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SionBayliss / PIRATE

A toolbox for pangenome analysis and threshold evaluation.
GNU General Public License v3.0
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PIRATE to Roary #46

Closed JParraV closed 4 years ago

JParraV commented 4 years ago

Hi,

I am trying to covert the PIRATE output to Roary. However, I got "input directory not found", even though it is there.

hsb18158@sipbsmicro ~/PIRATE % bin/PIRATE PIRATE_to_roary.pl -i /home/hsb18158/data/PIRATE_output/PIRATE.gene_families.tsv -o /home/hsb18158/data/PIRATE_to_roary/gene_families.csv
ERROR: input directory not
hsb18158@sipbsmicro ~/PIRATE % bin/PIRATE convert_to_roary.pl -i /home/hsb18158/data/PIRATE_output/PIRATE.gene_families.tsv -o /home/hsb18158/data/PIRATE_to_roary/gene_families.csv
ERROR: input directory not found.

Any suggestion?

Thank you, Parra

SionBayliss commented 4 years ago

Hi Parra,

It looks like you might be using an older version of the script. Try the most recent one from github.

All the best, Sion

JParraV commented 4 years ago

Hi,

I tried both. But I sorted it out. It was entirely my fault. I installed PIRATE by cloning the repository and I tried to run the script PIRATE_to_roary.pl from the bin folder. Sorry. It's amended and the results look great.

Thanks! Parra