snakemake: error: unrecognized arguments: -T

[TealFurnholm]

COMMAND

python3 go_metacompass.py -1 test_for.fastq -2 test_rev.fastq -l 250 -o MC_assembly -m 2 -t 10 -y 100 --clobber

###OUTPUT###
MetaCompass metagenome assembler version 2.0.0 by Victoria Cepeda (vcepeda@cs.umd.edu)

usage: snakemake [-h] [--dryrun] [--profile PROFILE] [--snakefile FILE]
[--cores [N]] [--local-cores N]
[--resources [NAME=INT [NAME=INT ...]]]
[--config [KEY=VALUE [KEY=VALUE ...]]] [--configfile FILE]
[--directory DIR] [--touch] [--keep-going] [--force]
[--forceall] [--forcerun [TARGET [TARGET ...]]]
[--prioritize TARGET [TARGET ...]]
[--until TARGET [TARGET ...]]
[--omit-from TARGET [TARGET ...]] [--rerun-incomplete]
[--shadow-prefix DIR] [--report HTMLFILE] [--export-cwl FILE]
[--list] [--list-target-rules] [--dag] [--rulegraph]
[--d3dag] [--summary] [--detailed-summary] [--archive FILE]
[--cleanup-metadata FILE [FILE ...]] [--cleanup-shadow]
[--unlock] [--list-version-changes] [--list-code-changes]
[--list-input-changes] [--list-params-changes]
[--list-untracked] [--delete-all-output]
[--delete-temp-output] [--bash-completion] [--version]
[--reason] [--gui [PORT]] [--printshellcmds] [--debug-dag]
[--stats FILE] [--nocolor] [--quiet] [--print-compilation]
[--verbose] [--force-use-threads] [--allow-ambiguity]
[--nolock] [--ignore-incomplete] [--latency-wait SECONDS]
[--wait-for-files [FILE [FILE ...]]] [--notemp]
[--keep-remote] [--keep-target-files]
[--allowed-rules ALLOWED_RULES [ALLOWED_RULES ...]]
[--max-jobs-per-second MAX_JOBS_PER_SECOND]
[--max-status-checks-per-second MAX_STATUS_CHECKS_PER_SECOND]
[--restart-times RESTART_TIMES] [--attempt ATTEMPT]
[--wrapper-prefix WRAPPER_PREFIX]
[--default-remote-provider {S3,GS,FTP,SFTP,S3Mocked,gfal,gridftp,iRODS}]
[--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}]
[--cluster CMD | --cluster-sync CMD | --drmaa [ARGS]]
[--cluster-config FILE] [--immediate-submit]
[--jobscript SCRIPT] [--jobname NAME]
[--cluster-status CLUSTER_STATUS] [--drmaa-log-dir DIR]
[--kubernetes [NAMESPACE]]
[--kubernetes-env ENVVAR [ENVVAR ...]]
[--container-image IMAGE] [--use-conda] [--list-conda-envs]
[--cleanup-conda] [--conda-prefix DIR] [--create-envs-only]
[--use-singularity] [--singularity-prefix DIR]
[--singularity-args ARGS]
[target [target ...]]
snakemake: error: unrecognized arguments: -T
ERROR: snakemake command failed; exiting..

SNAKEMAKE VERSION

$ snakemake -v
5.4.0

[gavinmdouglas]

I was having similar problems finding a compatible version of snakemake, but after some trial and error I was able to get snakemake v5.2.0 to work with go_metacompass.py.

[vcepeda]

Please make sure you have the required software versions.

[MMAThijssen]

I ran into the same problem. Commenting out

if not notimestamps:
    cmd += " -T"

in go_metacompass.py solved it for me.

[esraagithub]

I ran into the same problem. Commenting out

if not notimestamps:
    cmd += " -T"

in go_metacompass.py solved it for me.

@MMAThijssen
Could you give me more details how to do it, please?

[MMAThijssen]

I decided not to use MetaCompass because different errors kept coming up, but for this particular error I solved it by commenting out that part in the script go_metacompass.py in the MetaCompass folder (there is also a script go_metacompass.py in the subfolder workflows, did not touch that one). So move to your MetaCompass folder, open the script with nano go_metacompass.py, then you can search for 'if not notimestamps' with Ctrl+W and comment out or remove the two lines.

Does this help? @esraagithub