Open hdbeukel opened 10 months ago
Sorry for the late reply @hdbeukel but this seems to be a memory issue (from your nextflow.log
:
# There is insufficient memory for the Java Runtime Environment to continue.
You could try to increase the memory for the process by using a custom.config
file:
process {
withName: PICARD_MARKDUPLICATES {
memory = 72.GB
}
}
And then adding -c custom.config
to your Nextflow command
Description of the bug
When running the atac-seq pipeline on our SLURM cluster, it keeps failing at seemingly arbitrary points, with an error message saying that the process was "terminated for an unknown reason -- Likely it has been terminated by the external system" (see full error below).
When resuming the pipeline, without any changes in parameters or anything, it usually does get past the previously terminated process and then fails again at a later step, with the same error message. If I keep resuming the pipeline, eventually it does reach the end.
When a process fails, the working directory contains only two files:
.command.sh
.command.run
No
.out
,.trace
,.exitcode
, ... and also no symlinks to the input data have been created. If a manually submit the.command.run
script to the cluster, without making any changes, it succeeds without any problem and all the files are there.I have been in touch with our IT support in charge of managing the cluster but they also have no clue what is happening. We used to have a Sun Grid Engine cluster, on which the pipeline ran without problems. The issue started to appear when the cluster was migrated to SLURM.
Command used and terminal output
Relevant files
The config file only sets the working directory and the SLURM executor:
The parameter file contains these settings:
System information