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DaehwanKimLab / hisat-genotype

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ValueError: not enough values to unpack (expected 11, got 3) #46

Closed salonso65 closed 3 years ago

salonso65 commented 3 years ago

Hi Chris I have been failing to get hisatgenotype working, and after a week of missery I have decided to knock at your door for help. Here is my problem:

I have installed: hisatgenotype version 1.3.2 HISAT2 version 2.2.1 python Python 3.7.1 and RHEL 7.2

My command is:

hisatgenotype --base hla --locus-list A -1 ILMN/NA12892.extracted.1.fq.gz -2 ILMN/NA12892.extracted.2.fq.gz

Result (1):

No /MSA03/hisat-genotype/indicies/hla.snp file found (My comment: well, in fact there is one hla.out but empty) Building hla Database Except exception err_msg = multiprocessing.pool.RemoteTraceback: """ Traceback (most recent call last): File "/opt/conda/miniconda3/lib/python3.7/multiprocessing/pool.py", line 121, in worker result = (True, func(*args, *kwds)) File "/MSA03/hisat-genotype/hisatgenotype_modules/hisatgenotype_typing_core.py", line 2408, in genotyping_locus verbose >= 1) File "/MSA03/hisat-genotype/hisatgenotype_modules/hisatgenotype_typing_common.py", line 54, in wrapper func(args, **kwargs) File "/MSA03/hisat-genotype/hisatgenotype_modules/hisatgenotype_typing_common.py", line 568, in extract_database_if_not_exists verbose) File "/MSA03/hisat-genotype/hisatgenotype_modules/hisatgenotype_typing_process.py", line 390, in extract_vars temp_alleleid, flag, chr, left, , cigar_str = cols[:6] ValueError: not enough values to unpack (expected 6, got 3) """

The above exception was the direct cause of the following exception:

Traceback (most recent call last): File "/MSA03/hisat-genotype/hisatgenotype", line 738, in typing_process ofnlog.write(str(x.get())) File "/opt/conda/miniconda3/lib/python3.7/multiprocessing/pool.py", line 683, in get raise self._value ValueError: not enough values to unpack (expected 6, got 3)

If I now run it a second time (result-2):

    1: Extracting reads from NA12892.extracted.1.fq.gz

Traceback (most recent call last): File "/MSA03/hisat-genotype/hisatgenotype", line 845, in typing_process(args) File "/MSA03/hisat-genotype/hisatgenotype", line 553, in typing_process args.verbose) File "/MSA03/hisat-genotype/hisatgenotype_modules/hisatgenotype_typing_process.py", line 1776, in extract_reads verbose) File "/MSA03/hisat-genotype/hisatgenotype_modules/hisatgenotype_typing_process.py", line 1615, in work readname, flag, chr, pos, mapQ, cigar, , , , read, qual = cols[:11] ValueError: not enough values to unpack (expected 11, got 3)

(if it helps I have: line: HISAT2@HD VN:1.0 SO:unsorted cols: ['HISAT2@HD', 'VN:1.0', 'SO:unsorted'])

Any help welcome! Thanks!

chbe-helix commented 3 years ago

Hi Salonso,

Thanks for reaching out! It looks like there is an error in the database building for HLA. There is likely an incomplete database built in your hisat-genotype source directory as HISAT-genotype will not delete indices that fail to build properly.

I'd look in there for an indices folder and look at deleting any incomplete files. Alternatively, you can try rebuilding hisat-genotype manually according to the manual online. Let me know if this helps!

Thanks, Chris

salonso65 commented 3 years ago

Seems to be working now. I think tehproblem was a previous hisat2 install that was interfering. Thanks.