Comments (8)
A quick and ugly fix is to add errorStrategy = 'ignore'
to the macs
job in base.config. But then we don't see which macs jobs have failed (and we ignore other errors in the macs jobs too).
from chipseq.
Is there a special error code that MACS generates in such a case? That would be interesting to catch and issue a warning for that sample.
from chipseq.
You mean an exit code? Not sure. I was saying to @orzechoj that we could implement a similar strategy to the one that we have in the rnaseq pipeline though, where we check the log files:
https://github.com/nf-core/rnaseq/blob/d64b7f536b09b400c8d46533b150c4f05843b556/main.nf#L591-L595
https://github.com/nf-core/rnaseq/blob/d64b7f536b09b400c8d46533b150c4f05843b556/main.nf#L530-L549
from chipseq.
Yeah, exit code was in my mind actually. I thought the failing MACS process issues an exit code != 0
, therefore causing the pipeline to fail. If it just pushes something on stderr
, we can implement it the way you proposed - nice 👍
from chipseq.
The problem with the exit code is that it probably doesn’t differentiate for why it fails - we only want to catch these specific failures. I could be wrong though!
from chipseq.
I fear so, too! If I find some time I'll have a look.
from chipseq.
The exit code is 1, which isn't so informative. But stderr
has this error message
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.
from chipseq.
Closing in favour of #128
from chipseq.
Related Issues (20)
- No Space left on device error HOT 3
- Make subworkflows & modules available for nf-core tools HOT 1
- Default values for p-value and FDR HOT 2
- Get rid of checkIfExists for params paths HOT 1
- minor "samplesheet_pe.csv" format issue HOT 1
- PHANTOMPEAKQUALTOOLS throws stack overflow exception HOT 1
- MACS2: Too few paired peaks (0) so I can not build the model! HOT 2
- Error with NextSeq trimming HOT 2
- Error running the pipline test in the BWA index step HOT 2
- jobs failing with sigbus and unknown userid errors HOT 1
- Update MACS to v3 HOT 1
- There are multiple files for each of the following file names
- Can't run if there is no control HOT 2
- Improve website on parameters section Alignment Options for argument --save_unaligned HOT 1
- IDR analysis HOT 2
- Remove lib folder to get ready for v2.13.1 template merge HOT 1
- Macs2 Output HOT 2
- The "sample" field from the samplesheet is too lenient HOT 1
- Streamline nf-core/chipseq and nf-core/atacseq by using shared subworkflows
- Get rid of checksamplesheet.py and switch to nf-schema
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from chipseq.