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error: Have found no compatible reference specifications #89

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champa82 opened this issue Mar 20, 2023 · 1 comment
Open

error: Have found no compatible reference specifications #89

champa82 opened this issue Mar 20, 2023 · 1 comment
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@champa82
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error when running the HLA-LA app:

Have found no compatible reference specifications in /opt/conda/envs/hla-la/opt/hla-la/src/../graphs/PRG_MHC_GRCh38_withIMGT/knownReferences - create a file for this BAM file and try again. at /opt/conda/envs/hla-la/bin/HLA-LA.pl line 364.

Copied the following file to the knownReference directory but still giving error.

hg19_chr6_only.txt

Please suggest?

thanks
@AlexanderDilthey
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Hi @champa82, what output do you get when you do a samtools idxstats on your input BAM/CRAM? The reference specification file needs to contain exactly one entry for each contig in your reference.

Best wishes

Alex

@AlexanderDilthey AlexanderDilthey mentioned this issue Jul 17, 2023
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@AlexanderDilthey @champa82