Usegalaxy.org: Jobs ending with error "Unable to finish job" having details "TypeError: object of type 'NoneType' has no len()" -- RESOLVED, please rerun

Question: Usegalaxy.org: Jobs ending with error "Unable to finish job" having details "TypeError: object of type 'NoneType' has no len()" -- RESOLVED, please rerun

9 weeks ago by

francesca.cortini • 10

francesca.cortini • 10 wrote:

Hello,

I have problems with Map with BWA-MEM tool, I launch my Galaxy workflow but, two days ago it doesn't work at Map-BWA MEM step

error bwa bwa-mem galaxy • 377 views

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modified 9 weeks ago by Jennifer Hillman Jackson ♦ 25k • written 9 weeks ago by francesca.cortini • 10

Update 9-25-2018 10:30am EST

I found your bug report. This is a temporary cluster issue that we are working to resolve.

The current workaround is to directly set the cluster where the job is executed to be the Galaxy Cluster using the Job Resources Parameter near the end of the tool form. FAQ: https://galaxyproject.org/main/#choosing-computational-resources

For anyone else running into this problem, the error reported is in web interface will be:

Unable to finish job

With the full error Job Traceback reporting:

Traceback (most recent call last):
  File "/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/jobs/runners/pulsar.py", line 514, in finish_job
    remote_metadata_directory=remote_metadata_directory,
  File "/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/jobs/__init__.py", line 1445, in finish
    job.set_streams(job.stdout, job.stderr)
  File "/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/model/__init__.py", line 227, in set_streams
    if (len(stdout) > galaxy.util.DATABASE_MAX_STRING_SIZE):
TypeError: object of type 'NoneType' has no len()

Thanks for reporting the problem and we will close out this post once resolved.

Jen, Galaxy team

ADD REPLY • link modified 9 weeks ago • written 9 weeks ago by Jennifer Hillman Jackson ♦ 25k

9 weeks ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Update 9-25-2018 4pm EST

This issue is now fixed.

These jobs can be run without setting the Job Resources parameter (Galaxy chooses the cluster with available resources) or you can target one of the other clusters. Each cluster has a different profile (memory/walltime) -- Details: https://galaxyproject.org/main/

Avoid the development clusters or errors may come up unexpectedly. We really do use these for testing and no bug reports need to be sent in for odd job results when using them.

Note: There was another issue that triggered certain jobs to fail for not finding built-in indexes. This was also corrected and the specific error message can vary by tool. And there is one more issue that related to data input types that has been fixed but not applied to the server yet. This error message can also vary by the tool and does not impact all runs -- so try rerunning a few times to achieve a successful result (FastQC was one of the impacted tools).

Main point: If you had any odd job failures over the last few days, please rerun now. If the job fails, it can be sent in as a bug report or you can double check your inputs using the FAQ help here first: https://galaxyproject.org/support/tool-error/

Thanks to all for reporting the problems and for your patience while we corrected the problem.

Jen & the Galaxy team

ADD COMMENT • link written 9 weeks ago by Jennifer Hillman Jackson ♦ 25k

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