Failed to open key file profile_names/VIBRANT_pfam-plasmid_profiles.txt

[IBEXCluster]

Dear developers, We are trying to download VIBRANT (v 1.2.1) database and it's failed to open key file profile_names/VIBRANT_pfam-plasmid_profiles.txt.

This process will require 20GB of temporary free storage space, but the final size requirement is ~11.2GB in the form of pressed HMM databases.
Please be patient. This only needs to be run once and will take a few minutes.

Verifying Pfam, KEGG and VOG source websites are available for download ...

Downloading HMM profiles for Pfam, KEGG and VOG from their source websites ...
2023-06-18 12:00:37 URL: ftp://ftp.ebi.ac.uk/pub/databases/Pfam/releases/Pfam32.0/Pfam-A.hmm.gz [270995712] -> "Pfam-A.hmm.gz" [1]
2023-06-18 12:00:40 URL:https://fileshare.csb.univie.ac.at/vog/vog94/vog.hmm.tar.gz [329720997/329720997] -> "vog.hmm.tar.gz" [1]
2023-06-18 12:18:20 URL: ftp://ftp.genome.jp/pub/db/kofam/archives/2019-08-10/profiles.tar.gz [1173662460] -> "profiles.tar.gz" [1]

Unzipping profiles ...

Concatenating individual profiles ...
Extracting profiles used for VIBRANT ...
Error: Failed to open key file profile_names/VIBRANT_pfam-plasmid_profiles.txt
Error: Failed to open key file profile_names/VIBRANT_pfam-phage_profiles.txt
Error: Failed to open key file profile_names/VIBRANT_vog_profiles.txt
Error: Failed to open key file profile_names/VIBRANT_kegg_profiles.txt
Pressing profiles used for VIBRANT ...
Error: File format problem in trying to open HMM file VOGDB94_phage.HMM.
File exists, but appears to be empty?
Error: File format problem in trying to open HMM file Pfam-A_plasmid_v32.HMM.
File exists, but appears to be empty?
Error: File format problem in trying to open HMM file KEGG_profiles_prokaryotes.HMM.
File exists, but appears to be empty?
Error: File format problem in trying to open HMM file Pfam-A_phage_v32.HMM.
File exists, but appears to be empty?
Working...    done.
Pressed and indexed 17929 HMMs (17929 names and 17929 accessions).
Models pressed into binary file:   Pfam-A_v32.HMM.h3m
SSI index for binary model file:   Pfam-A_v32.HMM.h3i
Profiles (MSV part) pressed into:  Pfam-A_v32.HMM.h3f
Profiles (remainder) pressed into: Pfam-A_v32.HMM.h3p

Done. Several new databases are now in this folder.

VIBRANT should be ready to go. You can verify this by running VIBRANT_test_setup.py within this folder (databases/)

Any advise?

[KrisKieft]

How did you install VIBRANT? Where are the program files stored?

[IBEXCluster]

Dear @KrisKieft Here are the steps, I used to install the VIBRANT.

#!/bin/bash
mkdir -p vibrant/1.2.1/el7.9_conda3
cd vibrant/1.2.1/el7.9_conda3
curl -O https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
sh ./Miniconda3-latest-Linux-x86_64.sh -bufp /ibex/sw/csi/vibrant/1.2.1/el7.9_conda3/Miniconda3

export PATH=/ibex/sw/csi/vibrant/1.2.1/el7.9_conda3/Miniconda3/bin:$PATH
pip install biopython
pip install pandas
pip install matplotlib
pip install seaborn
pip install numpy
pip install pickle-mixin
conda install scikit-learn
conda install -c bioconda vibrant
export PATH=/ibex/sw/csi/vibrant/1.2.1/el7.9_conda3/Miniconda3/bin:$PATH
python ./Miniconda3/share/vibrant-1.0.1/databases/VIBRANT_setup.py
mv Pfam-A_* KEGG_profiles_prokaryotes.HMM VOGDB94_phage.HMM vibrant_data/

Looking for your advise.

[IBEXCluster]

Dear @KrisKieft, I was using VIBRANT_run.py script from installed version which was inappropriate. When we started using the VIBRANT_run.py from https://github.com/AnantharamanLab/VIBRANT GitHub repo. the issue disappeared. Please close this ticket and thanks for all your time.