Hello!
I have been trying to set up the DRAM databases and I keep getting this issue:
2023-03-01 12:31:00,046 - Database preparation started
2023-03-01 12:31:00,046 - Downloading kofam_hmm
2023-03-01 12:31:15,070 - Something went wrong with the download of the url: ftp://ftp.genome.jp/pub/db/kofam/profiles.tar.gz
2023-03-01 12:31:15,070 -
2023-03-01 12:31:15,517 - Something went wrong with the download of the url: https://www.genome.jp/ftp/db/kofam/profiles.tar.gz
2023-03-01 12:31:15,517 -
Here is the command I was using:
/home/nolin/miniconda3/envs/DRAM/bin/DRAM-setup.py prepare_databases --output_dir DRAM_data
Any help would be greatly appreciated!
I will also include the full log here:
2023-02-21 17:51:22,014 - Starting the process of downloading data
2023-02-21 17:51:22,014 - The kegg_loc argument was not used to specify a downloaded kegg file, and dram can not download it its self. So it is assumed that the user wants to
set up DRAM without it
2023-02-21 17:51:22,014 - The gene_ko_link_loc argument was not used to specify a downloaded gene_ko_link file, and dram can not download it its self. So it is assumed that t
he user wants to set up DRAM without it
2023-02-21 17:51:22,014 - Database preparation started
2023-02-21 17:51:22,014 - Downloading kofam_hmm
2023-02-21 17:55:50,166 - Downloading kofam_ko_list
2023-02-21 17:55:52,392 - Downloading uniref
2023-02-22 09:36:45,175 - Downloading pfam
2023-02-22 09:50:11,428 - Downloading pfam_hmm
2023-02-22 09:50:13,442 - Downloading dbcan
2023-02-22 09:50:15,585 - Downloading dbcan_fam_activities
2023-02-22 09:50:15,585 - Downloading dbCAN family activities from : https://bcb.unl.edu/dbCAN2/download/Databases/V11/CAZyDB.08062022.fam-activities.txt
2023-02-22 09:50:15,849 - Downloading dbcan_subfam_ec
2023-02-22 09:50:15,849 - Downloading dbCAN sub-family encumber from : https://bcb.unl.edu/dbCAN2/download/Databases/V11/CAZyDB.08062022.fam.subfam.ec.txt
2023-02-22 09:50:16,288 - Downloading vogdb
2023-02-22 09:54:02,461 - Downloading vog_annotations
2023-02-22 09:54:03,900 - Downloading viral
2023-02-22 09:54:08,078 - Downloading peptidase
2023-02-22 09:54:32,539 - Downloading genome_summary_form
2023-02-22 09:54:32,933 - Downloading module_step_form
2023-02-22 09:54:33,303 - Downloading function_heatmap_form
2023-02-22 09:54:33,533 - Downloading amg_database
2023-02-22 09:54:33,794 - Downloading etc_module_database
2023-02-22 09:54:33,996 - All raw data files were downloaded successfully
2023-02-22 09:54:33,996 - Processing kofam_hmm
2023-02-22 09:58:55,795 - KOfam database processed
2023-02-22 09:58:55,862 - Moved kofam_hmm to final destination, configuration updated
2023-02-22 09:58:55,863 - Processing kofam_ko_list
2023-02-22 09:58:55,920 - KOfam ko list processed
2023-02-22 09:58:55,922 - Moved kofam_ko_list to final destination, configuration updated
2023-02-22 09:58:55,922 - Processing uniref
2023-02-22 11:47:02,995 - UniRef database processed
2023-02-22 11:47:03,032 - Moved uniref to final destination, configuration updated
2023-02-22 11:47:03,032 - Processing pfam
2023-02-22 12:43:14,525 - PFAM database processed
2023-02-22 12:43:14,529 - Moved pfam to final destination, configuration updated
2023-02-22 12:43:14,533 - Moved pfam_hmm to final destination, configuration updated
2023-02-22 12:43:14,533 - Processing dbcan
2023-02-22 12:43:17,371 - dbCAN database processed
2023-02-22 12:43:17,374 - Moved dbcan to final destination, configuration updated
2023-02-22 12:43:17,376 - Moved dbcan_fam_activities to final destination, configuration updated
2023-02-22 12:43:17,377 - Moved dbcan_subfam_ec to final destination, configuration updated
2023-02-22 12:43:17,377 - Processing vogdb
2023-02-22 12:44:56,230 - VOGdb database processed
2023-02-22 12:44:56,258 - Moved vogdb to final destination, configuration updated
2023-02-22 12:44:56,259 - Moved vog_annotations to final destination, configuration updated
2023-02-22 12:44:56,259 - Processing viral
2023-02-22 12:45:13,109 - RefSeq viral database processed
2023-02-22 12:45:13,111 - Moved viral to final destination, configuration updated
2023-02-22 12:45:13,111 - Processing peptidase
2023-02-22 12:45:41,796 - MEROPS database processed
2023-02-22 12:45:41,799 - Moved peptidase to final destination, configuration updated
2023-02-22 12:45:41,800 - Moved genome_summary_form to final destination, configuration updated
2023-02-22 12:45:41,802 - Moved module_step_form to final destination, configuration updated
2023-02-22 12:45:41,803 - Moved function_heatmap_form to final destination, configuration updated
2023-02-22 12:45:41,805 - Moved amg_database to final destination, configuration updated
2023-02-22 12:45:41,806 - Moved etc_module_database to final destination, configuration updated
2023-02-22 12:45:41,806 - Populating the description db, this may take some time
2023-02-22 16:03:11,006 - Description updated for the uniref database
2023-02-22 16:03:37,082 - Description updated for the viral database
2023-02-22 16:04:25,617 - Description updated for the peptidase database
2023-02-22 16:04:26,791 - Description updated for the pfam database
2023-02-22 16:04:27,949 - Description updated for the dbcan database
2023-02-22 16:04:33,099 - Description updated for the vogdb database
2023-02-22 16:04:33,108 - DRAM description database populated
2023-02-22 16:04:33,217 - Database preparation completed
2023-03-01 12:31:00,034 - Starting the process of downloading data
2023-03-01 12:31:00,046 - The kegg_loc argument was not used to specify a downloaded kegg file, and dram can not download it its self. So it is assumed that the user wants to
set up DRAM without it
2023-03-01 12:31:00,046 - The gene_ko_link_loc argument was not used to specify a downloaded gene_ko_link file, and dram can not download it its self. So it is assumed that t
he user wants to set up DRAM without it
2023-03-01 12:31:00,046 - Database preparation started
2023-03-01 12:31:00,046 - Downloading kofam_hmm
2023-03-01 12:31:15,070 - Something went wrong with the download of the url: ftp://ftp.genome.jp/pub/db/kofam/profiles.tar.gz
2023-03-01 12:31:15,070 -
2023-03-01 12:31:15,517 - Something went wrong with the download of the url: https://www.genome.jp/ftp/db/kofam/profiles.tar.gz
2023-03-01 12:31:15,517 -
Hello! I have been trying to set up the DRAM databases and I keep getting this issue: 2023-03-01 12:31:00,046 - Database preparation started 2023-03-01 12:31:00,046 - Downloading kofam_hmm 2023-03-01 12:31:15,070 - Something went wrong with the download of the url: ftp://ftp.genome.jp/pub/db/kofam/profiles.tar.gz 2023-03-01 12:31:15,070 - 2023-03-01 12:31:15,517 - Something went wrong with the download of the url: https://www.genome.jp/ftp/db/kofam/profiles.tar.gz 2023-03-01 12:31:15,517 -
Here is the command I was using: /home/nolin/miniconda3/envs/DRAM/bin/DRAM-setup.py prepare_databases --output_dir DRAM_data
Any help would be greatly appreciated! I will also include the full log here:
2023-02-21 17:51:22,014 - Starting the process of downloading data 2023-02-21 17:51:22,014 - The kegg_loc argument was not used to specify a downloaded kegg file, and dram can not download it its self. So it is assumed that the user wants to set up DRAM without it 2023-02-21 17:51:22,014 - The gene_ko_link_loc argument was not used to specify a downloaded gene_ko_link file, and dram can not download it its self. So it is assumed that t he user wants to set up DRAM without it 2023-02-21 17:51:22,014 - Database preparation started 2023-02-21 17:51:22,014 - Downloading kofam_hmm 2023-02-21 17:55:50,166 - Downloading kofam_ko_list 2023-02-21 17:55:52,392 - Downloading uniref 2023-02-22 09:36:45,175 - Downloading pfam 2023-02-22 09:50:11,428 - Downloading pfam_hmm 2023-02-22 09:50:13,442 - Downloading dbcan 2023-02-22 09:50:15,585 - Downloading dbcan_fam_activities 2023-02-22 09:50:15,585 - Downloading dbCAN family activities from : https://bcb.unl.edu/dbCAN2/download/Databases/V11/CAZyDB.08062022.fam-activities.txt 2023-02-22 09:50:15,849 - Downloading dbcan_subfam_ec 2023-02-22 09:50:15,849 - Downloading dbCAN sub-family encumber from : https://bcb.unl.edu/dbCAN2/download/Databases/V11/CAZyDB.08062022.fam.subfam.ec.txt 2023-02-22 09:50:16,288 - Downloading vogdb 2023-02-22 09:54:02,461 - Downloading vog_annotations 2023-02-22 09:54:03,900 - Downloading viral 2023-02-22 09:54:08,078 - Downloading peptidase 2023-02-22 09:54:32,539 - Downloading genome_summary_form 2023-02-22 09:54:32,933 - Downloading module_step_form 2023-02-22 09:54:33,303 - Downloading function_heatmap_form 2023-02-22 09:54:33,533 - Downloading amg_database 2023-02-22 09:54:33,794 - Downloading etc_module_database 2023-02-22 09:54:33,996 - All raw data files were downloaded successfully 2023-02-22 09:54:33,996 - Processing kofam_hmm 2023-02-22 09:58:55,795 - KOfam database processed 2023-02-22 09:58:55,862 - Moved kofam_hmm to final destination, configuration updated 2023-02-22 09:58:55,863 - Processing kofam_ko_list 2023-02-22 09:58:55,920 - KOfam ko list processed 2023-02-22 09:58:55,922 - Moved kofam_ko_list to final destination, configuration updated 2023-02-22 09:58:55,922 - Processing uniref 2023-02-22 11:47:02,995 - UniRef database processed 2023-02-22 11:47:03,032 - Moved uniref to final destination, configuration updated 2023-02-22 11:47:03,032 - Processing pfam 2023-02-22 12:43:14,525 - PFAM database processed 2023-02-22 12:43:14,529 - Moved pfam to final destination, configuration updated 2023-02-22 12:43:14,533 - Moved pfam_hmm to final destination, configuration updated 2023-02-22 12:43:14,533 - Processing dbcan 2023-02-22 12:43:17,371 - dbCAN database processed 2023-02-22 12:43:17,374 - Moved dbcan to final destination, configuration updated 2023-02-22 12:43:17,376 - Moved dbcan_fam_activities to final destination, configuration updated 2023-02-22 12:43:17,377 - Moved dbcan_subfam_ec to final destination, configuration updated 2023-02-22 12:43:17,377 - Processing vogdb 2023-02-22 12:44:56,230 - VOGdb database processed 2023-02-22 12:44:56,258 - Moved vogdb to final destination, configuration updated 2023-02-22 12:44:56,259 - Moved vog_annotations to final destination, configuration updated 2023-02-22 12:44:56,259 - Processing viral 2023-02-22 12:45:13,109 - RefSeq viral database processed 2023-02-22 12:45:13,111 - Moved viral to final destination, configuration updated 2023-02-22 12:45:13,111 - Processing peptidase 2023-02-22 12:45:41,796 - MEROPS database processed 2023-02-22 12:45:41,799 - Moved peptidase to final destination, configuration updated 2023-02-22 12:45:41,800 - Moved genome_summary_form to final destination, configuration updated 2023-02-22 12:45:41,802 - Moved module_step_form to final destination, configuration updated 2023-02-22 12:45:41,803 - Moved function_heatmap_form to final destination, configuration updated 2023-02-22 12:45:41,805 - Moved amg_database to final destination, configuration updated 2023-02-22 12:45:41,806 - Moved etc_module_database to final destination, configuration updated 2023-02-22 12:45:41,806 - Populating the description db, this may take some time 2023-02-22 16:03:11,006 - Description updated for the uniref database 2023-02-22 16:03:37,082 - Description updated for the viral database 2023-02-22 16:04:25,617 - Description updated for the peptidase database 2023-02-22 16:04:26,791 - Description updated for the pfam database 2023-02-22 16:04:27,949 - Description updated for the dbcan database 2023-02-22 16:04:33,099 - Description updated for the vogdb database 2023-02-22 16:04:33,108 - DRAM description database populated 2023-02-22 16:04:33,217 - Database preparation completed 2023-03-01 12:31:00,034 - Starting the process of downloading data 2023-03-01 12:31:00,046 - The kegg_loc argument was not used to specify a downloaded kegg file, and dram can not download it its self. So it is assumed that the user wants to set up DRAM without it 2023-03-01 12:31:00,046 - The gene_ko_link_loc argument was not used to specify a downloaded gene_ko_link file, and dram can not download it its self. So it is assumed that t he user wants to set up DRAM without it 2023-03-01 12:31:00,046 - Database preparation started 2023-03-01 12:31:00,046 - Downloading kofam_hmm 2023-03-01 12:31:15,070 - Something went wrong with the download of the url: ftp://ftp.genome.jp/pub/db/kofam/profiles.tar.gz 2023-03-01 12:31:15,070 - 2023-03-01 12:31:15,517 - Something went wrong with the download of the url: https://www.genome.jp/ftp/db/kofam/profiles.tar.gz 2023-03-01 12:31:15,517 -