These are chat archives for nextflow-io/nextflow

16th
Mar 2016
Tiffany Delhomme
@tdelhomme
Mar 16 2016 09:33

Hi,
I have an endless process with this 4.5min-repeated line in the log :

Mar-16 10:16:19.480 [Thread-3] DEBUG n.processor.TaskPollingMonitor - !! executor lsf > tasks to be completed: 1 -- first: TaskHandler[jobId: 16964; id: 2; name: indel_realignment (MLT00BUU); status: SUBMITTED; exit: -; workDir: /mnt/beegfs/delhommet/nextflow_dev/bam_realignment/work/1b/af04ad7fc47382df8c91da02c25cab started: -; exited: -; ]

with this job status: 16964 delhomm EXIT normal hn cn01 *MLT00BUU) Mar 16 09:36

Paolo Di Tommaso
@pditommaso
Mar 16 2016 10:20
@tdelhomme um, could you check if a file named .exitcode exists in the folder
/mnt/beegfs/delhommet/nextflow_dev/bam_realignment/work/1b/af04ad7fc47382df8c91da02c25cab
Tiffany Delhomme
@tdelhomme
Mar 16 2016 12:52
There is no .exitcode file...
Paolo Di Tommaso
@pditommaso
Mar 16 2016 12:55
the most common explanation is that the cluster kill that job
Tiffany Delhomme
@tdelhomme
Mar 16 2016 12:57
yes I agree but why nextflow set the status of this job to SUBMITTED in the log? even after the probably killing
the fact is that the process was endless I guess because of this SUBMITTED status
Paolo Di Tommaso
@pditommaso
Mar 16 2016 13:00
can you share the .nextflow.log file?
Tiffany Delhomme
@tdelhomme
Mar 16 2016 13:22
hum I think I did not have the log anymore...
Paolo Di Tommaso
@pditommaso
Mar 16 2016 13:25
hard to say something without that
what should happen is that nextflow stops after a while that the job is not avail and that fle does not exist