Hello Ward,
I attached two logs, one with the sanity_check_paths in the config file
(sanity_on) and one without (sanity_off, causing the lib/lib64 error).
Thanks,
Oliver
________________________________________
From: [email protected] [[email protected]] on
behalf of Ward Poelmans [[email protected]]
Sent: Monday, August 10, 2015 4:45 PM
To: [email protected]
Subject: Re: [easybuild] Tarball Easyblock sanity_check fails
On Mon, Aug 10, 2015 at 4:39 PM, Stolpe, Oliver
<[email protected]> wrote:
> When I comment out the sanity_check part, then it complains that lib and
> lib64 are missing, but I there is nothing to check for easybuild and I
> didn't request them?
>
> Sanity check failed: no dir of ('lib', 'lib64')
Dear Oliver,
That's odd indeed. Can you show us the debug log?
Ward
== 2015-08-10 14:54:45,758 main.Tarball INFO This is EasyBuild 2.2.0 (framework: 2.2.0, easyblocks: 2.2.0) on host a4a19bc0d117.
== 2015-08-10 14:54:45,758 main.Tarball INFO This is easyblock Tarball from module easybuild.easyblocks.generic.tarball (/vol/fs01/tools/ubuntu14.04/easybuild/software/EasyBuild/2.2.0/lib/python2.7/site-packages/easybuild_easyblocks-2.2.0-py2.7.egg/easybuild/easyblocks/generic/tarball.pyc)
== 2015-08-10 14:54:45,759 main.Tarball INFO Build dir set to /vol/fs01/tools/ubuntu14.04/easybuild/build/svtyper/v0.0.2/dummy-dummy-Python-2.7.9
== 2015-08-10 14:54:45,759 main.Tarball INFO Install dir set to /vol/fs01/tools/ubuntu14.04/easybuild/software/svtyper/v0.0.2-Python-2.7.9
== 2015-08-10 14:54:45,759 main.Tarball INFO Init completed for application name svtyper version v0.0.2
== 2015-08-10 14:54:45,759 main.easyblock INFO Obtained application instance of for svtyper (easyblock: Tarball)
== 2015-08-10 14:54:45,759 main.Tarball INFO building and installing svtyper/v0.0.2-Python-2.7.9...
== 2015-08-10 14:54:45,759 main.Tarball INFO fetching files...
== 2015-08-10 14:54:45,760 main.Tarball INFO Starting fetch step
== 2015-08-10 14:54:45,761 main.Tarball INFO Running method fetch_step part of step fetch
== 2015-08-10 14:54:45,761 main.Tarball WARNING Easyconfig does not specify an EasyBuild-version (key 'easybuild_version')! Assuming the latest version
== 2015-08-10 14:54:45,761 main.filetools INFO Command eb found at /vol/fs01/tools/ubuntu14.04/easybuild/software/EasyBuild/2.2.0/bin/eb
== 2015-08-10 14:54:45,762 main.Tarball INFO Found file v0.0.2.tar.gz at /vol/fs01/tools/ubuntu14.04/easybuild/sources/s/svtyper/v0.0.2.tar.gz
== 2015-08-10 14:54:45,762 main.Tarball INFO Added sources: [{'path': '/vol/fs01/tools/ubuntu14.04/easybuild/sources/s/svtyper/v0.0.2.tar.gz', 'cmd': None, 'finalpath': '/vol/fs01/tools/ubuntu14.04/easybuild/build/svtyper/v0.0.2/dummy-dummy-Python-2.7.9', 'name': 'v0.0.2.tar.gz', 'checksum': None}]
== 2015-08-10 14:54:45,762 main.Tarball INFO no patches provided
== 2015-08-10 14:54:45,762 main.Tarball INFO md5 checksum for /vol/fs01/tools/ubuntu14.04/easybuild/sources/s/svtyper/v0.0.2.tar.gz: c799a67f0e8b00ee461708b18892ab06
== 2015-08-10 14:54:45,796 main.Tarball INFO Setting parallelism: 8
== 2015-08-10 14:54:45,796 main.Tarball INFO Checking dirs that need to be created: ['/vol/fs01/tools/ubuntu14.04/easybuild/software/svtyper', '/vol/fs01/tools/ubuntu14.04/easybuild/modules/all/svtyper', '/vol/fs01/tools/ubuntu14.04/easybuild/modules/bio/svtyper']
== 2015-08-10 14:54:45,796 main.Tarball INFO creating build dir, resetting environment...
== 2015-08-10 14:54:45,797 main.Tarball INFO Starting ready step
== 2015-08-10 14:54:45,798 main.Tarball INFO Running method check_readiness_step part of step ready
== 2015-08-10 14:54:45,802 main.Tarball WARNING Loaded modules detected: ['EasyBuild/2.2.0']
== 2015-08-10 14:54:45,824 main.Tarball INFO Running method make_builddir part of step ready
== 2015-08-10 14:54:45,824 main.Tarball INFO Found old directory /vol/fs01/tools/ubuntu14.04/easybuild/build/svtyper/v0.0.2/dummy-dummy-Python-2.7.9
== 2015-08-10 14:54:45,825 main.filetools INFO Path /vol/fs01/tools/ubuntu14.04/easybuild/build/svtyper/v0.0.2/dummy-dummy-Python-2.7.9 successfully removed.
== 2015-08-10 14:54:45,825 main.Tarball INFO Removed old directory /vol/fs01/tools/ubuntu14.04/easybuild/build/svtyper/v0.0.2/dummy-dummy-Python-2.7.9
== 2015-08-10 14:54:45,825 main.filetools INFO Creating directory /vol/fs01/tools/ubuntu14.04/easybuild/build/svtyper/v0.0.2/dummy-dummy-Python-2.7.9 (parents: True, set_gid: False, sticky: False)
== 2015-08-10 14:54:45,826 main.Tarball INFO Running method env_reset_changes part of step ready
== 2015-08-10 14:54:45,826 main.Tarball INFO Running method handle_iterate_opts part of step ready
== 2015-08-10 14:54:45,826 main.Tarball INFO unpacking...
== 2015-08-10 14:54:45,826 main.Tarball INFO Starting source step
== 2015-08-10 14:54:45,828 main.Tarball INFO Running method checksum_step part of step source
== 2015-08-10 14:54:45,828 main.Tarball INFO Checksum verification for /vol/fs01/tools/ubuntu14.04/easybuild/sources/s/svtyper/v0.0.2.tar.gz using None passed.
== 2015-08-10 14:54:45,828 main.Tarball INFO Running method extract_step part of step source
== 2015-08-10 14:54:45,828 main.Tarball INFO Unpacking source v0.0.2.tar.gz
== 2015-08-10 14:54:45,866 main.Tarball INFO patching...
== 2015-08-10 14:54:45,866 main.Tarball INFO Starting patch step
== 2015-08-10 14:54:45,867 main.Tarball INFO Running method patch_step part of step patch
== 2015-08-10 14:54:45,868 main.Tarball INFO preparing...
== 2015-08-10 14:54:45,868 main.Tarball INFO Starting prepare step
== 2015-08-10 14:54:45,869 main.Tarball INFO Running method prepare_step part of step prepare
== 2015-08-10 14:54:45,869 main.Dummy INFO prepare: toolchain dummy mode, dummy version; not loading dependencies
== 2015-08-10 14:54:45,869 main.Tarball INFO configuring...
== 2015-08-10 14:54:45,869 main.Tarball INFO Starting configure step
== 2015-08-10 14:54:45,870 main.Tarball INFO Running method configure_step part of step configure
== 2015-08-10 14:54:45,870 main.Tarball INFO building...
== 2015-08-10 14:54:45,871 main.Tarball INFO Starting build step
== 2015-08-10 14:54:45,872 main.Tarball INFO Running method build_step part of step build
== 2015-08-10 14:54:45,872 main.Tarball INFO testing...
== 2015-08-10 14:54:45,872 main.Tarball INFO Starting test step
== 2015-08-10 14:54:45,873 main.Tarball INFO Running method test_step part of step test
== 2015-08-10 14:54:45,873 main.Tarball INFO installing...
== 2015-08-10 14:54:45,873 main.Tarball INFO Starting install step
== 2015-08-10 14:54:45,874 main.Tarball INFO Running method stage_install_step part of step install
== 2015-08-10 14:54:45,875 main.Tarball INFO Running method make_installdir part of step install
== 2015-08-10 14:54:45,875 main.Tarball INFO Found old directory /vol/fs01/tools/ubuntu14.04/easybuild/software/svtyper/v0.0.2-Python-2.7.9
== 2015-08-10 14:54:45,875 main.filetools INFO Path /vol/fs01/tools/ubuntu14.04/easybuild/software/svtyper/v0.0.2-Python-2.7.9 successfully removed.
== 2015-08-10 14:54:45,875 main.Tarball INFO Removed old directory /vol/fs01/tools/ubuntu14.04/easybuild/software/svtyper/v0.0.2-Python-2.7.9
== 2015-08-10 14:54:45,876 main.filetools INFO Creating directory /vol/fs01/tools/ubuntu14.04/easybuild/software/svtyper/v0.0.2-Python-2.7.9 (parents: True, set_gid: False, sticky: False)
== 2015-08-10 14:54:45,876 main.Tarball INFO Running method install_step part of step install
== 2015-08-10 14:54:45,876 main.filetools INFO Path /vol/fs01/tools/ubuntu14.04/easybuild/software/svtyper/v0.0.2-Python-2.7.9 successfully removed.
== 2015-08-10 14:54:45,877 main.Tarball INFO taking care of extensions...
== 2015-08-10 14:54:45,878 main.Tarball INFO Starting extensions step
== 2015-08-10 14:54:45,879 main.Tarball INFO Running method extensions_step part of step extensions
== 2015-08-10 14:54:45,879 main.Tarball INFO postprocessing...
== 2015-08-10 14:54:45,879 main.Tarball INFO Starting postproc step
== 2015-08-10 14:54:45,880 main.Tarball INFO Running method post_install_step part of step postproc
== 2015-08-10 14:54:45,913 main.run INFO cmd "mkdir -p /vol/fs01/tools/ubuntu14.04/easybuild/software/svtyper/v0.0.2-Python-2.7.9/bin" exited with exitcode 0 and output:
== 2015-08-10 14:54:45,942 main.run INFO cmd "mv /vol/fs01/tools/ubuntu14.04/easybuild/software/svtyper/v0.0.2-Python-2.7.9/scripts/* /vol/fs01/tools/ubuntu14.04/easybuild/software/svtyper/v0.0.2-Python-2.7.9/bin" exited with exitcode 0 and output:
== 2015-08-10 14:54:45,971 main.run INFO cmd "mv /vol/fs01/tools/ubuntu14.04/easybuild/software/svtyper/v0.0.2-Python-2.7.9/svtyper /vol/fs01/tools/ubuntu14.04/easybuild/software/svtyper/v0.0.2-Python-2.7.9/bin" exited with exitcode 0 and output:
== 2015-08-10 14:54:45,971 main.Tarball INFO sanity checking...
== 2015-08-10 14:54:45,972 main.Tarball INFO Starting sanitycheck step
== 2015-08-10 14:54:45,973 main.Tarball INFO Running method sanity_check_step part of step sanitycheck
== 2015-08-10 14:54:45,973 main.Tarball INFO Using default sanity check paths: {'files': [], 'dirs': ['bin', ('lib', 'lib64')]}
== 2015-08-10 14:54:45,973 main.Tarball WARNING Sanity check: no dir of ('lib', 'lib64') in /vol/fs01/tools/ubuntu14.04/easybuild/software/svtyper/v0.0.2-Python-2.7.9
== 2015-08-10 14:54:45,974 main.filetools INFO Creating directory /tmp/eb-zyPVNp/tmpWWQRAp/all/svtyper (parents: True, set_gid: False, sticky: False)
== 2015-08-10 14:54:45,974 main.filetools INFO Creating directory /tmp/eb-zyPVNp/tmpWWQRAp/bio/svtyper (parents: True, set_gid: False, sticky: False)
== 2015-08-10 14:54:45,975 main.Tarball INFO Module file /tmp/eb-zyPVNp/tmpWWQRAp/all/svtyper/v0.0.2-Python-2.7.9 written: #%Module
proc ModulesHelp { } {
puts stderr { Bayesian genotyper for structural variants - Homepage: https://github.com/hall-lab/svtyper
}
}
module-whatis {Description: Bayesian genotyper for structural variants - Homepage: https://github.com/hall-lab/svtyper}
set root /vol/fs01/tools/ubuntu14.04/easybuild/software/svtyper/v0.0.2-Python-2.7.9
conflict svtyper
if { ![ is-loaded pysam/0.8.3-foss-2015a-Python-2.7.9 ] } {
module load pysam/0.8.3-foss-2015a-Python-2.7.9
}
if { ![ is-loaded Python/2.7.9-foss-2015a ] } {
module load Python/2.7.9-foss-2015a
}
prepend-path PATH $root/bin
setenv EBROOTSVTYPER "$root"
setenv EBVERSIONSVTYPER "v0.0.2"
setenv EBDEVELSVTYPER "$root/easybuild/svtyper-v0.0.2-Python-2.7.9-easybuild-devel"
# Built with EasyBuild version 2.2.0
== 2015-08-10 14:54:45,993 main.environment INFO Environment variable EBDEVELEASYBUILD set to /vol/fs01/tools/ubuntu14.04/easybuild/software/EasyBuild/2.2.0/easybuild/EasyBuild-2.2.0-easybuild-devel (previously undefined)
== 2015-08-10 14:54:45,993 main.environment INFO Environment variable PATH set to /vol/fs01/tools/ubuntu14.04/easybuild/software/EasyBuild/2.2.0/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin (previous value: '/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin')
== 2015-08-10 14:54:45,993 main.environment INFO Environment variable LIBRARY_PATH set to /vol/fs01/tools/ubuntu14.04/easybuild/software/EasyBuild/2.2.0/lib (previously undefined)
== 2015-08-10 14:54:45,993 main.environment INFO Environment variable PYTHONPATH set to /vol/fs01/tools/ubuntu14.04/easybuild/software/EasyBuild/2.2.0/lib/python2.7/site-packages:/vol/fs01/tools/ubuntu14.04/easybuild.local (previous value: '/vol/fs01/tools/ubuntu14.04/easybuild.local')
== 2015-08-10 14:54:45,993 main.environment INFO Environment variable EBROOTEASYBUILD set to /vol/fs01/tools/ubuntu14.04/easybuild/software/EasyBuild/2.2.0 (previously undefined)
== 2015-08-10 14:54:45,994 main.environment INFO Environment variable EBVERSIONEASYBUILD set to 2.2.0 (previously undefined)
== 2015-08-10 14:54:45,994 main.environment INFO Environment variable MODULEPATH set to /vol/fs01/tools/ubuntu14.04/easybuild/modules/all:/etc/environment-modules/modules:/usr/share/modules/versions:/usr/Modules/$MODULE_VERSION/modulefiles:/usr/share/modules/modulefiles (previous value: '/tmp/eb-zyPVNp/tmpWWQRAp/all:/vol/fs01/tools/ubuntu14.04/easybuild/modules/all:/etc/environment-modules/modules:/usr/share/modules/versions:/usr/Modules/$MODULE_VERSION/modulefiles:/usr/share/modules/modulefiles')
== 2015-08-10 14:54:45,994 main.environment INFO Environment variable _LMFILES_ set to /vol/fs01/tools/ubuntu14.04/easybuild/modules/all/EasyBuild/2.2.0 (previously undefined)
== 2015-08-10 14:54:45,994 main.environment INFO Environment variable LOADEDMODULES set to EasyBuild/2.2.0 (previously undefined)
== 2015-08-10 14:54:46,023 main.EnvironmentModulesC INFO $MODULEPATH set based on list of module paths (via 'module use'): /tmp/eb-zyPVNp/tmpWWQRAp/all:/vol/fs01/tools/ubuntu14.04/easybuild/modules/all:/etc/environment-modules/modules:/usr/share/modules/versions:/usr/Modules/$MODULE_VERSION/modulefiles:/usr/share/modules/modulefiles
== 2015-08-10 14:54:46,186 main.Tarball INFO Using specified sanity check commands: []
== 2015-08-10 14:54:46,200 main.filetools INFO Path /tmp/eb-zyPVNp/tmpWWQRAp successfully removed.
== 2015-08-10 14:54:46,201 main.environment INFO Environment variable PATH set to /vol/fs01/tools/ubuntu14.04/easybuild/software/EasyBuild/2.2.0/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin (previous value: '/vol/fs01/tools/ubuntu14.04/easybuild/software/Cython/0.22.1-foss-2015a-Python-2.7.9/bin:/vol/fs01/tools/ubuntu14.04/easybuild/software/Python/2.7.9-foss-2015a/bin:/vol/fs01/tools/ubuntu14.04/easybuild/software/Tk/8.6.3-foss-2015a-no-X11/bin:/vol/fs01/tools/ubuntu14.04/easybuild/software/SQLite/3.8.8.1-foss-2015a/bin:/vol/fs01/tools/ubuntu14.04/easybuild/software/Tcl/8.6.3-foss-2015a/bin:/vol/fs01/tools/ubuntu14.04/easybuild/software/libreadline/6.3-foss-2015a/bin:/vol/fs01/tools/ubuntu14.04/easybuild/software/ncurses/5.9-foss-2015a/bin:/vol/fs01/tools/ubuntu14.04/easybuild/software/bzip2/1.0.6-foss-2015a/bin:/vol/fs01/tools/ubuntu14.04/easybuild/software/FFTW/3.3.4-gompi-2015a/bin:/vol/fs01/tools/ubuntu14.04/easybuild/software/OpenBLAS/0.2.13-GCC-4.9.2-LAPACK-3.5.0/bin:/vol/fs01/tools/ubuntu14.04/easybuild/software/OpenMPI/1.8.4-GCC-4.9.2/bin:/vol/fs01/tools/ubuntu14.04/easybuild/software/hwloc/1.10.0-GCC-4.9.2/bin:/vol/fs01/tools/ubuntu14.04/easybuild/software/numactl/2.0.10-GCC-4.9.2/bin:/vol/fs01/tools/ubuntu14.04/easybuild/software/GCC/4.9.2/bin:/vol/fs01/tools/ubuntu14.04/easybuild/software/EasyBuild/2.2.0/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin')
== 2015-08-10 14:54:46,201 main.environment INFO Environment variable LD_LIBRARY_PATH set to /vol/fs01/tools/ubuntu14.04/easybuild/software/EasyBuild/2.2.0/lib (previous value: '/vol/fs01/tools/ubuntu14.04/easybuild/software/pysam/0.8.3-foss-2015a-Python-2.7.9/lib:/vol/fs01/tools/ubuntu14.04/easybuild/software/Cython/0.22.1-foss-2015a-Python-2.7.9/lib:/vol/fs01/tools/ubuntu14.04/easybuild/software/Python/2.7.9-foss-2015a/lib:/vol/fs01/tools/ubuntu14.04/easybuild/software/Tk/8.6.3-foss-2015a-no-X11/lib:/vol/fs01/tools/ubuntu14.04/easybuild/software/SQLite/3.8.8.1-foss-2015a/lib:/vol/fs01/tools/ubuntu14.04/easybuild/software/Tcl/8.6.3-foss-2015a/lib:/vol/fs01/tools/ubuntu14.04/easybuild/software/libreadline/6.3-foss-2015a/lib:/vol/fs01/tools/ubuntu14.04/easybuild/software/ncurses/5.9-foss-2015a/lib:/vol/fs01/tools/ubuntu14.04/easybuild/software/zlib/1.2.8-foss-2015a/lib:/vol/fs01/tools/ubuntu14.04/easybuild/software/bzip2/1.0.6-foss-2015a/lib:/vol/fs01/tools/ubuntu14.04/easybuild/software/ScaLAPACK/2.0.2-gompi-2015a-OpenBLAS-0.2.13-LAPACK-3.5.0/lib:/vol/fs01/tools/ubuntu14.04/easybuild/software/FFTW/3.3.4-gompi-2015a/lib:/vol/fs01/tools/ubuntu14.04/easybuild/software/OpenBLAS/0.2.13-GCC-4.9.2-LAPACK-3.5.0/lib:/vol/fs01/tools/ubuntu14.04/easybuild/software/OpenMPI/1.8.4-GCC-4.9.2/lib:/vol/fs01/tools/ubuntu14.04/easybuild/software/hwloc/1.10.0-GCC-4.9.2/lib:/vol/fs01/tools/ubuntu14.04/easybuild/software/numactl/2.0.10-GCC-4.9.2/lib:/vol/fs01/tools/ubuntu14.04/easybuild/software/GCC/4.9.2/lib/gcc/x86_64-unknown-linux-gnu/4.9.2:/vol/fs01/tools/ubuntu14.04/easybuild/software/GCC/4.9.2/lib64:/vol/fs01/tools/ubuntu14.04/easybuild/software/GCC/4.9.2/lib:/vol/fs01/tools/ubuntu14.04/easybuild/software/EasyBuild/2.2.0/lib')
== 2015-08-10 14:54:46,201 main.environment INFO Environment variable LIBRARY_PATH set to /vol/fs01/tools/ubuntu14.04/easybuild/software/EasyBuild/2.2.0/lib (previous value: '/vol/fs01/tools/ubuntu14.04/easybuild/software/pysam/0.8.3-foss-2015a-Python-2.7.9/lib:/vol/fs01/tools/ubuntu14.04/easybuild/software/Cython/0.22.1-foss-2015a-Python-2.7.9/lib:/vol/fs01/tools/ubuntu14.04/easybuild/software/Python/2.7.9-foss-2015a/lib:/vol/fs01/tools/ubuntu14.04/easybuild/software/Tk/8.6.3-foss-2015a-no-X11/lib:/vol/fs01/tools/ubuntu14.04/easybuild/software/SQLite/3.8.8.1-foss-2015a/lib:/vol/fs01/tools/ubuntu14.04/easybuild/software/Tcl/8.6.3-foss-2015a/lib:/vol/fs01/tools/ubuntu14.04/easybuild/software/libreadline/6.3-foss-2015a/lib:/vol/fs01/tools/ubuntu14.04/easybuild/software/ncurses/5.9-foss-2015a/lib:/vol/fs01/tools/ubuntu14.04/easybuild/software/zlib/1.2.8-foss-2015a/lib:/vol/fs01/tools/ubuntu14.04/easybuild/software/bzip2/1.0.6-foss-2015a/lib:/vol/fs01/tools/ubuntu14.04/easybuild/software/ScaLAPACK/2.0.2-gompi-2015a-OpenBLAS-0.2.13-LAPACK-3.5.0/lib:/vol/fs01/tools/ubuntu14.04/easybuild/software/FFTW/3.3.4-gompi-2015a/lib:/vol/fs01/tools/ubuntu14.04/easybuild/software/OpenBLAS/0.2.13-GCC-4.9.2-LAPACK-3.5.0/lib:/vol/fs01/tools/ubuntu14.04/easybuild/software/OpenMPI/1.8.4-GCC-4.9.2/lib:/vol/fs01/tools/ubuntu14.04/easybuild/software/hwloc/1.10.0-GCC-4.9.2/lib:/vol/fs01/tools/ubuntu14.04/easybuild/software/numactl/2.0.10-GCC-4.9.2/lib:/vol/fs01/tools/ubuntu14.04/easybuild/software/GCC/4.9.2/lib64:/vol/fs01/tools/ubuntu14.04/easybuild/software/GCC/4.9.2/lib:/vol/fs01/tools/ubuntu14.04/easybuild/software/EasyBuild/2.2.0/lib')
== 2015-08-10 14:54:46,201 main.environment INFO Environment variable PYTHONPATH set to /vol/fs01/tools/ubuntu14.04/easybuild/software/EasyBuild/2.2.0/lib/python2.7/site-packages:/vol/fs01/tools/ubuntu14.04/easybuild.local (previous value: '/vol/fs01/tools/ubuntu14.04/easybuild/software/pysam/0.8.3-foss-2015a-Python-2.7.9/lib/python2.7/site-packages:/vol/fs01/tools/ubuntu14.04/easybuild/software/Cython/0.22.1-foss-2015a-Python-2.7.9/lib/python2.7/site-packages:/vol/fs01/tools/ubuntu14.04/easybuild/software/EasyBuild/2.2.0/lib/python2.7/site-packages:/vol/fs01/tools/ubuntu14.04/easybuild.local')
== 2015-08-10 14:54:46,201 main.environment INFO Environment variable _LMFILES_ set to /vol/fs01/tools/ubuntu14.04/easybuild/modules/all/EasyBuild/2.2.0 (previous value: '/vol/fs01/tools/ubuntu14.04/easybuild/modules/all/EasyBuild/2.2.0:/vol/fs01/tools/ubuntu14.04/easybuild/modules/all/GCC/4.9.2:/vol/fs01/tools/ubuntu14.04/easybuild/modules/all/numactl/2.0.10-GCC-4.9.2:/vol/fs01/tools/ubuntu14.04/easybuild/modules/all/hwloc/1.10.0-GCC-4.9.2:/vol/fs01/tools/ubuntu14.04/easybuild/modules/all/OpenMPI/1.8.4-GCC-4.9.2:/vol/fs01/tools/ubuntu14.04/easybuild/modules/all/OpenBLAS/0.2.13-GCC-4.9.2-LAPACK-3.5.0:/vol/fs01/tools/ubuntu14.04/easybuild/modules/all/gompi/2015a:/vol/fs01/tools/ubuntu14.04/easybuild/modules/all/FFTW/3.3.4-gompi-2015a:/vol/fs01/tools/ubuntu14.04/easybuild/modules/all/ScaLAPACK/2.0.2-gompi-2015a-OpenBLAS-0.2.13-LAPACK-3.5.0:/vol/fs01/tools/ubuntu14.04/easybuild/modules/all/foss/2015a:/vol/fs01/tools/ubuntu14.04/easybuild/modules/all/bzip2/1.0.6-foss-2015a:/vol/fs01/tools/ubuntu14.04/easybuild/modules/all/zlib/1.2.8-foss-2015a:/vol/fs01/tools/ubuntu14.04/easybuild/modules/all/ncurses/5.9-foss-2015a:/vol/fs01/tools/ubuntu14.04/easybuild/modules/all/libreadline/6.3-foss-2015a:/vol/fs01/tools/ubuntu14.04/easybuild/modules/all/Tcl/8.6.3-foss-2015a:/vol/fs01/tools/ubuntu14.04/easybuild/modules/all/SQLite/3.8.8.1-foss-2015a:/vol/fs01/tools/ubuntu14.04/easybuild/modules/all/Tk/8.6.3-foss-2015a-no-X11:/vol/fs01/tools/ubuntu14.04/easybuild/modules/all/Python/2.7.9-foss-2015a:/vol/fs01/tools/ubuntu14.04/easybuild/modules/all/Cython/0.22.1-foss-2015a-Python-2.7.9:/vol/fs01/tools/ubuntu14.04/easybuild/modules/all/pysam/0.8.3-foss-2015a-Python-2.7.9')
== 2015-08-10 14:54:46,202 main.environment INFO Environment variable LOADEDMODULES set to EasyBuild/2.2.0 (previous value: 'EasyBuild/2.2.0:GCC/4.9.2:numactl/2.0.10-GCC-4.9.2:hwloc/1.10.0-GCC-4.9.2:OpenMPI/1.8.4-GCC-4.9.2:OpenBLAS/0.2.13-GCC-4.9.2-LAPACK-3.5.0:gompi/2015a:FFTW/3.3.4-gompi-2015a:ScaLAPACK/2.0.2-gompi-2015a-OpenBLAS-0.2.13-LAPACK-3.5.0:foss/2015a:bzip2/1.0.6-foss-2015a:zlib/1.2.8-foss-2015a:ncurses/5.9-foss-2015a:libreadline/6.3-foss-2015a:Tcl/8.6.3-foss-2015a:SQLite/3.8.8.1-foss-2015a:Tk/8.6.3-foss-2015a-no-X11:Python/2.7.9-foss-2015a:Cython/0.22.1-foss-2015a-Python-2.7.9:pysam/0.8.3-foss-2015a-Python-2.7.9')
== 2015-08-10 14:54:46,203 main ERROR Sanity check failed: no dir of ('lib', 'lib64') in /vol/fs01/tools/ubuntu14.04/easybuild/software/svtyper/v0.0.2-Python-2.7.9 (at easybuild/software/EasyBuild/2.2.0/lib/python2.7/site-packages/easybuild_framework-2.2.0-py2.7.egg/easybuild/framework/easyblock.py:1653 in sanity_check_step)
== 2015-08-10 14:54:46,204 main.easyblock WARNING build failed (first 300 chars): Sanity check failed: no dir of ('lib', 'lib64') in /vol/fs01/tools/ubuntu14.04/easybuild/software/svtyper/v0.0.2-Python-2.7.9
== 2015-08-10 14:54:46,204 main.Tarball INFO Closing log for application name svtyper version v0.0.2
== 2015-08-10 14:51:54,152 main.Tarball INFO This is EasyBuild 2.2.0 (framework: 2.2.0, easyblocks: 2.2.0) on host a4a19bc0d117.
== 2015-08-10 14:51:54,152 main.Tarball INFO This is easyblock Tarball from module easybuild.easyblocks.generic.tarball (/vol/fs01/tools/ubuntu14.04/easybuild/software/EasyBuild/2.2.0/lib/python2.7/site-packages/easybuild_easyblocks-2.2.0-py2.7.egg/easybuild/easyblocks/generic/tarball.pyc)
== 2015-08-10 14:51:54,153 main.Tarball INFO Build dir set to /vol/fs01/tools/ubuntu14.04/easybuild/build/svtyper/v0.0.2/dummy-dummy-Python-2.7.9
== 2015-08-10 14:51:54,153 main.Tarball INFO Install dir set to /vol/fs01/tools/ubuntu14.04/easybuild/software/svtyper/v0.0.2-Python-2.7.9
== 2015-08-10 14:51:54,153 main.Tarball INFO Init completed for application name svtyper version v0.0.2
== 2015-08-10 14:51:54,154 main.easyblock INFO Obtained application instance of for svtyper (easyblock: Tarball)
== 2015-08-10 14:51:54,154 main.Tarball INFO building and installing svtyper/v0.0.2-Python-2.7.9...
== 2015-08-10 14:51:54,154 main.Tarball INFO fetching files...
== 2015-08-10 14:51:54,155 main.Tarball INFO Starting fetch step
== 2015-08-10 14:51:54,157 main.Tarball INFO Running method fetch_step part of step fetch
== 2015-08-10 14:51:54,158 main.Tarball WARNING Easyconfig does not specify an EasyBuild-version (key 'easybuild_version')! Assuming the latest version
== 2015-08-10 14:51:54,158 main.filetools INFO Command eb found at /vol/fs01/tools/ubuntu14.04/easybuild/software/EasyBuild/2.2.0/bin/eb
== 2015-08-10 14:51:54,159 main.Tarball INFO Found file v0.0.2.tar.gz at /vol/fs01/tools/ubuntu14.04/easybuild/sources/s/svtyper/v0.0.2.tar.gz
== 2015-08-10 14:51:54,159 main.Tarball INFO Added sources: [{'path': '/vol/fs01/tools/ubuntu14.04/easybuild/sources/s/svtyper/v0.0.2.tar.gz', 'cmd': None, 'finalpath': '/vol/fs01/tools/ubuntu14.04/easybuild/build/svtyper/v0.0.2/dummy-dummy-Python-2.7.9', 'name': 'v0.0.2.tar.gz', 'checksum': None}]
== 2015-08-10 14:51:54,160 main.Tarball INFO no patches provided
== 2015-08-10 14:51:54,160 main.Tarball INFO md5 checksum for /vol/fs01/tools/ubuntu14.04/easybuild/sources/s/svtyper/v0.0.2.tar.gz: c799a67f0e8b00ee461708b18892ab06
== 2015-08-10 14:51:54,194 main.Tarball INFO Setting parallelism: 8
== 2015-08-10 14:51:54,194 main.Tarball INFO Checking dirs that need to be created: ['/vol/fs01/tools/ubuntu14.04/easybuild/software/svtyper', '/vol/fs01/tools/ubuntu14.04/easybuild/modules/all/svtyper', '/vol/fs01/tools/ubuntu14.04/easybuild/modules/bio/svtyper']
== 2015-08-10 14:51:54,195 main.Tarball INFO creating build dir, resetting environment...
== 2015-08-10 14:51:54,195 main.Tarball INFO Starting ready step
== 2015-08-10 14:51:54,197 main.Tarball INFO Running method check_readiness_step part of step ready
== 2015-08-10 14:51:54,202 main.Tarball WARNING Loaded modules detected: ['EasyBuild/2.2.0']
== 2015-08-10 14:51:54,225 main.Tarball INFO Running method make_builddir part of step ready
== 2015-08-10 14:51:54,225 main.Tarball INFO Found old directory /vol/fs01/tools/ubuntu14.04/easybuild/build/svtyper/v0.0.2/dummy-dummy-Python-2.7.9
== 2015-08-10 14:51:54,226 main.filetools INFO Path /vol/fs01/tools/ubuntu14.04/easybuild/build/svtyper/v0.0.2/dummy-dummy-Python-2.7.9 successfully removed.
== 2015-08-10 14:51:54,227 main.Tarball INFO Removed old directory /vol/fs01/tools/ubuntu14.04/easybuild/build/svtyper/v0.0.2/dummy-dummy-Python-2.7.9
== 2015-08-10 14:51:54,227 main.filetools INFO Creating directory /vol/fs01/tools/ubuntu14.04/easybuild/build/svtyper/v0.0.2/dummy-dummy-Python-2.7.9 (parents: True, set_gid: False, sticky: False)
== 2015-08-10 14:51:54,227 main.Tarball INFO Running method env_reset_changes part of step ready
== 2015-08-10 14:51:54,228 main.Tarball INFO Running method handle_iterate_opts part of step ready
== 2015-08-10 14:51:54,228 main.Tarball INFO unpacking...
== 2015-08-10 14:51:54,228 main.Tarball INFO Starting source step
== 2015-08-10 14:51:54,230 main.Tarball INFO Running method checksum_step part of step source
== 2015-08-10 14:51:54,231 main.Tarball INFO Checksum verification for /vol/fs01/tools/ubuntu14.04/easybuild/sources/s/svtyper/v0.0.2.tar.gz using None passed.
== 2015-08-10 14:51:54,231 main.Tarball INFO Running method extract_step part of step source
== 2015-08-10 14:51:54,231 main.Tarball INFO Unpacking source v0.0.2.tar.gz
== 2015-08-10 14:51:54,264 main.Tarball INFO patching...
== 2015-08-10 14:51:54,264 main.Tarball INFO Starting patch step
== 2015-08-10 14:51:54,266 main.Tarball INFO Running method patch_step part of step patch
== 2015-08-10 14:51:54,267 main.Tarball INFO preparing...
== 2015-08-10 14:51:54,267 main.Tarball INFO Starting prepare step
== 2015-08-10 14:51:54,269 main.Tarball INFO Running method prepare_step part of step prepare
== 2015-08-10 14:51:54,269 main.Dummy INFO prepare: toolchain dummy mode, dummy version; not loading dependencies
== 2015-08-10 14:51:54,269 main.Tarball INFO configuring...
== 2015-08-10 14:51:54,270 main.Tarball INFO Starting configure step
== 2015-08-10 14:51:54,272 main.Tarball INFO Running method configure_step part of step configure
== 2015-08-10 14:51:54,272 main.Tarball INFO building...
== 2015-08-10 14:51:54,272 main.Tarball INFO Starting build step
== 2015-08-10 14:51:54,274 main.Tarball INFO Running method build_step part of step build
== 2015-08-10 14:51:54,275 main.Tarball INFO testing...
== 2015-08-10 14:51:54,275 main.Tarball INFO Starting test step
== 2015-08-10 14:51:54,277 main.Tarball INFO Running method test_step part of step test
== 2015-08-10 14:51:54,277 main.Tarball INFO installing...
== 2015-08-10 14:51:54,278 main.Tarball INFO Starting install step
== 2015-08-10 14:51:54,280 main.Tarball INFO Running method stage_install_step part of step install
== 2015-08-10 14:51:54,280 main.Tarball INFO Running method make_installdir part of step install
== 2015-08-10 14:51:54,280 main.Tarball INFO Found old directory /vol/fs01/tools/ubuntu14.04/easybuild/software/svtyper/v0.0.2-Python-2.7.9
== 2015-08-10 14:51:54,281 main.filetools INFO Path /vol/fs01/tools/ubuntu14.04/easybuild/software/svtyper/v0.0.2-Python-2.7.9 successfully removed.
== 2015-08-10 14:51:54,281 main.Tarball INFO Removed old directory /vol/fs01/tools/ubuntu14.04/easybuild/software/svtyper/v0.0.2-Python-2.7.9
== 2015-08-10 14:51:54,282 main.filetools INFO Creating directory /vol/fs01/tools/ubuntu14.04/easybuild/software/svtyper/v0.0.2-Python-2.7.9 (parents: True, set_gid: False, sticky: False)
== 2015-08-10 14:51:54,282 main.Tarball INFO Running method install_step part of step install
== 2015-08-10 14:51:54,282 main.filetools INFO Path /vol/fs01/tools/ubuntu14.04/easybuild/software/svtyper/v0.0.2-Python-2.7.9 successfully removed.
== 2015-08-10 14:51:54,285 main.Tarball INFO taking care of extensions...
== 2015-08-10 14:51:54,286 main.Tarball INFO Starting extensions step
== 2015-08-10 14:51:54,288 main.Tarball INFO Running method extensions_step part of step extensions
== 2015-08-10 14:51:54,288 main.Tarball INFO postprocessing...
== 2015-08-10 14:51:54,288 main.Tarball INFO Starting postproc step
== 2015-08-10 14:51:54,290 main.Tarball INFO Running method post_install_step part of step postproc
== 2015-08-10 14:51:54,321 main.run INFO cmd "mkdir -p /vol/fs01/tools/ubuntu14.04/easybuild/software/svtyper/v0.0.2-Python-2.7.9/bin" exited with exitcode 0 and output:
== 2015-08-10 14:51:54,354 main.run INFO cmd "mv /vol/fs01/tools/ubuntu14.04/easybuild/software/svtyper/v0.0.2-Python-2.7.9/scripts/* /vol/fs01/tools/ubuntu14.04/easybuild/software/svtyper/v0.0.2-Python-2.7.9/bin" exited with exitcode 0 and output:
== 2015-08-10 14:51:54,383 main.run INFO cmd "mv /vol/fs01/tools/ubuntu14.04/easybuild/software/svtyper/v0.0.2-Python-2.7.9/svtyper /vol/fs01/tools/ubuntu14.04/easybuild/software/svtyper/v0.0.2-Python-2.7.9/bin" exited with exitcode 0 and output:
== 2015-08-10 14:51:54,384 main.Tarball INFO sanity checking...
== 2015-08-10 14:51:54,384 main.Tarball INFO Starting sanitycheck step
== 2015-08-10 14:51:54,385 main.Tarball INFO Running method sanity_check_step part of step sanitycheck
== 2015-08-10 14:51:54,385 main.Tarball INFO Using specified sanity check paths: {'files': ['bin/svtyper', 'bin/sv_counts', 'bin/vcf_group_multiline.py', 'bin/vcf_paste.py', 'LICENSE', 'README.md'], 'dirs': []}
== 2015-08-10 14:51:54,386 main.Tarball WARNING Sanity check: no file of ('bin/sv_counts',) in /vol/fs01/tools/ubuntu14.04/easybuild/software/svtyper/v0.0.2-Python-2.7.9
== 2015-08-10 14:51:54,386 main.filetools INFO Creating directory /tmp/eb-V8DNkW/tmpZ69oUG/all/svtyper (parents: True, set_gid: False, sticky: False)
== 2015-08-10 14:51:54,386 main.filetools INFO Creating directory /tmp/eb-V8DNkW/tmpZ69oUG/bio/svtyper (parents: True, set_gid: False, sticky: False)
== 2015-08-10 14:51:54,387 main.Tarball INFO Module file /tmp/eb-V8DNkW/tmpZ69oUG/all/svtyper/v0.0.2-Python-2.7.9 written: #%Module
proc ModulesHelp { } {
puts stderr { Bayesian genotyper for structural variants - Homepage: https://github.com/hall-lab/svtyper
}
}
module-whatis {Description: Bayesian genotyper for structural variants - Homepage: https://github.com/hall-lab/svtyper}
set root /vol/fs01/tools/ubuntu14.04/easybuild/software/svtyper/v0.0.2-Python-2.7.9
conflict svtyper
if { ![ is-loaded pysam/0.8.3-foss-2015a-Python-2.7.9 ] } {
module load pysam/0.8.3-foss-2015a-Python-2.7.9
}
if { ![ is-loaded Python/2.7.9-foss-2015a ] } {
module load Python/2.7.9-foss-2015a
}
prepend-path PATH $root/bin
setenv EBROOTSVTYPER "$root"
setenv EBVERSIONSVTYPER "v0.0.2"
setenv EBDEVELSVTYPER "$root/easybuild/svtyper-v0.0.2-Python-2.7.9-easybuild-devel"
# Built with EasyBuild version 2.2.0
== 2015-08-10 14:51:54,405 main.environment INFO Environment variable EBDEVELEASYBUILD set to /vol/fs01/tools/ubuntu14.04/easybuild/software/EasyBuild/2.2.0/easybuild/EasyBuild-2.2.0-easybuild-devel (previously undefined)
== 2015-08-10 14:51:54,405 main.environment INFO Environment variable PATH set to /vol/fs01/tools/ubuntu14.04/easybuild/software/EasyBuild/2.2.0/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin (previous value: '/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin')
== 2015-08-10 14:51:54,406 main.environment INFO Environment variable LIBRARY_PATH set to /vol/fs01/tools/ubuntu14.04/easybuild/software/EasyBuild/2.2.0/lib (previously undefined)
== 2015-08-10 14:51:54,406 main.environment INFO Environment variable PYTHONPATH set to /vol/fs01/tools/ubuntu14.04/easybuild/software/EasyBuild/2.2.0/lib/python2.7/site-packages:/vol/fs01/tools/ubuntu14.04/easybuild.local (previous value: '/vol/fs01/tools/ubuntu14.04/easybuild.local')
== 2015-08-10 14:51:54,406 main.environment INFO Environment variable EBROOTEASYBUILD set to /vol/fs01/tools/ubuntu14.04/easybuild/software/EasyBuild/2.2.0 (previously undefined)
== 2015-08-10 14:51:54,407 main.environment INFO Environment variable EBVERSIONEASYBUILD set to 2.2.0 (previously undefined)
== 2015-08-10 14:51:54,407 main.environment INFO Environment variable MODULEPATH set to /vol/fs01/tools/ubuntu14.04/easybuild/modules/all:/etc/environment-modules/modules:/usr/share/modules/versions:/usr/Modules/$MODULE_VERSION/modulefiles:/usr/share/modules/modulefiles (previous value: '/tmp/eb-V8DNkW/tmpZ69oUG/all:/vol/fs01/tools/ubuntu14.04/easybuild/modules/all:/etc/environment-modules/modules:/usr/share/modules/versions:/usr/Modules/$MODULE_VERSION/modulefiles:/usr/share/modules/modulefiles')
== 2015-08-10 14:51:54,407 main.environment INFO Environment variable _LMFILES_ set to /vol/fs01/tools/ubuntu14.04/easybuild/modules/all/EasyBuild/2.2.0 (previously undefined)
== 2015-08-10 14:51:54,407 main.environment INFO Environment variable LOADEDMODULES set to EasyBuild/2.2.0 (previously undefined)
== 2015-08-10 14:51:54,438 main.EnvironmentModulesC INFO $MODULEPATH set based on list of module paths (via 'module use'): /tmp/eb-V8DNkW/tmpZ69oUG/all:/vol/fs01/tools/ubuntu14.04/easybuild/modules/all:/etc/environment-modules/modules:/usr/share/modules/versions:/usr/Modules/$MODULE_VERSION/modulefiles:/usr/share/modules/modulefiles
== 2015-08-10 14:51:54,604 main.Tarball INFO Using specified sanity check commands: []
== 2015-08-10 14:51:54,617 main.filetools INFO Path /tmp/eb-V8DNkW/tmpZ69oUG successfully removed.
== 2015-08-10 14:51:54,617 main.environment INFO Environment variable PATH set to /vol/fs01/tools/ubuntu14.04/easybuild/software/EasyBuild/2.2.0/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin (previous value: '/vol/fs01/tools/ubuntu14.04/easybuild/software/Cython/0.22.1-foss-2015a-Python-2.7.9/bin:/vol/fs01/tools/ubuntu14.04/easybuild/software/Python/2.7.9-foss-2015a/bin:/vol/fs01/tools/ubuntu14.04/easybuild/software/Tk/8.6.3-foss-2015a-no-X11/bin:/vol/fs01/tools/ubuntu14.04/easybuild/software/SQLite/3.8.8.1-foss-2015a/bin:/vol/fs01/tools/ubuntu14.04/easybuild/software/Tcl/8.6.3-foss-2015a/bin:/vol/fs01/tools/ubuntu14.04/easybuild/software/libreadline/6.3-foss-2015a/bin:/vol/fs01/tools/ubuntu14.04/easybuild/software/ncurses/5.9-foss-2015a/bin:/vol/fs01/tools/ubuntu14.04/easybuild/software/bzip2/1.0.6-foss-2015a/bin:/vol/fs01/tools/ubuntu14.04/easybuild/software/FFTW/3.3.4-gompi-2015a/bin:/vol/fs01/tools/ubuntu14.04/easybuild/software/OpenBLAS/0.2.13-GCC-4.9.2-LAPACK-3.5.0/bin:/vol/fs01/tools/ubuntu14.04/easybuild/software/OpenMPI/1.8.4-GCC-4.9.2/bin:/vol/fs01/tools/ubuntu14.04/easybuild/software/hwloc/1.10.0-GCC-4.9.2/bin:/vol/fs01/tools/ubuntu14.04/easybuild/software/numactl/2.0.10-GCC-4.9.2/bin:/vol/fs01/tools/ubuntu14.04/easybuild/software/GCC/4.9.2/bin:/vol/fs01/tools/ubuntu14.04/easybuild/software/EasyBuild/2.2.0/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin')
== 2015-08-10 14:51:54,617 main.environment INFO Environment variable LD_LIBRARY_PATH set to /vol/fs01/tools/ubuntu14.04/easybuild/software/EasyBuild/2.2.0/lib (previous value: '/vol/fs01/tools/ubuntu14.04/easybuild/software/pysam/0.8.3-foss-2015a-Python-2.7.9/lib:/vol/fs01/tools/ubuntu14.04/easybuild/software/Cython/0.22.1-foss-2015a-Python-2.7.9/lib:/vol/fs01/tools/ubuntu14.04/easybuild/software/Python/2.7.9-foss-2015a/lib:/vol/fs01/tools/ubuntu14.04/easybuild/software/Tk/8.6.3-foss-2015a-no-X11/lib:/vol/fs01/tools/ubuntu14.04/easybuild/software/SQLite/3.8.8.1-foss-2015a/lib:/vol/fs01/tools/ubuntu14.04/easybuild/software/Tcl/8.6.3-foss-2015a/lib:/vol/fs01/tools/ubuntu14.04/easybuild/software/libreadline/6.3-foss-2015a/lib:/vol/fs01/tools/ubuntu14.04/easybuild/software/ncurses/5.9-foss-2015a/lib:/vol/fs01/tools/ubuntu14.04/easybuild/software/zlib/1.2.8-foss-2015a/lib:/vol/fs01/tools/ubuntu14.04/easybuild/software/bzip2/1.0.6-foss-2015a/lib:/vol/fs01/tools/ubuntu14.04/easybuild/software/ScaLAPACK/2.0.2-gompi-2015a-OpenBLAS-0.2.13-LAPACK-3.5.0/lib:/vol/fs01/tools/ubuntu14.04/easybuild/software/FFTW/3.3.4-gompi-2015a/lib:/vol/fs01/tools/ubuntu14.04/easybuild/software/OpenBLAS/0.2.13-GCC-4.9.2-LAPACK-3.5.0/lib:/vol/fs01/tools/ubuntu14.04/easybuild/software/OpenMPI/1.8.4-GCC-4.9.2/lib:/vol/fs01/tools/ubuntu14.04/easybuild/software/hwloc/1.10.0-GCC-4.9.2/lib:/vol/fs01/tools/ubuntu14.04/easybuild/software/numactl/2.0.10-GCC-4.9.2/lib:/vol/fs01/tools/ubuntu14.04/easybuild/software/GCC/4.9.2/lib/gcc/x86_64-unknown-linux-gnu/4.9.2:/vol/fs01/tools/ubuntu14.04/easybuild/software/GCC/4.9.2/lib64:/vol/fs01/tools/ubuntu14.04/easybuild/software/GCC/4.9.2/lib:/vol/fs01/tools/ubuntu14.04/easybuild/software/EasyBuild/2.2.0/lib')
== 2015-08-10 14:51:54,617 main.environment INFO Environment variable LIBRARY_PATH set to /vol/fs01/tools/ubuntu14.04/easybuild/software/EasyBuild/2.2.0/lib (previous value: '/vol/fs01/tools/ubuntu14.04/easybuild/software/pysam/0.8.3-foss-2015a-Python-2.7.9/lib:/vol/fs01/tools/ubuntu14.04/easybuild/software/Cython/0.22.1-foss-2015a-Python-2.7.9/lib:/vol/fs01/tools/ubuntu14.04/easybuild/software/Python/2.7.9-foss-2015a/lib:/vol/fs01/tools/ubuntu14.04/easybuild/software/Tk/8.6.3-foss-2015a-no-X11/lib:/vol/fs01/tools/ubuntu14.04/easybuild/software/SQLite/3.8.8.1-foss-2015a/lib:/vol/fs01/tools/ubuntu14.04/easybuild/software/Tcl/8.6.3-foss-2015a/lib:/vol/fs01/tools/ubuntu14.04/easybuild/software/libreadline/6.3-foss-2015a/lib:/vol/fs01/tools/ubuntu14.04/easybuild/software/ncurses/5.9-foss-2015a/lib:/vol/fs01/tools/ubuntu14.04/easybuild/software/zlib/1.2.8-foss-2015a/lib:/vol/fs01/tools/ubuntu14.04/easybuild/software/bzip2/1.0.6-foss-2015a/lib:/vol/fs01/tools/ubuntu14.04/easybuild/software/ScaLAPACK/2.0.2-gompi-2015a-OpenBLAS-0.2.13-LAPACK-3.5.0/lib:/vol/fs01/tools/ubuntu14.04/easybuild/software/FFTW/3.3.4-gompi-2015a/lib:/vol/fs01/tools/ubuntu14.04/easybuild/software/OpenBLAS/0.2.13-GCC-4.9.2-LAPACK-3.5.0/lib:/vol/fs01/tools/ubuntu14.04/easybuild/software/OpenMPI/1.8.4-GCC-4.9.2/lib:/vol/fs01/tools/ubuntu14.04/easybuild/software/hwloc/1.10.0-GCC-4.9.2/lib:/vol/fs01/tools/ubuntu14.04/easybuild/software/numactl/2.0.10-GCC-4.9.2/lib:/vol/fs01/tools/ubuntu14.04/easybuild/software/GCC/4.9.2/lib64:/vol/fs01/tools/ubuntu14.04/easybuild/software/GCC/4.9.2/lib:/vol/fs01/tools/ubuntu14.04/easybuild/software/EasyBuild/2.2.0/lib')
== 2015-08-10 14:51:54,618 main.environment INFO Environment variable PYTHONPATH set to /vol/fs01/tools/ubuntu14.04/easybuild/software/EasyBuild/2.2.0/lib/python2.7/site-packages:/vol/fs01/tools/ubuntu14.04/easybuild.local (previous value: '/vol/fs01/tools/ubuntu14.04/easybuild/software/pysam/0.8.3-foss-2015a-Python-2.7.9/lib/python2.7/site-packages:/vol/fs01/tools/ubuntu14.04/easybuild/software/Cython/0.22.1-foss-2015a-Python-2.7.9/lib/python2.7/site-packages:/vol/fs01/tools/ubuntu14.04/easybuild/software/EasyBuild/2.2.0/lib/python2.7/site-packages:/vol/fs01/tools/ubuntu14.04/easybuild.local')
== 2015-08-10 14:51:54,618 main.environment INFO Environment variable _LMFILES_ set to /vol/fs01/tools/ubuntu14.04/easybuild/modules/all/EasyBuild/2.2.0 (previous value: '/vol/fs01/tools/ubuntu14.04/easybuild/modules/all/EasyBuild/2.2.0:/vol/fs01/tools/ubuntu14.04/easybuild/modules/all/GCC/4.9.2:/vol/fs01/tools/ubuntu14.04/easybuild/modules/all/numactl/2.0.10-GCC-4.9.2:/vol/fs01/tools/ubuntu14.04/easybuild/modules/all/hwloc/1.10.0-GCC-4.9.2:/vol/fs01/tools/ubuntu14.04/easybuild/modules/all/OpenMPI/1.8.4-GCC-4.9.2:/vol/fs01/tools/ubuntu14.04/easybuild/modules/all/OpenBLAS/0.2.13-GCC-4.9.2-LAPACK-3.5.0:/vol/fs01/tools/ubuntu14.04/easybuild/modules/all/gompi/2015a:/vol/fs01/tools/ubuntu14.04/easybuild/modules/all/FFTW/3.3.4-gompi-2015a:/vol/fs01/tools/ubuntu14.04/easybuild/modules/all/ScaLAPACK/2.0.2-gompi-2015a-OpenBLAS-0.2.13-LAPACK-3.5.0:/vol/fs01/tools/ubuntu14.04/easybuild/modules/all/foss/2015a:/vol/fs01/tools/ubuntu14.04/easybuild/modules/all/bzip2/1.0.6-foss-2015a:/vol/fs01/tools/ubuntu14.04/easybuild/modules/all/zlib/1.2.8-foss-2015a:/vol/fs01/tools/ubuntu14.04/easybuild/modules/all/ncurses/5.9-foss-2015a:/vol/fs01/tools/ubuntu14.04/easybuild/modules/all/libreadline/6.3-foss-2015a:/vol/fs01/tools/ubuntu14.04/easybuild/modules/all/Tcl/8.6.3-foss-2015a:/vol/fs01/tools/ubuntu14.04/easybuild/modules/all/SQLite/3.8.8.1-foss-2015a:/vol/fs01/tools/ubuntu14.04/easybuild/modules/all/Tk/8.6.3-foss-2015a-no-X11:/vol/fs01/tools/ubuntu14.04/easybuild/modules/all/Python/2.7.9-foss-2015a:/vol/fs01/tools/ubuntu14.04/easybuild/modules/all/Cython/0.22.1-foss-2015a-Python-2.7.9:/vol/fs01/tools/ubuntu14.04/easybuild/modules/all/pysam/0.8.3-foss-2015a-Python-2.7.9')
== 2015-08-10 14:51:54,618 main.environment INFO Environment variable LOADEDMODULES set to EasyBuild/2.2.0 (previous value: 'EasyBuild/2.2.0:GCC/4.9.2:numactl/2.0.10-GCC-4.9.2:hwloc/1.10.0-GCC-4.9.2:OpenMPI/1.8.4-GCC-4.9.2:OpenBLAS/0.2.13-GCC-4.9.2-LAPACK-3.5.0:gompi/2015a:FFTW/3.3.4-gompi-2015a:ScaLAPACK/2.0.2-gompi-2015a-OpenBLAS-0.2.13-LAPACK-3.5.0:foss/2015a:bzip2/1.0.6-foss-2015a:zlib/1.2.8-foss-2015a:ncurses/5.9-foss-2015a:libreadline/6.3-foss-2015a:Tcl/8.6.3-foss-2015a:SQLite/3.8.8.1-foss-2015a:Tk/8.6.3-foss-2015a-no-X11:Python/2.7.9-foss-2015a:Cython/0.22.1-foss-2015a-Python-2.7.9:pysam/0.8.3-foss-2015a-Python-2.7.9')
== 2015-08-10 14:51:54,619 main ERROR Sanity check failed: no file of ('bin/sv_counts',) in /vol/fs01/tools/ubuntu14.04/easybuild/software/svtyper/v0.0.2-Python-2.7.9 (at easybuild/software/EasyBuild/2.2.0/lib/python2.7/site-packages/easybuild_framework-2.2.0-py2.7.egg/easybuild/framework/easyblock.py:1653 in sanity_check_step)
== 2015-08-10 14:51:54,620 main.easyblock WARNING build failed (first 300 chars): Sanity check failed: no file of ('bin/sv_counts',) in /vol/fs01/tools/ubuntu14.04/easybuild/software/svtyper/v0.0.2-Python-2.7.9
== 2015-08-10 14:51:54,620 main.Tarball INFO Closing log for application name svtyper version v0.0.2
