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v-mikhaylov / tfold-release

TFold v1.0
Apache License 2.0
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issue with running peptides with sequence #5

Closed seanwangsalad closed 4 months ago

seanwangsalad commented 4 months ago

Hello developers,

Great software! I was able to run many peptides. However, when running peptides using a sequence, I am getting an error (below). I attached my test1.csv file. I have pep and MHCII sequence separated by a /

If I changed MHC sequence to MHC allele and use HLA-DRA01:01/DRB101:01, it runs.

test1.csv

Aligning MHC sequences. Traceback (most recent call last): File "/choncc/tfold-release/tfold/modeling/make_inputs.py", line 211, in map_one_mhc_seq mhc_a=seq_tools.mhc_from_seq(sA) File "/choncc/tfold-release/tfold/utils/seq_tools.py", line 614, in mhc_from_seq hits=blast_prot(seq,['MHC'],species=species) File "/choncc/tfold-release/tfold/utils/seq_tools.py", line 433, in blast_prot stdout,stderr=blastp_cline() File "/home/mhc/miniforge3/envs/tfold-env/lib/python3.8/site-packages/Bio/Application/init.py", line 574, in call raise ApplicationError(return_code, str(self), stdout_str, stderr_str) Bio.Application.ApplicationError: Non-zero return code 127 from 'blastp -out /choncc/tfold-release/tmp/IKEEHVIIQA5137303316.xml -outfmt 5 -query /choncc/tfold-release/tmp/IKEEHVIIQA5137303316.fasta -db /choncc/tfold-release/data/seq_tools/db/MHC.fasta', message '/bin/sh: 1: blastp: not found'

Thanks!

v-mikhaylov commented 4 months ago

Hi Sean! To align MHC to IMGT numbering, it uses blastp. You need to install BLAST and make sure blastp is available as a command line command. The version that I used was "Protein-Protein BLAST 2.9.0+" -- not sure if it works with the newer ones.

seanwangsalad commented 4 months ago

Sorry for the delayed response (got busy with school) This works! Thanks