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AnantharamanLab / VIBRANT

Virus Identification By iteRative ANnoTation
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VIBRANT error: could not identify Pfam HMM files in database directory. Please run VIBRANT_setup.py - After download-db #98

Open gadieid opened 2 weeks ago

gadieid commented 2 weeks ago

After download-db, and although no errors found in the VIBRANT_setup.log, the VIBRANT_run.py exit with error on missing db files.

During download-db the hmmpress certed only the .h3i file and not all other indexes (.h3f and so on) both for PFAM and VOG HMM so Vibrant_tun.py failed.

It might be related to the subprocess and parallelism

Workaround in the database directory to manually run hmmpress like this:

hmmpress VOGDB94_phage.HMM rm VOGDB94_phage.HMM.h3i (hmmpress will not run if several of the binary files exists) hmmpress VOGDB94_phage.HMM

bernt-matthias commented 1 week ago

Same here.

Workaround mentioned above works. One can simply uses hmmpress -f VOGDB94_phage.HMM (and analogous for the other two HMM files).