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@TransGirlCodes
Last active May 16, 2022 17:43
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Slurm executor problem
#!/us/bin/env nextflow
// Configuration & parameters
nextflow.enable.dsl = 2
// Processes
// ---------
process pullHifiReads {
input:
path tarball
output:
path '**hifi_reads.fastq.gz'
shell:
'''
tar -xvf !{tarball} $(tar -tf !{tarball} | grep hifi_reads.fastq.gz)
'''
}
// Workflows
// ---------
workflow {
channel
.fromPath(["data/raw/pacbio-ccs/**Demultiplex_Barcodes_CCS_Analysis.tar", "data/raw/pacbio-ccs/**Demultiplex_Barcodes_CCS_Analysis.tar.gz"]) \
| pullHifiReads
}
profiles {
standard {
process.executor = 'local'
}
cluster {
process {
executor = 'slurm'
queue = 'ei-long'
memory = '100 GB'
cpus = 8
//withLabel: KAT {
// container = 'singularity_imgs/kat.img'
//}
}
}
}
N E X T F L O W ~ version 22.04.0
Launching `main.nf` [nauseous_goldberg] DSL2 - revision: 2650970915
[- ] process > pullHifiReads -
[- ] process > pullHifiReads [ 0%] 0 of 1
Error executing process > 'pullHifiReads (1)'
Caused by:
java.io.IOException: Cannot run program "sbatch" (in directory "/ei/projects/d/d2c0bfb1-c37a-4211-9493-86b15d4e773e/scratch/work/6d/a97531ebf595145049576f078ca246"): error=2, No such file or directory
Command executed:
sbatch .command.run
Command exit status:
-
Command output:
(empty)
Work dir:
/ei/projects/d/d2c0bfb1-c37a-4211-9493-86b15d4e773e/scratch/work/6d/a97531ebf595145049576f078ca246
Tip: when you have fixed the problem you can continue the execution adding the option `-resume` to the run command line
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