Error executing process > 'mixMHC2pred

beijish commented 2 years ago

Good afternoon, thanks for sharing nextNEOpi, it's a very useful resource. I am working on HPC (LMOD), using singularity, nextflow version 22.04.4., nextNEOpi v.1.3 & 1.3.2, hla-hd v.1.5.0, VEP v.105 & 106.1, hg38.

It runs smoothly up to mixMHC2pred, when it gets stuck with the following error:

_Error executing process > 'mixMHC2pred (PB-16-002)'

Caused by: Process mixMHC2pred (PB-16-002) terminated with an error exit status (1)

Command executed:

/XXX/work/MixMHC2pred/MixMHC2pred_unix \ -i PB-16-002_peptides.fasta \ -o PB-16-002_mixMHC2pred.tsv \ -a DRB1_15_01 DRB1_12_01 DRB3_01_01 DRB5_01_01 parse_mixMHC2pred.py \ --vep_vcf PB-16-002_vep_somatic_gx.vcf.gz \ --pep_fasta PB-16-002_peptides.fasta \ --mixMHC2pred_result PB-16-002_mixMHC2pred.tsv \ --out PB-16-002_mixMHC2pred_all.tsv \ --sample_name PB-16-002_tumor \ --normal_name PB-16-002_normal awk \ '{ if ($0 ~ /#/) { print } else { if ($18 <= 2) { print } } }' PB-16-002_mixMHC2pred_all.tsv > PB-16-002_mixMHC2pred_filtered.tsv

Command exit status: 1

Command output: Runing MixMHC2pred (v1.2) for peptide file: PB-16-002_peptides.fasta Imported 27848 peptides. Computing now the scores from each peptide. Finished the computations.

Command error: Traceback (most recent call last): File "/XXX/bin/parse_mixMHC2pred.py", line 181, in out_file.write("\t".join(map(str, vcf_map[key].values())) + "\t" + line) KeyError: 'ENSG00000285238_ENST00000644480.2_911-912GAGAA/G'

Work dir: /XXX/work/89/b85145dc36f106bca16fa3f0c7007d

Tip: when you have fixed the problem you can continue the execution adding the option -resume to the run command line_

I have been trying for weeks to find out to understand where the problem is, my sys admins think it could be a glitch with parse_mixMHC2pred.py but I am not a python person to try and do this myself. I would really benefit from some help, please. Thanks in advance

SV

riederd commented 2 years ago

Hi, do you mind sharing/mailing the following files, so that I can check what happens:

/XXX/work/89/b85145dc36f106bca16fa3f0c7007d/PB-16-002_vep_somatic_gx.vcf.gz
/XXX/work/89/b85145dc36f106bca16fa3f0c7007d/PB-16-002_peptides.fasta
/XXX/work/89/b85145dc36f106bca16fa3f0c7007d/PB-16-002_mixMHC2pred.tsv
/XXX/work/89/b85145dc36f106bca16fa3f0c7007d/PB-16-002_mixMHC2pred.tsv

Thanks

beijish commented 2 years ago

Sure, see zipped folder, please let me know if you prefer me to send it by email. Thank you a lot

SV Archive.zip

riederd commented 2 years ago

Thanks for reporting this issue. There seem to occur rare situations where VEP can not assign a gene symbol to annotate a mutation, this caused the problem with our mixMHC2pred parser.

I fixed the problem now and made a new release.

You may also just download the fixed parser script from https://github.com/icbi-lab/nextNEOpi/raw/master/bin/parse_mixMHC2pred.py and place it into your nextNEOpi bin directory and resume the pipeline with the -resume command line option.

beijish commented 2 years ago

Lucky me who picked up the VEP exception! Thank s a lot

Sara

On 3 Aug 2022, at 10:21, Dietmar Rieder @.***> wrote:

Thanks for reporting this issue. There seem to occur rare situations where VEP can not assign a gene symbol to annotate a mutation, this caused the problem with our mixMHC2pred parser.

I fixed the problem now and made a new release.

You may also just download the fixed parser script from https://github.com/icbi-lab/nextNEOpi/raw/master/bin/parse_mixMHC2pred.py and place it into your nextNEOpi bin directory and resume the pipeline with the -resume command line option.

— Reply to this email directly, view it on GitHubhttps://github.com/icbi-lab/nextNEOpi/issues/10#issuecomment-1203700205, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AHLJWQ7DCZZLIXSN6HROOIDVXI2X7ANCNFSM55KYCZUA. You are receiving this because you authored the thread.Message ID: @.***>

icbi-lab / nextNEOpi

Error executing process > 'mixMHC2pred #10