Question: Trinity jobs stalled at
gravatar for magdawarzecha6
18 months ago by
magdawarzecha610 wrote:

Hello, my trinity job is still waiting to run (for two days). Are there still some problems with server ?


ADD COMMENTlink modified 18 months ago by Jennifer Hillman Jackson25k • written 18 months ago by magdawarzecha610

Hello! Thanks for reporting the problem. I am both running test jobs and have asked our admin for feedback about the PCS Bridges connection. I did notice that your inputs are quite large, but we won't know if it is too large until executed.

We'll post an update soon. Thanks, Jen, Galaxy team

ADD REPLYlink modified 18 months ago • written 18 months ago by Jennifer Hillman Jackson25k
gravatar for Jennifer Hillman Jackson
18 months ago by
United States
Jennifer Hillman Jackson25k wrote:


Rerunning stalled Trinity jobs is how I was able to get test runs to be processed. I suggest that you and others with jobs stalled longer than 24 hrs do the same.

For your data, I reran the originally stalled job and it came back with a green success dataset. However, it is empty due to a problem with the fastq input identifier format. Review the stderr from the job for full error details (on the "i" view details info page).

In short, the fastq data has @ identifier lines formatted like this (below). Trinity is not able to parse these into forward and reverse fasta reads when fastq dataset are submitted to the tool.

example1: @SRR3101501.1 1/1
example2: @SRR3101501.185 185/2

I am not sure how these data were generated as they are a merge of datasets not included in the same history, but better identifiers would be formatted like:

example1: @SRR3101501.1/1
example2: @SRR3101501.185/2

Reprocess the data from the source or use the reformatting tools in the group Text Manipulation to correct before running Trinity. If you want to submit fasta files directly that is also an option to test out. Use the tool FASTQ to FASTA converter.

Hope this helps and our apologies for reoccurring issues with the connection to PCS Bridges.

Jen, Galaxy team

ADD COMMENTlink written 18 months ago by Jennifer Hillman Jackson25k

Hi Jen, thank you, I will try to correct my files, but right now, all jobs at are stalled.


ADD REPLYlink written 18 months ago by magdawarzecha610

Hi Magda, I can confirm this problem and our administrator has made a correction. Jobs should start up soon and we have some test runs to track/confirm that. The update when all clear will be posted here:

ADD REPLYlink written 18 months ago by Jennifer Hillman Jackson25k

Jobs starting running again later yesterday. Please launch new rerun jobs if the prior queued jobs have not started up yet (this tool only, as far as I know). Other queued jobs should be allowed to process as resource becomes available to avoid losing original queue placeholder.

ADD REPLYlink written 18 months ago by Jennifer Hillman Jackson25k
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