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huguesrichard / Allopipe

AlloPipe is a computational method to assess the alloreactivity expected from a donor/recipient transplantation pair
MIT License
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af-AMS run: Broken pipe #5

Open PierreLaville opened 8 months ago

PierreLaville commented 8 months ago

When launching the AAMS run: python aams_pipeline.py -M ../output/runs/test_run/run_tables/test_pair_test_run_mismatches_20_400_5_gq_20_0.8_bl_3.tsv -T ../output/runs/test_run/run_tables/test_pair_test_run_transcripts_pair_codons_20_400_5_gq_20_0.8_bl_3.tsv -E ../tutorial/Ensembl/Homo_sapiens.GRCh38.cdna.all.fa -P ../tutorial/Ensembl/Homo_sapiens.GRCh38.pep.all.fa -R ../tutorial/Ensembl/Homo_sapiens.GRCh38.103.refseq.tsv -n test_run -p test_pair -l 9 --el_rank 2 -a HLA-A*01:01,HLA-A*02:01,HLA-B*08:01,HLA-B*27:05,HLA-C*01:02,HLA-C*07:01

Error (starting line 2 for 4 lines, see below), output pasted for context:

Entering netMHCpan handler : running netMHCpan will last a long time
paste: write error: Broken pipe
paste: write error
paste: write error: Broken pipe
paste: write error
0   Pos    Peptide               ID     Ave      NB
1     0  AISFLGCIT  ENSG00000112462  0.0001       0
2     0  ISFLGCITQ  ENSG00000112462  0.0002       0
3     0  SFLGCITQL  ENSG00000112462  0.0220       0
4     0  FLGCITQLH  ENSG00000112462  0.0014       0
5     0  LGCITQLHF  ENSG00000112462  0.0010       0
..   ..        ...              ...     ...     ...
677   0  SSQGCPECR  ENSG00000009765  0.0009       0
678   0  SQGCPECRS  ENSG00000009765  0.0000       0
679   0  QGCPECRSG  ENSG00000009765  0.0000       0
680   0  GCPECRSGD  ENSG00000009765  0.0000       0
681   0  CPECRSGDC  ENSG00000009765  0.0000       0

[681 rows x 5 columns]
34

Not sure wether it comes from Python or NetMHCpan. It doesn't seem to affect the ouptut though, which is fitting to the expected value (but maybe it does for some of the output).

huguesrichard commented 8 months ago

I searched for a paste command in the code, didn't find one. One way to test would be to store the call of the command and to print it on the terminal before it's launched (it's at this position in the file: https://github.com/huguesrichard/Allopipe/blob/4b4c37191e404575725d285e9bbec2c92f1a46f4/src/tools/aams_helpers.py#L373)

PierreLaville commented 8 months ago

If I understood correctly, the printed call of the command is the following (running with the tutorial example data): netMHCpan -BA -f ../output/runs/test_run/aams_run_tables/test_pair_test_run_netmhc_fasta.fa -inptype 0 -l 9 -xls -xlsfile ../output/runs/test_run/netMHCpan_out/test_pair.out -a HLA-A01:01,HLA-A02:01,HLA-B08:01,HLA-B27:05,HLA-C01:02,HLA-C07:01 > ../output/runs/test_run/netMHCpan_out/test_pair_full_run_information.txt