Hi Hans-Rudolf,
many thanks for pointing me to the right direction. samtools was
installed, it was indeed a problem with $PATH.
There are actually path setting scripts provides with the tools,
also for samtools, e.g.
database/dependencies/samtools/0.1.19/devteam/package_samtools_0_1_19/95d2c4aefb5f/env.sh
but it seems that they don't get executed automatically on server
start. I did it manually and bwa-mem runs now without errors.
We will have to see whether other tools besides samtools are
affected. Would you recommend that we put such path setting scripts
into run.sh?
Best,
Georgios
On 05/22/2017 08:11 AM, Hans-Rudolf
Hotz wrote:
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.nikolis@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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