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snakemake / snakemake-executor-plugin-slurm

A Snakemake executor plugin for submitting jobs to a SLURM cluster
MIT License
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main.py: error: argument --executor/-e: invalid choice: 'slurm-jobstep' (choose from 'local', 'dryrun', 'touch') #50

Closed Carsten-Ke closed 3 months ago

Carsten-Ke commented 3 months ago

Hi,

I am trying to run a test pipeline. Locally it works fine but wen I try to run in on our slurm cluster using

snakemake --snakefile pipeline.txt --executor slurm --jobs 10

I get the following error:

usage: main.py [-h] [--dry-run] [--profile PROFILE] [--workflow-profile WORKFLOW_PROFILE] [--cache [RULE ...]] [--snakefile FILE] [--cores N] [--jobs N] [--local-cores N] [--resources NAME=INT [NAME=INT ...]] [--set-threads RULE=THREADS [RULE=THREADS ...]] [--max-threads MAX_THREADS] [--set-resources RULE:RESOURCE=VALUE [RULE:RESOURCE=VALUE ...]] [--set-scatter NAME=SCATTERITEMS [NAME=SCATTERITEMS ...]] [--set-resource-scopes RESOURCE=[global|local] [RESOURCE=[global|local] ...]] [--default-resources [NAME=INT ...]] [--preemptible-rules [PREEMPTIBLE_RULES ...]] [--preemptible-retries PREEMPTIBLE_RETRIES] [--config [KEY=VALUE ...]] [--configfile FILE [FILE ...]] [--envvars VARNAME [VARNAME ...]] [--directory DIR] [--touch] [--keep-going] [--rerun-triggers {code,input,mtime,params,software-env} [{code,input,mtime,params,software-env} ...]] [--force] [--executor {local,dryrun,touch}] [--forceall] [--forcerun [TARGET ...]] [--prioritize TARGET [TARGET ...]] [--batch RULE=BATCH/BATCHES] [--until TARGET [TARGET ...]] [--omit-from TARGET [TARGET ...]] [--rerun-incomplete] [--shadow-prefix DIR] [--scheduler [{ilp,greedy}]] [--wms-monitor [WMS_MONITOR]] [--wms-monitor-arg [NAME=VALUE ...]] [--scheduler-ilp-solver {GLPK_CMD,PULP_CBC_CMD,COIN_CMD}] [--scheduler-solver-path SCHEDULER_SOLVER_PATH] [--conda-base-path CONDA_BASE_PATH] [--no-subworkflows] [--precommand PRECOMMAND] [--groups GROUPS [GROUPS ...]] [--group-components GROUP_COMPONENTS [GROUP_COMPONENTS ...]] [--report [FILE]] [--report-stylesheet CSSFILE] [--reporter PLUGIN] [--draft-notebook TARGET] [--edit-notebook TARGET] [--notebook-listen IP:PORT] [--lint [{text,json}]] [--generate-unit-tests [TESTPATH]] [--containerize] [--export-cwl FILE] [--list-rules] [--list-target-rules] [--dag] [--rulegraph] [--filegraph] [--d3dag] [--summary] [--detailed-summary] [--archive FILE] [--cleanup-metadata FILE [FILE ...]] [--cleanup-shadow] [--skip-script-cleanup] [--unlock] [--list-changes {code,input,params}] [--list-input-changes] [--list-params-changes] [--list-untracked] [--delete-all-output | --delete-temp-output] [--keep-incomplete] [--drop-metadata] [--deploy-sources QUERY CHECKSUM] [--version] [--printshellcmds] [--debug-dag] [--nocolor] [--quiet [{all,progress,rules} ...]] [--print-compilation] [--verbose] [--force-use-threads] [--allow-ambiguity] [--nolock] [--ignore-incomplete] [--max-inventory-time SECONDS] [--latency-wait SECONDS] [--wait-for-files [FILE ...]] [--wait-for-files-file FILE] [--queue-input-wait-time SECONDS] [--notemp] [--all-temp] [--unneeded-temp-files FILE [FILE ...]] [--keep-storage-local-copies] [--target-files-omit-workdir-adjustment] [--allowed-rules ALLOWED_RULES [ALLOWED_RULES ...]] [--target-jobs TARGET_JOBS [TARGET_JOBS ...]] [--local-groupid LOCAL_GROUPID] [--max-jobs-per-second MAX_JOBS_PER_SECOND] [--max-status-checks-per-second MAX_STATUS_CHECKS_PER_SECOND] [--seconds-between-status-checks SECONDS_BETWEEN_STATUS_CHECKS] [--retries RETRIES] [--attempt ATTEMPT] [--wrapper-prefix WRAPPER_PREFIX] [--default-storage-provider DEFAULT_STORAGE_PROVIDER] [--default-storage-prefix DEFAULT_STORAGE_PREFIX] [--local-storage-prefix LOCAL_STORAGE_PREFIX] [--shared-fs-usage {input-output,persistence,software-deployment,source-cache,sources,storage-local-copies,none} [{input-output,persistence,software-deployment,source-cache,sources,storage-local-copies,none} ...]] [--scheduler-greediness SCHEDULER_GREEDINESS] [--no-hooks] [--debug] [--runtime-profile FILE] [--mode {default,remote,subprocess}] [--show-failed-logs] [--log-handler-script FILE] [--log-service {none,slack,wms}] [--job-deploy-sources] [--container-image IMAGE] [--immediate-submit] [--jobscript SCRIPT] [--jobname NAME] [--flux] [--software-deployment-method {apptainer,conda,env-modules} [{apptainer,conda,env-modules} ...]] [--container-cleanup-images] [--use-conda] [--conda-not-block-search-path-envvars] [--list-conda-envs] [--conda-prefix DIR] [--conda-cleanup-envs] [--conda-cleanup-pkgs [{tarballs,cache}]] [--conda-create-envs-only] [--conda-frontend {conda,mamba}] [--use-apptainer] [--apptainer-prefix DIR] [--apptainer-args ARGS] [--use-envmodules] [--report-html-path VALUE] [--report-html-stylesheet-path VALUE] [targets ...] main.py: error: argument --executor/-e: invalid choice: 'slurm-jobstep' (choose from 'local', 'dryrun', 'touch')

snakmake: 8.5.4 snakemake-executor-plugin-slurm: 0.4.1 snakemake-executor-plugin-slurm-jobstep: 0.1.10

Could you please help me to solve the problem?

Carsten-Ke commented 3 months ago

Sorry, the plugin was not installed on the cluster it was running on it seems