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WrightonLabCSU / DRAM

Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes
GNU General Public License v3.0
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Downloading CAMPER db #313

Closed ZarulHanifah closed 7 months ago

ZarulHanifah commented 7 months ago

Hello DRAM developers,

Thank you for the wonderful software.

I am using DRAM v1.4.6, downloaded via conda. I have been using DRAM just fine all this while; here is the dbs that I have been using:

2023-11-11 16:03:27,287 - Logging to console
Processed search databases
KEGG db: None
KOfam db: /fs03/ie79/db/DRAM_data/kofam_profiles.hmm
KOfam KO list: /fs03/ie79/db/DRAM_data/kofam_ko_list.tsv
UniRef db: None
Pfam db: /fs03/ie79/db/DRAM_data/pfam.mmspro
dbCAN db: /fs03/ie79/db/DRAM_data/dbCAN-HMMdb-V11.txt
RefSeq Viral db: /fs03/ie79/db/DRAM_data/refseq_viral.20230117.mmsdb
MEROPS peptidase db: /fs03/ie79/db/DRAM_data/peptidases.20230117.mmsdb
VOGDB db: /fs03/ie79/db/DRAM_data/vog_latest_hmms.txt

Descriptions of search database entries
Pfam hmm dat: /fs03/ie79/db/DRAM_data/Pfam-A.hmm.dat.gz
dbCAN family activities: /fs03/ie79/db/DRAM_data/CAZyDB.08062022.fam-activities.txt
VOG annotations: /fs03/ie79/db/DRAM_data/vog_annotations_latest.tsv.gz

Description db: /fs03/ie79/db/DRAM_data/description_db.sqlite

DRAM distillation sheets
Genome summary form: /fs03/ps45/Zarul/workflow_dram/upd/genome_summary_form.20231111.tsv
Module step form: /fs03/ps45/Zarul/workflow_dram/upd/module_step_form.20231111.tsv
ETC module database: /fs03/ps45/Zarul/workflow_dram/upd/etc_mdoule_database.20231111.tsv
Function heatmap form: /fs03/ps45/Zarul/workflow_dram/upd/function_heatmap_form.20231111.tsv
AMG database: /fs03/ps45/Zarul/workflow_dram/upd/amg_database.20231111.tsv+

When I look at the Github page, I noticed that there are other dbs like camper and fegenie. Where do I get that? I went through the Github issues and found #212 , so I tried:

DRAM-setup.py prepare_databases --output_dir test \
    --skip_uniref \
    --threads 10 \
    --camper_tar_gz_loc CAMPER_v1.0.0-beta.1.tar.gz

But I got this:

usage: DRAM-setup.py [-h]
                     {version,prepare_databases,set_database_locations,mv_db_folder,update_description_db,update_dram_forms,print_config,print_settings,import_config,export_config}
                     ...
DRAM-setup.py: error: unrecognized arguments: --camper_tar_gz_loc CAMPER_v1.0.0-beta.1.tar.gz

Why? Need help please :pray:

jrr-microbio commented 7 months ago

camper is a new database that the lab just released - it hasn't been updated here yet. However, you can manually download and activate CAMPER by following the github here: https://github.com/WrightonLabCSU/CAMPER . The biorxiv for this paper can be found here: https://www.biorxiv.org/content/10.1101/2023.09.24.559193v1

Fegenie as well as some of the other databases were moreso just experimental for this current version of DRAM. An improved version of DRAM using those dbs will be available once DRAM2 is released!