error despite success

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error despite success

Matthias Bernt
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,
[hidden email], 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
-------------------------------------------
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MACS2 Error

Deepak Tanwar
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 ()


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

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Re: error despite success

Marius van den Beek
In reply to this post by Matthias Bernt
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 <[hidden email]> 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/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 <a href="tel:%2B49%20341%20235%20482296" value="+49341235482296" target="_blank">+49 341 235 482296,
[hidden email], 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/

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 http://galaxyproject.org/search/


___________________________________________________________
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Re: MACS2 Error

Deepak Tanwar
In reply to this post by Deepak Tanwar
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 <[hidden email]> 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 ()


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:
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Re: MACS2 Error

Devon Ryan-2

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 <[hidden email]> 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 ()

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: [hidden email]

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Re: MACS2 Error

Deepak Tanwar
I am using Galaxy via Docker.

On Oct 18, 2017, at 11:51 AM, Devon Ryan <[hidden email]> 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 <[hidden email]> 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 ()

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: [hidden email]


___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
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Re: MACS2 Error

Devon Ryan-2

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 <[hidden email]> 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 <[hidden email]> 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 ()

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: [hidden email]


-- 
Devon Ryan, PhD
Bioinformatician / Data manager
Bioinformatics Core Facility
Max Planck Institute for Immunobiology and Epigenetics
Email: [hidden email]

___________________________________________________________
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/