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)
- mergeBed ERROR: Requested column 10, but database file - only has fields 1 - 9. HOT 18
- Normalisation of bigwig files
- package or namespace load failed for ‘UpSetR’ HOT 3
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from chipseq.