Question: Fatal error in Trimmomatic
0
gravatar for binibe
18 months ago by
binibe70
binibe70 wrote:

Hi all,

I have been trying to run a Trimmomatic trim on my data since Friday. Trimmomatic will be running for a few seconds up to an hour before terminating with following error:

Fatal error: Exit code 1 - Trimmomatic did not finish successfully

Have others experienced the same issue - or is there something wrong with my data?

Thank you!

Cheers, B

rna-seq trimmomatic • 655 views
ADD COMMENTlink modified 18 months ago • written 18 months ago by binibe70
1
gravatar for Jennifer Hillman Jackson
18 months ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

There is most likely a problem with the input data. Check that the file is loaded completely and is in fastqsanger format.

If problems continue, you can send in a bug report from the error dataset. Do this from the server http://usegalaxy.org and include a link to this post in the comments. Even if you are not currently working at this server, testing to see if the problem can be reproduced there is informative.

How to submit a bug report: https://wiki.galaxyproject.org/Support#Reporting_tool_errors

Thanks, Jen, Galaxy team

ADD COMMENTlink written 18 months ago by Jennifer Hillman Jackson25k
0
gravatar for binibe
18 months ago by
binibe70
binibe70 wrote:

Thank you, Jennifer!

I trimmed the same data (with a different Phred score) Friday morning before the error occurred and it worked fine. The files are completely loaded and in fastqsanger format.

The bug was reported earlier this morning (from usegalaxy.org) since it continued to show the error. Will wait and see what happens :-)

Cheers, Birgitte

ADD COMMENTlink written 18 months ago by binibe70
1

Yes, I found your ticket. More feedback soon. Jen

ADD REPLYlink written 18 months ago by Jennifer Hillman Jackson25k

Thank you!

Don't know if this will help locate the error, but I just did a Headcrop with Trimmomatic on the data, and it worked like a charm. I then tried the IlluminaClip (Truseq3, additional) again - and the error came up again. The issue might be with the adapter trimming in some way.

ADD REPLYlink written 17 months ago by binibe70
1

Yes, this is now a confirmed tool issue. Please follow here for updates on the fix: https://github.com/galaxyproject/galaxy/issues/3691

Thanks to you and others for reporting the problem! Jen

ADD REPLYlink written 17 months ago by Jennifer Hillman Jackson25k
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