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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
105 stars 16 forks source link

error in step mgefinder formatbam #41

Closed Oelsakha closed 1 year ago

Oelsakha commented 1 year ago

Hi all please, if anyone can help me I am trying to run this code (mgefinder) lololly-MBP MGEfinder % mgefinder formatbam s5.sam s5.bam
but gave me this error

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 Traceback (most recent call last): File "/Users/lololly/miniconda3/envs/mgefinder/bin/mgefinder", line 5, in from mgefinder.main import cli File "/Users/lololly/miniconda3/envs/mgefinder/lib/python3.6/site-packages/mgefinder/main.py", line 38, in check_dependencies() File "/Users/lololly/miniconda3/envs/mgefinder/lib/python3.6/site-packages/mgefinder/dependencies.py", line 39, in check_dependencies bowtie2_checker.check(extract_version=lambda x: x.split()[2]) File "/Users/lololly/miniconda3/envs/mgefinder/lib/python3.6/site-packages/mgefinder/dependencies.py", line 12, in check output = shell(cmd.format(tool=self.tool), read=True).decode('utf-8').strip() File "/Users/lololly/miniconda3/envs/mgefinder/lib/python3.6/site-packages/snakemake/shell.py", line 88, in new raise sp.CalledProcessError(retcode, cmd) subprocess.CalledProcessError: Command 'bowtie2 --version 2>&1' returned non-zero exit status 255.

Oelsakha commented 1 year ago

never mind, it solved

durrantmm commented 1 year ago

Great!