DRAM
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WrightonLabCSU
AttributeError: 'NoneType' object has no attribute 'split'
Hi,
I used the DRAM in conda environment with some errors. Can you tell me how to fix it, Thanks.
$DRAM-v.py annotate -i /data/liaohp/project1/virus/Virsorter-SOP/all-final--viral-combined-derep.fa -o annotation
2021-08-05 11:15:49.638597: Viral annotation started
0:00:00.944904: Retrieved database locations and descriptions
0:00:00.944963: Annotating NODE_27_length_79927_cov_6.839818||full
0:00:02.643946: Turning genes from prodigal to mmseqs2 db
/data/software/conda2/envs/DRAM/lib/python3.9/site-packages/mag_annotator/annotate_bins.py:739: UserWarning: No KEGG source provided so distillation will be of limited use.
warnings.warn('No KEGG source provided so distillation will be of limited use.')
0:00:04.774285: Getting forward best hits from viral
0:00:05.556976: Getting reverse best hits from viral
0:00:06.177756: Getting descriptions of hits from viral
0:00:06.194178: Getting forward best hits from peptidase
0:00:07.080629: Getting reverse best hits from peptidase
0:00:07.776862: Getting descriptions of hits from peptidase
0:00:07.781495: Getting hits from pfam
0:00:16.991231: Getting hits from dbCAN
0:00:18.395969: Getting hits from VOGDB
/data/software/conda2/envs/DRAM/lib/python3.9/site-packages/mag_annotator/database_handler.py:42: UserWarning: No descriptions were found for your id's. Does this VOG02708 look like an id from vogdb_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 "/data/software/conda2/envs/DRAM/bin/DRAM-v.py", line 140, in
Here are the database in config.
(DRAM) [liaohp@ubuntu DRAM-master] /data/software/DRAM-master $DRAM-setup.py print_config KEGG db: None KOfam db: /data/software/DRAM-master/db-dramv/database_files/kofam_profiles.hmm KOfam KO list: None UniRef db: None Pfam db: /data/software/DRAM-master/db-dramv/database_files/pfam.mmspro Pfam hmm dat: /data/software/DRAM-master/db-dramv/Pfam-A.hmm.dat.gz dbCAN db: /data/software/DRAM-master/db-dramv/database_files/dbCAN-HMMdb-V9.txt dbCAN family activities: /data/software/DRAM-master/db-dramv/CAZyDB.07302020.fam-activities.txt RefSeq Viral db: /data/software/DRAM-master/db-dramv/database_files/refseq_viral.20210804.mmsdb MEROPS peptidase db: /data/software/DRAM-master/db-dramv/database_files/peptidases.20210804.mmsdb VOGDB db: /data/software/DRAM-master/db-dramv/database_files/vog_latest_hmms.txt VOG annotations: None Description db: None Genome summary form: /data/software/DRAM-master/db-dramv/database_files/genome_summary_form.20210804.tsv Module step form: /data/software/DRAM-master/db-dramv/database_files/module_step_form.20210804.tsv ETC module database: /data/software/DRAM-master/db-dramv/database_files/etc_mdoule_database.20210804.tsv Function heatmap form: /data/software/DRAM-master/db-dramv/database_files/function_heatmap_form.20210804.tsv AMG database: /data/software/DRAM-master/db-dramv/database_files/amg_database.20210804.tsv
Hi @hannet91,
Sorry for the slow response. I have been off for a chunk of August and it has taken me a bit to catch up.
It looks like something failed during the set up of DRAM since you do not have the VOG annotations or description DB present in your config. Were any errors present when you set up DRAM?
Mike
