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bhattlab / MGEfinder

A toolbox for identifying mobile genetic element (MGE) insertions from short-read sequencing data of bacterial isolates.
MIT License
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No output file, no error message #28

Closed Kylies5 closed 3 years ago

Kylies5 commented 3 years ago

Hello, I have tried running mgefinder on multiple data sets. Some have worked and some have not. My latest run produced this:

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: /scratch/aubksw/MGEfinder/MGEfinder/cluster5 cores: 1 memory: 16000 unlock: False rerun_incomplete: False keep_going: False sensitive: True #################### COMMAND: snakemake -s /home/aubksw/anaconda3/envs/mgefinder/lib/python3.6/site-packages/mgefinder/workflow/denovo.sensitive.Snakefile --config wd=/scratch/aubksw/MGEfinder/MGEfinder/cluster5 memory=16000 --cores 1 --configfile /home/aubksw/anaconda3/envs/mgefinder/lib/python3.6/site-packages/mgefinder/workflow/denovo.sensitive.config.yml Provided cores: 1 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

There were no output files created and no error messages so I am not sure what went wrong. Please let me know if there is a solution. Thank you

durrantmm commented 3 years ago

This looks like an issue with the directory structure. Could you show me the files in your working directory?

Kylies5 commented 3 years ago
Screen Shot 2021-06-22 at 10 16 55 AM
durrantmm commented 3 years ago

I need to see the files in the directories 00.assembly, 00.bam, and 00.genome.

Kylies5 commented 3 years ago

aubksw@dmcvlogin4:cluster5> cd 00.assembly (base) aubksw@dmcvlogin4:00.assembly> ls XtranslucensF5.fna (base) aubksw@dmcvlogin4:00.assembly> cd .. (base) aubksw@dmcvlogin4:cluster5> cd 00.genome (base) aubksw@dmcvlogin4:00.genome> ls XtranslucensDSM18974.fsa (base) aubksw@dmcvlogin4:00.genome> cd .. (base) aubksw@dmcvlogin4:cluster5> cd 00.bam (base) aubksw@dmcvlogin4:00.bam> ls XtranslucensF5.XtranslucensDSM18974.bam XtranslucensF5.XtranslucensDSM18974.bam.bai

Kylies5 commented 3 years ago

XtranslucensDSM18974.fsa.zip XtranslucensF5.XtranslucensDSM18974.bam.bai.zip XtranslucensF5.fna.zip

durrantmm commented 3 years ago

Ok, the way the files are named needs to match what is described here. The 00.genome file must end in .fna not .fsa.