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this is why I use the slack clients though
N E X T F L O W ~ version 19.01.0
Launching `RNAseqPipe/main.nf` [thirsty_hamilton] - revision: a2f41a936f
This workflow requires Nextflow version 0.26 or greater -- You are running version 19.01.0
ERROR ~ GTF file not found: $workDir/Genome/gencode.chr22.gtf
-- Check '.nextflow.log' file for details
Hi all, I'm trying to help NGI Sweden debug an issue where 19.01.0 incorrectly thinks slurm jobs are gone and give up, but am not sure how much farther I'm gonna get without some tips.
I've gotten down to checkActiveStatus in ./modules/nextflow/src/main/groovy/nextflow/executor/AbstractGridExecutor.groovy
Feb-27 08:46:35.309 [Task monitor] TRACE n.executor.AbstractGridExecutor - [SLURM] queue (node) status > map does not contain jobId: 557670
but I also have an strace for this controller run, and have lines like
30833 write(1, "557514 CD\n557315 CD\n557670 R\n557671 R\n", 38 <unfinished ...>
for all the invocations of squeue (any attempt to get queue status that has gotten so far as execv). I also see corresponding read lines.
For some of these I see
Feb-27 08:38:55.328 [Task monitor] TRACE n.executor.AbstractGridExecutor - [SLURM] queue (node) status > cmd exit: 0
557514 CD
557315 CD
557670 R
557671 R
Feb-27 08:38:55.335 [Task monitor] TRACE n.executor.AbstractGridExecutor - [SLURM] queue (node) status >
job: 557514: DONE
job: 557315: DONE
job: 557670: RUNNING
job: 557671: RUNNING
which is fine, but I also see quite a few
Feb-27 08:39:55.354 [Task monitor] TRACE n.executor.AbstractGridExecutor - [SLURM] queue (node) status > cmd exit: 0
Feb-27 08:39:55.355 [Task monitor] TRACE n.executor.AbstractGridExecutor - [SLURM] queue (node) status >
(empty)
leading up to
Feb-27 08:39:55.355 [Task monitor] TRACE n.executor.AbstractGridExecutor - [SLURM] queue (node) status > map does not contain jobId: 557670
Any tips on getting further with this?