155796 killed

[TKsh6]

Here is my command, DRAM-setup.py prepare_databases --output_dir DRAM And this is de report error,

/beegfs/home/syl/anaconda3/envs/vs2/lib/python3.10/site-packages/mag_annotator/database_handler.py:166: UserWarning: Database does not exist at path None
  warnings.warn(
/beegfs/home/syl/anaconda3/envs/vs2/lib/python3.10/site-packages/mag_annotator/database_handler.py:123: UserWarning: Database does not exist at path None
  warnings.warn("Database does not exist at path %s" % description_loc)
2023-04-03 16:30:47,437 - Starting the process of downloading data
2023-04-03 16:30:47,437 - 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
2023-04-03 16:30:47,438 - 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 the user wants to set up DRAM without it
2023-04-03 16:30:47,438 - Database preparation started
2023-04-03 16:30:47,439 - Downloading kofam_hmm
2023-04-03 16:54:55,729 - Downloading kofam_ko_list
2023-04-03 16:54:57,800 - Downloading uniref
2023-04-05 16:45:21,789 - Downloading pfam
2023-04-05 17:08:02,945 - Downloading pfam_hmm
2023-04-05 17:08:06,268 - Downloading dbcan
2023-04-05 17:08:32,464 - Downloading dbcan_fam_activities
2023-04-05 17:08:32,465 - Downloading dbCAN family activities from : https://bcb.unl.edu/dbCAN2/download/Databases/V11/CAZyDB.08062022.fam-activities.txt
2023-04-05 17:08:33,628 - Downloading dbcan_subfam_ec
2023-04-05 17:08:33,629 - Downloading dbCAN sub-family encumber from : https://bcb.unl.edu/dbCAN2/download/Databases/V11/CAZyDB.08062022.fam.subfam.ec.txt
2023-04-05 17:08:35,471 - Downloading vogdb
2023-04-05 17:09:28,911 - Downloading vog_annotations
2023-04-05 17:09:31,049 - Downloading viral
2023-04-05 17:09:52,573 - Downloading peptidase
2023-04-05 17:10:49,035 - Downloading genome_summary_form
2023-04-05 17:15:22,073 - Downloading module_step_form
2023-04-05 17:15:23,704 - Downloading function_heatmap_form
2023-04-05 17:19:58,550 - Downloading amg_database
2023-04-05 17:19:59,313 - Downloading etc_module_database
2023-04-05 17:20:00,201 - All raw data files were downloaded successfully
2023-04-05 17:20:00,202 - Processing kofam_hmm
2023-04-05 17:25:18,339 - KOfam database processed
2023-04-05 17:25:18,479 - Moved kofam_hmm to final destination, configuration updated
2023-04-05 17:25:18,480 - Processing kofam_ko_list
2023-04-05 17:25:18,600 - KOfam ko list processed
2023-04-05 17:25:18,604 - Moved kofam_ko_list to final destination, configuration updated
2023-04-05 17:25:18,605 - Processing uniref
2023-04-06 00:54:59,043 - UniRef database processed
2023-04-06 00:54:59,057 - Moved uniref to final destination, configuration updated
2023-04-06 00:54:59,058 - Processing pfam
2023-04-06 04:20:33,296 - PFAM database processed
2023-04-06 04:20:33,397 - Moved pfam to final destination, configuration updated
2023-04-06 04:20:33,400 - Moved pfam_hmm to final destination, configuration updated
2023-04-06 04:20:33,401 - Processing dbcan
2023-04-06 04:20:37,185 - dbCAN database processed
2023-04-06 04:20:37,190 - Moved dbcan to final destination, configuration updated
2023-04-06 04:20:37,193 - Moved dbcan_fam_activities to final destination, configuration updated
2023-04-06 04:20:37,197 - Moved dbcan_subfam_ec to final destination, configuration updated
2023-04-06 04:20:37,197 - Processing vogdb
2023-04-06 04:25:14,642 - VOGdb database processed
2023-04-06 04:25:14,658 - Moved vogdb to final destination, configuration updated
2023-04-06 04:25:14,662 - Moved vog_annotations to final destination, configuration updated
2023-04-06 04:25:14,663 - Processing viral
2023-04-06 04:26:10,787 - RefSeq viral database processed
2023-04-06 04:26:10,792 - Moved viral to final destination, configuration updated
2023-04-06 04:26:10,793 - Processing peptidase
2023-04-06 04:27:50,398 - MEROPS database processed
2023-04-06 04:27:50,403 - Moved peptidase to final destination, configuration updated
2023-04-06 04:27:50,406 - Moved genome_summary_form to final destination, configuration updated
2023-04-06 04:27:50,408 - Moved module_step_form to final destination, configuration updated
2023-04-06 04:27:50,411 - Moved function_heatmap_form to final destination, configuration updated
2023-04-06 04:27:50,414 - Moved amg_database to final destination, configuration updated
2023-04-06 04:27:50,416 - Moved etc_module_database to final destination, configuration updated
2023-04-06 04:27:50,417 - Populating the description db, this may take some time
/bin/bash: line 1: 155796 Killed                  DRAM-setup.py prepare_databases --output_dir DRAM
****

Can you help me to solve this? yours

[saras224]

Hey! @TKsh6 Even I got the same error, were you able to resolve it later? if yes then how?

Thanks

[sahilrishav2]

I am also facing the same issue. Have you resolved it? Please help me also then.

[jianshu93]

Hello all,

How long does it take for the populating step to be killed after the previous step? It has been 5 hours on my machine. It is a pity that such as useful tool updated without help from the original authors. NO idea what happened, I am pretty sure that the memory is not a problem on my machine (I have 1.5T memory).

Thanks.

Jianshu

[TKsh6]

Sorry, I didn't solve this problem, but in the end, I completed the installation by relying on conda. conda install @jianshu93 @saras224 @sahilrishav2

[sahilrishav2]

@TKsh6, You installed through conda, what does this mean ? Did you able to set up the database also through conda, please explain the step then.

[sahilrishav2]

@jianshu93 , were you able to complete the database setup process

[jianshu93]

Yes. I was able to solve it. The populating step takes more than 25 hours (other steps before it only several hours). Just be patient and allow at least 600G memory.

Jianshu

[sahilrishav2]

@jianshu93 , do you know how to perform only the last step Populating the description db, this may take some time as my other steps have been done but got killed in this last step only, so, instead of doing all the steps from the start, I want to do this last step only.