Question: TopHat Error After Updating Galaxy
gravatar for irinadominova
2.6 years ago by
irinadominova10 wrote:


After updating Galaxy I have some problems with running TopHat because permanently appear message "This job is waiting to run", but running of job don't start. Please solve this problem or answer me what I do wrong.

Thank you!

Kind regards, Irina

tophat • 690 views
ADD COMMENTlink modified 2.6 years ago by Jennifer Hillman Jackson25k • written 2.6 years ago by irinadominova10

Please share more details about the instance and configuration. Is this a local or cloud Galaxy? Have any advanced configuration steps been done, and if so, which? Thanks, Jen, Galaxy team

ADD REPLYlink written 2.6 years ago by Jennifer Hillman Jackson25k

Hello Jen,

I use cloud Galaxy and TopHat with default parameters except Bowtie -n mode (Yes) and Set Bowtie2 setting (Yes, Sensitive) for mapping RNA-seq data to reference genome (rn5).

Thank you in advance for any kind of feedback! Irina.

ADD REPLYlink written 2.6 years ago by irinadominova10
gravatar for Jennifer Hillman Jackson
2.6 years ago by
United States
Jennifer Hillman Jackson25k wrote:

Hi Irina,

Thanks for sending more information. After a cloud update, make sure to restart the instance and double check that all services are running (found on the admin page). If you are the only one using the instance, jobs can be run on the master node, but you can also add in one extra node to test that out (and kill it after if not needed or when not needed).

If the tool still has trouble, start by uninstalling and reinstalling Tophat using managed dependencies. The tool status itself is also in the admin section where it can be reviewed.

I am assuming the upgrade was made through the admin interface to Galaxy version 16.04, that Tophat has run well before under 16.01, that the reference genome was created with data managers: loaded genome (fetch fasta), followed by samtools indexes once that complete, picard indexes after samtools indexes complete, and tophat indexes after picard indexes complete (using bowtie index DM with option to include tophat indexed checked off). Also creating a twoBit index is a good idea - this can be run after the genome is loaded and is not dependent on the other indexes - you can run it anytime or in parallel with the others.

Let us know how this goes and if there are still problems, we can get more help from the cloudman developers to troubleshoot.

Thanks, Jen, Galaxy team

ADD COMMENTlink written 2.6 years ago by Jennifer Hillman Jackson25k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 181 users visited in the last hour