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mskcc / tempo

CCS research pipeline to process WES and WGS TN pairs
https://cmotempo.netlify.com/
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Selective lines of neoantigen maf truncated #708

Closed gongyixiao closed 4 years ago

gongyixiao commented 4 years ago

See https://github.com/taylor-lab/neoantigen-dev/issues/8

gongyixiao commented 4 years ago

Solving here: https://github.com/taylor-lab/neoantigen-dev/pull/9

Need to update the docker file to use the git repository of neoantigen instead of a local tar.gz file: https://github.com/mskcc/tempo/blob/f8e437bc91df936a2f135c0d0c0c5b79ac00c4e8/containers/neoantigen/Dockerfile#L48

I guess the reason that we use downloaded neoantigen-dev-0.3.0.tar.gz is because the repository is not publicly available. So ignore this maybe for now.

gongyixiao commented 4 years ago

And I also run into problem recreating the docker image using this docker file, since I don't know what exact change need to be made to this file and I can't find this file anywhere data.netmhcpan.tar.gz: https://github.com/mskcc/tempo/blob/f8e437bc91df936a2f135c0d0c0c5b79ac00c4e8/containers/neoantigen/Dockerfile#L38-L40

Tried doing this: 

    && wget http://www.cbs.dtu.dk/services/NetMHCpan-4.0/data.Linux.tar.gz \
    && gunzip -c data.Linux.tar.gz | tar xvf - \
    && find ./ -type d | xargs -n1 chmod o+rw \
    && find ./ -type f | xargs -n1 chmod o+r \

Doesn't seem to work.

Error I'm getting is like below, not sure if that's the consequence of the above issue:

[gongy@juno output]$ cat /juno/work/ccs/gongy/output/work/b4/643fbc11e0876b4fc433bd7c99ab73/.command.log
nxf-scratch-dir jb16:/scratch/gongy/nxf.3fSph8ewAa
12-06-2019 17:34:45: INFO: Starting neoantigen prediction run
12-06-2019 17:34:45: INFO:  Log file: .//neoantigen_run.log
12-06-2019 17:34:45: INFO:  --config_file:/usr/local/bin/neoantigen/neoantigen-docker.config
12-06-2019 17:34:45: INFO:  --normal_bam: None
12-06-2019 17:34:45: INFO:  --maf_file: DU874145-T__DU874145-N.facets.zygosity.maf
12-06-2019 17:34:45: INFO:  --output_dir: ./
12-06-2019 17:34:45: INFO: Generating mutated peptides FASTA
12-06-2019 17:34:45: INFO: Loading reference CDS/cDNA sequences...
12-06-2019 17:35:46: INFO: Finished loading reference CDS/cDNA sequences...
12-06-2019 17:35:46: INFO: Reading MAF file and constructing mutated peptides...
12-06-2019 17:35:46: INFO:  MAF mutations summary
12-06-2019 17:35:46: INFO:      # mutations: 2
12-06-2019 17:35:46: INFO:      # non-syn: 1 (# with missing CDS: 0)
12-06-2019 17:35:46: INFO:
12-06-2019 17:35:46: INFO: Running MHC--peptide binding predictions using NetMHCpan 4.0...
12-06-2019 17:35:46: INFO: Starting NetMHCpan 4.0...
12-06-2019 17:35:46: INFO: Predicting on the following HLA-alleles: HLA-A01:01,HLA-A31:01,HLA-B08:01,HLA-B14:01,HLA-C07:01
12-06-2019 17:35:46: ERROR: Error while running NetMHCpan and NetMHC
12-06-2019 17:35:46: ERROR: Traceback (most recent call last):
  File "/usr/local/bin/neoantigen/neoantigen.py", line 332, in main
    execute_cmd(run_netmhcpan_cmd)
  File "/usr/local/bin/neoantigen/neoantigen.py", line 518, in execute_cmd
    output = subprocess.check_output(cmd, shell=True, stderr=subprocess.STDOUT)
  File "/usr/lib/python2.7/subprocess.py", line 223, in check_output
    raise CalledProcessError(retcode, cmd, output=output)
CalledProcessError: Command 'rm -f .//DU874145-T__DU874145-N.netmhcpan4.output.txt; /usr/local/bin/netMHCpan-4.0/netMHCpan -s -BA  -a HLA-A01:01,HLA-A31:01,HLA-B08:01,HLA-B14:01,HLA-C07:01 -f .//DU874145-T__DU874145-N.mutated_sequences.fa -l 9,10 -inptype 0  -xls  -xlsfile .//DU874145-T__DU874145-N.netmhcpan4.output.xls  > .//DU874145-T__DU874145-N.netmhcpan4.output.txt' returned non-zero exit status 126

12-06-2019 17:35:46: INFO: Cleaning up NetMHCpan run directory
kpjonsson commented 4 years ago

@gongyixiao

May be a matter of setting the right permission. In the docker container:

drwxr-xr-x 4 root root  244 Oct 11  2017 data

But locally, after dowloading and upacking the data.Linux.tar.gz file:

drwxr-x---   14 jonssonp  MSKCC\Domain Users   448B Oct 11  2017 data/
gongyixiao commented 4 years ago

Yes, I did notice that. I changed it using: 

    && wget http://www.cbs.dtu.dk/services/NetMHCpan-4.0/data.Linux.tar.gz \
    && gunzip -c data.Linux.tar.gz | tar xvf - \
    && find ./ -type d | xargs -n1 chmod o+rw \
    && find ./ -type f | xargs -n1 chmod o+r \
gongyixiao commented 4 years ago

Yes, the above permission change need to be done.

But permission changes also need to be done for netMHCpan directory as well.

Solved here https://github.com/mskcc/tempo/pull/722