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GRIDSS: the Genomic Rearrangement IDentification Software Suite
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long chromosomes that require .csi index lead to htsjdk error #602

Open jjuod opened 2 years ago

jjuod commented 2 years ago

Hi, I'm working with long chromosomes (barley) that require .csi indexing instead of .bai. Is this currently supported in gridss? The specific error that I'm getting is:

ERROR   2022-10-14 15:20:31     AssemblyEvidenceSource  Fatal error during assembly 
java.util.concurrent.ExecutionException: htsjdk.samtools.SAMException: Exception when processing alignment for BAM index asm53-20404 161b aligned to contig2:536877234-536877371.
        at java.base/java.util.concurrent.FutureTask.report(FutureTask.java:122)
        at java.base/java.util.concurrent.FutureTask.get(FutureTask.java:191)
        at au.edu.wehi.idsv.AssemblyEvidenceSource.runTasks(AssemblyEvidenceSource.java:168)
        at au.edu.wehi.idsv.AssemblyEvidenceSource.assembleBreakends(AssemblyEvidenceSource.java:108)
        at gridss.AssembleBreakends.doWork(AssembleBreakends.java:43)
        at gridss.cmdline.MultipleSamFileCommandLineProgram.doWork(MultipleSamFileCommandLineProgram.java:173)
        at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:305)
        at gridss.AssembleBreakends.main(AssembleBreakends.java:35)
Caused by: htsjdk.samtools.SAMException: Exception when processing alignment for BAM index asm53-20404 16
1b aligned to contig2:536877234-536877371.                                                                       at htsjdk.samtools.BAMFileWriter.writeAlignment(BAMFileWriter.java:141)
        at htsjdk.samtools.SAMFileWriterImpl.addAlignment(SAMFileWriterImpl.java:185)
        at htsjdk.samtools.AsyncSAMFileWriter.synchronouslyWrite(AsyncSAMFileWriter.java:36)
        at htsjdk.samtools.AsyncSAMFileWriter.synchronouslyWrite(AsyncSAMFileWriter.java:16)
        at htsjdk.samtools.util.AbstractAsyncWriter$WriterRunnable.run(AbstractAsyncWriter.java:123)
        at java.base/java.lang.Thread.run(Thread.java:829)
Caused by: htsjdk.samtools.SAMException: Exception creating BAM index for record asm53-20404 161b aligned
 to contig2:536877234-536877371.                                                                                 at htsjdk.samtools.BAMIndexer.processAlignment(BAMIndexer.java:132)
        at htsjdk.samtools.BAMFileWriter.writeAlignment(BAMFileWriter.java:138)
        ... 5 more
Caused by: java.lang.IllegalStateException: Read position too high for BAI bin indexing.
        at htsjdk.samtools.SAMRecord.computeIndexingBin(SAMRecord.java:1576)
        at htsjdk.samtools.BAMIndexer$BAMIndexBuilder$1.getIndexingBin(BAMIndexer.java:250)
        at htsjdk.samtools.BinningIndexBuilder.processFeature(BinningIndexBuilder.java:96)
        at htsjdk.samtools.BAMIndexer$BAMIndexBuilder.processAlignment(BAMIndexer.java:238)
        at htsjdk.samtools.BAMIndexer.processAlignment(BAMIndexer.java:130)
        ... 6 more

Googling I find some more issues with csi support in htsjdk, so not sure if this something that can be fixed within gridss, or is this out of your hands? Thanks!

d-cameron commented 1 year ago

I'll look into it further but that is indeed likely to be the case.