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AlexanderLabWHOI / EUKulele

Automatic eukaryotic taxonomic classification
MIT License
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How can I run with existing database? #43

Closed jolespin closed 2 years ago

jolespin commented 2 years ago

I want to run EUKulele with proteins from MAGs I have so I ran the following command: 

EUKulele -m mags --p_ext faa -f --scratch tmp -o eukulele_output --sample_dir S005_R2_POST-PE-N728-S516-1_S23/output/genomes/ --database /usr/local/scratch/CORE/jespinoz/db/eukulele

but I got the following error: 

Running EUKulele with command line arguments, as no valid configuration file was provided.
Setting things up...
Could not successfully install all external dependent software.
Check DIAMOND, BLAST, BUSCO, and TransDecoder installation.
Specified reference directory, reference FASTA, and protein map/taxonomy table not found. Using database in location: /usr/local/scratch/core/jespinoz/db/eukulele.
mkdir: cannot create directory ‘/usr/local/scratch/core’: Permission denied
Automatically downloading database /usr/local/scratch/core/jespinoz/db/eukulele . If you intended to use an existing database folder, be sure a reference FASTA, protein map, and taxonomy table are provided. Check the documentation for details.
Specified reference database, /usr/local/scratch/core/jespinoz/db/eukulele is not supported.

What should I do to run EUKulele with an existing database that I've already downloaded (EukProt)?

jolespin commented 2 years ago

Got it, you have to specify the subdirectory: 

EUKulele -m mags --p_ext faa -f --scratch tmp -o eukulele_output --sample_dir S005_R2_POST-PE-N728-S516-1_S23/output/genomes/ --reference_dir /usr/local/scratch/CORE/jespinoz/db/eukulele/eukprot/ --alignment_choice diamond