snakemake: error: argument **-T/--restart-times: expected one argument**

[esraagithub]

hello i found this error when running metacompass please help me to understand what is that error mean and how to solve it

usage: snakemake [-h] [--dry-run] [--profile PROFILE] [--cache [RULE ...]] [--snakefile FILE] [--cores [N]] [--jobs [N]] [--local-cores N] [--resources [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 ...]] [--default-resources [NAME=INT ...]] [--preemption-default PREEMPTION_DEFAULT] [--preemptible-rules PREEMPTIBLE_RULES [PREEMPTIBLE_RULES ...]] [--config [KEY=VALUE ...]] [--configfile FILE [FILE ...]] [--envvars VARNAME [VARNAME ...]] [--directory DIR] [--touch] [--keep-going] [--force] [--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 {COIN_CMD}] [--scheduler-solver-path SCHEDULER_SOLVER_PATH] [--conda-base-path CONDA_BASE_PATH] [--no-subworkflows] [--groups GROUPS [GROUPS ...]] [--group-components GROUP_COMPONENTS [GROUP_COMPONENTS ...]] [--report [FILE]] [--report-stylesheet CSSFILE] [--draft-notebook TARGET] [--edit-notebook TARGET] [--notebook-listen IP:PORT] [--lint [{text,json}]] [--generate-unit-tests [TESTPATH]] [--containerize] [--export-cwl FILE] [--list] [--list-target-rules] [--dag] [--rulegraph] [--filegraph] [--d3dag] [--summary] [--detailed-summary] [--archive FILE] [--cleanup-metadata FILE [FILE ...]] [--cleanup-shadow] [--skip-script-cleanup] [--unlock] [--list-version-changes] [--list-code-changes] [--list-input-changes] [--list-params-changes] [--list-untracked] [--delete-all-output] [--delete-temp-output] [--bash-completion] [--keep-incomplete] [--drop-metadata] [--version] [--reason] [--gui [PORT]] [--printshellcmds] [--debug-dag] [--stats FILE] [--nocolor] [--quiet] [--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] [--notemp] [--all-temp] [--keep-remote] [--keep-target-files] [--allowed-rules ALLOWED_RULES [ALLOWED_RULES ...]] [--local-groupid LOCAL_GROUPID] [--max-jobs-per-second MAX_JOBS_PER_SECOND] [--max-status-checks-per-second MAX_STATUS_CHECKS_PER_SECOND] [-T RESTART_TIMES] [--attempt ATTEMPT] [--wrapper-prefix WRAPPER_PREFIX] [--default-remote-provider {S3,GS,FTP,SFTP,S3Mocked,gfal,gridftp,iRODS,AzBlob,XRootD}] [--default-remote-prefix DEFAULT_REMOTE_PREFIX] [--no-shared-fs] [--greediness GREEDINESS] [--no-hooks] [--overwrite-shellcmd OVERWRITE_SHELLCMD] [--debug] [--runtime-profile FILE] [--mode {0,1,2}] [--show-failed-logs] [--log-handler-script FILE] [--log-service {none,slack,wms}] [--cluster CMD | --cluster-sync CMD | --drmaa [ARGS]] [--cluster-config FILE] [--immediate-submit] [--jobscript SCRIPT] [--jobname NAME] [--cluster-status CLUSTER_STATUS] [--cluster-cancel CLUSTER_CANCEL] [--cluster-cancel-nargs CLUSTER_CANCEL_NARGS] [--cluster-sidecar CLUSTER_SIDECAR] [--drmaa-log-dir DIR] [--kubernetes [NAMESPACE]] [--container-image IMAGE] [--tibanna] [--tibanna-sfn TIBANNA_SFN] [--precommand PRECOMMAND] [--tibanna-config TIBANNA_CONFIG [TIBANNA_CONFIG ...]] [--google-lifesciences] [--google-lifesciences-regions GOOGLE_LIFESCIENCES_REGIONS [GOOGLE_LIFESCIENCES_REGIONS ...]] [--google-lifesciences-location GOOGLE_LIFESCIENCES_LOCATION] [--google-lifesciences-keep-cache] [--tes URL] [--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-singularity] [--singularity-prefix DIR] [--singularity-args ARGS] [--use-envmodules] [target ...] snakemake: error: argument -T/--restart-times: expected one argument

snakemake -v 7.3.4

[vcepeda]

did you run the Readme examples without errors? which command and samples did you run?

[esraagithub]

@vcepeda thank you for your quick reply yes i used the example in the readme file and get that error python3 go_metacompass.py -r tutorial/Candidatus_Carsonella_ruddii_HT_Thao2000.fasta -P tutorial/thao2000.1.fq,tutorial/thao2000.2.fq -o example1_outpt -m 3 -t 4

[lxsteiner]

Same issue on tutorial example.

$  snakemake -v
7.32.4

Managed to get around it with --notimestamps but the command failed elsewhere.