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⛏ HLA predictions from NGS shotgun data
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HLA-I_II_CDS.fasta not working #23

Closed zaqnq closed 2 years ago

zaqnq commented 2 years ago

Hi,

I tried the sample codes in file HPRArnaseq_classI.sh, only changing the HLA_ABC_CDS.fasta into HLA-I_II_CDS.fasta because I want to obtain the results for both HLA I and II. But it is not working. I tried it with HLA_ABC_CDS.fasta but it worked.

The slurm output shows:

[bwa_aln] 17bp reads: max_diff = 2 [bwa_aln] 38bp reads: max_diff = 3 [bwa_aln] 64bp reads: max_diff = 4 [bwa_aln] 93bp reads: max_diff = 5 [bwa_aln] 124bp reads: max_diff = 6 [bwa_aln] 157bp reads: max_diff = 7 [bwa_aln] 190bp reads: max_diff = 8 [bwa_aln] 225bp reads: max_diff = 9 [bwa_aln_core] calculate SA coordinate... /var/spool/slurmd/job950335/slurm_script: line 2: 346271 Segmentation fault (core dumped) bwa aln -e 0 -o 0 ../hlaminer/HLAminer-1.4/HLAminer_v1.4/database/HLA-I_II_CDS.fasta ../hlaminer/HLAminer-1.4/HLAminer_v1.4/test-demo/rd1.fq > aln_test.1.sai [fread] Unexpected end of file

Is there anything wrong with the file?

Thanks, Q

warrenlr commented 2 years ago

nothing wrong with the file to my knowledge, although the HLA sequences they comprise may not be complete (Please refer to the readme for updating the databases and indices before running HLAminer).

If you are interested in HLA class I and II, why not run: HPRArnaseq_classI-II.sh ?

Thank you for your interest in HLAminer

github-actions[bot] commented 2 years ago

This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs. Thank you for your interest in HLAminer!