Question: Diffbind and repmatch fatal error
gravatar for jenyka_dm
8 months ago by
jenyka_dm10 wrote:

Hi! I have 3 chip replicates and I want to find common peaks within them. I used diffbind to do so, however when I run diffbind on my replicates, I get a fatal error Fatal error: An undefined error occured, please check your intput carefully and contact your administrator. 1-831 Inf ER Reg 1 raw 2-831 Inf ER Reg 2 raw 4-831 Inf ER Reg 3 raw Warning message: No contrasts added. Perhaps try more categories, or lower value for minMembers. Error in pv.DBA(DBA, method, bSubControl, bFullLibrarySize, bTagwise = bTagwise, : Unable to perform analysis: no contrasts specified. Calls: dba.analyze -> pv.DBA Warning message: No contrasts added. Perhaps try more categories, or lower value for minMembers.

I also tried to use repmatch to match paired peaks within my replicates, but I also get an error. Unable to parse file "/galaxy-repl/main/files/024/118/dataset_24118100.dat", exception: list index out of range

I am not quite sure what happened here. Could you please help me with that. Thanks!

diffbind chip-seq • 343 views
ADD COMMENTlink modified 8 months ago by Jennifer Hillman Jackson25k • written 8 months ago by jenyka_dm10
gravatar for Jennifer Hillman Jackson
8 months ago by
United States
Jennifer Hillman Jackson25k wrote:


These both look like usage problems. Double check that you are using the most current version of the tool and that the inputs were all mapped correctly to the same genome build used in all steps of your analysis. Any reference annotation must also be a match for that genome build. You also might want to go back and run FastQC on your original fastq datasets to check for quality problems.

If you cannot determine the problem, a bug report can be sent in. I know that you know how to do this, but for others that may read this, how-to is described in this prior Q&A: and here in this support FAQ:

The Galaxy Main server was recently upgraded, however, our testing with the updated tool version was successful. The prior Q&A above also includes a link to the test history that can be reviewed to better understand usage/proper inputs.

Galaxy tutorials:

Thanks! Jen, Galaxy team

ADD COMMENTlink written 8 months 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: 172 users visited in the last hour