thread 'main' panicked error

[GuidoGallo]

thread 'main' panicked error

[GuidoGallo]

Dear Matt
Thank you so much for the rapid answer. You are right, one of the the bam files I was using had an inconsistency with the chromosomes as defined in the vcf header, I didn't realize it.
Thanks again and congratulations for the great tool, it worked perfectly :)

[holtjma]

Hi @GuidoGallo,

So assuming you're on the latest version, it's getting an error at this point in the code:

HiPhase/src/block_gen.rs

Line 636 in 9b01d7e

bam.fetch((chrom, pos, pos+1)).unwrap();

That line is trying to fetch a region in the BAM file. I've never actually encountered an error there before, so I'm going to do some guessing as to what might be causing it, most of which involve a deviation from "normal" processing that is leaving BAMs and/or VCFs in an inconsistent state:

1. It looks like you're using multiple BAM files. Is it possible that one or more of the BAM files is missing one or more chromosomes from the dataset? This may be a missing entry in the header. It may also be a chromosome with no alignments to it, I'm not sure what the fetch would do in that instance (if this is the case, we may need to patch it).
2. Were the VCFs processed in a way that their chromosome lists do not match the BAM headers? If so, it may be trying to fetch a region from the VCF that does match exist in the BAM.
3. Are you able to tell roughly where this is happening in the processing? In other words, is it happening on a "core" chromosome, or is it throwing errors somewhere in an ALT contig or similar? That may help provide some clues if neither of the above is true.

Hope this helps,
Matt

[holtjma]

Great, glad it worked out! I'll make a note to improve the messaging there. Hopefully future users won't encounter a cryptic panic message and instead get something a little more insightful.