DRAM
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WrightonLabCSU
Peptidase database
Hello, I install DRAM using conda recently. When I run the annotate command, it shows the error:
DRAM.py annotate -i 'test/*.fna' -o annotation --threads 10
2 fastas found
2021-02-16 11:54:54.257147: Annotation started
0:00:00.040343: Retrieved database locations and descriptions
0:00:00.040376: Annotating METABAT_84
0:01:48.909865: Turning genes from prodigal to mmseqs2 db
0:01:51.289461: Getting hits from kofam
0:21:55.120991: Getting forward best hits from peptidase
0:22:19.253644: Getting reverse best hits from peptidase
0:22:21.115586: Getting descriptions of hits from peptidase
/opt/Miniconda3/envs/DRAM/lib/python3.9/site-packages/mag_annotator/database_handler.py:42: UserWarning: No descriptions were found for your id's. Does this MER0378710 look like an id from peptidase_description
warn("No descriptions were found for your id's. Does this %s look like an id from %s" % (list(ids)[0],
Traceback (most recent call last):
File "/opt/Miniconda3/envs/DRAM/bin/DRAM.py", line 145, in
I had to manually put the database's path because the prepare_database command did not do this for me. Here are the settings: KEGG db: None KOfam db: /data/DRAM_data/kofam_profiles.hmm KOfam KO list: /data/DRAM_data/kofam_ko_list.tsv UniRef db: /data/DRAM_data/uniref90.20210216.mmsdb Pfam db: /data/DRAM_data/pfam.mmspro Pfam hmm dat: /data/DRAM_data/Pfam-A.hmm.dat.gz dbCAN db: /data/DRAM_data/dbCAN-HMMdb-V8.txt dbCAN family activities: /data/DRAM_data/CAZyDB.07312019.fam-activities.txt RefSeq Viral db: /data/DRAM_data/refseq_viral.20210216.mmsdb MEROPS peptidase db: /data/DRAM_data/peptidases.20210216.mmsdb VOGDB db: /data/DRAM_data/vog_latest_hmms.txt VOG annotations: /data/DRAM_data/vog_annotations_latest.tsv.gz Description db: /data/DRAM_data/description_db.sqlite Genome summary form: /data/DRAM_data/genome_summary_form.20210216.tsv Module step form: /data/DRAM_data/module_step_form.20210216.tsv ETC module database: /data/DRAM_data/etc_mdoule_database.20210216.tsv Function heatmap form: /data/DRAM_data/function_heatmap_form.20210216.tsv AMG database: /data/DRAM_data/amg_database.20210216.tsv
Thank you
Hello,
When you ran DRAM-setup.py prepare_databases did it finish with an error or did it not have the MEROPs database in place even after finishing successfully?
My hunch is that for some reason the MEROPs identifiers didn't get added to the database. As a result you will need to rebuild the description database. You can do this by running DRAM-setup.py update_description_db.
Hello,
When you ran
DRAM-setup.py prepare_databasesdid it finish with an error or did it not have the MEROPs database in place even after finishing successfully?My hunch is that for some reason the MEROPs identifiers didn't get added to the database. As a result you will need to rebuild the description database. You can do this by running
DRAM-setup.py update_description_db.
Hi, thank you for the quick reply.
I not exactly sure because I run the DRAM-setup.py prepare_databases with "nohup and &". My nohup file was empty, so no error.
I tried to do the DRAM-setup.py update_description_db: 0:00:00.000004: Populating description database 0:00:01.476084: Database connection established 0:00:01.476123: KEGG descriptions added to description database Dead
It seems a problem with Memory.
Hmm. Can you try running with more memory available if you have some. @mw55309 also created some scripts to deal with this issue that you could try out https://github.com/mw55309/DRAM_hacks.
We need to re-profile DRAM build With the modifications to the 1.4 release cycle, but for now I am closing this issue.
