program error on calling with hs38DH.fa about octopus HOT 6 CLOSED

Ignore that - have now reproduced. Will work on a fix!

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Thanks for reporting this Greg. The error is raised when Htslib does not successfully load a contig for VCF/BCF streaming. I'll investigate...

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Thanks Dan. My open file limit was:

$ ulimit -Sn
16384

Not sure if that could be a factor here or not.

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Hi Greg, I'm having trouble reproducing this. Could you check if there are any reads mapped to HLA-A*01:01:01:01 in any of the BAMs please? Also, do you get the error if you just try to call this contig?

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This was due to htslib not being able to parse :s in contig names (see here). Octopus creates temporary .bcf files - one for each contig - when using multithreading. During the merging of these temporaries after calling, the error was thrown. I've 'fixed' this by using ".vcf" temporary files for contig names with : (37a3329).

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aha...great!...thanks very much Dan

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