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bowmanjeffs / paprica

paprica - PAthway PRediction by phylogenetIC plAcement
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FileNotFoundError: [Errno 2] No such file or directory: 'test.bacteria.phylum_reps.edpllist.csv' #87

Closed lee-s17 closed 3 years ago

lee-s17 commented 3 years ago

Hi, I am installing paprica via git clone https://github.com/bowmanjeffs/paprica.git When running ./paprica-run.sh test bacteria, the error pops up. testrun.txt

Previously when I downloaded paprica v6 using "wget https://github.com/bowmanjeffs/paprica/archive/paprica_v0.6.tar.gz", it runs fine without error, so wondering what might lead to this error.

*Just realised this is the same error in#86. I tried reinstalling but the issue persists.

bowmanjeffs commented 3 years ago

Lee, I can't reproduce with a fresh clone of the repository. Can you re-clone and try again?

lee-s17 commented 3 years ago

Thanks for the reply. Unfortunately, I tried to reclone but the same error persists. Attaching an image with the output files from running ./paprica-run.sh test bacteria. Screenshot 2021-02-11 001855

bowmanjeffs commented 3 years ago

It looks like your version of gappa doesn't understand the --tree-file-prefix option. Can you update gappa and try again?

bowmanjeffs commented 3 years ago

Looking closer at this I looks like gappa is naming your EDPL file differently than expected (paprica expects edplelist.csv and you're getting edpledple_list.csv). It looks like you're running the same gappa version as our test box, but let me know how you installed an what platform you're running on. Perhaps there are differences...

bowmanjeffs commented 3 years ago

It looks like this is caused by a recent update to gappa. Should have a fix implemented shortly. Standy by...

bowmanjeffs commented 3 years ago

Okay should be good. Reopen this issue if problems persist.