Question: Cuffmerge "Matched on error" - Check for problematic input format
0
gravatar for gunes.kutlu
2.1 years ago by
gunes.kutlu0 wrote:

Hi,

This is my first time analyzing RNASeq data. I mapped and aligned my reads using tophat and cufflinks. Now I am trying to create an assembled transcript on Cuffmerge using my Cufflink data but I keep getting the error below. Is there a solution to this? What might I be doing wrong? Thank you for your help.

Gunes

Fatal error: Matched on Error Error running cuffmerge.

[Wed Sep 28 07:34:31 2016] Beginning transcriptome assembly merge

[Wed Sep 28 07:34:31 2016] Preparing output location cm_output/ Traceback (most recent call last): File "/galaxy/main/deps/cufflinks/2.2.1/devteam/package_cufflinks_2_2_1/899067a260d1/bin/cuffmerge", line 580, in <module> sys.exit(main()) File "/galaxy/main/deps/cufflinks/2.2.1/devteam/package_cufflinks_2_2_1/899067a260d1/bin/cuffmerge", line 546, in main chrom_info = get_gtf_chrom_info(gtf, chrom_info) File "/galaxy/main/deps/cufflinks/2.2.1/devteam/package_cufflinks_2_2_1/899067a260d1/bin/cuffmerge", line 476, in get_gtf_chrom_info left = int(cols[3]) ValueError: invalid literal for int() with base 10: 'transcript'

ADD COMMENTlink modified 2.1 years ago by Jennifer Hillman Jackson25k • written 2.1 years ago by gunes.kutlu0
1
gravatar for Jennifer Hillman Jackson
2.1 years ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

This looks like a problem with one of the inputs. Are there extra lines at the start of any of the files - I suspect one of them has a header that should be removed or files were concatenated together introducing a header line in the middle of a dataset.

If that checks out, then double check that the same exact reference genome was used for all steps and that each input dataset has that assigned as the genome build. This error is generally thrown by this tool suite when there is an input that is .tar compressed, or is incomplete (uploaded problem is a possible but check the original file), or has extra content not in specification, or there is a genome-mismatch problem. https://wiki.galaxyproject.org/Support#Reference_genomes

Thanks, Jen, Galaxy team

ADD COMMENTlink written 2.1 years ago by Jennifer Hillman Jackson25k

Update: Try your data with the earlier tool version 0.0.6. There may be a new issue with v 2.1.1 - our team is looking into it. This ticket is tracking the problem and resolution: https://github.com/galaxyproject/galaxy/issues/2989

ADD REPLYlink written 2.1 years ago by Jennifer Hillman Jackson25k
0
gravatar for gunes.kutlu
2.1 years ago by
gunes.kutlu0 wrote:

Hi, Thanks for your reply. I found out that one of the cufflink output files was causing this problem. I re-ran Cufflinks and Cuffmerge worked fine

Gunes

ADD COMMENTlink written 2.1 years ago by gunes.kutlu0

wonder how do you solve this problem at last,and would like to share more details about this problem? BIG THANKS!

ADD REPLYlink written 23 months ago by gswang0
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