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====== Main locations for most Databases on PERUN ======

/misc/db1/
    /scratch3/rogerlab_databases/other_dbs/
    /scratch4/db/
    /scratch5/db/       
**BLAST databases**
    /db1/blast-may-2024/nr.pal                   (updated May 2024)
    /db1/blast-may-2024/refseq_protein.pal       (updated May 2024)
    /db1/blast-may-2024/nt.nal                   (updated May 2024)

/scratch3/rogerlab_databases/other_dbs/blast_protein_database/    (updated Apr 2024)
    /scratch3/rogerlab_databases/other_dbs/nr_010621                  (updated Jun 2021)
    /opt/perun/share/extra-data-sets/uniprot/                         (updated Jul 25, 2017)
    /db1/extra-data-sets/MMETSP/MMETSP_db/ (2018, Kolisko et al. cleaned up with WinstoneCleaner see README file in he directory for more information)
    /opt/perun/share/extra-data-sets/CAM_P_0001000.nt.fa (old marine metagenome database)
** PLAST databases**
   /db1/extra-data-sets/nr-fasta.jun2024/nr.fasta (updated Jun, 2024)
   /scratch3/rogerlab_databases/other_dbs/nt_Jun2024/nt/nt.fasta (updated Jun, 2024)   
Note: Plast need to use the fasta file to run, and cannot use new format of v5 NCBI nr and nt databases
   
   
** DIAMOND:**
   /scratch5/db/Eukfinder/Diamond/nr.dmnd                                 (updated Nov 2025)
   /scratch3/rogerlab_databases/other_dbs/nt_Jun2024/nr/nr.dmnd           (updated Dec 2024)
   /scratch3/rogerlab_databases/other_dbs/nr_March252023/diamond/nr.dmnd  (updated Mar 2023)
   /scratch3/rogerlab_databases/other_dbs/nr_032121/nr.dmnd               (updated Mar 2021)
   /scratch3/rogerlab_databases/other_dbs/nr_06162020/nr.dmnd             (updated Jun 2020)

** CENTRIFUGE **
   /scratch2/software/centrifuge-1.0.3/          (updated 2019)
To use: the base index is "nt", which corresponds to the large nucleotide ncbi database in centrifuge format.

Centrifuge Database for Eukfinder:    
   /scratch3/Eukfinder/DB/Centrifuge_DB/
   The base index is Centrifuge_NewDB_Sept2020

** CheckM2 **

/scratch5/db/checkm2/CheckM2_database/         (updated Mar 2021)

** EGGNOG **
Several databases that are available at 
   /opt/perun/share/extra-data-sets/eggnog/
   /scratch4/db/eggnog-mapper-2.1.4/
   /db1/extra-data-sets/eggnog_5.0/                  (updated Dec 2024)

**PRESSED databases  **
   Full archaea hmm profiles : archaea_DB.hmmer
   Full bacteria hmm profiles : BACT_DB.hmmer
   Full eukaryotes hmm profiles : EUK_DB.hmmer    
Virus and virus-like: 
         Picornavirales.hmmer, Retrotranscribing.hmmer, Retroviridae.hmmer, ssDNA.hmmer, ssRNA.hmmer, 
         ssRNA_negative.hmmer, ssRNA_positive.hmmer, Tymovirales.hmmer, Viruses.hmmer, Nidovirales.hmmer
if you need all domains together (bacteria, archaea and eukarya): 
      /opt/perun/share/extra-data-sets/eggnog/fulleggnogdb/fullEggNOGDB.hmmer
**NOT PRESSED (individual profiles):**\\
   hmm for bacteria at /opt/perun/share/extra-data-sets/eggnog/bactNOG_hmm
   hmm for archaea at /opt/perun/share/extra-data-sets/eggnog/arNOG_hmm
   hmm for eukaryotes at /opt/perun/share/extra-data-sets/eggnog/euNOG_hmm
   hmm for bacteria-archaea-eukaryotes at /opt/perun/share/extra-data-sets/eggnog/NOG_hmm   
**EggNOG ANNOTATIONS** are within each of the directories for individual profiles (Not pressed), except for NOG (NOG.annotations.tsv) which is in the 
   /opt/perun/share/extra-data-sets/eggnog

**PANTHER hmm database:**\\
PANTHER 17 Classification:
    /scratch3/rogerlab_databases/other_dbs/PANTHER17.0/
PANTHER fasta files by family:
   /scratch3/rogerlab_databases/other_dbs/PANTHER17.0/books (updated Jan 2022)

**EukProt:**

/scratch3/rogerlab_databases/other_dbs/EukProt_V3/proteins/  (updated Mar 2022)   
   /scratch4/db/EukProtv3/                                      (updated Aug 2022)

**foldseek:**
   /scratch5/db/foldseek  
   /scratch5/db/foldseek-gpu/

**Kraken2:**

/scratch3/rogerlab_databases/other_dbs/kraken2/hash.k2d   (updated Nov 2023) 
    /scratch4/db/kraken2/                                     (16S, EUK_SSU)
    /scratch4/db/Kraken2PlusPFP/Kraken2_Standard_Jun2024/hash.k2d   (Standard, updated Jun 2024)
    /scratch4/db/Kraken2PlusPFP/Kraken2PlusPFP_Jun2024/hash.k2d     (PlusPFP, updated Jun 2024) 
    /scratch4/db/Kraken2PlusPFP/hash.k2d                            (PlusPFP, updated July 2025) 
      
The Most updated Kraken2 databases can be downloaded from here:
   https://benlangmead.github.io/aws-indexes/k2

**Acc2tax:**
   /db1/extra-data-sets/Acc2tax/
   /db1/extra-data-sets/Acc2tax/Acc2Tax_04_01_2024
   /scratch3/rogerlab_databases/other_dbs/Acc2Tax_March252023   
   /scratch5/db/Eukfinder/Acc2tax                    (Nov 2025)

**gtdbtk**
    gtdbtk-2.0.0: /scratch4/db/gtdbtk-2.0.0/ (Mar 2022)
    gtdbtk-2.0.0: /scratch4/db/gtdbtk-1.5.0/   
    /scratch5/db/gtdbtk/                      (Apr 2025)

**Pfam** 
    /scratch3/rogerlab_databases/other_dbs/Pfam_Feb2025

**Eukfinder**
Updated Database Locations for Eukfinder (v1.2.4)

Centrifuge: /scratch3/Eukfinder/DB/Centrifuge_DB/  (Sept 2020, gut environment focused)
               /scratch3/Eukfinder/DB/Centrifuge_DB_2024/    (Nov 2024, marine environment focused)
               /scratch5/db/Eukfinder/Centrifuge/ABV/        (Apr 2025, Bacteria/Archaea/Virus refseq)
   PLAST:      /scratch3/Eukfinder/DB/PLAST_DB/  (Sept 2020, gut environment focused)
               /misc/scratch3/Eukfinder/DB/PLAST_DB_2024/    (Nov 2024, marine environment focused)

//Important Notes for v1.2.4//

1. The newest version removes the need for acc2tax.

2. Only Centrifuge_DB and PLAST_DB are required.

<del>3. Eukfinder v1.2.4 is not yet installed globally on Perun.</del>

//How to Run Eukfinder v1.2.4 on Perun//

source /scratch5/software/miniconda3/etc/profile.d/conda.sh
   conda activate eukfinder
   Eukfinder=/misc/scratch3/Eukfinder/eukfinder.py
   python $Eukfinder [arguments]

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