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createIndices caused Unable to locate a modulefile for 'slurm'

See original GitHub issue

Hi, I ran createIndices in the below way but I got ModuleCmd_Load.c(208):ERROR:105: Unable to locate a modulefile for 'slurm'. Our cluster is using PBSpro and therefore I would like to use only one compute node. How can I remove the slurm error?

snakepipes> createIndices --genomeURL /scratch/waterhouse_team/benth/dbg2olc-40x/scaffolds_FINAL.fasta -o snakePipes-output --tempdir snakePipes-tmp dbg2olc-40x
Building DAG of jobs...
Using shell: /bin/bash
Provided cluster nodes: 5
Job counts:
	count	jobs
	1	all
	1	bowtie2Index
	1	bwaIndex
	1	bwamethIndex
	1	computeEffectiveGenomeSize
	1	createGenomeFasta
	1	fastaIndex
	1	hisat2Index
	1	make2bit
	1	starIndex
	10

[Sun Oct 14 01:10:10 2018]
rule createGenomeFasta:
    output: /lustre/scratch/waterhouse_team/benth/dbg2olc-40x/snakepipes/snakePipes-output/genome_fasta/genome.fa
    jobid: 7

ModuleCmd_Load.c(208):ERROR:105: Unable to locate a modulefile for 'slurm'
/bin/sh: SlurmEasy: command not found
Error submitting jobscript (exit code 127):

Job failed, going on with independent jobs.
Exiting because a job execution failed. Look above for error message
Complete log: /lustre/scratch/waterhouse_team/benth/dbg2olc-40x/snakepipes/snakePipes-output/.snakemake/log/2018-10-14T011009.735531.snakemake.log
Error: snakemake returned an error code of 1, so processing is incomplete!

Thank you in advance,

Michal

Issue Analytics

State:
Created 5 years ago
Comments:5 (3 by maintainers)

Top GitHub Comments

1reaction

steffenheynecommented, Oct 15, 2018

Hi Michal, if you just want to use one computer, each workflow has the option --local By that, snakePipes (and Snakemake) ignores any cluster configuration. With -j one can then control the max number of cores used on one machine.

Is that what you want to achieve?

0reactions

mictadlocommented, Oct 15, 2018

Hi @steffenheyne , Yes that is what I tried to achieve.

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