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appliedbinf / el_gato

MIT License
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Output directory 'output2019_mlst' exists and overwrite is turned off. Exiting #3

Closed tbazilegith closed 1 year ago

tbazilegith commented 1 year ago

HI Alan, I tried to run el-gato on two samples, using this command for samp in $(cat samples.txt); do /home/myUser/el_gato/el_gato/el_gato.py --assembly ../assemblies/${samp}_assembly.fasta --out output2019_mlst done

The run failed with this error: Output directory 'output2019_mlst' exists and overwrite is turned off. Exiting Any ideas? Thanks! TJ

Alan-Collins commented 1 year ago

Hi TJ,

As I said here el_gato wants you to provide a different output directory for each sample. It writes output files with the same filenames each run so you can't write outputs from multiple runs in the same directory

Alan

tbazilegith commented 1 year ago

Thanks! I caught the issue by adding the sample name as subdirectory of the output dir.