search

bhattlab / MGEfinder

A toolbox for identifying mobile genetic element (MGE) insertions from short-read sequencing data of bacterial isolates.
MIT License
105 stars 16 forks source link

No Output File #43

Open REMOUS-MAX opened 1 year ago

REMOUS-MAX commented 1 year ago

mgefinder workflow denovo --cores 4 ../fastqtrim/

CHECKING DEPENDENCIES

Current version of snakemake: 3.13.3 Expected version of snakemake: 3.13.3 Current version of einverted: EMBOSS:6.6.0.0 Expected version of einverted: EMBOSS:6.6.0.0 Current version of bowtie2: 2.3.5 Expected version of bowtie2: 2.3.5 Current version of samtools: 1.9 Expected version of samtools: 1.9 Current version of cd-hit: 4.8.1 Expected version of cd-hit: 4.8.1 ############################### Get help documentation with --help. Get version with --version.

PARAMETERS

command: workflow workdir: ../fastqtrim/ cores: 4 memory: 16000 unlock: False rerun_incomplete: False keep_going: False sensitive: False #################### COMMAND: snakemake -s /home/biobootcamp/anaconda3/envs/mgefinder/lib/python3.6/site-packages/mgefinder/workflow/denovo.original.Snakefile --config wd=../fastqtrim/ memory=16000 --cores 4 --configfile /home/biobootcamp/anaconda3/envs/mgefinder/lib/python3.6/site-packages/mgefinder/workflow/denovo.original.config.yml Provided cores: 4 Rules claiming more threads will be scaled down. Job counts: count jobs 1 all 1

rule all: jobid: 0

Finished job 0. 1 of 1 steps (100%) done

durrantmm commented 1 year ago

This looks like an issue with how you are setting up the working directory, please follow the tutorial closely.