Question: MACS2 Error while running a shared workflow
gravatar for smitha.ijee
8 days ago by
smitha.ijee0 wrote:

Hi, I used a workflow for ChIP seq, " ChIP seq analysis for intersect"; owner: klaourakis, June13 2016. It shows MACS2 error; Fatal error: Exit code 1 (). Please help.

ADD COMMENTlink modified 8 days ago by Jennifer Hillman Jackson24k • written 8 days ago by smitha.ijee0
gravatar for Jennifer Hillman Jackson
8 days ago by
United States
Jennifer Hillman Jackson24k wrote:


Tools can fail for many reasons. Sometimes this is related to input formatting problems and sometimes because of data content and/or parameters.

MACS2 often fails this way due to data content. If you click on the Job Details icon within the failed dataset ("i" icon), then click on either stderr or stdout on the report, the full error details can be reviewed. This is the end of your error (thanks for the bug report!) and is common when there were upstream mapping problems (resulting in low mapping rates) or settings made with MACS2 that do not fit the data well. (I didn't post anything private here - this is the same error that many receive under similar circumstances).

WARNING @ Wed, 11 Apr 2018 10:33:13: Too few paired peaks (0) so I can
not build the model! Broader your MFOLD range parameter may erase this
error. If it still can't build the model, we suggest to use --nomodel
and --extsize 147 or other fixed number instead.  WARNING @ Wed, 11
Apr 2018 10:33:13: Process for pairing-model is terminated!

The MACS2 manual and google group are the best resources for learning how to tune parameters.

Your inputs were purged already, so I cannot double check those, but the troubleshooting help here may help: I would suggest checking the quality of the fastq reads (FastQC) and the mapping rates first to eliminate those as issues. Once those are confirmed, then go forward with testing different MACS2 parameters for a successful job.

Galaxy tutorials for ChIP-seq, fastq QA/QC, and other protocols:

Thanks! Jen, Galaxy team

ADD COMMENTlink written 8 days ago by Jennifer Hillman Jackson24k
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