Error running GenomeSTRiP --RCCache: index file is truncated: for cram.rc.bin.idx

When running gs_preprocess.sh, I am getting the error "index file is truncatated" on a number of files.

Any suggestions for dealing with this?

Is there a command to reindex the file?

ERROR 13:50:58,287 FunctionEdge - Contents of /restricted/projectnb/casa/wgs.hg38/sv/gs/metadata/logs/SVPreprocess-19738.out:
INFO  13:42:05,283 HelpFormatter - --------------------------------------------------------
INFO  13:42:05,288 HelpFormatter - Program Name: org.broadinstitute.sv.apps.MergeReadCounts
INFO  13:42:05,296 HelpFormatter - Program Args: -I /restricted/projectnb/casa/wgs.hg38/pipelines/sv/gs/metadata/rccache.list -O /restricted/projectnb/casa/wgs.hg38/pipelines/sv/gs/metadata/rccache.merge/P0233.rccache.bin -R Homo_sapiens_assembly38/Homo_sapiens_assembly38.fasta -L chr14:40000001-50000000
INFO  13:42:05,302 HelpFormatter - Executing as [email protected] on Linux 2.6.32-696.10.3.el6.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_92-b14.
INFO  13:42:05,302 HelpFormatter - Date/Time: 2018/03/03 13:42:05
INFO  13:42:05,303 HelpFormatter - --------------------------------------------------------
INFO  13:42:05,303 HelpFormatter - --------------------------------------------------------
Exception in thread "main" org.broadinstitute.sv.commandline.ArgumentException: RCCache: index file is truncated: /restricted/projectnb/casa/wgs.hg38/pipelines/sv/gs/metadata/rccache/A-IIAA-IA000139-BL-NCR-14AD67283.hg38.realign.bqsr.cram.rc.bin.idx
        at org.broadinstitute.sv.metadata.depth.ReadCountIndexReader.initIntervalList(ReadCountIndexReader.java:195)
        at org.broadinstitute.sv.metadata.depth.ReadCountIndexReader.readHeader(ReadCountIndexReader.java:98)
        at org.broadinstitute.sv.metadata.depth.ReadCountIndexReader.open(ReadCountIndexReader.java:54)
        at org.broadinstitute.sv.metadata.depth.ReadCountFileReader.initIndexReader(ReadCountFileReader.java:363)
        at org.broadinstitute.sv.metadata.depth.ReadCountFileReader.access$500(ReadCountFileReader.java:41)
        at org.broadinstitute.sv.metadata.depth.ReadCountFileReader$ReadCountDataIterator.<init>(ReadCountFileReader.java:412)
        at org.broadinstitute.sv.metadata.depth.ReadCountFileReader.getReadCountDataIteratorInternal(ReadCountFileReader.java:313)
        at org.broadinstitute.sv.metadata.depth.ReadCountFileReader.getReadCountDataIterator(ReadCountFileReader.java:282)
        at org.broadinstitute.sv.metadata.depth.ReadCountFileMerger$MergeIterator.setInterval(ReadCountFileMerger.java:338)
        at org.broadinstitute.sv.metadata.depth.ReadCountFileMerger.mergeFilesInternal(ReadCountFileMerger.java:99)
        at org.broadinstitute.sv.metadata.depth.ReadCountFileMerger.mergeFiles(ReadCountFileMerger.java:78)
        at org.broadinstitute.sv.apps.MergeReadCounts.run(MergeReadCounts.java:67)
        at org.broadinstitute.sv.commandline.CommandLineProgram.execute(CommandLineProgram.java:54)
        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.apps.MergeReadCounts.main(MergeReadCounts.java:53)
ERROR 13:50:58,291 FunctionEdge - Error:  'java'  '-Xmx8192m'  '-XX:+UseParallelOldGC'  '-XX:ParallelGCThreads=4'  '-XX:GCTimeLimit=50'  '-XX:GCHeapFreeLimit=10'  '-Djava.io.tmpdir=/restricted/projectnb/casa/wgs.hg38/sv/gs/tmp'  '-cp' '/restricted/projectnb/casa/wgs.hg38/pipelines/sv/gs/svtoolkit/lib/SVToolkit.jar:/restricted/projectnb/casa/wgs.hg38/pipelines/sv/gs/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/restricted/projectnb/casa/wgs.hg38/pipelines/sv/gs/svtoolkit/lib/gatk/gatk-queue-3.7.jar'  '-cp' '/restricted/projectnb/casa/wgs.hg38/pipelines/sv/gs/svtoolkit/lib/SVToolkit.jar:/restricted/projectnb/casa/wgs.hg38/pipelines/sv/gs/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/restricted/projectnb/casa/wgs.hg38/pipelines/sv/gs/svtoolkit/lib/gatk/gatk-queue-3.7.jar'  'org.broadinstitute.sv.apps.MergeReadCounts'  '-I' '/restricted/projectnb/casa/wgs.hg38/pipelines/sv/gs/metadata/rccache.list'  '-O' '/restricted/projectnb/casa/wgs.hg38/pipelines/sv/gs/metadata/rccache.merge/P0278.rccache.bin'  '-R' 'Homo_sapiens_assembly38/Homo_sapiens_assembly38.fasta'  -L chr20:40000001-50000000
ERROR 13:50:58,295 FunctionEdge - Contents of /restricted/projectnb/casa/wgs.hg38/sv/gs/metadata/logs/SVPreprocess-19828.out:
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Answers

  • jfarrelljfarrell Member

    Thanks Bob!

    Deleting the idx.done files for the corrupted index solved the issue. The script then executed the IndexReadCountFile tool for the affected files.

    Regarding what triggered the error, GenomeSTRiP was being run on 4815 crams. Only about 35 of those had this error. It looked like it was triggered by a memory error which occurred on these samples on the initial run. Once I added the -memLimit 8 parameter, the memory error went away.

    'java' '-Xmx8192m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/restricted/projectnb/casa/wgs.hg38/sv/gs/tmp' '-cp' '/restricted/projectnb/casa/wgs.hg38/pipelines/sv/gs/svtoolkit/lib/SVToolkit.jar:/restricted/projectnb/casa/wgs.hg38/pipelines/sv/gs/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/restricted/projectnb/casa/wgs.hg38/pipelines/sv/gs/svtoolkit/lib/gatk/gatk-queue-3.7.jar' '-cp' '/restricted/projectnb/casa/wgs.hg38/pipelines/sv/gs/svtoolkit/lib/SVToolkit.jar:/restricted/projectnb/casa/wgs.hg38/pipelines/sv/gs/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/restricted/projectnb/casa/wgs.hg38/pipelines/sv/gs/svtoolkit/lib/gatk/gatk-queue-3.7.jar' 'org.broadinstitute.sv.apps.IndexReadCountFile' '-I' '/restricted/projectnb/casa/wgs.hg38/pipelines/sv/gs/metadata/rccache/A-IIAA-IA000257-BL-NCR-14AD67402.hg38.realign.bqsr.cram.rc.bin' '-O' '/restricted/projectnb/casa/wgs.hg38/pipelines/sv/gs/metadata/rccache/A-IIAA-IA000257-BL-NCR-14AD67402.hg38.realign.bqsr.cram.rc.bin.idx'

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