Long processing time during DRAM annotate, step "Getting forward best hits from kegg"

[ganiatgithub]

Hi developers,

I was wondering whether you can share some insights on what I've noticed in running DRAM annotate. Occasionally, the "Getting forward best hits from kegg" takes days to finish. Here I attach a log file showing it has taken 5 days.

2024-11-12 09:41:11,811 - 10 FASTAs found
2024-11-12 09:41:11,945 - Starting the Annotation of Bins with database configuration: 
 

KEGG db:
    Description_Db_Updated: 05/13/2023, 12:52:43
    Citation:  M. Kanehisa, M. Furumichi, Y. Sato, M. Ishiguro-Watanabe, and M. Tanabe, "Kegg: integrating viruses and cellular organisms," Nucleic acids research, vol. 49, no. D1, pp. D545–D551, 2021.
KOfam db:
...
...
... # removed text for simplicity
Genome summary form:
    Branch: master
    Download Time: 05/13/2023, 11:40:10
    Origin: Downloaded by DRAM
Module step form:
    Branch: master
    Download Time: 05/13/2023, 11:40:11
    Origin: Downloaded by DRAM
ETC module database:
    Branch: master
    Download Time: 05/13/2023, 11:40:12
    Origin: Downloaded by DRAM
Function heatmap form:
    Branch: master
    Download Time: 05/13/2023, 11:40:11
    Origin: Downloaded by DRAM
AMG database:
    Branch: master
    Download Time: 05/13/2023, 11:40:11
    Origin: Downloaded by DRAM
2024-11-12 09:41:11,946 - Retrieved database locations and descriptions
2024-11-12 09:41:11,947 - Annotating 11_GN_calf_175_refined_bin.225
2024-11-12 09:41:19,741 - Turning genes from prodigal to mmseqs2 db
2024-11-12 09:41:21,690 - Getting forward best hits from kegg
2024-11-17 12:45:10,947 - Getting reverse best hits from kegg
2024-11-17 12:45:44,746 - Getting descriptions of hits from kegg
2024-11-17 12:47:14,421 - Getting forward best hits from peptidase
2024-11-17 12:47:23,164 - Getting reverse best hits from peptidase
2024-11-17 12:47:25,652 - Getting descriptions of hits from peptidase
2024-11-17 12:47:30,950 - Getting hits from pfam
2024-11-17 12:47:42,104 - Getting hits from dbCAN
2024-11-17 12:47:49,922 - Merging ORF annotations
2024-11-17 12:48:10,139 - Annotating 11_GN_calf_148_refined_bin.201
2024-11-17 12:48:12,825 - Turning genes from prodigal to mmseqs2 db
2024-11-17 12:48:14,402 - Getting forward best hits from kegg
2024-11-17 13:25:12,910 - Getting reverse best hits from kegg
2024-11-17 13:25:52,678 - Getting descriptions of hits from kegg
2024-11-17 13:27:08,258 - Getting forward best hits from peptidase
2024-11-17 13:27:13,865 - Getting reverse best hits from peptidase
2024-11-17 13:27:15,080 - Getting descriptions of hits from peptidase
2024-11-17 13:27:15,568 - Getting hits from pfam
2024-11-17 13:27:24,055 - Getting hits from dbCAN
2024-11-17 13:27:27,325 - Merging ORF annotations
2024-11-17 13:27:32,511 - No tRNAs were detected, no trnas.tsv file will be created.
2024-11-17 13:27:33,868 - Annotating 00_GN_BF177_ref_50_10_bin.54
 ...# removed other genome annotation log

For the other jobs I ran for the another subset of the genomes, the analysis was fine:

2024-11-12 09:41:11,811 - The log file is created at /home/gnii0001/075_succession/result/DRAM/normal_queue_additional1/chunk_124/annotation/annotate.log.
2024-11-12 09:41:11,812 - 10 FASTAs found
2024-11-12 09:41:11,945 - Starting the Annotation of Bins with database configuration: 
 
...
...
... # removed text for simplicity
2024-11-12 09:41:11,947 - Retrieved database locations and descriptions
2024-11-12 09:41:11,947 - Annotating 11_GN_calf_155_refined_bin.146
2024-11-12 09:41:17,007 - Turning genes from prodigal to mmseqs2 db
2024-11-12 09:41:18,697 - Getting forward best hits from kegg
2024-11-12 11:20:04,036 - Getting reverse best hits from kegg
2024-11-12 11:20:25,303 - Getting descriptions of hits from kegg
2024-11-12 11:21:09,581 - Getting forward best hits from peptidase
2024-11-12 11:21:18,976 - Getting reverse best hits from peptidase
2024-11-12 11:21:21,365 - Getting descriptions of hits from peptidase
2024-11-12 11:21:25,825 - Getting hits from pfam
2024-11-12 11:24:27,187 - Getting hits from dbCAN
2024-11-12 11:24:34,783 - Merging ORF annotations
2024-11-12 11:24:44,422 - Annotating 11_GN_calf_171_refined_bin.81
...
...
... # removed text for simplicity
2024-11-12 15:20:04,400 - Completed annotations

I'm using DRAM version 1.4.6, mamba installation, and here is my code:

DRAM.py annotate -i "$MAG_DIR/*" -o "$DRAM_OUT_DIR"/annotation --threads "$thread"
DRAM.py distill -i "$DRAM_OUT_DIR"/annotation/annotations.tsv -o "$DRAM_OUT_DIR"/genome_summaries --trna_path "$DRAM_OUT_DIR"/annotation/trnas.tsv --rrna_path "$DRAM_OUT_DIR"/annotation/rrnas.tsv

Any suggestions to look further is much appreciated.

Best regards,
Gaofeng