Mccortex Path not accepted

[ronald-jaepel]

running this command: /well/iqbal/people/ronaldj/apps/atlas/mykatlas/atlas_main.py walk DRR002017 /well/iqbal/people/ronaldj/gn-amr-genes.fasta --memory 2GB --skeleton_dir /well/iqbal/people/ronaldj/skeletons/ --mccortex31_path /well/iqbal/people/ronaldj/apps/atlas/mccortex/bin/mccortex31 --kmer 31 --ctx /well/iqbal/people/ronaldj/ena_ecolis/cortex/DRR002017/binaries/cleaned/k31/DRR002017.kmer31.q10cleaned_10.ctx

I get this error: ERROR:mykatlas.cortex.server:Couldn't start McCortex is mccortex31 in path? : [Errno 2] No such file or directory

but just running /well/iqbal/people/ronaldj/apps/atlas/mccortex/bin/mccortex31 works just fine and calls mccortex

[Phelimb]

I was able to run

atlas walk DRR002017 /well/iqbal/people/ronaldj/gn-amr-genes.fasta --memory 2GB --skeleton_dir /well/iqbal/people/ronaldj/skeletons/ --mccortex31_path /well/iqbal/people/ronaldj/apps/atlas/mccortex/bin/mccortex31 --kmer 31 --ctx /well/iqbal/people/ronaldj/ena_ecolis/cortex/DRR002017/binaries/cleaned/k31/DRR002017.kmer31.q10cleaned_10.ctx

On cycloid without a problem.

bash-4.1$ atlas --version atlas v0.3.9-0-g407127f-dirty

Does this also fail or only on the cluster?

[Phelimb]

@ronald-jaepel what's the status on this? Can you get a run to fail on cycloid?

[ronald-jaepel]

Runs fail on cycloid if the mccortex path is not in the PATH variable, regardless of whether or not --mccortex31_path /well/iqbal/people/ronaldj/apps/atlas/mccortex/bin/mccortex31 has been used.

[ronald-jaepel]

Error messages: calling it with --mccortex31_path

(venv)-bash-4.1$ atlas walk DRR002017 /well/iqbal/people/ronaldj/gn-amr-genes.fasta --memory 2GB --skeleton_dir /well/iqbal/people/ronaldj/skeletons/ --mccortex31_path /well/iqbal/people/ronaldj/apps/atlas/mccortex/bin/mccortex31 --kmer 31 --ctx /well/iqbal/people/ronaldj/ena_ecolis/cortex/DRR002017/binaries/cleaned/k31/DRR002017.kmer31.q10cleaned_10.ctx
WARNING:mykatlas.typing.typer.genotyper:Failed to parse ['kpc?name=kpc&version=16', '0', '0', '0', '']
WARNING:mykatlas.typing.typer.genotyper:Failed to parse ['kpc?name=kpc&version=16', '0', '0', '0', '']
DEBUG:mykatlas.cmds.walk:Loading binary
ERROR:mykatlas.cortex.server:Couldn't start McCortex is mccortex31 in path? : [Errno 20] Not a directory 

calling it without --mccortex31_path:

(venv)-bash-4.1$ atlas walk DRR002017 /well/iqbal/people/ronaldj/gn-amr-genes.fasta --memory 2GB --skeleton_dir /well/iqbal/people/ronaldj/skeletons/ --kmer 31 --ctx /well/iqbal/people/ronaldj/ena_ecolis/cortex/DRR002017/binaries/cleaned/k31/DRR002017.kmer31.q10cleaned_10.ctx
DEBUG:mykatlas.cortex.mccortex:running mccortex31 geno -t 1 -m 2GB -k 31 -o /tmp//DRR002017-31_gn-amr-genes.covgs -g /well/iqbal/people/ronaldj/ena_ecolis/cortex/DRR002017/binaries/cleaned/k31/DRR002017.kmer31.q10cleaned_10.ctx -c /well/iqbal/people/ronaldj/gn-amr-genes.fasta /tmp//DRR002017-31_gn-amr-genes.ctx
Traceback (most recent call last):
  File "/data2/apps/atlas/venv/bin/atlas", line 9, in <module>
    load_entry_point('mykatlas==0.3.9', 'console_scripts', 'atlas')()
  File "/data2/apps/atlas/venv/lib/python2.7/site-packages/mykatlas/atlas_main.py", line 245, in main
    args.func(parser, args)
  File "/data2/apps/atlas/venv/lib/python2.7/site-packages/mykatlas/atlas_main.py", line 47, in run_subtool
    run(parser, args)
  File "/data2/apps/atlas/venv/lib/python2.7/site-packages/mykatlas/cmds/walk.py", line 130, in run
    _out_dict = run_genotype(parser, args)
  File "/data2/apps/atlas/venv/lib/python2.7/site-packages/mykatlas/cmds/genotype.py", line 27, in run_main
    cp.run()
  File "/data2/apps/atlas/venv/lib/python2.7/site-packages/mykatlas/typing/typer/genotyper.py", line 73, in run
    self._run_cortex()
  File "/data2/apps/atlas/venv/lib/python2.7/site-packages/mykatlas/typing/typer/genotyper.py", line 90, in _run_cortex
    self.mc_cortex_runner.run()
  File "/data2/apps/atlas/venv/lib/python2.7/site-packages/mykatlas/cortex/mccortex.py", line 161, in run
    self._run_cortex()
  File "/data2/apps/atlas/venv/lib/python2.7/site-packages/mykatlas/cortex/mccortex.py", line 175, in _run_cortex
    self._run_coverage_if_required()
  File "/data2/apps/atlas/venv/lib/python2.7/site-packages/mykatlas/cortex/mccortex.py", line 208, in _run_coverage_if_required
    subprocess.check_output(self.coverages_cmd)
  File "/apps/well/python/2.7.7-venv/lib/python2.7/subprocess.py", line 566, in check_output
    process = Popen(stdout=PIPE, *popenargs, **kwargs)
  File "/apps/well/python/2.7.7-venv/lib/python2.7/subprocess.py", line 710, in __init__
    errread, errwrite)
  File "/apps/well/python/2.7.7-venv/lib/python2.7/subprocess.py", line 1327, in _execute_child
    raise child_exception
OSError: [Errno 20] Not a directory

[Phelimb]

This should be fixed in 0.3.10