VIBRANT error: could not identify Pfam HMM files in database directory. Please run VIBRANT_setup.py - After download-db

[gadieid]

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]

Same here.

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

[mattewchen]

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

@gadieid
Hi, I encountered a similar issue:
VIBRANT error: could not identify KEGG HMM files in database directory. Please run VIBRANT_setup.py.

However, all the KEGG database files (.h3f, .h3i, .h3p, .h3m) are present in my directory.
I also tried regenerating these files using the hmmpress command, but the same error still occurs.

Could you please help me understand what might be causing this issue and how to resolve it?
Thank you very much!

[KrisKieft]

Where are the databases located relative to the run command and what is your directory setup? Are you on a laptop or server or cluster?

[ShevchenkoAlla]

I have the same issue, can anyone have found a solution?

The db folder have everything, I have run VIBRANT_setup.py but it didn't helped.
Any ideas?
I work on the cluster, what are i my db folder -

KEGG_profiles_prokaryotes.HMM KEGG_profiles_prokaryotes.HMM.h3m Pfam-A_v32.HMM.h3f Pfam-A_v32.HMM.h3p VIBRANT_setup.py VOGDB94_phage.HMM.h3i
KEGG_profiles_prokaryotes.HMM.h3f KEGG_profiles_prokaryotes.HMM.h3p Pfam-A_v32.HMM.h3i profile_names VOGDB94_phage.HMM VOGDB94_phage.HMM.h3m
KEGG_profiles_prokaryotes.HMM.h3i Pfam-A_v32.HMM Pfam-A_v32.HMM.h3m VIBRANT_setup.log VOGDB94_phage.HMM.h3f VOGDB94_phage.HMM.h3p