alisDRI
alisDRI
Hi, I am having the same problem. Here is the output of the DRAM-setup.py print_config DRAM-setup.py print_config /home/alis/anaconda3/envs/DRAM/lib/python3.9/site-packages/mag_annotator/database_handler.py:51: UserWarning: Database does not exist at path None warnings.warn('Database does not exist...
Hi @pulidofabs and @rmFlynn Unfortunately, The solution mentioned by @pulidofabs did not help. I am still getting this error: DRAM-setup.py set_database_locations --kofam_hmm_loc /home/alis/DRAM_database_files/profiles.tar.gz --update_description_db /home/alis/anaconda3/envs/DRAM/lib/python3.9/site-packages/mag_annotator/database_handler.py:51: UserWarning: Database does not exist...
Hi @rmFlynn Thank you for your prompt reply. **Here is the error:** 2022-03-23 11:45:32.239066: Database preparation started 0:00:02.435158: dbCAN database processed 1:40:27.374766: UniRef database processed 2:25:16.347554: PFAM database processed 2:25:28.864731:...
@rmFlynn I tried the gunzip /home/alis/DRAM_database_files/kofam_ko_list.tsv.gz and I am getting this error gunzip /home/alis/DRAM_database_files/kofam_ko_list.tsv gzip: /home/alis/DRAM_database_files/kofam_ko_list.tsv: unknown suffix -- ignored Something is wrong with the gunzip tool?!
@rmFlynn I tried to run the DRAM setup.py after moving the kofam_ko_list.tsv.gz to /data/alis/DRAM_database It got mad at me. It's telling me that the file exists. Do you think changing...
OK, I'll try it.
@rmFlynn Hi, Thank you for your help. I was able to fix the problem. I simply transferred the kofam_ko_list.tsv.gz and Vog.annotation.tsv.gz file to the folder that asked DRAM to build...
One question: Where can I get this kofam_ko_list.tsv.gz file? I downloaded a text file from the Kofam database called ko_list then I converted that file to a tsv file. Alireza...
@rmFlynn Hi, unfortunately, I am having the same problem as everyone else. Any suggestions? DRAM-v.py annotate -i /home/alis/NASA_DRAMV_Files/VAL_A09_dramv.fa -v /home/alis/NASA_DRAMV_Files/VAL_A09_viral-affi_dramv.tab -o VAL_A09_dramv-annotation-result --skip_trnascan --threads 28 --min_contig_size 1000 2022-03-29 16:17:08.610389: Viral...
Hi @rmFlynn, Thank you for fixing the problem with the DRAM annotation step. Should I update my database again? or should I update the DRAM version to fix the annotation...