python subprocess OSError when running bwa-mem
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
___________________________________________________________ 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/
Hi run.sh On 05/24/2017 10:51 AM, Georgios Nikolis wrote:
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?
yes, at least for samtools, I guess this is currently the best option. Regards, Hans-Rudolf
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
___________________________________________________________ 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/
participants (2)
-
Georgios Nikolis -
Hans-Rudolf Hotz