These are chat archives for nextflow-io/nextflow

12th
Sep 2018
Paolo Di Tommaso
@pditommaso
Sep 12 2018 07:11
my understanding is that minio is s3 api compatibile, in this extent it should work
interested to know if you try it
Karin Lagesen
@karinlag
Sep 12 2018 08:36
would queueSize under slurm go towards the number of Running jobs, or does that also include Pending?
Paolo Di Tommaso
@pditommaso
Sep 12 2018 08:39
only running
Karin Lagesen
@karinlag
Sep 12 2018 08:58
@pditommaso thanks :)
Paolo Di Tommaso
@pditommaso
Sep 12 2018 09:15
:+1:
Crabime
@Crabime
Sep 12 2018 11:34
hello, i am running NF scripts in docker and return 137 exit code, so if there are some methods to resolve it?
which kinds of condition will let docker container OOM. As i seen,there are still enough server resources
Luca Cozzuto
@lucacozzuto
Sep 12 2018 11:35
have you checked the amount of memory used?
Crabime
@Crabime
Sep 12 2018 11:36
yeah, there are still enough memory in such node
Luca Cozzuto
@lucacozzuto
Sep 12 2018 11:37
try to understand why that node killed the job
it is not NF killing it, the exit code is from that job
Crabime
@Crabime
Sep 12 2018 11:38
en, i'm reproducing such error and do not remove such container when running jobs
Luca Cozzuto
@lucacozzuto
Sep 12 2018 11:39
?
Crabime
@Crabime
Sep 12 2018 11:40
start docker without --rm option
Luca Cozzuto
@lucacozzuto
Sep 12 2018 11:41
if you launch outside nextflow does it work?
Crabime
@Crabime
Sep 12 2018 11:46
i'm writing it in nextflow.config file, docker.remove=true