HISAT2 "OSError: [Errno 2] No such file or directory" (Samtools install problem on a local Galaxy)

Question: HISAT2 "OSError: [Errno 2] No such file or directory" (Samtools install problem on a local Galaxy)

2.1 years ago by

djevo1 • 60

djevo1 • 60 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 • 1.3k views

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modified 2.1 years ago by Jennifer Hillman Jackson ♦ 25k • written 2.1 years ago by djevo1 • 60

2.1 years ago by

Nate Coraor ♦ 3.2k

United States

Nate Coraor ♦ 3.2k 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 COMMENT • link written 2.1 years ago by Nate Coraor ♦ 3.2k

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 REPLY • link written 2.1 years ago by djevo1 • 60

How did you start Galaxy after that?

ADD REPLY • link written 2.1 years ago by Nate Coraor ♦ 3.2k

Simply ran sh run.sh

ADD REPLY • link written 2.1 years ago by djevo1 • 60

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 REPLY • link written 2.1 years ago by Nate Coraor ♦ 3.2k

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

ADD REPLY • link written 2.1 years ago by djevo1 • 60

Ok, good to know, thanks!

ADD REPLY • link written 2.1 years ago by Jennifer Hillman Jackson ♦ 25k

2.1 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k 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 COMMENT • link modified 2.1 years ago • written 2.1 years ago by Jennifer Hillman Jackson ♦ 25k

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

ADD REPLY • link written 2.1 years ago by djevo1 • 60

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

ADD REPLY • link written 2.1 years ago by Jennifer Hillman Jackson ♦ 25k

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 REPLY • link written 2.1 years ago by djevo1 • 60

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