/FALCON-make' make[1]: Leaving directory '/build/falcon-LwwdoQ/falcon-1.8.8' debian/rules override_dh_install make[1]: Entering directory '/build/falcon-LwwdoQ/falcon-1.8.8' dh_install -XLICENSE make[1]: Leaving directory '/build/falcon-LwwdoQ/falcon-1.8.8' dh_installdocs -a dh_installchangelogs -a dh_installexamples -a dh_installman -a dh_python2 -a dh_lintian -a dh_perl -a dh_link -a dh_strip_nondeterminism -a dh_compress -a dh_fixperms -a dh_missing -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb -a dh_gencontrol -a dh_md5sums -a dh_builddeb -a dpkg-deb: building package 'falcon' in '../falcon_1.8.8-1_amd64.deb'. dpkg-deb: building package 'falcon-dbgsym' in '../falcon-dbgsym_1.8.8-1_amd64.deb'. dpkg-genbuildinfo --build=any dpkg-genchanges --build=any >../falcon_1.8.8-1_amd64.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build falcon-1.8.8 dpkg-buildpackage: info: binary-only upload (no source included) I: running special hook: sync-out /build/falcon-LwwdoQ /tmp/falcon-1.8.8-12256qcfx I: cleaning package lists and apt cache... W: deleting files in /tmp: pytest-of-builduser I: creating tarball... I: done I: removing tempdir /tmp/mmdebstrap.SAG5NvxJ_M... I: success in 1781.2442 seconds md5: falcon-dbgsym_1.8.8-1_amd64.deb: OK md5: falcon_1.8.8-1_amd64.deb: OK sha1: falcon-dbgsym_1.8.8-1_amd64.deb: OK sha1: falcon_1.8.8-1_amd64.deb: OK sha256: falcon-dbgsym_1.8.8-1_amd64.deb: OK sha256: falcon_1.8.8-1_amd64.deb: OK Checksums: OK