Closed ingewortel closed 6 years ago
Hi @ingewortel , Sorry about that this is a silly mistake on my side, the genomic anchors file should be semicolon separated and not coma separated. You can hardfix this locally by replacing comas by semicolons in the gene anchors file of your interest (either in the directory IGoR models have been installed into, or before installation) This is something I should have fixed earlier, I will try and release a new version of IGoR containing this fix along other bug fixes in the next few days. Again my apologies for this silly mistake...
Hi @qmarcou
Thanks for the quick reply, the semicolons indeed fixed the problem!
Best wishes, Inge
Hi @ingewortel , I have uploaded IGoRv1.3.0 release in which your problem has been addressed, along many others and new features were added. Check it out! I'll thus close this issue since the problem is solved. Best wished
Hi @qmarcou!
I am trying to run IGoR with the standard mouse beta chain model but have some problems with the alignment:
igor -set_wd . -batch foo -read_seqs myseqs.fasta -species mouse -chain beta -align --all
yields the following output:
Batch name set to: foo_
FASTA extension detected for the input sequence file
Species parameter set to: mouse
Chain parameter set to: beta
Working directory set to: "./"
[IGoR] ERROR: Exception caught while reading V CDR3 anchors.
[IGoR] ERROR: stoi
[IGoR] ERROR: Use "man igor", "igor -help" or visit https://bitbucket.org/qmarcou/igor to see available commands and their effects.
[IGoR] ERROR: Please report any bug to: quentin.marcou@lpt.ens.fr
[IGoR] ERROR: Terminating IGoR...
Note that I don't have this problem when I just read the sequences with
igor -set_wd . -batch foo -read_seqs myseqs.fasta
or try the alignment on the human model withigor -set_wd . -batch foo -read_seqs myseqs.fasta -species human -chain beta -align --all
But I do get the same error about V CDR3 anchors even when I try to align only the J genes:igor -set_wd . -batch foo -read_seqs myseqs.fasta -species mouse -chain beta -align --J
So the issue seems to be in the mouse model itself somewhere and probably has something to do with the _V_gene_CDR3anchors.csv file.
I looked into the _V_gene_CDR3anchors.csv file provided, and noticed that some of the TRBV genes that occur in the genomicVs.fasta file and the _modelparms.txt file are missing from the anchor file (for example, TRBV11*01). Could this be why IGoR crashes? Or am I doing something wrong?
Thanks!
Inge