Unclear error code while testing

[DCGenomics]

(cwl) Bens-MBP:amr_finder benbusby$ ./amrfinder -p test_prot.fa
Required supplementary data not present, downloading via ftp.
Fetching AMR.LIB...success!
Fetching AMRProt...success!
Fetching AMR_CDS...success!
Fetching fam.tab...success!
Fetching changes.txt...success!
['cwl-runner', '--user-space-docker-cmd', 'udocker', '/Users/benbusby/experiments/amr_finder/wf_amr_prot.cwl', '/var/folders/fd/2wlv763j4nd6kmpg89701kd80000gn/T/amr_params_rsfl0e.yaml']
Return code: 1
None

Docker is installed on this system but not udocker.

[slottad]

amrfinder only tries to run udocker when it can't find docker in the path.

What happens when you type docker run hello-world at the same prompt?

[clinardi]

Hi, I have the same problem and I was able to run "docker run hello-world" but I still have the following error.

cl:/amr_finder$ ./amrfinder -p test_prot.fa -g test_prot.gff
Required supplementary data not present, downloading via ftp.
Fetching AMR.LIB...success!
Fetching AMRProt...success!
Fetching AMR_CDS...success!
Fetching fam.tab...success!
Fetching changes.txt...success!
['cwl-runner', '/home/cl/amr_finder/wf_amr_prot.cwl', '/tmp/amr_params_deU2W4.yaml']
Return code: 1
None
cl:/amr_finder$ ./amrfinder -p test_prot.fa -g test_prot.gff
['cwl-runner', '/home/cl/amr_finder/wf_amr_prot.cwl', '/tmp/amr_params_QsuswL.yaml']
Return code: 1
None

Do you know what might be the problem?

[slottad]

This doesn't look exactly like the same problem, since it is not trying to run udocker. Can you try running it again with the -s option and post the output?

[clinardi]

I get the following error

cl@bal2:~/amr_finder$ ./amrfinder -p test_prot.fa -g test_prot.gff -s
Traceback (most recent call last):
File "/home/cl/miniconda2/bin/cwl-runner", line 7, in
from cwltool.main import main
File "/home/cl/miniconda2/lib/python2.7/site-packages/cwltool/main.py", line 21, in
from schema_salad import validate
File "/home/cl/miniconda2/lib/python2.7/site-packages/schema_salad/init.py", line 10, in
from .utils import onWindows
File "/home/cl/miniconda2/lib/python2.7/site-packages/schema_salad/utils.py", line 8, in
from typing_extensions import Text # pylint: disable=unused-import
File "/home/cl/miniconda2/lib/python2.7/site-packages/typing_extensions.py", line 4, in
from typing import (
ImportError: cannot import name Counter
['cwl-runner', '/home/cl/amr_finder/wf_amr_prot.cwl', '/tmp/amr_params_nMQ1IA.yaml']
Return code: 1
None

[slottad]

There is something broken about your installation. Counter is part of typing, which extends collections, which is part of the standard package for python. Did you install this in a python virtualenv? Or forget to activate it?

I suggest creating a virtenv and reinstalling cwl.

[clinardi]

I get the following error when trying to make a virtualenv

cl@l:~$ virtualenv --python=python2 cwl
Running virtualenv with interpreter /home/cl/miniconda2/bin/python2
New python executable in /home/cl/cwl/bin/python2
Also creating executable in /home/cl/cwl/bin/python
Installing setuptools, pip, wheel...
Complete output from command /home/cl/cwl/bin/python2 - setuptools pip wheel:
Traceback (most recent call last):
File "", line 11, in
ImportError: cannot import name main

...Installing setuptools, pip, wheel...done.
Traceback (most recent call last):
File "/home/cl/miniconda2/lib/python2.7/site-packages/virtualenv.py", line 2343, in
main()
File "/home/cl/miniconda2/lib/python2.7/site-packages/virtualenv.py", line 712, in main
symlink=options.symlink)
File "/home/cl/miniconda2/lib/python2.7/site-packages/virtualenv.py", line 947, in create_environment
download=download,
File "/home/cl/miniconda2/lib/python2.7/site-packages/virtualenv.py", line 904, in install_wheel
call_subprocess(cmd, show_stdout=False, extra_env=env, stdin=SCRIPT)
File "/home/cl/miniconda2/lib/python2.7/site-packages/virtualenv.py", line 796, in call_subprocess
% (cmd_desc, proc.returncode))
OSError: Command /home/cl/cwl/bin/python2 - setuptools pip wheel failed with error code 1

[slottad]

What OS is this? You are using a version of python from your home directory, not the system one. You might try: virtualenv --python=/usr/bin/python cwl

[clinardi]

I was using ubuntu so I used the command

virtualenv -p /usr/bin/python cwl

It works perfectly now! Thank you so much for your help!