Question: Cufflinks tool locally cached 'hg38' malformed; error reads: 'An invalid option was selected for index, u'hg38', please verify'
0
gravatar for theresa
5 weeks ago by
theresa0
theresa0 wrote:

Greetings, I am trying to use the Cufflinks tool in the main/public instance of Galaxy to generate FPKMs for my BAM files against hg38. The tool throws an error having to do with the locally cached hg38 reference. Below I include the steps to reproduce the error with BAM files aligned to hg38.

In the main Cufflinks options, when in 'Perform Bias Correction', I enter 'yes', and in 'Reference sequence data', I enter 'locally cached', and in 'Using reference genome' I select 'hg38',

when I click 'Execute'- I get the following error message:

"An invalid option was selected for index, u'hg38', please verify" .

Again, the error indicates the problem is with the locally (Galaxy) cached hg38 reference (or code to access it), not a file I've uploaded or pulled from UCSC GB.

Thanks so much! Apologizes in advanced if my blunder is obvious.

rna-seq cufflinks cuffdiff • 101 views
ADD COMMENTlink modified 5 weeks ago by Jennifer Hillman Jackson24k • written 5 weeks ago by theresa0
0
gravatar for Jennifer Hillman Jackson
5 weeks ago by
United States
Jennifer Hillman Jackson24k wrote:

Hello,

We are reviewing the job failure. You are cc'd on the bug report I sent to our internal team and we will get back to you there about the problem.

This might be related to a known issue on the server involving duplicated indexes or it may be just a simple cluster error. We do not have enough information to know which is the case yet.

For now, I would suggest trying a rerun. If the job errors again, please submit a bug report and include a link to this post in the comments for reference. FAQs: https://galaxyproject.org/support/#unexpected-results

Thanks! Jen, Galaxy team

ADD COMMENTlink modified 5 weeks ago • written 5 weeks ago by Jennifer Hillman Jackson24k

Please check your email for feedback. We were not able to find an error dataset with the problem described in this post, and how to move forward is explained (rerun, then a bug report as needed). If you are not working at Galaxy Main https://usegalaxy.org, help for that situation is also explained.

ADD REPLYlink written 5 weeks ago by Jennifer Hillman Jackson24k
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