CNVDiscoveryPipeline 2 Jobs Fail

EADGEADG KielMember ✭✭✭
edited February 2017 in GenomeSTRiP

HI,

Iam running GenomeStrip (lattest version) locally in a Docker-Container with wdl. I can run SVPrepross without any errors for my samples. For saving time I run GenomeStrip only on Chr11/14. When I start CNVDiscoveryPipeline it process 279 jobs fine...another one fail. But when I take a look at the logs the job finish successfully.

My commandline:

   set -o pipefail
   export SV_DIR=${SV_Dir}
   tar -xf ${metaData_archive} &&  cd svRun &&\
   java -Xmx12g -cp ${classpath} \
     org.broadinstitute.gatk.queue.QCommandLine \
     -S ${SV_Dir}/qscript/discovery/cnv/CNVDiscoveryPipeline.q \
     -S ${SV_Dir}/qscript/SVQScript.q \
     -cp ${classpath} \
     -gatk ${SV_Dir}/lib/gatk/GenomeAnalysisTK.jar \
     -configFile ${SV_Dir}/conf/genstrip_parameters.txt \
     -R ${ref_fasta} \
     -I ${input_bam} \
     -md metadata \
     -jobRunner Shell -gatkJobRunner Shell \
     -runDirectory run1 \
     -jobLogDir run1/logs \
     -l DEBUG \
     -intervalList ${intervalList} \
     -tilingWindowSize 1000 \
     -tilingWindowOverlap 500 \
     -maximumReferenceGapLength 1000 \
     -boundaryPrecision 100 \
     -minimumRefinedLength 500 \
     -run

The stderr from wdl (part)

INFO  09:48:19,662 QGraph - Failed:   'java'  '-Xmx4096m'  '-XX:+UseParallelOldGC'  '-XX:ParallelGCThreads=4'  '-XX:GCTimeLimit=50'  '-XX:GCHeapFreeLimit=10'  '-Djava.io.tmpdir=/root/Translocat [...]

INFO  09:48:19,662 QGraph - Log:     /root/TranslocationWorkflow/da98e721-c0ff-438e-86f3-14a63bc1cb46/call-CNVDiscovery/execution/svRun/run1/cnv_stage2/seq_chr11/logs/CNVDiscoveryStage2-231.out

INFO  09:48:19,663 QCommandLine - Script failed: 8 Pend, 0 Run, 1 Fail, 269 Done

DEBUG 10:23:12,115 IOUtils - Deleted /root/TranslocationWorkflow/da98e721-c0ff-438e-86f3-14a63bc1cb46/call-CNVDiscovery/execution/svRun/.queue/tmp/.exec4114067890890442215[...]

ERROR 10:23:12,117 FunctionEdge - Error:  'java'  '-Xmx2048m'  '-XX:+UseParallelOldGC'  '-XX:ParallelGCThreads=4'  '-XX:GCTimeLimit=50'  '-XX:GCHeapFreeLimit=10'  '-Djava.io.tmpdir=/root/Transl[...]

ERROR 10:23:12,133 FunctionEdge - Contents of /root/TranslocationWorkflow/da98e721-c0ff-438e-86f3-14a63bc1cb46/call-CNVDiscovery/execution/svRun/run1/logs/CNVDiscoveryPipeline-9.out:

CNVDiscoveryStage2-231.out

INFO  09:39:55,282 HelpFormatter - -----------------------------------------------------------------------------------------
INFO  09:39:55,286 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.5.GS-r1678-6-gf101448, Compiled 2017/01/24 12:43:00
INFO  09:39:55,286 HelpFormatter - Copyright (c) 2010 The Broad Institute
INFO  09:39:55,287 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
INFO  09:39:55,294 HelpFormatter - Program Args: -T SVGenotyperWalker -R /root/TranslocationWorkflow/da98e721-c0ff-438e-86f3-14a63bc1cb46/call-CNVDiscovery/inputs/data/reference/meta/metadata/ref/Homo_sapiens_assembly38/Homo_sapiens_assem$
INFO  09:39:55,298 HelpFormatter - Executing as [email protected] on Linux 3.16.0-4-amd64 amd64; OpenJDK 64-Bit Server VM 1.8.0_111-8u111-b14-2~bpo8+1-b14.
INFO  09:39:55,299 HelpFormatter - Date/Time: 2017/02/21 09:39:55
INFO  09:39:55,299 HelpFormatter - -----------------------------------------------------------------------------------------
INFO  09:39:55,300 HelpFormatter - -----------------------------------------------------------------------------------------
INFO  09:39:55,399 21-Feb-2017 GenomeAnalysisEngine - Strictness is SILENT
INFO  09:39:55,735 21-Feb-2017 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
INFO  09:39:55,886 21-Feb-2017 IntervalUtils - Processing 1 bp from intervals
INFO  09:39:55,983 21-Feb-2017 GenomeAnalysisEngine - Preparing for traversal
INFO  09:39:55,984 21-Feb-2017 GenomeAnalysisEngine - Done preparing for traversal
INFO  09:39:55,984 21-Feb-2017 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
INFO  09:39:55,985 21-Feb-2017 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
INFO  09:39:55,985 21-Feb-2017 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
INFO  09:39:55,989 21-Feb-2017 SVGenotyper - Opening reference sequence ...
INFO  09:39:55,990 21-Feb-2017 SVGenotyper - Opened reference sequence.
INFO  09:39:55,990 21-Feb-2017 SVGenotyper - Initializing input data set ...
INFO  09:39:56,070 21-Feb-2017 SVGenotyper - Initialized data set: 1 file, 1 read group, 1 sample.
INFO  09:39:56,071 21-Feb-2017 MetaData - Opening metadata ...
INFO  09:39:56,071 21-Feb-2017 MetaData - Adding metadata directory metadata ...
INFO  09:39:56,072 21-Feb-2017 MetaData - Opened metadata.
INFO  09:39:56,168 21-Feb-2017 MetaData - Loading insert size distributions ...
INFO  09:39:56,276 21-Feb-2017 ReadCountDiskCache - Initializing read count disk cache [metadata/rccache.bin] ...
INFO  09:39:56,277 21-Feb-2017 ReadCountDiskCache - Initialized read count disk cache with 1 file.
INFO  09:39:59,322 21-Feb-2017 ProgressMeter -            done         0.0     3.0 s       5.5 w      100.0%     3.0 s       0.0 s
INFO  09:39:59,322 21-Feb-2017 ProgressMeter - Total runtime 3.34 secs, 0.06 min, 0.00 hours
INFO  09:40:00,579 21-Feb-2017 GATKRunReport - Uploaded run statistics report to AWS S3

Any suggestions to fix this ?
Thanks!

Greetings EADG:)

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