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GRIDSS: the Genomic Rearrangement IDentification Software Suite
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Exception in thread "main" java.lang.RuntimeException: java.lang.RuntimeException: #600

Open jigaoxiang opened 2 years ago

jigaoxiang commented 2 years ago

Dear Dr： When I used the Gridss with the parameter gridss -r ref.fasta -t 20 --useproperpair -o gridss_output/Sample.vcf.gz Sample.bam. There are some error happened. Please give some advice for this.

Exception in thread "main" java.lang.RuntimeException: java.lang.RuntimeException: Exception when running gridss.cmdline.ByReadNameSinglePassSamProgram$WrappedSinglePassSamProgram
        at picard.analysis.SinglePassSamProgram.makeItSo(SinglePassSamProgram.java:253)
        at picard.analysis.SinglePassSamProgram.makeItSo(SinglePassSamProgram.java:134)
        at picard.analysis.SinglePassSamProgram.makeItSo(SinglePassSamProgram.java:126)
        at picard.analysis.CollectMultipleMetrics.doWork(CollectMultipleMetrics.java:598)
        at gridss.analysis.CollectGridssMetrics.doWork(CollectGridssMetrics.java:80)
        at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:305)
        at picard.cmdline.CommandLineProgram.instanceMainWithExit(CommandLineProgram.java:196)
        at gridss.CollectGridssMetricsAndExtractSVReads.main(CollectGridssMetricsAndExtractSVReads.java:56)
Caused by: java.lang.RuntimeException: Exception when running gridss.cmdline.ByReadNameSinglePassSamProgram$WrappedSinglePassSamProgram
        at picard.analysis.SinglePassSamProgram.raiseAsyncException(SinglePassSamProgram.java:282)
        at picard.analysis.SinglePassSamProgram.asyncAcceptRead(SinglePassSamProgram.java:273)
        at picard.analysis.SinglePassSamProgram.asyncAcceptReads(SinglePassSamProgram.java:263)
        at picard.analysis.SinglePassSamProgram.makeItSo(SinglePassSamProgram.java:216)
        ... 7 more
Caused by: java.lang.NullPointerException
        at htsjdk.samtools.SAMUtils.validateCigar(SAMUtils.java:937)
        at htsjdk.samtools.SAMRecord.validateCigar(SAMRecord.java:1806)
        at htsjdk.samtools.BAMRecord.getCigar(BAMRecord.java:284)
        at gridss.ExtractSVReads.isFullyMapped(ExtractSVReads.java:94)
        at gridss.ExtractSVReads.hasReadAlignmentConsistentWithReference(ExtractSVReads.java:75)
        at gridss.ExtractSVReads.shouldExtract(ExtractSVReads.java:158)
        at gridss.ExtractSVReads.acceptFragment(ExtractSVReads.java:171)
        at gridss.cmdline.ByReadNameSinglePassSamProgram$WrappedSinglePassSamProgram.acceptRead(ByReadNameSinglePassSamProgram.java:162)
        at picard.analysis.SinglePassSamProgram$SinglePassSamProgramRunner.run(SinglePassSamProgram.java:320)
        at java.base/java.lang.Thread.run(Thread.java:834)
[W::bgzf_read_block] EOF marker is absent. The input is probably truncated
samtools sort: truncated file. Aborting
d-cameron commented 2 years ago

That looks like an input file error. Can you successfully run Picard tools ValidateSam on your input bam?

On Mon, 5 Sep 2022, 13:31 jigaoxiang, @.***> wrote:

Dear Dr： When I used the Gridss with the parameter gridss -r ref.fasta -t 20 --useproperpair -o gridss_output/Sample.vcf.gz Sample.bam. There are some error happened. Please give some advice for this.

Exception in thread "main" java.lang.RuntimeException: java.lang.RuntimeException: Exception when running gridss.cmdline.ByReadNameSinglePassSamProgram$WrappedSinglePassSamProgram

    at picard.analysis.SinglePassSamProgram.makeItSo(SinglePassSamProgram.java:253)

    at picard.analysis.SinglePassSamProgram.makeItSo(SinglePassSamProgram.java:134)

    at picard.analysis.SinglePassSamProgram.makeItSo(SinglePassSamProgram.java:126)

    at picard.analysis.CollectMultipleMetrics.doWork(CollectMultipleMetrics.java:598)

    at gridss.analysis.CollectGridssMetrics.doWork(CollectGridssMetrics.java:80)

    at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:305)

    at picard.cmdline.CommandLineProgram.instanceMainWithExit(CommandLineProgram.java:196)

    at gridss.CollectGridssMetricsAndExtractSVReads.main(CollectGridssMetricsAndExtractSVReads.java:56)

Caused by: java.lang.RuntimeException: Exception when running gridss.cmdline.ByReadNameSinglePassSamProgram$WrappedSinglePassSamProgram

    at picard.analysis.SinglePassSamProgram.raiseAsyncException(SinglePassSamProgram.java:282)

    at picard.analysis.SinglePassSamProgram.asyncAcceptRead(SinglePassSamProgram.java:273)

    at picard.analysis.SinglePassSamProgram.asyncAcceptReads(SinglePassSamProgram.java:263)

    at picard.analysis.SinglePassSamProgram.makeItSo(SinglePassSamProgram.java:216)

    ... 7 more

Caused by: java.lang.NullPointerException

    at htsjdk.samtools.SAMUtils.validateCigar(SAMUtils.java:937)

    at htsjdk.samtools.SAMRecord.validateCigar(SAMRecord.java:1806)

    at htsjdk.samtools.BAMRecord.getCigar(BAMRecord.java:284)

    at gridss.ExtractSVReads.isFullyMapped(ExtractSVReads.java:94)

    at gridss.ExtractSVReads.hasReadAlignmentConsistentWithReference(ExtractSVReads.java:75)

    at gridss.ExtractSVReads.shouldExtract(ExtractSVReads.java:158)

    at gridss.ExtractSVReads.acceptFragment(ExtractSVReads.java:171)

    at gridss.cmdline.ByReadNameSinglePassSamProgram$WrappedSinglePassSamProgram.acceptRead(ByReadNameSinglePassSamProgram.java:162)

    at picard.analysis.SinglePassSamProgram$SinglePassSamProgramRunner.run(SinglePassSamProgram.java:320)

    at java.base/java.lang.Thread.run(Thread.java:834)

[W::bgzf_read_block] EOF marker is absent. The input is probably truncated

samtools sort: truncated file. Aborting

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jigaoxiang commented 2 years ago

Thank you for reply! At first, I also thought maybe my bam file have some problem. But using the picard check bam file, there is no error on my input bam. So it is confused me long time. There is the check out of picard ValidateSamFile my input bam.

## HISTOGRAM    java.lang.String
Error Type  Count
WARNING:QUALITY_NOT_STORED  1

[Mon Sep 05 20:20:05 CST 2022] picard.sam.ValidateSamFile done. Elapsed time: 6.33 minutes.
Runtime.totalMemory()=1068498944
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp