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nextflow-io / nextflow

A DSL for data-driven computational pipelines
http://nextflow.io
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Queue status command fail on LSF version 8 #910

Closed tomas-pluskal closed 5 years ago

tomas-pluskal commented 6 years ago

Bug report

Hi! After upgrading to nextflow 18.10.1 from 0.32.0, I started seeing this message repeatedly in nextflow output:

WARN: [LSF] queue status cannot be fetched > exit status: 255

WARN: [LSF] queue status cannot be fetched > exit status: 255

WARN: [LSF] queue status cannot be fetched > exit status: 255

WARN: [LSF] queue status cannot be fetched > exit status: 255

WARN: [LSF] queue status cannot be fetched > exit status: 255

WARN: [LSF] queue status cannot be fetched > exit status: 255

WARN: [LSF] queue status cannot be fetched > exit status: 255

All cluster jobs, however, seem to be working fine, and the nextflow pipeline is producing all files normally.

This is my nextflow.config file:

process.executor = "lsf"
executor.queueSize = 1000

env.PATH = "/lab/solexa_weng/testtube/trinityrnaseq-Trinity-v2.8.4:/lab/solexa_weng/testtube/TransDecoder-TransDecoder-v5.0.2:/lab/solexa_weng/testtube/transrate-1.0.3-linux-x86_64:/lab/solexa_weng/testtube/signalp-4.1:/lab/solexa_weng/testtube/tmhmm-2.0c/bin:/lab/solexa_weng/testtube/ncbi-blast-2.7.1+/bin:/lab/solexa_weng/testtube/bowtie2-2.3.4.3-linux-x86_64:$PATH"

report.enabled = true