error: Have found no compatible reference specifications

DiltheyLab / HLA-LA

Fast HLA type inference from whole-genome data

GNU General Public License v3.0

120 stars 40 forks source link

error: Have found no compatible reference specifications #89

Open champa82 opened 1 year ago

champa82 commented 1 year ago

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 commented 11 months ago

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