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Tophat, Tophat2, Bowtie2 ending with metadata warning #62
Jobs are ending with a metadata warning. The "autodetect" button does not resolve the problem. Datasets cannot be used or in some cases downloaded (.bam.bai files) until resolved.
How can I tell if my job has a metadata error? A yellow warning box will appear in the dataset.
Temporary workaround: (updated 11-14-17)
Bowtie2 is now ending with this error:
Error on stampede and jetstream. Success on roundup.
Similiar to #61
Could these be memory failures? A few reports of multi-core jobs ending this way, or with metadata problems, have come in starting around Thurs 11/9, also linked to jetstream/stampede.
The second error is due to the SSL certs on our staging Galaxy servers expiring. I'd renewed all of our certs last month and deployed them, but apparently missed these two servers. Jetstream jobs should run now. Still looking at the metadata issue, which is unrelated.
Bowtie2 job on
BWA job on
Agree - the default cluster Roundup (Job resource left at default or this cluster specifically chosen) or Jetstream should be used when using a built-in index (aka locally cached data) when running Tophat, Tophat2, or HISAT2. Let's leave this ticket open until the transition to Stampede2 .. unless you'd prefer a distinct ticket, and reference this one?
For those running mapping jobs at https://usegalaxy.org: Avoid sending these jobs to the cluster Stampede unless you are using a custom genome from the history. Instead, specify the Job Resource parameter to use Jetstream instead. The option is the last one on the tool form, immediately above the "submit" button:
For more details about job resource selections, please see this FAQ: https://galaxyproject.org/main/#resouces-available-to-main-site
Note: When inputting fastqsanger.gz formatted data, you may get this warning in the comment fields of the output datasets when using Jetstream (but not the default cluster Roundup):
This warning does not impact the mapping job's results. They are valid and can be used directly as inputs to downstream tools.
We are doing more testing to see if this warning impacts other tools/use cases and will update this ticket with a link to the new issue if a problem is discovered.