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I expect the pipeline to run, but its requesting a error code and times out after 4.5 minutes while my pipeline is still running, even if i try a retry strat or anything, the pipeline is STILL executing in the background..
Steps to reproduce the problem
nextflow run myworkflow.nf
Program output
ERROR ~ Error executing process > 'TASK2'
Caused by:
Process TASK2 terminated for an unknown reason -- Likely it has been terminated by the external system
Command exit status:
Command output:
(empty)
Feb-24 18:41:30.804 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor slurm > tasks to be completed: 1 -- submitted tasks are shown below
~> TaskHandler[jobId: 2998128; id: 2; name: TASK2; status: RUNNING; exit: -; error: -; workDir: [/path/to]/work/b4/9b7db98b055639f6058494719b451e started: 1740422190792; exited: -; ]
Feb-24 18:43:30.814 [Task monitor] DEBUG nextflow.executor.GridTaskHandler - Failed to get exit status for process TaskHandler[jobId: 2998128; id: 2; name: TASK2; status: RUNNING; exit: -; error: -; workDir: [/path/to]/work/b4/9b7db98b055639f6058494719b451e started: 1740422190792; exited: -; ] -- exitStatusReadTimeoutMillis: 270000; delta: 270020
Current queue status:
> (empty)
Environment
Nextflow version: [?]
Java version:
openjdk 11.0.26 2025-01-21
OpenJDK Runtime Environment (build 11.0.26+4-post-Ubuntu-1ubuntu122.04)
OpenJDK 64-Bit Server VM (build 11.0.26+4-post-Ubuntu-1ubuntu122.04, mixed mode, sharing)
Bug report
Expected behavior and actual behavior
I expect the pipeline to run, but its requesting a error code and times out after 4.5 minutes while my pipeline is still running, even if i try a retry strat or anything, the pipeline is STILL executing in the background..
Steps to reproduce the problem
nextflow run myworkflow.nf
Program output
ERROR ~ Error executing process > 'TASK2'
Caused by:
Process
TASK2
terminated for an unknown reason -- Likely it has been terminated by the external systemCommand exit status:
Command output:
(empty)
Environment
openjdk 11.0.26 2025-01-21
OpenJDK Runtime Environment (build 11.0.26+4-post-Ubuntu-1ubuntu122.04)
OpenJDK 64-Bit Server VM (build 11.0.26+4-post-Ubuntu-1ubuntu122.04, mixed mode, sharing)
LSB Version: core-11.1.0ubuntu4-noarch:printing-11.1.0ubuntu4-noarch:security-11.1.0ubuntu4-noarch
Distributor ID: Ubuntu
Description: Ubuntu 22.04.5 LTS
Release: 22.04
Codename: jammy
$SHELL --version
)GNU bash, version 5.1.16(1)-release (x86_64-pc-linux-gnu)
Additional context
running on SLURM.
Similar to these issues.
#2672
#1045
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