Question: "No such file or directory" when using mpileup
gravatar for kep
2.4 years ago by
United Kingdom
kep10 wrote:


We have a local install of galaxy which has the mpileup 0.0.3 tool installed (we can't go higher as we need to use a 1.1.x version of samtools).  When we run the tool it appears to run for a reasonable amount of time and the result dataset is written to disk and is of a non-zero size however we get the following errors:

Stack trace:

Traceback (most recent call last):
  File "/data/galaxy/app/lib/galaxy/jobs/runners/", line 129, in queue_job
    job_wrapper.finish( stdout, stderr, exit_code )
  File "/data/galaxy/app/lib/galaxy/jobs/", line 1204, in finish
    dataset.datatype.set_meta( dataset, overwrite=False )
  File "/data/galaxy/app/lib/galaxy/datatypes/", line 502, in set_meta
    proc = subprocess.Popen( args=command, stderr=open( stderr_name, 'wb' ) )
  File "/usr/lib64/python2.6/", line 642, in __init__
    errread, errwrite)
  File "/usr/lib64/python2.6/", line 1238, in _execute_child
    raise child_exception
OSError: [Errno 2] No such file or directory


Unable to finish job

We have seen the same error with the 0.0.2 version as well.

Any assistance you can give to why we are seeing this would be gratefully received!



mpileup • 1.1k views
ADD COMMENTlink modified 2.4 years ago by Wolfgang Maier510 • written 2.4 years ago by kep10
gravatar for Wolfgang Maier
2.4 years ago by
Wolfgang Maier510 wrote:

Apart from Jen's comments, is bcftools available in your $PATH?

The error you are seeing seems to be caused by Galaxy trying to index the file after its been created. In the case of a BCF file, I think it relies on the bcftools index command to do so.

ADD COMMENTlink written 2.4 years ago by Wolfgang Maier510

Adding the samtools path system wide fixed the issue.  Many thanks for the assistance!


ADD REPLYlink written 2.3 years ago by kep10
gravatar for Jennifer Hillman Jackson
2.4 years ago by
United States
Jennifer Hillman Jackson24k wrote:


First, older versions of this tool may be problematic due to other Galaxy updates (are now incompatible, unless also running an earlier Galaxy distribution from the same time frame).

Using the most current version is recommended (more that one version of samtool can be installed on a Galaxy as far as I know).

BUT - before you upgrade, please know that Mpileup v2.x has some known issues right now.

Best, Jen, Galaxy team

ADD COMMENTlink written 2.4 years ago by Jennifer Hillman Jackson24k
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