Question: HISAT2 incompatible with CuffDiff ?
0
gravatar for willtun1991
2.6 years ago by
willtun199110
United Kingdom
willtun199110 wrote:

Hey

I'm trying to compare the transcript expression levels between two conditions. I have put my data through HISAT2 on galaxy. However when I put the HISAT2 outputs from condition 1 and condition 2 into cuffdiff, no matter what parameters and references I use, the galaxy run fails every time I try and implement cuffdiff.

Any one else finding the same problem?

software error alignment • 915 views
ADD COMMENTlink modified 2.6 years ago by Jennifer Hillman Jackson25k • written 2.6 years ago by willtun199110

There is a current issue with Main that the team is investigating. This is most likely the reason for the job failures. More feedback soon. Thanks for your patience. Jen, Galaxy team

ADD REPLYlink written 2.6 years ago by Jennifer Hillman Jackson25k

Ok. Where can I find this feedback message that tells me cuffdiff works again?

ADD REPLYlink written 2.6 years ago by willtun199110

Our team will post back here directly in reply to inquiries about the cluster performance (including yours). This should come today or tomorrow.

I can let you know now that all nodes are/were not impacted as of late yesterday. Many users have had success with re-running jobs a few times. I also had this type of result while testing. (Same job, re-run, some result in failure, others succeed).

Thanks for your patience. The core group is at an important meeting through today.

ADD REPLYlink modified 2.6 years ago • written 2.6 years ago by Jennifer Hillman Jackson25k
0
gravatar for Jennifer Hillman Jackson
2.6 years ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

The recent errors due to the cluster issues are now cleared. Please re-run the failed job(s) and let us know if problems persist via a new bug report from the latest failure (from today). We can help to diagnose the issue and get it resolved.

Thanks for your patience while we worked on the solution, Jen, Galaxy team

ADD COMMENTlink written 2.6 years ago by Jennifer Hillman Jackson25k
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