Dear Genome STRiP users,
I am running SVCNVDiscovery pipeline to 10686 samples with successfully completed SVPreprocesse. I met two "java.lang.RuntimeException" errors in the output.
Exception in thread "main" java.lang.RuntimeException: Read count cache file file:///proj/yunligrp/users/minzhi/gs/freeze6-AA_chr16/svpre_freeze6-AA_chr16_standard_full_single_1-500000over1-500000_parallel_success/md_tempdir/rccache.bin is truncated
at org.broadinstitute.sv.commandline.CommandLineProgram.execute(CommandLineProgram.java:65)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:256)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:158)
at org.broadinstitute.sv.commandline.CommandLineProgram.runAndReturnResult(CommandLineProgram.java:29)
at org.broadinstitute.sv.commandline.CommandLineProgram.run(CommandLineProgram.java:25)
at org.broadinstitute.sv.genotyping.RefineCNVBoundaries.main(RefineCNVBoundaries.java:133)
Caused by: java.lang.RuntimeException: Read count cache file file:///proj/yunligrp/users/minzhi/gs/freeze6-AA_chr16/svpre_freeze6-AA_chr16_standard_full_single_1-500000over1-500000_parallel_success/md_tempdir/rccache.bin is truncated
at org.broadinstitute.sv.metadata.depth.ReadCountFileReader$ReadCountDataIterator.decodeRow(ReadCountFileReader.java:516)
at org.broadinstitute.sv.metadata.depth.ReadCountFileReader$ReadCountDataIterator.getReadCacheItems(ReadCountFileReader.java:470)
at org.broadinstitute.sv.metadata.depth.ReadCountFileReader$ReadCountDataIterator.aggregateSampleReadCounts(ReadCountFileReader.java:476)
at org.broadinstitute.sv.metadata.depth.ReadCountFileReader.getReadCounts(ReadCountFileReader.java:266)
at org.broadinstitute.sv.common.ReadCountCache.getReadCounts(ReadCountCache.java:100)
at org.broadinstitute.sv.genotyping.GenotypingDepthModule.computeRefReadCounts(GenotypingDepthModule.java:295)
at org.broadinstitute.sv.genotyping.GenotypingDepthModule.computeRefReadCounts(GenotypingDepthModule.java:245)
at org.broadinstitute.sv.genotyping.GenotypingDepthModule.getReadCounts(GenotypingDepthModule.java:230)
at org.broadinstitute.sv.genotyping.GenotypingDepthModule.getCnpReadCounts(GenotypingDepthModule.java:217)
at org.broadinstitute.sv.genotyping.GenotypingDepthModule.genotypeCnp(GenotypingDepthModule.java:141)
at org.broadinstitute.sv.genotyping.BoundaryRefinementAlgorithm.genotypeCnp(BoundaryRefinementAlgorithm.java:287)
at org.broadinstitute.sv.genotyping.BoundaryRefinementAlgorithm.refineOneBoundary(BoundaryRefinementAlgorithm.java:633)
at org.broadinstitute.sv.genotyping.BoundaryRefinementAlgorithm.refineBoundaryStep(BoundaryRefinementAlgorithm.java:553)
at org.broadinstitute.sv.genotyping.BoundaryRefinementAlgorithm.refineBoundaries(BoundaryRefinementAlgorithm.java:536)
at org.broadinstitute.sv.genotyping.BoundaryRefinementAlgorithm.processVariant(BoundaryRefinementAlgorithm.java:232)
at org.broadinstitute.sv.genotyping.RefineCNVBoundaries.run(RefineCNVBoundaries.java:204)
at org.broadinstitute.sv.commandline.CommandLineProgram.execute(CommandLineProgram.java:54)
... 5 more
INFO 23:29:51,212 QGraph - Writing incremental jobs reports...
INFO 23:29:51,213 QGraph - 4 Pend, 5 Run, 1 Fail, 33 Done
INFO 23:30:51,242 FunctionEdge - Done: 'java' '-Xmx102400m' ...
...
INFO 23:25:21,377 MetaData - Opened metadata.
INFO 23:25:21,436 RefineCNVBoundaries - Initializing input data set ...
INFO 23:25:31,820 RefineCNVBoundaries - Initialized data set: 1 file, 121337 read groups, 10148 samples.
INFO 23:25:32,452 ReadCountCache - Initializing read count cache with 1 file.
mInputFile=file:///proj/yunligrp/users/minzhi/gs/freeze6-AA_chr16/svpre_freeze6-AA_chr16_standard_full_single_1-500000over1-500000_parallel_success/md_tempdir/rccache.bin mCurrentSequenceName=chr16; mCurrentPosition=500001
Exception in thread "main" java.lang.RuntimeException: Read count cache file file:///proj/yunligrp/users/minzhi/gs/freeze6-AA_chr16/svpre_freeze6-AA_chr16_standard_full_single_1-500000over1-500000_parallel_success/md_tempdir/rccache.bin is truncated
at org.broadinstitute.sv.commandline.CommandLineProgram.execute(CommandLineProgram.java:65)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:256)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:158)
at org.broadinstitute.sv.commandline.CommandLineProgram.runAndReturnResult(CommandLineProgram.java:29)
at org.broadinstitute.sv.commandline.CommandLineProgram.run(CommandLineProgram.java:25)
at org.broadinstitute.sv.genotyping.RefineCNVBoundaries.main(RefineCNVBoundaries.java:133)
Caused by: java.lang.RuntimeException: Read count cache file file:///proj/yunligrp/users/minzhi/gs/freeze6-AA_chr16/svpre_freeze6-AA_chr16_standard_full_single_1-500000over1-500000_parallel_success/md_tempdir/rccache.bin is truncated
at org.broadinstitute.sv.metadata.depth.ReadCountFileReader$ReadCountDataIterator.decodeRow(ReadCountFileReader.java:516)
at org.broadinstitute.sv.metadata.depth.ReadCountFileReader$ReadCountDataIterator.getReadCacheItems(ReadCountFileReader.java:470)
at org.broadinstitute.sv.metadata.depth.ReadCountFileReader$ReadCountDataIterator.aggregateSampleReadCounts(ReadCountFileReader.java:476)
at org.broadinstitute.sv.metadata.depth.ReadCountFileReader.getReadCounts(ReadCountFileReader.java:266)
at org.broadinstitute.sv.common.ReadCountCache.getReadCounts(ReadCountCache.java:100)
at org.broadinstitute.sv.genotyping.GenotypingDepthModule.computeRefReadCounts(GenotypingDepthModule.java:295)
at org.broadinstitute.sv.genotyping.GenotypingDepthModule.computeRefReadCounts(GenotypingDepthModule.java:245)
at org.broadinstitute.sv.genotyping.GenotypingDepthModule.getReadCounts(GenotypingDepthModule.java:230)
at org.broadinstitute.sv.genotyping.GenotypingDepthModule.getCnpReadCounts(GenotypingDepthModule.java:217)
at org.broadinstitute.sv.genotyping.GenotypingDepthModule.genotypeCnp(GenotypingDepthModule.java:141)
at org.broadinstitute.sv.genotyping.BoundaryRefinementAlgorithm.genotypeCnp(BoundaryRefinementAlgorithm.java:287)
at org.broadinstitute.sv.genotyping.BoundaryRefinementAlgorithm.refineOneBoundary(BoundaryRefinementAlgorithm.java:633)
at org.broadinstitute.sv.genotyping.BoundaryRefinementAlgorithm.refineBoundaryStep(BoundaryRefinementAlgorithm.java:558)
at org.broadinstitute.sv.genotyping.BoundaryRefinementAlgorithm.refineBoundaries(BoundaryRefinementAlgorithm.java:536)
at org.broadinstitute.sv.genotyping.BoundaryRefinementAlgorithm.processVariant(BoundaryRefinementAlgorithm.java:232)
at org.broadinstitute.sv.genotyping.RefineCNVBoundaries.run(RefineCNVBoundaries.java:204)
at org.broadinstitute.sv.commandline.CommandLineProgram.execute(CommandLineProgram.java:54)
... 5 more
INFO 23:42:51,601 QGraph - Writing incremental jobs reports...
INFO 23:42:51,602 QGraph - 4 Pend, 0 Run, 2 Fail, 37 Done
INFO 23:42:51,605 QCommandLine - Writing final jobs report...
INFO 23:42:51,606 QCommandLine - Done with errors
INFO 23:42:51,609 QGraph - -------
INFO 23:42:51,609 QGraph - Failed: 'java' '-Xmx102400m' ...
...
Has anyone met such error? Does it related to the original .bam files or my SVPreprocess is broken? May I have your suggestions? Thank you very much.
Best regards,
Wusheng