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Singularity Builder Robot Logger, reporting for duty!

Installing Singularity Dependencies
Preparing logging... Logs available at http://10.138.0.6/ # SINGULARITY SINGULARITY_REPO: https://github.com/cclerget/singularity.git The Singularity repository being cloned by the builder. SINGULARITY_BRANCH: feature-squashbuild-secbuild-2.4.3 The branch of the repository being used. SINGULARITY_COMMIT: If defined, a particular commit to checkout. # SETTINGS SREGISTRY_USER_REPO: https://github.com/eilon-s/sherlock_vep Your repository we are building from! SINGULARITY_RECIPE: Singularity The recipe file in queue for build! SREGISTRY_USER_BRANCH: master The branch we are cloning to do your build. SREGISTRY_USER_TAG: latest The tag for the image. SREGISTRY_GOOGLE_STORAGE_PRIVATE: false Building a private image? # Installing Singularity git clone -b feature-squashbuild-secbuild-2.4.3 https://github.com/cclerget/singularity.git Using commit 4cd89c97d338362e6e91ed1f90f128f984d60d61 Install return value 0 /usr/local/bin/singularity Cloning User Repository https://github.com/eilon-s/sherlock_vep git clone -b master https://github.com/eilon-s/sherlock_vep Using commit c76f5591cb09e7d24b485872c5983e1208cec509 Found recipe: Singularity Start Time: Tue Mar 20 02:24:10 UTC 2018. Using container recipe deffile: Singularity Sanitizing environment Adding base Singularity environment to container Docker image path: index.docker.io/willmclaren/ensembl-vep:latest Cache folder set to /root/.singularity/docker [1/20] ||----------------------------------| 0.0% [1/20] |=|---------------------------------| 5.0% [2/20] |===|-------------------------------| 10.0% [3/20] |=====|-----------------------------| 15.0% [4/20] |=======|---------------------------| 20.0% [5/20] |========|--------------------------| 25.0% [6/20] |==========|------------------------| 30.0% [7/20] |============|----------------------| 35.0% [8/20] |==============|--------------------| 40.0% [9/20] |===============|-------------------| 45.0% [10/20] |=================|-----------------| 50.0% [11/20] |===================|---------------| 55.0% [12/20] |=====================|-------------| 60.0% [13/20] |======================|------------| 65.0% [14/20] |========================|----------| 70.0% [15/20] |==========================|--------| 75.0% [16/20] |============================|------| 80.0% [17/20] |=============================|-----| 85.0% [18/20] |===============================|---| 90.0% [19/20] |=================================|-| 95.0% [20/20] |===================================| 100.0% User defined %runscript found! Taking priority. Adding environment to container Running post scriptlet Setting up directories - fetching BioPerl - unpacking ./Bio/tmp/release-1-6-924.zip - moving files Attempting to install Bio::DB::HTS and htslib. >>> If this fails, try re-running with --NO_HTSLIB - checking out HTSLib - building HTSLIB in ./htslib In /htslib echo '/* Empty config.h generated by Makefile */' > config.h gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -c -o kfunc.o kfunc.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -c -o knetfile.o knetfile.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -c -o kstring.o kstring.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -c -o bgzf.o bgzf.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -c -o faidx.o faidx.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -c -o hfile.o hfile.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -c -o hfile_net.o hfile_net.c echo '#define HTS_VERSION "1.3.2-dirty"' > version.h gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -c -o hts.o hts.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -c -o md5.o md5.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -c -o regidx.o regidx.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -c -o sam.o sam.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -c -o synced_bcf_reader.o synced_bcf_reader.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -c -o vcf_sweep.o vcf_sweep.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -c -o tbx.o tbx.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -c -o vcf.o vcf.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -c -o vcfutils.o vcfutils.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -c -o cram/cram_codecs.o cram/cram_codecs.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -c -o cram/cram_decode.o cram/cram_decode.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -c -o cram/cram_encode.o cram/cram_encode.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -c -o cram/cram_external.o cram/cram_external.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -c -o cram/cram_index.o cram/cram_index.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -c -o cram/cram_io.o cram/cram_io.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -c -o cram/cram_samtools.o cram/cram_samtools.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -c -o cram/cram_stats.o cram/cram_stats.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -c -o cram/files.o cram/files.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -c -o cram/mFILE.o cram/mFILE.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -c -o cram/open_trace_file.o cram/open_trace_file.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -c -o cram/pooled_alloc.o cram/pooled_alloc.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -c -o cram/rANS_static.o cram/rANS_static.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -c -o cram/sam_header.o cram/sam_header.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -c -o cram/string_alloc.o cram/string_alloc.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -c -o cram/thread_pool.o cram/thread_pool.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -c -o cram/vlen.o cram/vlen.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -c -o cram/zfio.o cram/zfio.c ar -rc libhts.a kfunc.o knetfile.o kstring.o bgzf.o faidx.o hfile.o hfile_net.o hts.o md5.o regidx.o sam.o synced_bcf_reader.o vcf_sweep.o tbx.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_samtools.o cram/cram_stats.o cram/files.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/rANS_static.o cram/sam_header.o cram/string_alloc.o cram/thread_pool.o cram/vlen.o cram/zfio.o ranlib libhts.a gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -fpic -c -o kfunc.pico kfunc.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -fpic -c -o knetfile.pico knetfile.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -fpic -c -o kstring.pico kstring.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -fpic -c -o bgzf.pico bgzf.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -fpic -c -o faidx.pico faidx.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -fpic -c -o hfile.pico hfile.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -fpic -c -o hfile_net.pico hfile_net.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -fpic -c -o hts.pico hts.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -fpic -c -o md5.pico md5.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -fpic -c -o regidx.pico regidx.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -fpic -c -o sam.pico sam.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -fpic -c -o synced_bcf_reader.pico synced_bcf_reader.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -fpic -c -o vcf_sweep.pico vcf_sweep.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -fpic -c -o tbx.pico tbx.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -fpic -c -o vcf.pico vcf.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -fpic -c -o vcfutils.pico vcfutils.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -fpic -c -o cram/cram_codecs.pico cram/cram_codecs.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -fpic -c -o cram/cram_decode.pico cram/cram_decode.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -fpic -c -o cram/cram_encode.pico cram/cram_encode.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -fpic -c -o cram/cram_external.pico cram/cram_external.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -fpic -c -o cram/cram_index.pico cram/cram_index.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -fpic -c -o cram/cram_io.pico cram/cram_io.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -fpic -c -o cram/cram_samtools.pico cram/cram_samtools.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -fpic -c -o cram/cram_stats.pico cram/cram_stats.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -fpic -c -o cram/files.pico cram/files.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -fpic -c -o cram/mFILE.pico cram/mFILE.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -fpic -c -o cram/open_trace_file.pico cram/open_trace_file.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -fpic -c -o cram/pooled_alloc.pico cram/pooled_alloc.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -fpic -c -o cram/rANS_static.pico cram/rANS_static.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -fpic -c -o cram/sam_header.pico cram/sam_header.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -fpic -c -o cram/string_alloc.pico cram/string_alloc.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -fpic -c -o cram/thread_pool.pico cram/thread_pool.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -fpic -c -o cram/vlen.pico cram/vlen.c gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -fpic -c -o cram/zfio.pico cram/zfio.c gcc -shared -Wl,-soname,libhts.so.1 -pthread -o libhts.so kfunc.pico knetfile.pico kstring.pico bgzf.pico faidx.pico hfile.pico hfile_net.pico hts.pico md5.pico regidx.pico sam.pico synced_bcf_reader.pico vcf_sweep.pico tbx.pico vcf.pico vcfutils.pico cram/cram_codecs.pico cram/cram_decode.pico cram/cram_encode.pico cram/cram_external.pico cram/cram_index.pico cram/cram_io.pico cram/cram_samtools.pico cram/cram_stats.pico cram/files.pico cram/mFILE.pico cram/open_trace_file.pico cram/pooled_alloc.pico cram/rANS_static.pico cram/sam_header.pico cram/string_alloc.pico cram/thread_pool.pico cram/vlen.pico cram/zfio.pico -lz -lm ln -sf libhts.so libhts.so.1 gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -c -o bgzip.o bgzip.c gcc -pthread -o bgzip bgzip.o libhts.a -lz gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -c -o htsfile.o htsfile.c gcc -pthread -o htsfile htsfile.o libhts.a -lz gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -c -o tabix.o tabix.c gcc -pthread -o tabix tabix.o libhts.a -lz gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -c -o test/fieldarith.o test/fieldarith.c gcc -pthread -o test/fieldarith test/fieldarith.o libhts.a -lz gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -c -o test/hfile.o test/hfile.c gcc -pthread -o test/hfile test/hfile.o libhts.a -lz gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -c -o test/sam.o test/sam.c gcc -pthread -o test/sam test/sam.o libhts.a -lz gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -c -o test/test-regidx.o test/test-regidx.c gcc -pthread -o test/test-regidx test/test-regidx.o libhts.a -lz gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -c -o test/test_view.o test/test_view.c gcc -pthread -o test/test_view test/test_view.o libhts.a -lz gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -c -o test/test-vcf-api.o test/test-vcf-api.c gcc -pthread -o test/test-vcf-api test/test-vcf-api.o libhts.a -lz gcc -g -Wall -O2 -fPIC -Wno-unused -Wno-unused-result -I. -c -o test/test-vcf-sweep.o test/test-vcf-sweep.c gcc -pthread -o test/test-vcf-sweep test/test-vcf-sweep.o libhts.a -lz - unpacking ./Bio/tmp/biodbhts.zip to ./Bio/tmp/ ./Bio/tmp/Bio-DB-HTS-2.9 - moving files to ./biodbhts - making Bio::DB:HTS Created MYMETA.yml and MYMETA.json Creating new 'Build' script for 'Bio-DB-HTS' version '2.9' Building Bio-DB-HTS x86_64-linux-gnu-gcc -I/htslib/htslib -I/usr/lib/x86_64-linux-gnu/perl/5.22/CORE -DXS_VERSION="2.9" -DVERSION="2.9" -fPIC -D_IOLIB=2 -D_FILE_OFFSET_BITS=64 -Wno-error -Wno-unused-result -c -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fwrapv -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -g -o lib/Bio/DB/HTS.o lib/Bio/DB/HTS.c ExtUtils::Mkbootstrap::Mkbootstrap('blib/arch/auto/Bio/DB/HTS/HTS.bs') x86_64-linux-gnu-gcc -shared -L/usr/local/lib -fstack-protector-strong -o blib/arch/auto/Bio/DB/HTS/HTS.so lib/Bio/DB/HTS.o -L/htslib -Wl,-rpath,/htslib -lhts -lpthread -lz x86_64-linux-gnu-gcc -I/htslib/htslib -I/usr/lib/x86_64-linux-gnu/perl/5.22/CORE -DXS_VERSION="2.9" -DVERSION="2.9" -fPIC -D_IOLIB=2 -D_FILE_OFFSET_BITS=64 -Wno-error -Wno-unused-result -c -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fwrapv -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -g -o lib/Bio/DB/HTS/Faidx.o lib/Bio/DB/HTS/Faidx.c ExtUtils::Mkbootstrap::Mkbootstrap('blib/arch/auto/Bio/DB/HTS/Faidx/Faidx.bs') x86_64-linux-gnu-gcc -shared -L/usr/local/lib -fstack-protector-strong -o blib/arch/auto/Bio/DB/HTS/Faidx/Faidx.so lib/Bio/DB/HTS/Faidx.o -L/htslib -Wl,-rpath,/htslib -lhts -lpthread -lz Downloading required Ensembl API files - fetching ensembl - unpacking ./Bio/tmp/ensembl.zip - moving files - getting version information - fetching ensembl-variation - unpacking ./Bio/tmp/ensembl-variation.zip - moving files - getting version information - fetching ensembl-funcgen - unpacking ./Bio/tmp/ensembl-funcgen.zip - moving files - getting version information - fetching ensembl-io - unpacking ./Bio/tmp/ensembl-io.zip - moving files - getting version information Testing VEP installation /home/vep/src/ensembl-vep/t/TranscriptTree.t ................................. ok /home/vep/src/ensembl-vep/t/Utils.t .......................................... ok /home/vep/src/ensembl-vep/t/OutputFactory.t .................................. ok /home/vep/src/ensembl-vep/t/AnnotationSource_File_BED.t ...................... ok /home/vep/src/ensembl-vep/t/Stats.t .......................................... ok /home/vep/src/ensembl-vep/t/AnnotationSource_Cache.t ......................... ok /home/vep/src/ensembl-vep/t/InputBuffer.t .................................... ok /home/vep/src/ensembl-vep/t/OutputFactory_VCF.t .............................. ok /home/vep/src/ensembl-vep/t/Parser.t ......................................... ok /home/vep/src/ensembl-vep/t/Runner.t ......................................... ok /home/vep/src/ensembl-vep/t/Parser_VEP_input.t ............................... ok /home/vep/src/ensembl-vep/t/version.t ........................................ ok /home/vep/src/ensembl-vep/t/bam_edit.t ....................................... ok /home/vep/src/ensembl-vep/t/AnnotationSource_Database_RegFeat.t .............. ok /home/vep/src/ensembl-vep/t/Haplo_AnnotationSource_File_GTF.t ................ ok /home/vep/src/ensembl-vep/t/AnnotationSource_Cache_Transcript.t .............. ok /home/vep/src/ensembl-vep/t/AnnotationSource_Cache_VariationTabix.t .......... ok /home/vep/src/ensembl-vep/t/AnnotationSource_File.t .......................... ok /home/vep/src/ensembl-vep/t/OutputFactory_VEP_output.t ....................... ok /home/vep/src/ensembl-vep/t/AnnotationSource_Database_StructuralVariation.t .. ok /home/vep/src/ensembl-vep/t/Haplo_AnnotationSource_Database_Transcript.t ..... ok /home/vep/src/ensembl-vep/t/Haplo_AnnotationSource_File_GFF.t ................ ok /home/vep/src/ensembl-vep/t/AnnotationSourceAdaptor.t ........................ ok /home/vep/src/ensembl-vep/t/Parser_HGVS.t .................................... ok /home/vep/src/ensembl-vep/t/AnnotationSource.t ............................... ok /home/vep/src/ensembl-vep/t/AnnotationSource_Cache_Variation.t ............... ok /home/vep/src/ensembl-vep/t/AnnotationSource_Database_Variation.t ............ ok /home/vep/src/ensembl-vep/t/VariantRecoder.t ................................. ok /home/vep/src/ensembl-vep/t/Parser_ID.t ...................................... ok /home/vep/src/ensembl-vep/t/AnnotationSource_File_VCF.t ...................... ok /home/vep/src/ensembl-vep/t/AnnotationSource_Database_Transcript.t ........... ok /home/vep/src/ensembl-vep/t/CacheDir.t ....................................... ok /home/vep/src/ensembl-vep/t/Haplo_Parser_VCF.t ............................... ok /home/vep/src/ensembl-vep/t/OutputFactory_Tab.t .............................. ok /home/vep/src/ensembl-vep/t/AnnotationSource_File_GTF.t ...................... ok /home/vep/src/ensembl-vep/t/AnnotationSource_Cache_RegFeat.t ................. ok /home/vep/src/ensembl-vep/t/Config.t ......................................... ok /home/vep/src/ensembl-vep/t/Parser_Region.t .................................. ok /home/vep/src/ensembl-vep/t/Haplo_AnnotationSource_Cache_Transcript.t ........ ok /home/vep/src/ensembl-vep/t/Haplo_Runner.t ................................... ok /home/vep/src/ensembl-vep/t/Haplo_InputBuffer.t .............................. ok /home/vep/src/ensembl-vep/t/BaseVEP.t ........................................ ok /home/vep/src/ensembl-vep/t/AnnotationSource_File_GFF.t ...................... ok /home/vep/src/ensembl-vep/t/OutputFactory_JSON.t ............................. ok /home/vep/src/ensembl-vep/t/FilterSet.t ...................................... ok /home/vep/src/ensembl-vep/t/Parser_VCF.t ..................................... ok /home/vep/src/ensembl-vep/t/AnnotationSource_File_BigWig.t ................... ok All tests successful. Files=47, Tests=1785, 95 wallclock secs ( 0.30 usr 0.06 sys + 90.30 cusr 2.82 csys = 93.48 CPU) Result: PASS - OK! - getting list of available cache files - downloading ftp://ftp.ensembl.org/pub/release-91/variation/VEP/saccharomyces_cerevisiae_vep_91_R64-1-1.tar.gz - unpacking saccharomyces_cerevisiae_vep_91_R64-1-1.tar.gz - converting cache, this may take some time but will allow VEP to look up variants and frequency data much faster - use CTRL-C to cancel if you do not wish to convert this cache now (you may run convert_cache.pl later) 2018-03-20 02:28:10 - Processing saccharomyces_cerevisiae 2018-03-20 02:28:10 - Processing version 91_R64-1-1 2018-03-20 02:28:10 - Processing _var cache type [> ] [ 0% ] [===> ] [ 9% ] [======> ] [ 14% ] [=========> ] [ 19% ] [============> ] [ 23% ] [==================> ] [ 33% ] [====================> ] [ 38% ] [=======================> ] [ 42% ] [=============================> ] [ 52% ] [================================> ] [ 57% ] [===================================> ] [ 61% ] [======================================> ] [ 66% ] [========================================> ] [ 71% ] [===========================================> ] [ 76% ] [==============================================> ] [ 80% ] [=================================================> ] [ 85% ] [=======================================================> ] [ 95% ] [===========================================================] [ 100% ] 2018-03-20 02:28:13 - All done! - downloading Saccharomyces_cerevisiae.R64-1-1.dna.toplevel.fa.gz - downloading Saccharomyces_cerevisiae.R64-1-1.dna.toplevel.fa.gz.fai - downloading Saccharomyces_cerevisiae.R64-1-1.dna.toplevel.fa.gz.gzi The FASTA file should be automatically detected by the VEP when using --cache or --offline. If it is not, use "--fasta /home/vep/.vep/saccharomyces_cerevisiae/91_R64-1-1/Saccharomyces_cerevisiae.R64-1-1.dna.toplevel.fa.gz" All done Setting up directories - fetching BioPerl - unpacking ./Bio/tmp/release-1-6-924.zip - moving files Attempting to install Bio::DB::HTS and htslib. >>> If this fails, try re-running with --NO_HTSLIB - checking out HTSLib - building HTSLIB in ./htslib In /htslib make: Nothing to be done for 'all'. - unpacking ./Bio/tmp/biodbhts.zip to ./Bio/tmp/ ./Bio/tmp/Bio-DB-HTS-2.9 - moving files to ./biodbhts - making Bio::DB:HTS Created MYMETA.yml and MYMETA.json Creating new 'Build' script for 'Bio-DB-HTS' version '2.9' Building Bio-DB-HTS x86_64-linux-gnu-gcc -I/htslib/htslib -I/usr/lib/x86_64-linux-gnu/perl/5.22/CORE -DXS_VERSION="2.9" -DVERSION="2.9" -fPIC -D_IOLIB=2 -D_FILE_OFFSET_BITS=64 -Wno-error -Wno-unused-result -c -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fwrapv -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -g -o lib/Bio/DB/HTS/Faidx.o lib/Bio/DB/HTS/Faidx.c ExtUtils::Mkbootstrap::Mkbootstrap('blib/arch/auto/Bio/DB/HTS/Faidx/Faidx.bs') x86_64-linux-gnu-gcc -shared -L/usr/local/lib -fstack-protector-strong -o blib/arch/auto/Bio/DB/HTS/Faidx/Faidx.so lib/Bio/DB/HTS/Faidx.o -L/htslib -Wl,-rpath,/htslib -lhts -lpthread -lz x86_64-linux-gnu-gcc -I/htslib/htslib -I/usr/lib/x86_64-linux-gnu/perl/5.22/CORE -DVERSION="2.9" -DXS_VERSION="2.9" -fPIC -D_IOLIB=2 -D_FILE_OFFSET_BITS=64 -Wno-error -Wno-unused-result -c -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fwrapv -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -g -o lib/Bio/DB/HTS.o lib/Bio/DB/HTS.c ExtUtils::Mkbootstrap::Mkbootstrap('blib/arch/auto/Bio/DB/HTS/HTS.bs') x86_64-linux-gnu-gcc -shared -L/usr/local/lib -fstack-protector-strong -o blib/arch/auto/Bio/DB/HTS/HTS.so lib/Bio/DB/HTS.o -L/htslib -Wl,-rpath,/htslib -lhts -lpthread -lz Downloading required Ensembl API files - fetching ensembl - unpacking ./Bio/tmp/ensembl.zip - moving files - getting version information - fetching ensembl-variation - unpacking ./Bio/tmp/ensembl-variation.zip - moving files - getting version information - fetching ensembl-funcgen - unpacking ./Bio/tmp/ensembl-funcgen.zip - moving files - getting version information - fetching ensembl-io - unpacking ./Bio/tmp/ensembl-io.zip - moving files - getting version information Testing VEP installation /home/vep/src/ensembl-vep/t/TranscriptTree.t ................................. ok /home/vep/src/ensembl-vep/t/Utils.t .......................................... ok /home/vep/src/ensembl-vep/t/OutputFactory.t .................................. ok /home/vep/src/ensembl-vep/t/AnnotationSource_File_BED.t ...................... ok /home/vep/src/ensembl-vep/t/Stats.t .......................................... ok /home/vep/src/ensembl-vep/t/AnnotationSource_Cache.t ......................... ok /home/vep/src/ensembl-vep/t/InputBuffer.t .................................... ok /home/vep/src/ensembl-vep/t/OutputFactory_VCF.t .............................. ok /home/vep/src/ensembl-vep/t/Parser.t ......................................... ok /home/vep/src/ensembl-vep/t/Runner.t ......................................... ok /home/vep/src/ensembl-vep/t/Parser_VEP_input.t ............................... ok /home/vep/src/ensembl-vep/t/version.t ........................................ ok /home/vep/src/ensembl-vep/t/bam_edit.t ....................................... ok /home/vep/src/ensembl-vep/t/AnnotationSource_Database_RegFeat.t .............. ok /home/vep/src/ensembl-vep/t/Haplo_AnnotationSource_File_GTF.t ................ ok /home/vep/src/ensembl-vep/t/AnnotationSource_Cache_Transcript.t .............. ok /home/vep/src/ensembl-vep/t/AnnotationSource_Cache_VariationTabix.t .......... ok /home/vep/src/ensembl-vep/t/AnnotationSource_File.t .......................... ok /home/vep/src/ensembl-vep/t/OutputFactory_VEP_output.t ....................... ok /home/vep/src/ensembl-vep/t/AnnotationSource_Database_StructuralVariation.t .. ok /home/vep/src/ensembl-vep/t/Haplo_AnnotationSource_Database_Transcript.t ..... ok /home/vep/src/ensembl-vep/t/Haplo_AnnotationSource_File_GFF.t ................ ok /home/vep/src/ensembl-vep/t/AnnotationSourceAdaptor.t ........................ ok /home/vep/src/ensembl-vep/t/Parser_HGVS.t .................................... ok /home/vep/src/ensembl-vep/t/AnnotationSource.t ............................... ok /home/vep/src/ensembl-vep/t/AnnotationSource_Cache_Variation.t ............... ok /home/vep/src/ensembl-vep/t/AnnotationSource_Database_Variation.t ............ ok /home/vep/src/ensembl-vep/t/VariantRecoder.t ................................. ok /home/vep/src/ensembl-vep/t/Parser_ID.t ...................................... ok /home/vep/src/ensembl-vep/t/AnnotationSource_File_VCF.t ...................... ok /home/vep/src/ensembl-vep/t/AnnotationSource_Database_Transcript.t ........... ok /home/vep/src/ensembl-vep/t/CacheDir.t ....................................... ok /home/vep/src/ensembl-vep/t/Haplo_Parser_VCF.t ............................... ok /home/vep/src/ensembl-vep/t/OutputFactory_Tab.t .............................. ok /home/vep/src/ensembl-vep/t/AnnotationSource_File_GTF.t ...................... ok /home/vep/src/ensembl-vep/t/AnnotationSource_Cache_RegFeat.t ................. ok /home/vep/src/ensembl-vep/t/Config.t ......................................... ok /home/vep/src/ensembl-vep/t/Parser_Region.t .................................. ok /home/vep/src/ensembl-vep/t/Haplo_AnnotationSource_Cache_Transcript.t ........ ok /home/vep/src/ensembl-vep/t/Haplo_Runner.t ................................... ok /home/vep/src/ensembl-vep/t/Haplo_InputBuffer.t .............................. ok /home/vep/src/ensembl-vep/t/BaseVEP.t ........................................ ok /home/vep/src/ensembl-vep/t/AnnotationSource_File_GFF.t ...................... ok /home/vep/src/ensembl-vep/t/OutputFactory_JSON.t ............................. ok /home/vep/src/ensembl-vep/t/FilterSet.t ...................................... ok /home/vep/src/ensembl-vep/t/Parser_VCF.t ..................................... ok /home/vep/src/ensembl-vep/t/AnnotationSource_File_BigWig.t ................... ok All tests successful. Files=47, Tests=1785, 91 wallclock secs ( 0.29 usr 0.08 sys + 86.86 cusr 2.61 csys = 89.84 CPU) Result: PASS - OK! - getting list of available cache files - downloading ftp://ftp.ensembl.org/pub/release-91/variation/VEP/homo_sapiens_vep_91_GRCh37.tar.gz - unpacking homo_sapiens_vep_91_GRCh37.tar.gz - converting cache, this may take some time but will allow VEP to look up variants and frequency data much faster - use CTRL-C to cancel if you do not wish to convert this cache now (you may run convert_cache.pl later) 2018-03-20 02:39:57 - Processing homo_sapiens 2018-03-20 02:39:57 - Processing version 91_GRCh37 2018-03-20 02:39:57 - Processing _var cache type [> ] [ 0% ] [> ] [ 0% ] [> ] [ 1% ] [=> ] [ 5% ] [=> ] [ 6% ] [====> ] [ 11% ] [=======> ] [ 15% ] [=========> ] [ 18% ] [==========> ] [ 20% ] [==========> ] [ 21% ] [===========> ] [ 21% ] [============> ] [ 24% ] [================> ] [ 31% ] [=================> ] [ 31% ] [=================> ] [ 32% ] [==================> ] [ 34% ] [===================> ] [ 35% ] [=====================> ] [ 38% ] [=======================> ] [ 43% ] [========================> ] [ 43% ] [========================> ] [ 44% ] [=========================> ] [ 45% ] [=========================> ] [ 46% ] [==========================> ] [ 47% ] [==========================> ] [ 48% ] [===========================> ] [ 48% ] [===========================> ] [ 49% ] [============================> ] [ 51% ] [=============================> ] [ 51% ] [=============================> ] [ 52% ] [=============================> ] [ 53% ] [================================> ] [ 56% ] [================================> ] [ 57% ] [===================================> ] [ 62% ] [===================================> ] [ 63% ] [====================================> ] [ 64% ] [=====================================> ] [ 65% ] [=========================================> ] [ 72% ] [===========================================> ] [ 76% ] [============================================> ] [ 76% ] [============================================> ] [ 77% ] [==============================================> ] [ 80% ] [==============================================> ] [ 81% ] [===============================================> ] [ 83% ] [================================================> ] [ 83% ] [==================================================> ] [ 88% ] [===================================================> ] [ 88% ] [===================================================> ] [ 89% ] [====================================================> ] [ 90% ] [======================================================> ] [ 94% ] [========================================================> ] [ 98% ] [=========================================================> ] [ 98% ] [=========================================================> ] [ 99% ] [===========================================================] [ 100% ] 2018-03-20 04:22:42 - All done! WARNING: Changing FTP URL for GRCh37 - downloading Homo_sapiens.GRCh37.75.dna.primary_assembly.fa.gz - converting sequence data to bgzip format, this may take some time... - conversion successful - indexing FASTA file - indexing OK The FASTA file should be automatically detected by the VEP when using --cache or --offline. If it is not, use "--fasta /home/vep/.vep/homo_sapiens/91_GRCh37/Homo_sapiens.GRCh37.75.dna.primary_assembly.fa.gz" All done Adding runscript Adding runscript help Finalizing Singularity container Calculating final size for metadata... Skipping checks Building Singularity image... Singularity container built: c76f5591cb09e7d24b485872c5983e1208cec509.simg Cleaning up... Return value of 0. End Time: Tue Mar 20 05:03:37 UTC 2018. Upload with format: [storage-bucket] : sregistry-vanessa [github-namespace] : github.com/[container]/[branch]/[commit] [container] : eilon-s/sherlock_vep [commit] : c76f5591cb09e7d24b485872c5983e1208cec509 [branch] : master [sha256sum] : 591c0bd8879547909a98966ef43b17ce8d1a50712121d547b0e823f7452443fe [tag] : latest gs://[storage-bucket]/github.com/[github-namespace]/[sha256sum]:[tag].simg gs://sregistry-vanessa/github.com/eilon-s/sherlock_vep/master/c76f5591cb09e7d24b485872c5983e1208cec509/591c0bd8879547909a98966ef43b17ce8d1a50712121d547b0e823f7452443fe:latest.simg gsutil cp -a public-read c76f5591cb09e7d24b485872c5983e1208cec509.simg gs://sregistry-vanessa/github.com/eilon-s/sherlock_vep/master/c76f5591cb09e7d24b485872c5983e1208cec509/591c0bd8879547909a98966ef43b17ce8d1a50712121d547b0e823f7452443fe:latest.simg