snakemake: error: unrecognized arguments: -T

TealFurnholm commented 3 years ago

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 commented 3 years ago

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 commented 3 years ago

Please make sure you have the required software versions.

MMAThijssen commented 2 years ago

I ran into the same problem. Commenting out

if not notimestamps:
    cmd += " -T"

in go_metacompass.py solved it for me.

esraagithub commented 2 years ago

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 commented 2 years ago

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

marbl / MetaCompass