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phac-nml / mob-suite

MOB-suite: Software tools for clustering, reconstruction and typing of plasmids from draft assemblies
Apache License 2.0
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mob_cluster: Duplicated path during copy of 'references_updated.fasta' file #81

Closed dfornika closed 3 years ago

dfornika commented 3 years ago

The update_fasta variable is initialized here as the out_dir/references_updated.fasta:

https://github.com/phac-nml/mob-suite/blob/40ec14b7322d4d0ad8506a65b77e28275b826fe0/mob_suite/mob_cluster.py#L566

...then when it is used here for a file copy, the out_dir is prepended again:

https://github.com/phac-nml/mob-suite/blob/40ec14b7322d4d0ad8506a65b77e28275b826fe0/mob_suite/mob_cluster.py#L623

...resulting in out_dir/out_dir/references_updated.fasta, which is giving an error:

FileNotFoundError: [Error 2] No such file or directory: 'out_dir/out_dir/references_updated.fasta