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DiltheyLab / HLA-LA

Fast HLA type inference from whole-genome data
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Error: Have found no compatible reference specifications #79

Closed Sahu-Mousumi closed 11 months ago

Sahu-Mousumi commented 1 year ago

Hi! I am trying to use HLA-LA for HLA typing but ending up generating error as below. I am also attaching output of the samtools idxstats of my bam file.

I was wondering if anyone can help me resolving this!

Error:

Identified paths:

   samtools_bin: /usr/local/apps/samtools/1.9/bin/samtools
   bwa_bin: /usr/local/apps/bwa/0.7.17/bwa
   java_bin: /usr/bin/java
  picard_sam2fastq_bin: /usr/local/apps/picard/2.9.2/build/libs/picard.jar
  General working directory: /gpfs/gsfs11/users/Gourh_Lab/hla-la
  Sample-specific working directory: /gpfs/gsfs11/users/Gourh_Lab/hla-la/bqsrS10

Have found no compatible reference specifications in /usr/local/apps/HLA-LA/1.0.1/src/../graphs/PRG_MHC_GRCh38_withIMGT/knownReferences - create a file for this BAM file and try again. at /usr/local/apps/HLA-LA/1.0.1/src/HLA-LA.pl line 309.

Thanks!

reference_extraction.txt

AlexanderDilthey commented 11 months ago

Solved after email exchange.