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Mapping jobs failing on Jetstream cluster #257

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jennaj opened this issue Oct 1, 2019 · 4 comments

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@jennaj jennaj commented Oct 1, 2019

Bowtie2 & HISAT2 test history: https://usegalaxy.org/u/jen/h/test-mappers-and-clusters

For the workaround until resolved, please see this Galaxy Help post: https://help.galaxyproject.org/t/hisat2-not-working/2189/7?u=jennaj

Reminder: Stampede should never be as a target cluster for any mapping jobs. Using default settings will not send jobs to that cluster, but it is possible to directly select that cluster on the tool form. Avoid Stampede or reliably expect the job to remain in the "queued" state and eventually fail. Prior ticket: #214

@jennaj jennaj added this to To Consider: Inbox in Bugs being fixed Oct 1, 2019
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@jennaj jennaj commented Oct 9, 2019

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@jennaj jennaj commented Oct 10, 2019

Fixed.

Note to all end users running mapping: Using all defaults for the "Job Resources" parameter is a good choice now again. No need to target a particular cluster anymore. Allowing Galaxy to choose the target cluster based on the currently available resources, at the time of job submission, is the fastest way to run tools.

@jennaj jennaj closed this Oct 10, 2019
@jennaj jennaj moved this from To Consider: Inbox to Done in Bugs being fixed Oct 10, 2019
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@jennaj jennaj commented Oct 11, 2019

All mapping tools are Ok except for RNA-Star when sent to PCS Bridges cluster.

@jmchilton thinks they need up update their version of Galaxy

@natefoo can you help?

For end-users: Workaround pending testing (in the same test history above). Checking to see if targeting the "Jetstream" or "Galaxy cluster" under the Job Resources option will run successful jobs (similar to the prior workaround included in the Galaxy Help post above).

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@jennaj jennaj commented Oct 11, 2019

Fixed

@jennaj jennaj closed this Oct 11, 2019
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