DiltheyLab/HLA-LA

No contigs for extraction specified

kvaldez opened this issue · 3 comments

kvaldez commented

Hello! I created an extraction file for my data based on the documentation, however I'm running into this error:

No contigs for extraction specified in /opt/conda/envs/hla-la/opt/hla-la/src/../graphs/PRG_MHC_GRCh38_withIMGT/knownReferences/hla-la_hg19_Compass.txt? at /opt/conda/envs/hla-la/bin/HLA-LA.pl line 391.

I attached my file here, can you suggest a solution?
hla-la_hg19_Compass.txt

Thanks,
Kristin

Zoeyoungxy commented

Hello! I met the same question. Have you solved the problem?
The error message:
Using /home/anaconda3/envs/hlala/opt/hla-la/src/../graphs/PRG_MHC_GRCh38_withIMGT/knownReferences/reference_extraction_UNIX.txt as reference file.
No contigs for extraction specified in /home/anaconda3/envs/hlala/opt/hla-la/src/../graphs/PRG_MHC_GRCh38_withIMGT/knownReferences/reference_extraction_UNIX.txt? at /home/anaconda3/envs/hlala/bin/HLA-LA.pl line 391.

The samtools idxstats file and reference_extraction file:
reference_extraction_UNIX.txt
sample.idxstats.txt

Any suggestions will be highly appreciated.

Thanks,
-Zoey

kvaldez commented

Hi Zoey! No unfortunately I haven't resolved the issue either.

Kristin

AlexanderDilthey commented

Hi @kvaldez and @Zoeyoungxy,

The issue is that the file does not specify any genomic locations as targets for the extraction process - i.e. there are no values / only 0 in the columns ExtractCompleteContig, PartialExtraction_Start, and PartialExtraction_Stop.

Check out e.g. https://github.com/DiltheyLab/HLA-LA/blob/master/additionalReferences/PRG_MHC_GRCh38_withIMGT/G1000_Ymasked.txt for an example - the general strategy should be to mark the complete MHC for extraction, plus any alternative MHC or HLA allele contigs.

Best wishes,

Alex