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Slurm executor problem
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#!/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 | |
} |
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profiles { | |
standard { | |
process.executor = 'local' | |
} | |
cluster { | |
process { | |
executor = 'slurm' | |
queue = 'ei-long' | |
memory = '100 GB' | |
cpus = 8 | |
//withLabel: KAT { | |
// container = 'singularity_imgs/kat.img' | |
//} | |
} | |
} | |
} |
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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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