collection in workflow fail
by Alexander Vowinkel
Hi,
I'm running cutadapt (from TS) on a collection with 96 datasets, started
from a workflow as an intermediate step.
About half of them fail with this message.
Traceback (most recent call last):
File "/mnt/galaxy/galaxy-app/lib/galaxy/jobs/runners/__init__.py",
line 590, in finish_job
job_state.job_wrapper.finish( stdout, stderr, exit_code )
File "/mnt/galaxy/galaxy-app/lib/galaxy/jobs/__init__.py", line
1261, in finish
ActionBox.execute(self.app, self.sa_session, pja.post_job_action, job)
File "/mnt/galaxy/galaxy-app/lib/galaxy/jobs/actions/post.py", line
532, in execute
ActionBox.actions[pja.action_type].execute(app, sa_session, pja,
job, replacement_dict)
File "/mnt/galaxy/galaxy-app/lib/galaxy/jobs/actions/post.py", line
405, in execute
for input_dataset in [x.dataset for x in j2c.input_datasets if
x.dataset.creating_job.workflow_invocation_step and
x.dataset.creating_job.workflow_invocation_step.workflow_invocation ==
wfi]:
AttributeError: 'NoneType' object has no attribute 'input_datasets'
Running release 15.07 rev cf29f6c4a7
<https://github.com/galaxyproject/galaxy/commit/cf29f6c4a77a084bcf4732ddf1...>
Is that Known? How to avoid?
Best,
Alexander
6 years, 9 months
Call for Tool Shed Admins
by Martin Čech
Hi everybody,
similar to the existing mailing list of Galaxy instance admins we are
putting together a mailing list of admins of Tool Shed instances
(especially the public ones) so if you administer one (or more) please
respond to me privately and I will put you on it.
Thank you very much.
Martin, Galaxy Team
6 years, 9 months
configuring job runner slurm on cloudman
by Alexander Vowinkel
Hi,
I have adopted /mnt/galaxy/galaxy-app/config/job_conf.xml:
I added a destination with following param:
<param id="nativeSpecification">-N1 --cpus-per-task 1
--mem-per-cpu=4G</param>
Galaxy service was restarted after chaning this.
Now I get the error "Unable to run job due to a misconfiguration of the
Galaxy job running system. Please contact a site administrator." when I try
to run a job.
Looking in the log gives:
galaxy.jobs.runners.drmaa DEBUG 2015-07-06 22:50:40,187 (493)
submitting file
/mnt/galaxy/tmp/job_working_directory/000/493/galaxy_493.sh
> galaxy.jobs.runners.drmaa DEBUG 2015-07-06 22:50:40,187 (493) native specification is: -N1 --cpus-per-task 1 --mem-per-cpu=4G
> galaxy.jobs.runners.drmaa ERROR 2015-07-06 22:50:40,187 (493) drmaa.Session.runJob() failed unconditionally
> Traceback (most recent call last):
> [...]
> InvalidAttributeValueException: code 14: Invalid native specification: -N1 --cpus-per-task 1 --mem-per-cpu=4G
Well. running this as galaxy user in the console with
$ srun -N1 --cpus-per-task 1 --mem-per-cpu=4G
> /mnt/galaxy/tmp/job_working_directory/000/494/galaxy_494.sh
, it actually runs good.
I was wondering if this is connected with the fact that the log states "
galaxy.jobs.runners.drmaa" and not something like galaxy.jobs.runners.slurm,
like defined in the job_conf.xml: <plugin id="slurm" type="runner"
load="galaxy.jobs.runners.slurm:SlurmJobRunner" />
So - What is going wrong here? Am I working on the wrong job_conf.xml?
What does galaxy do here?
Thanks for help!Alexander
6 years, 9 months
