Question: HISAT2 "OSError: [Errno 2] No such file or directory" (Samtools install problem on a local Galaxy)
0
gravatar for djevo1
14 months ago by
djevo160
djevo160 wrote:

I believe I had posted this under another account but cannot seem to find a solution to this issue. I installed hisat and added samtools to my PATH on my galaxy install machine. I attempt to run a job and receive the following near the end of the job from hisat. I am not sure what other issue could be causing hisat to fail.

Traceback (most recent call last):
  File "/home/eclark28/galaxy_production/galaxy/lib/galaxy/jobs/runners/__init__.py", line 609, in finish_job
    job_state.job_wrapper.finish( stdout, stderr, exit_code )
  File "/home/eclark28/galaxy_production/galaxy/lib/galaxy/jobs/__init__.py", line 1265, in finish
    dataset.datatype.set_meta( dataset, overwrite=False )
  File "/home/eclark28/galaxy_production/galaxy/lib/galaxy/datatypes/binary.py", line 347, in set_meta
    exit_code = subprocess.call( args=command, stderr=open( stderr_name, 'wb' ) )
  File "/home/eclark28/galaxy_production/python/lib/python2.7/subprocess.py", line 523, in call
    return Popen(*popenargs, **kwargs).wait()
  File "/home/eclark28/galaxy_production/python/lib/python2.7/subprocess.py", line 711, in __init__
    errread, errwrite)
  File "/home/eclark28/galaxy_production/python/lib/python2.7/subprocess.py", line 1343, in _execute_child
    raise child_exception
OSError: [Errno 2] No such file or directory
hisat admin error local samtools • 722 views
ADD COMMENTlink modified 14 months ago by Jennifer Hillman Jackson23k • written 14 months ago by djevo160
1
gravatar for Nate Coraor
14 months ago by
Nate Coraor3.1k
United States
Nate Coraor3.1k wrote:

You mentioned having installed samtools on $PATH. Could you explain the steps you used to do this? It seems as though it's still not found in the post-job environment.

ADD COMMENTlink written 14 months ago by Nate Coraor3.1k

I installed samtools by using the configure --prefix flag in this case to a folder in my home directory. I then ran the following command

export PATH=/home/eclark28/galaxy_production/samtools/bin:$PATH
ADD REPLYlink written 14 months ago by djevo160

How did you start Galaxy after that?

ADD REPLYlink written 14 months ago by Nate Coraor3.1k

Simply ran sh run.sh

ADD REPLYlink written 14 months ago by djevo160
1

Galaxy should inherit the environment then. You're not setting $PATH in a job destination or anything like that, are you?

You may need to add some debugging output to determine exactly what environment the metadata script is being run under. You can also disable job cleanup in galaxy.ini to see what the job script files are.

ADD REPLYlink written 14 months ago by Nate Coraor3.1k
1

I was able to fix this, there was an issue with the samtools install.

ADD REPLYlink written 14 months ago by djevo160

Ok, good to know, thanks!

ADD REPLYlink written 14 months ago by Jennifer Hillman Jackson23k
0
gravatar for Jennifer Hillman Jackson
14 months ago by
United States
Jennifer Hillman Jackson23k wrote:

Hello,

If working at http://usegalaxy.org, this indicates an error from the cluster. Re-running the job generally resolves this type of issue.

On a local, you'll need to do some admin detective work:

  • Try a re-run
  • Try other tools that use Samtools to ensure that is intact
  • Try a different dataset to make sure the inputs are not the problem, double checking the tool form instructions.

If those fail too:

  • Make sure you are upgraded to the latest Galaxy build: https://docs.galaxyproject.org/en/master/releases/16.07_announce.html
  • If you have not upgraded the database away from SQlite, do that: http://usegalaxy.org see "Advanced Config" link outs
  • If you are using a cluster and no jobs run there successfully, then the set up is likely problematic. Use the wiki resources or provide more details about your server config and the error (log) from this job run and post to galaxy-dev@lists.galaxyproject.org for development community support. Strip any API keys/user/pass info. We may get some replies here, but that is the core hub for admin help.

Thanks, Jen, Galaxy team

ADD COMMENTlink modified 14 months ago • written 14 months ago by Jennifer Hillman Jackson23k

I apologize, I meant to say I am running my own galaxy instance.

ADD REPLYlink written 14 months ago by djevo160

Yes, that was my mistake, I didn't read the entire title (!). Advice now is for a local.

ADD REPLYlink written 14 months ago by Jennifer Hillman Jackson23k

OK I am still using an sqlite database as we are going to migrate this instance. If I installed samtools nit system-wide, but instead in a dedicated folder, what is the proper method to have it identified by galaxy?

ADD REPLYlink written 14 months ago by djevo160
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