Dear list, today I got an erroneous result (red) despite the output of the tool to be seems fine. Seemingly there was an error during setting the metadata. ``` Fatal error: An error occured during execution, see stderr and stdout for more information Reading reference gene model /gpfs1/data/galaxy_server/galaxy-dev/database/files/002/dataset_2992.dat ... Done Loading SAM/BAM file ... Finished Total 62188 usable reads were sampled Traceback (most recent call last): File "/gpfs1/data/galaxy_server/galaxy-dev/jobs_dir/001/1858/set_metadata_Ad6q_v.py", line 1, in from galaxy_ext.metadata.set_metadata import set_metadata; set_metadata() File "/gpfs1/data/galaxy_server/galaxy-dev/lib/galaxy_ext/metadata/set_metadata.py", line 85, in set_metadata datatypes_registry.load_datatypes(root_dir=galaxy_root, config=datatypes_config) File "/gpfs1/data/galaxy_server/galaxy-dev/lib/galaxy/datatypes/registry.py", line 109, in load_datatypes tree = galaxy.util.parse_xml(config) File "/gpfs1/data/galaxy_server/galaxy-dev/lib/galaxy/util/__init__.py", line 214, in parse_xml root = tree.parse(fname, parser=ElementTree.XMLParser(target=DoctypeSafeCallbackTarget())) File "/global/apps/bioinf/galaxy/bin/Python-2.7.13/lib/python2.7/xml/etree/ElementTree.py", line 647, in parse source = open(source, "rb") IOError: [Errno 2] No such file or directory: '/gpfs1/data/galaxy_server/galaxy-dev/database/tmp/tmp_uHZbW' ``` Are there any suggestions how to continue with such a behavior. The file system on our cluster seems to be slow at the moment, could this be the cause? Best, Matthias -- ------------------------------------------- Matthias Bernt Bioinformatics Service Molekulare Systembiologie (MOLSYB) Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 482296, m.bernt@ufz.de, www.ufz.de Sitz der Gesellschaft/Registered Office: Leipzig Registergericht/Registration Office: Amtsgericht Leipzig Handelsregister Nr./Trade Register Nr.: B 4703 Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Wissenschaftlicher Geschäftsführer/Scientific Managing Director: Prof. Dr. Dr. h.c. Georg Teutsch Administrative Geschäftsführerin/ Administrative Managing Director: Prof. Dr. Heike Graßmann -------------------------------------------
Hi all, There is some problem with MACS2: export/galaxy-central/database/job_working_directory/000/380/tool_script.sh: line 25: macs2: command not found Fatal error: Exit code 127 () Tool installed: /shed_tools/toolshed.g2.bx.psu.edu/repos/iuc/macs2/f5d67c722d67/macs2<http://toolshed.g2.bx.psu.edu/repos/iuc/macs2/f5d67c722d67/macs2> Dependency Resolver Details Dependency Version Resolver Exact version Current Installation Status macs2 2.1.1.20160309 Conda True [http://192.168.99.100:32811/static/june_2007_style/blue/ok_small.png] gawk 4.1.3 Conda True [http://192.168.99.100:32811/static/june_2007_style/blue/ok_small.png] Thank you, Deepak
Hello, I am still facing problem. I have tried to reinstall MACS2 but nothing helped. Thank you! Deepak On Oct 16, 2017, at 4:00 PM, Deepak Tanwar <dktanwar@hotmail.com<mailto:dktanwar@hotmail.com>> wrote: Hi all, There is some problem with MACS2: export/galaxy-central/database/job_working_directory/000/380/tool_script.sh: line 25: macs2: command not found Fatal error: Exit code 127 () Tool installed: /shed_tools/toolshed.g2.bx.psu.edu/repos/iuc/macs2/f5d67c722d67/macs2<http://toolshed.g2.bx.psu.edu/repos/iuc/macs2/f5d67c722d67/macs2> Dependency Resolver Details Dependency Version Resolver Exact version Current Installation Status macs2 2.1.1.20160309 Conda True [http://192.168.99.100:32811/static/june_2007_style/blue/ok_small.png] gawk 4.1.3 Conda True [http://192.168.99.100:32811/static/june_2007_style/blue/ok_small.png] Thank you, Deepak
Assuming you don't have galaxy set to clean up job working directories upon failure, have a look at the tool_script.sh in that directory and see if you can discern the issue. Also check the conda activation log file (under working/ I think) in that directory to see if it has anything useful. Devon On 10/18/2017 05:46 PM, Deepak Tanwar wrote:
Hello,
I am still facing problem. I have tried to reinstall MACS2 but nothing helped.
Thank you! Deepak
On Oct 16, 2017, at 4:00 PM, Deepak Tanwar <dktanwar@hotmail.com <mailto:dktanwar@hotmail.com>> wrote:
Hi all,
There is some problem with MACS2:
export/galaxy-central/database/job_working_directory/000/380/tool_script.sh: line 25: macs2: command not found Fatal error: Exit code 127 () Tool installed: /shed_tools/toolshed.g2.bx.psu.edu/repos/iuc/macs2/f5d67c722d67/macs2 <http://toolshed.g2.bx.psu.edu/repos/iuc/macs2/f5d67c722d67/macs2>
Dependency Resolver Details Dependency Version Resolver Exact version Current Installation Status macs2 2.1.1.20160309 Conda True gawk 4.1.3 Conda True
Thank you, Deepak
___________________________________________________________ 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/
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-- Devon Ryan, PhD Bioinformatician / Data manager Bioinformatics Core Facility Max Planck Institute for Immunobiology and Epigenetics Email: dpryan79@gmail.com
I am using Galaxy via Docker. On Oct 18, 2017, at 11:51 AM, Devon Ryan <dpryan79@gmail.com<mailto:dpryan79@gmail.com>> wrote: Assuming you don't have galaxy set to clean up job working directories upon failure, have a look at the tool_script.sh in that directory and see if you can discern the issue. Also check the conda activation log file (under working/ I think) in that directory to see if it has anything useful. Devon On 10/18/2017 05:46 PM, Deepak Tanwar wrote: Hello, I am still facing problem. I have tried to reinstall MACS2 but nothing helped. Thank you! Deepak On Oct 16, 2017, at 4:00 PM, Deepak Tanwar <dktanwar@hotmail.com<mailto:dktanwar@hotmail.com>> wrote: Hi all, There is some problem with MACS2: export/galaxy-central/database/job_working_directory/000/380/tool_script.sh: line 25: macs2: command not found Fatal error: Exit code 127 () Tool installed: /shed_tools/toolshed.g2.bx.psu.edu/repos/iuc/macs2/f5d67c722d67/macs2<http://toolshed.g2.bx.psu.edu/repos/iuc/macs2/f5d67c722d67/macs2> Dependency Resolver Details Dependency Version Resolver Exact version Current Installation Status macs2 2.1.1.20160309 Conda True [http://192.168.99.100:32811/static/june_2007_style/blue/ok_small.png] gawk 4.1.3 Conda True [http://192.168.99.100:32811/static/june_2007_style/blue/ok_small.png] Thank you, Deepak ___________________________________________________________ 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/ -- Devon Ryan, PhD Bioinformatician / Data manager Bioinformatics Core Facility Max Planck Institute for Immunobiology and Epigenetics Email: dpryan79@gmail.com<mailto:dpryan79@gmail.com>
That doesn't change anything, I also using Galaxy within docker. On 10/18/2017 06:27 PM, Deepak Tanwar wrote:
I am using Galaxy via Docker.
On Oct 18, 2017, at 11:51 AM, Devon Ryan <dpryan79@gmail.com <mailto:dpryan79@gmail.com>> wrote:
Assuming you don't have galaxy set to clean up job working directories upon failure, have a look at the tool_script.sh in that directory and see if you can discern the issue. Also check the conda activation log file (under working/ I think) in that directory to see if it has anything useful.
Devon
On 10/18/2017 05:46 PM, Deepak Tanwar wrote:
Hello,
I am still facing problem. I have tried to reinstall MACS2 but nothing helped.
Thank you! Deepak
On Oct 16, 2017, at 4:00 PM, Deepak Tanwar <dktanwar@hotmail.com <mailto:dktanwar@hotmail.com>> wrote:
Hi all,
There is some problem with MACS2:
export/galaxy-central/database/job_working_directory/000/380/tool_script.sh: line 25: macs2: command not found Fatal error: Exit code 127 () Tool installed: /shed_tools/toolshed.g2.bx.psu.edu/repos/iuc/macs2/f5d67c722d67/macs2 <http://toolshed.g2.bx.psu.edu/repos/iuc/macs2/f5d67c722d67/macs2>
Dependency Resolver Details Dependency Version Resolver Exact version Current Installation Status macs2 2.1.1.20160309 Conda True gawk 4.1.3 Conda True
Thank you, Deepak
___________________________________________________________ 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/
-- Devon Ryan, PhD Bioinformatician / Data manager Bioinformatics Core Facility Max Planck Institute for Immunobiology and Epigenetics Email:dpryan79@gmail.com
-- Devon Ryan, PhD Bioinformatician / Data manager Bioinformatics Core Facility Max Planck Institute for Immunobiology and Epigenetics Email: dpryan79@gmail.com
Hi Matthias, any chance https://github.com/galaxyproject/galaxy/pull/4644 would fix this for you ? Best, Marius On 16 October 2017 at 20:12, Matthias Bernt <m.bernt@ufz.de> wrote:
Dear list,
today I got an erroneous result (red) despite the output of the tool to be seems fine. Seemingly there was an error during setting the metadata.
``` Fatal error: An error occured during execution, see stderr and stdout for more information Reading reference gene model /gpfs1/data/galaxy_server/gala xy-dev/database/files/002/dataset_2992.dat ... Done Loading SAM/BAM file ... Finished Total 62188 usable reads were sampled Traceback (most recent call last): File "/gpfs1/data/galaxy_server/galaxy-dev/jobs_dir/001/1858/set_metadata_Ad6q_v.py", line 1, in from galaxy_ext.metadata.set_metadata import set_metadata; set_metadata() File "/gpfs1/data/galaxy_server/galaxy-dev/lib/galaxy_ext/metadata/set_metadata.py", line 85, in set_metadata datatypes_registry.load_datatypes(root_dir=galaxy_root, config=datatypes_config) File "/gpfs1/data/galaxy_server/galaxy-dev/lib/galaxy/datatypes/registry.py", line 109, in load_datatypes tree = galaxy.util.parse_xml(config) File "/gpfs1/data/galaxy_server/galaxy-dev/lib/galaxy/util/__init__.py", line 214, in parse_xml root = tree.parse(fname, parser=ElementTree.XMLParser(t arget=DoctypeSafeCallbackTarget())) File "/global/apps/bioinf/galaxy/bin/Python-2.7.13/lib/python2.7/xml/etree/ElementTree.py", line 647, in parse source = open(source, "rb") IOError: [Errno 2] No such file or directory: '/gpfs1/data/galaxy_server/galaxy-dev/database/tmp/tmp_uHZbW' ```
Are there any suggestions how to continue with such a behavior. The file system on our cluster seems to be slow at the moment, could this be the cause?
Best, Matthias
--
------------------------------------------- Matthias Bernt Bioinformatics Service Molekulare Systembiologie (MOLSYB) Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany <https://maps.google.com/?q=Permoserstra%C3%9Fe+15,+04318+Leipzig,+Germany&entry=gmail&source=g> Phone +49 341 235 482296, m.bernt@ufz.de, www.ufz.de
Sitz der Gesellschaft/Registered Office: Leipzig Registergericht/Registration Office: Amtsgericht Leipzig Handelsregister Nr./Trade Register Nr.: B 4703 Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Wissenschaftlicher Geschäftsführer/Scientific Managing Director: Prof. Dr. Dr. h.c. Georg Teutsch Administrative Geschäftsführerin/ Administrative Managing Director: Prof. Dr. Heike Graßmann ------------------------------------------- ___________________________________________________________ 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 (4)
-
Deepak Tanwar -
Devon Ryan -
Marius van den Beek -
Matthias Bernt