Question: CuffDiff not working with CXB files
1
gravatar for Mark Lindsay
6 months ago by
Mark Lindsay70
United Kingdom
Mark Lindsay70 wrote:

Hi

when attempting to run CuffDiff with Cuffquant files, all the conditions end up loading condition 2 i.e. if you select CXB files with condition 1 and 2, condition 1 defaults to condition 2 so you end up comparing condition 2 and 2.

Hopefully this makes sense!!!

error select rna-seq input dataset • 236 views
ADD COMMENTlink modified 5 months ago by Jennifer Hillman Jackson25k • written 6 months ago by Mark Lindsay70

Hi - I've seen similar behavior with other tools with multiple-select inputs over the last week. I haven't run into it today. I'll do some more testing and open a ticket for the developers to review/fix. Because of this, I don't think the problem is with cxb data, but I'll test that too.

Meanwhile, I had success before even with this problem going on by rerunning the job (actually using the rerun button), choosing the inputs again, and executing the job. In some cases, it took a few attempts. You can always permanently delete the jobs that didn't capture all the inputs - you can usually tell even while the job is queued by the dataset name (includes a list of the inputs by dataset number). Only so many datasets can be listed, so this is of limited use if there are several inputs (more than 3 or 4), but might help.

Thanks for reporting this and more feedback very soon. Jen, Galaxy team

ADD REPLYlink written 6 months ago by Jennifer Hillman Jackson25k
1
gravatar for Jennifer Hillman Jackson
5 months ago by
United States
Jennifer Hillman Jackson25k wrote:

Update 6/5/2018

The issue is confirmed fixed now from our testing. Please let us know if you run into this again. Applies to everyone, using this tool/cxb input or any other tools that accept multiple inputs.

Thanks! Jen, Galaxy team

ADD COMMENTlink written 5 months ago by Jennifer Hillman Jackson25k
0
gravatar for Jennifer Hillman Jackson
6 months ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

The developers are still looking at the problem and we consider this a priority fix. I created a ticket specifically for this problem (using a simpler tool, but one that presents with the same behavior), please follow for updates: https://github.com/galaxyproject/usegalaxy-playbook/issues/125

Thanks for reporting the problem! And definitely try the "rerun" workaround as not all submitted jobs with multiple selects end up in this state (we are not exactly sure why yet).

Thanks for reporting the problem! Jen, Galaxy team

ADD COMMENTlink written 6 months ago by Jennifer Hillman Jackson25k
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