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Illumina / strelka

Strelka2 germline and somatic small variant caller
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Strelka 2.9.3 FATAL_ERROR: Unexpected return value from htslib sam_itr_next function '-2' while attempting to read BAM/CRAM #56

Open burakonal89 opened 6 years ago

burakonal89 commented 6 years ago

Hi,

I am getting this error: 2018-07-06T10:48:27.499694345Z [2018-07-06T10:48:27.499530Z] [4beb0927f133] [14_1] [WorkflowRunner] [ERROR] [2018-07-06T10:48:10.850255Z] [4beb0927f133] [14_1] [getChromDepth_sample000_estimateChromDepth_021_22] FATAL_ERROR: Unexpected return value from htslib sam_itr_next function '-2' while attempting to read BAM/CRAM file:

When I use normal and tumor bams for strelka 1.0.5, it works. But the same bams result in error.

ctsa commented 6 years ago

Both strelka1 and 2 are accessing the alignment file through samtools/htslib, but using significantly different versions of the library. It would help to understand whether the input file is bam or cram and what version of strelka2 this is?

Also, the error message should report both the bam/cram filename and the queried region. If you use a recent version of htslib/samtools (1.8+), and query this same file and region using samtools view, does samtools return the same error?