Hi there

I am working on a local instance of Galaxy constructed from the docker image galaxy-stable:18.01.

Like in this topic (https://biostar.usegalaxy.org/p/14328/) (I don't know if I should have posted there instead of opening a new topic) I have an problem with a job in red saying "Unable to finish job" but the output datasets seem to be OK. The tool I used is RSEM calculate expression (package RSEM, owner "jjohnson", revision 14267d364365).

Stdout and Stderr are empty.

I've checked that samtools are installed first. I have plenty of space on my disk and I allowed 16G of RAM in my job_conf.xml file.

Here's the last line of my uwsgi.log file :

galaxy.model.metadata DEBUG 2018-05-17 08:19:07,889 [p:319,w:2,m:0] [LocalRunner.work_thread-0] setting metadata externally failed for HistoryDatasetAssociation 7: 'samtools returned with error 1: stdout=, stderr=samtools index: failed to create index for "/export/galaxy-central/database/files/000/dataset_7.dat": Bad file descriptor\n'
[E::hts_idx_push] Chromosome blocks not continuous
galaxy.jobs.runners.local ERROR 2018-05-17 08:19:08,186 [p:319,w:2,m:0] [LocalRunner.work_thread-0] Job wrapper finish method failed
Traceback (most recent call last):
  File "lib/galaxy/jobs/runners/local.py", line 152, in queue_job
    self._finish_or_resubmit_job(job_state, stdout, stderr, exit_code)
  File "lib/galaxy/jobs/runners/__init__.py", line 432, in _finish_or_resubmit_job
    job_state.job_wrapper.finish(stdout, stderr, exit_code, check_output_detected_state=check_output_detected_state)
  File "lib/galaxy/jobs/__init__.py", line 1288, in finish
    dataset.datatype.set_meta(dataset, overwrite=False)
  File "lib/galaxy/datatypes/binary.py", line 401, in set_meta
    pysam.index(dataset.file_name, index_file.file_name)
  File "/galaxy_venv/local/lib/python2.7/site-packages/pysam/utils.py", line 75, in __call__
    stderr))
SamtoolsError: 'samtools returned with error 1: stdout=, stderr=samtools index: failed to create index for "/export/galaxy-central/database/files/000/dataset_7.dat": Resource temporarily unavailable\n'
galaxy.tools.error_reports DEBUG 2018-05-17 08:19:08,726 [p:319,w:2,m:0] [LocalRunner.work_thread-0] Bug report plugin <galaxy.tools.error_reports.plugins.sentry.SentryPlugin object at 0x7fd38ac07f50> generated response None
galaxy.tools.error_reports DEBUG 2018-05-17 08:19:08,726 [p:319,w:2,m:0] [LocalRunner.work_thread-0] Bug report plugin <galaxy.tools.error_reports.plugins.sentry.SentryPlugin object at 0x7fd38ac07f50> generated response None
galaxy.tools.error_reports DEBUG 2018-05-17 08:19:08,726 [p:319,w:2,m:0] [LocalRunner.work_thread-0] Bug report plugin <galaxy.tools.error_reports.plugins.sentry.SentryPlugin object at 0x7fd38ac07f50> generated response None
galaxy.tools.error_reports DEBUG 2018-05-17 08:19:08,726 [p:319,w:2,m:0] [LocalRunner.work_thread-0] Bug report plugin <galaxy.tools.error_reports.plugins.sentry.SentryPlugin object at 0x7fd38ac07f50> generated response None
galaxy.tools.error_reports DEBUG 2018-05-17 08:19:08,726 [p:319,w:2,m:0] [LocalRunner.work_thread-0] Bug report plugin <galaxy.tools.error_reports.plugins.sentry.SentryPlugin object at 0x7fd38ac07f50> generated response None
galaxy.model.metadata DEBUG 2018-05-17 08:19:08,729 [p:319,w:2,m:0] [LocalRunner.work_thread-0] Cleaning up external metadata files
galaxy.model.metadata DEBUG 2018-05-17 08:19:08,754 [p:319,w:2,m:0] [LocalRunner.work_thread-0] Failed to cleanup MetadataTempFile temp files from /export/galaxy-central/database/job_working_directory/000/5/metadata_out_HistoryDatasetAssociation_7_uppgiR: No JSON object could be decoded
172.17.0.1 - - [17/May/2018:08:19:09 +0000] "GET /api/histories/f597429621d6eb2b/contents?order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2018-05-17T08%3A19%3A05.000Z&qv=False&qv=False HTTP/1.1" 200 - "http://localhost:8002/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fjjohnson%2Frsem%2Frsem_calculate_expression%2F1.1.17&version=1.1.17&__identifer=1hja2xls8wx" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/66.0.3359.170 Safari/537.36"
[pid: 319|app: 0|req: 35/71] 172.17.0.1 () {44 vars in 1204 bytes} [Thu May 17 08:19:09 2018] GET /api/histories/f597429621d6eb2b/contents?order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2018-05-17T08%3A19%3A05.000Z&qv=False&qv=False => generated 2477 bytes in 90 msecs (HTTP/1.1 200) 3 headers in 124 bytes (1 switches on core 1)
172.17.0.1 - - [17/May/2018:08:19:09 +0000] "POST /api/tools/toolshed.g2.bx.psu.edu/repos/jjohnson/rsem/rsem_calculate_expression/1.1.17/build HTTP/1.1" 200 - "http://localhost:8002/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fjjohnson%2Frsem%2Frsem_calculate_expression%2F1.1.17&version=1.1.17&__identifer=1hja2xls8wx" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/66.0.3359.170 Safari/537.36"
[pid: 316|app: 0|req: 37/72] 172.17.0.1 () {50 vars in 1224 bytes} [Thu May 17 08:19:09 2018] POST /api/tools/toolshed.g2.bx.psu.edu/repos/jjohnson/rsem/rsem_calculate_expression/1.1.17/build => generated 44870 bytes in 76 msecs (HTTP/1.1 200) 3 headers in 124 bytes (1 switches on core 0)
172.17.0.1 - - [17/May/2018:08:19:09 +0000] "GET /api/histories/f597429621d6eb2b?keys=size%2Cnon_ready_jobs%2Ccontents_active%2Chid_counter HTTP/1.1" 200 - "http://localhost:8002/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fjjohnson%2Frsem%2Frsem_calculate_expression%2F1.1.17&version=1.1.17&__identifer=1hja2xls8wx" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/66.0.3359.170 Safari/537.36"
[pid: 319|app: 0|req: 36/73] 172.17.0.1 () {44 vars in 1100 bytes} [Thu May 17 08:19:09 2018] GET /api/histories/f597429621d6eb2b?keys=size%2Cnon_ready_jobs%2Ccontents_active%2Chid_counter => generated 120 bytes in 73 msecs (HTTP/1.1 200) 3 headers in 124 bytes (1 switches on core 3)
172.17.0.1 - - [17/May/2018:08:19:10 +0000] "GET /api/users/f2db41e1fa331b3e HTTP/1.1" 200 - "http://localhost:8002/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fjjohnson%2Frsem%2Frsem_calculate_expression%2F1.1.17&version=1.1.17&__identifer=1hja2xls8wx" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/66.0.3359.170 Safari/537.36"
[pid: 316|app: 0|req: 39/74] 172.17.0.1 () {44 vars in 975 bytes} [Thu May 17 08:19:10 2018] GET /api/users/f2db41e1fa331b3e => generated 278 bytes in 89 msecs (HTTP/1.1 200) 3 headers in 124 bytes (1 switches on core 2)
172.17.0.1 - - [17/May/2018:08:19:10 +0000] "POST /api/tools/toolshed.g2.bx.psu.edu/repos/jjohnson/rsem/rsem_calculate_expression/1.1.17/build HTTP/1.1" 200 - "http://localhost:8002/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fjjohnson%2Frsem%2Frsem_calculate_expression%2F1.1.17&version=1.1.17&__identifer=1hja2xls8wx" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/66.0.3359.170 Safari/537.36"
[pid: 316|app: 0|req: 39/75] 172.17.0.1 () {50 vars in 1224 bytes} [Thu May 17 08:19:10 2018] POST /api/tools/toolshed.g2.bx.psu.edu/repos/jjohnson/rsem/rsem_calculate_expression/1.1.17/build => generated 44870 bytes in 131 msecs (HTTP/1.1 200) 3 headers in 124 bytes (1 switches on core 3)

Any idea of how I could solve this?

Thank your for your help.

Hello,

Did you prepare the input with the tool "RSEM prepare reference" first?

If so, there might be a bug in the tool suite versus the latest Galaxy version. These tools were last updated in 2016 and much has changed since then.

First, check the required tool dependencies and that are these correctly installed (check under Admin). You could uninstall/reinstall to make sure these are intact. If any are missing versus what is reported as a dependency in the Tool Shed, then try to install anything missing. This tool uses an older dependency management protocol (largely replace by Conda now).

If that doesn't work, the tool author can be contacted through the Tool Shed https://usegalaxy.org/toolshed to report the problem (create account or login, navigate to the tool, then use the upper right corner menu for Repository Actions >> Contact repository owner.

I also asked the developer for direct feedback about this at the IUC Gitter channel here: https://gitter.im/galaxy-iuc/iuc?at=5afdcf7fb84be71db915a006. Please feel free to jump into the conversation.

Thanks! Jen, Galaxy team

Hello

Thank you for your answer.

Yes I prepared my input with "RSEM trinity fasta to gene map" and "RSEM prepare reference". I'm currently preparing an instance of Galaxy for a training given next week, and I'm following a (tested) tutorial given by the trainer to test the tools so I'll trust my data and procedure :)

I've also checked that all the dependencies are correctly installed. The only thing was that it didn't install the latest version of package "rsem_datatypes" but updating it didn't change anything.

Thank you for reporting the bug to the tool author on Gitter. I'll do the same through the toolshed.