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python subprocess OSError when running bwa-mem

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python subprocess OSError when running bwa-mem

Georgios Nikolis
Dear all,
we are currently working on a new local Galaxy instance (17.01) and we encounter an error when running bwa-mem jobs. The jobs fail with a python subprocess OSError triggered in the module lib/galaxy/datatypes/binary.py
Here is the traceback:
Traceback (most recent call last):
  File "/opt/galaxy/galaxy/lib/galaxy/jobs/runners/__init__.py", line 624, in finish_job
    job_state.job_wrapper.finish( stdout, stderr, exit_code )
  File "/opt/galaxy/galaxy/lib/galaxy/jobs/__init__.py", line 1350, in finish
    dataset.datatype.set_meta( dataset, overwrite=False )
  File "/opt/galaxy/galaxy/lib/galaxy/datatypes/binary.py", line 391, in set_meta
    exit_code = subprocess.call( args=command, stderr=open( stderr_name, 'wb' ))
  File "/usr/lib64/python2.7/subprocess.py", line 524, in call
    return Popen(*popenargs, **kwargs).wait()
  File "/usr/lib64/python2.7/subprocess.py", line 711, in __init__
    errread, errwrite)
  File "/usr/lib64/python2.7/subprocess.py", line 1327, in _execute_child
    raise child_exception
OSError: [Errno 2] No such file or directory
Has anyone seen this error before? Is there anything we can do to get rid of it?

Thanks a lot!

Best,
Georgios


--
Georgios Nikolis
Genomics and
Proteomics Core Facility
High Throughput Sequencing (W190)
IT Management Genomics Proteomics

German Cancer Research Center (DKFZ)
Foundation under Public Law
Im Neuenheimer Feld 580
69120 Heidelberg
Germany
phone: +49 6221 42-4659

g.nikolis@...
www.dkfz.de

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Management Board: Prof. Dr. Michael Baumann, Prof. Dr. Josef Puchta
VAT-ID No.: DE143293537




    

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Re: python subprocess OSError when running bwa-mem

Hans-Rudolf Hotz
Hi Georgios

I am just guessing here, but the error looks familiar:

Do you have samtools installed? and is it in $PATH?
(for a similar case, see: https://biostar.usegalaxy.org/p/19938/ )


Regards, Hans-Rudolf


On 05/19/2017 10:03 AM, Georgios Nikolis wrote:

> Dear all,
> we are currently working on a new local Galaxy instance (17.01) and we
> encounter an error when running bwa-mem jobs. The jobs fail with a
> python subprocess OSError triggered in the module
> lib/galaxy/datatypes/binary.py
> Here is the traceback:
>> Traceback (most recent call last):
>>    File "/opt/galaxy/galaxy/lib/galaxy/jobs/runners/__init__.py", line 624, in finish_job
>>      job_state.job_wrapper.finish( stdout, stderr, exit_code )
>>    File "/opt/galaxy/galaxy/lib/galaxy/jobs/__init__.py", line 1350, in finish
>>      dataset.datatype.set_meta( dataset, overwrite=False )
>>    File "/opt/galaxy/galaxy/lib/galaxy/datatypes/binary.py", line 391, in set_meta
>>      exit_code = subprocess.call( args=command, stderr=open( stderr_name, 'wb' ))
>>    File "/usr/lib64/python2.7/subprocess.py", line 524, in call
>>      return Popen(*popenargs, **kwargs).wait()
>>    File "/usr/lib64/python2.7/subprocess.py", line 711, in __init__
>>      errread, errwrite)
>>    File "/usr/lib64/python2.7/subprocess.py", line 1327, in _execute_child
>>      raise child_exception
>> OSError: [Errno 2] No such file or directory
> Has anyone seen this error before? Is there anything we can do to get
> rid of it?
>
> Thanks a lot!
>
> Best,
> Georgios
>
>
> --
> *Georgios Nikolis*
> Genomics and Proteomics Core Facility
> High Throughput Sequencing (W190)
> IT Management Genomics Proteomics
>
> German Cancer Research Center (DKFZ)
> Foundation under Public Law
> Im Neuenheimer Feld 580
> 69120 Heidelberg
> Germany
> phone: +49 6221 42-4659
>
> [hidden email] <http://www.dkfz.de/>
> www.dkfz.de <http://www.dkfz.de/>
>
> logo <http://www.dkfz.de>
>
> Management Board: Prof. Dr. Michael Baumann, Prof. Dr. Josef Puchta
> VAT-ID No.: DE143293537
>
>
>
>
>
> ___________________________________________________________
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>    https://lists.galaxyproject.org/
>
> To search Galaxy mailing lists use the unified search at:
>    http://galaxyproject.org/search/
>
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/
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