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MuTect2 ->Reference name for '1283' not found in sequence dictionary
t1000
Member
Hi, I am trying to runjava -jar GenomeAnalysisTK.jar -T MuTect2 -R ucsc.hg19.fasta -I:tumor tumor_rg.bam -I:normal normal_rg.bam -o output.vcf
I am using ucsc.hg19.fasta as a reference and I used:
1. samtools faidx to create the ucsc.hg19.fasta.fai file
2. java -jar picard.jar CreateSequenceDictionary REFERENCE=ucsc.hg19.fasta OUTPUT=ucsc.hg19.fasta.dict
I added a ReadGroup to my two BAM Files:java -jar picard.jar AddOrReplaceReadGroups I=normal.bam O=normal_rg.bam RGID=4 RGLB=lib1 RGPL=illumina RGPU=unit1 RGSM=20
I also validated the BAM files
Now I get the following error:
##### ERROR MESSAGE: SAM/BAM/CRAM file /analysis/tumnormalor.bam is malformed. Error details: Reference name for '1283' not found in sequence dictionary.
If I exchange the tumor and normal .bam files as command line arguments I get the error ##### ERROR MESSAGE: SAM/BAM/CRAM file /analysis/tumor.bam is malformed. Error details: Reference name for '1283' not found in sequence dictionary.
I tried to google it and found nothing. Can someone give me a clue where to look ?
Is the file ucsc.hg19.fasta.dict the sequence dictionary ?
Answers
@t1000
Hi,
Can you post the BAM file header and the FASTA dict file here? Specifically, I need to see if the @SQ lines in the BAM file match the ones in your dict file.
Thanks,
Sheila
Hi,
I'm having a similar issue with MuTect2 (GATK version 4.0.3.0).
I'm trying to run:
gatk Mutect2 \ -R human_g1k_v37_decoy.fasta \ -I ${TUMOUR}.recal.bam \ -tumor ${TUMOUR} \ -I ${NORMAL}.recal.bam \ -normal ${NORMAL} \ --germline-resource af-only-gnomad.raw.sites.b37.vcf \ --af-of-alleles-not-in-resource 0.00003125 \ -O ${TUMOUR}_${NORMAL}.vcfAnd I'm getting this error, with a different number after reference name each time:
[August 8, 2018 3:55:11 PM BST] org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2 done. Elapsed time: 0.14 minutes. Runtime.totalMemory()=2076049408 java.lang.IllegalArgumentException: Reference name for '3223094' not found in sequence dictionary. at htsjdk.samtools.SAMRecord.resolveNameFromIndex(SAMRecord.java:569) at htsjdk.samtools.SAMRecord.setReferenceIndex(SAMRecord.java:422) at htsjdk.samtools.BAMRecord.<init>(BAMRecord.java:87) at htsjdk.samtools.DefaultSAMRecordFactory.createBAMRecord(DefaultSAMRecordFactory.java:42) at htsjdk.samtools.BAMRecordCodec.decode(BAMRecordCodec.java:210) at htsjdk.samtools.BAMFileReader$BAMFileIterator.getNextRecord(BAMFileReader.java:829) at htsjdk.samtools.BAMFileReader$BAMFileIndexIterator.getNextRecord(BAMFileReader.java:981) at htsjdk.samtools.BAMFileReader$BAMFileIterator.advance(BAMFileReader.java:803) at htsjdk.samtools.BAMFileReader$BAMFileIndexIterator.<init>(BAMFileReader.java:963) at htsjdk.samtools.BAMFileReader.createIndexIterator(BAMFileReader.java:918) at htsjdk.samtools.BAMFileReader.query(BAMFileReader.java:575) at htsjdk.samtools.SamReader$PrimitiveSamReaderToSamReaderAdapter.query(SamReader.java:528) at htsjdk.samtools.SamReader$PrimitiveSamReaderToSamReaderAdapter.queryOverlapping(SamReader.java:400) at org.broadinstitute.hellbender.utils.iterators.SamReaderQueryingIterator.loadNextIterator(SamReaderQueryingIterator.java:125) at org.broadinstitute.hellbender.utils.iterators.SamReaderQueryingIterator.<init>(SamReaderQueryingIterator.java:66) at org.broadinstitute.hellbender.engine.ReadsDataSource.prepareIteratorsForTraversal(ReadsDataSource.java:404) at org.broadinstitute.hellbender.engine.ReadsDataSource.iterator(ReadsDataSource.java:330) at org.broadinstitute.hellbender.engine.MultiIntervalLocalReadShard.iterator(MultiIntervalLocalReadShard.java:134) at org.broadinstitute.hellbender.engine.AssemblyRegionIterator.<init>(AssemblyRegionIterator.java:109) at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.processReadShard(AssemblyRegionWalker.java:286) at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.traverse(AssemblyRegionWalker.java:271) at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:893) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:134) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:179) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:198) at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:160) at org.broadinstitute.hellbender.Main.mainEntry(Main.java:203) at org.broadinstitute.hellbender.Main.main(Main.java:289)I've checked the @SQ lines of both the .dict file and the .bam files, but can't see any obvious differences. Here is my .dict file:
and here are the @SQ lines from the ${TUMOUR}.recal.bam file:
I did use samtools reheader to change something in the header of my ${NORMAL}.recal.bam file (not the @SQ lines), and I notice that in this topic a ReadGroup was added to the bam file. Could this be the issue?
Thanks,
Michael
@michaelmc
Hi Michael,
Can you confirm this happens with the latest version?
-Sheila
Yes, I've tried it with 4.0.8.0 and I get the same error
@michaelmc
Hi Michael,
Thanks. I need to ask the developer and get back to you.
-Sheila
EDIT: This has been resolved in this thread.