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

g.niko...@dkfz.de <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





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