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DiltheyLab / HLA-LA

Fast HLA type inference from whole-genome data
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No compatible reference #98

Closed angyonghaseyo closed 8 months ago

angyonghaseyo commented 11 months ago

image

@AlexanderDilthey Any ideas on how to solve this error? Please do help as I have tried to solve with many other ways, but to no avail. Like doing https://github.com/DiltheyLab/HLA-LA/issues/27 wont work for me.

idxstats.txt PRG_MHC_GRCh38_withIMGT.txt

AlexanderDilthey commented 11 months ago

Hi @angyonghaseyo,

I have added a reference specification file for your reference (https://github.com/DiltheyLab/HLA-LA/blob/master/additionalReferences/PRG_MHC_GRCh38_withIMGT/Additional_B38_3.txt) - do a fresh pull from GitHub and you should be able to process your BAM.

Best wishes

Alex

angyonghaseyo commented 11 months ago

Hi @AlexanderDilthey, Im still facing the same error, any advice on that?

AlexanderDilthey commented 11 months ago

Could you do an ls on the folder specified in the error message and post the results here?

angyonghaseyo commented 11 months ago

Hi, u mean this? (base) angyong@comp1:~/HLA-LA/graphs/PRG_MHC_GRCh38_withIMGT/knownReferences$ ls 1000G_B37_noChr.txt 1000G_B38.txt Additional_B38_3.txt B37_generic_noChr.txt PRG_MHC_GRCh38_withIMGT.txt

AlexanderDilthey commented 11 months ago

Yes, thank you!

Could you also send me the contents of the directory ~/HLA-LA/src/additionalReferences/PRG_MHC_GRCh38_withIMGT?

angyonghaseyo commented 11 months ago

Hi, the contents of the directory are as following:

Additional_B38_2.txt B37_generic_noChr_withHHV.txt chm13v2.txt hg19.txt Additional_B38_3.txt B37_noChr_noGL.txt G1000_Ymasked.txt Illumina_B38.txt Additional_B38.txt B37_withChr_M2.txt GEL_B38.txt PRG_MHC_GRCh38_withIMGT.txt B37_for_Nobuyuki.txt B37_withChr.txt GRCh38.p12.genome.XY_idxstats.txt Valentin_B38.txt

angyonghaseyo commented 11 months ago

@AlexanderDilthey do let me know if theres any info, I suspect my idxstats file is showing contig number instead of accession number(will try to change and see if the not compatible reference specs error still pops up

AlexanderDilthey commented 11 months ago

OK, this sounds like a plan - let me know if this works!

pablosoro commented 11 months ago

Hi @AlexanderDilthey

I'm facing the same problem with Have found no compatible reference specifications in /nemo/stp/babs/working/barriop/.conda/envs/HLA_typing/opt/hla-la/src/../graphs/PRG_MHC_GRCh38_withIMGT/knownReferences - create a file for this BAM file and try again. at /camp/stp/babs/working/barriop/.conda/envs/HLA_typing/bin/HLA-LA.pl line 364.

Should I upload my idxstats file(s) here o create a new issue? Many thanks in advance.

Best, Pablo

AlexanderDilthey commented 8 months ago

Hey @pablosoro, I just saw that you opened a fresh issue for this - thank you, I will respond there!