Differences

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--- databases_locations [2025/10/30 12:39] – 64.66.218.10
+++ databases_locations [2026/01/20 09:58] (current) – 172.20.19.4
@@ Line 1: / Line 1: @@
 ====== Main locations for most Databases on PERUN ======
-    /misc/db1/
+    /db1/
     /scratch3/rogerlab_databases/other_dbs/
     /scratch4/db/
-**BLAST databases**
+    /scratch5/db/
-    /db1/blast-may-2024/nr.pal (updated May 2024)
-    /db1/blast-may-2024/refseq_protein.pal (updated May 2024)
+===== Databases in /db1 =====
-    /db1/blast-may-2024/nt.nal  (updated May 2024)
-    /scratch3/rogerlab_databases/other_dbs/nr_010621
-    /opt/perun/share/extra-data-sets/uniprot/ (updated Jul 25, 2017)
+    /db1/blast-may-2024: nt, nr                   (updated May 2024)
+    /db1/alphafold3                               (updated Mar 2025)
+    /db1/funannotate                              (updated Jan 2026)
+    /db1extra-data-sets/eggnog_5.0                (updated Sep 2016)
+===== 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**
+===== 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)
@@ Line 19: / Line 34: @@
-** DIAMOND:**
+===== DIAMOND =====
+   /scratch5/db/Eukfinder/Diamond/nr.dmnd                                 (updated Nov 2025)
+   /scratch5/db/Eukfinder/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_032121/nr.dmnd               (updated Mar 2021)
-   /scratch3/rogerlab_databases/other_dbs/nr_06162020/nr.dmnd  (updated Jun 2020)
+   /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.
+===== OTHER Tools =====
+==== 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
+   The base index is Centrifuge_NewDB_Sept2020
+==== CheckM2 ====
+   /scratch5/db/checkm2/CheckM2_database/         (updated Mar 2021)
+==== EGGNOG ====
-** 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  **
@@ Line 53: / Line 83: @@
    /opt/perun/share/extra-data-sets/eggnog
-**PANTHER hmm database:**\\
+==== PANTHER hmm database ====
 PANTHER 17 Classification:
     /scratch3/rogerlab_databases/other_dbs/PANTHER17.0/
@@ Line 60: / Line 92: @@
-**EukProt:**
+==== 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/EukProt_V3/proteins/  (updated Dec 2023)
-   /scratch4/db/EukProtv3/
-**Kraken2:**
     /scratch3/rogerlab_databases/other_dbs/kraken2/hash.k2d   (updated Nov 2023)
     /scratch4/db/kraken2/                                     (16S, EUK_SSU)
-    /scratch4/db/Kraken2PlusPFP/                              (updated Jun 2024)
+    /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:
+The Most updated Kraken2 databases can be downloaded from here:
    https://benlangmead.github.io/aws-indexes/k2
+==== Acc2tax ====
-**Acc2tax:**
    /db1/extra-data-sets/Acc2tax/
    /db1/extra-data-sets/Acc2tax/Acc2Tax_04_01_2024
+   /scratch3/rogerlab_databases/other_dbs/Acc2Tax_March252023
-**gtdbtk**
+   /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 ====
-**Eukfinder**
 Updated Database Locations for Eukfinder (v1.2.4)
@@ Line 91: / Line 141: @@
    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//
-. The newest version removes the need for acc2tax.
-. Only Centrifuge_DB and PLAST_DB are required.
-. Eukfinder v1.2.4 is not yet installed globally on Perun.
-//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]
-<Last updated by Dandan Zhao on Oct 30, 2025>
+<Last updated by Dandan Zhao on Jan 20, 2026>