Cufflinks tool locally cached 'hg38' malformed; error reads: 'An invalid option was selected for index, u'hg38', please verify'

Question: Cufflinks tool locally cached 'hg38' malformed; error reads: 'An invalid option was selected for index, u'hg38', please verify'

10 months ago by

theresa • 0

theresa • 0 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 • 478 views

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modified 10 months ago by Jennifer Hillman Jackson ♦ 25k • written 10 months ago by theresa • 0

10 months ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k 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

https://galaxyproject.org/issues/#usage-problem-reporting

Thanks! Jen, Galaxy team

ADD COMMENT • link modified 10 months ago • written 10 months ago by Jennifer Hillman Jackson ♦ 25k

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 REPLY • link written 10 months ago by Jennifer Hillman Jackson ♦ 25k

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