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Database download interrupted #392

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baidefeng opened this issue Dec 17, 2024 · 0 comments
Open

Database download interrupted #392

baidefeng opened this issue Dec 17, 2024 · 0 comments

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@baidefeng
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An error occurred during the database download process, is there anyone know how to fix it?

/data5/baidefeng/miniconda3/envs/DRAM/lib/python3.10/site-packages/mag_annotator/database_handler.py:126: UserWarning: Database does not exist at path None
warnings.warn("Database does not exist at path %s" % description_loc)
2024-12-15 20:50:15,835 - Starting the process of downloading data
2024-12-15 20:50:15,835 - 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
2024-12-15 20:50:15,835 - 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
2024-12-15 20:50:15,835 - Database preparation started
2024-12-15 20:50:15,835 - Downloading kofam_hmm
2024-12-16 01:40:50,265 - Downloading kofam_ko_list
2024-12-16 01:40:54,414 - Downloading uniref
2024-12-17 06:53:56,976 - Downloading pfam
2024-12-17 11:54:54,661 - Downloading pfam_hmm
2024-12-17 11:54:57,444 - Downloading dbcan
2024-12-17 12:03:24,002 - Downloading dbcan_fam_activities
2024-12-17 12:03:24,002 - Downloading dbCAN family activities from : https://bcb.unl.edu/dbCAN2/download/Databases/V11/CAZyDB.08062022.fam-activities.txt
2024-12-17 12:03:25,573 - Downloading dbcan_subfam_ec
2024-12-17 12:03:25,573 - Downloading dbCAN sub-family encumber from : https://bcb.unl.edu/dbCAN2/download/Databases/V11/CAZyDB.08062022.fam.subfam.ec.txt
2024-12-17 12:03:29,276 - Downloading vogdb
2024-12-17 12:14:06,856 - Downloading vog_annotations
2024-12-17 12:14:09,575 - Downloading viral
2024-12-17 12:15:36,975 - Downloading peptidase
2024-12-17 12:24:04,223 - Downloading genome_summary_form
2024-12-17 12:24:04,290 - Something went wrong with the download of the url: https://raw.githubusercontent.com/WrightonLabCSU/DRAM/master/data/genome_summary_form.tsv
2024-12-17 12:24:04,291 - <urlopen error [Errno 111] Connection refused>
Traceback (most recent call last):
File "/data5/baidefeng/miniconda3/envs/DRAM/bin/DRAM-setup.py", line 187, in
args.func(**args_dict)
File "/data5/baidefeng/miniconda3/envs/DRAM/lib/python3.10/site-packages/mag_annotator/database_processing.py", line 595, in prepare_databases
locs[i] = download_functions[i](
File "/data5/baidefeng/miniconda3/envs/DRAM/lib/python3.10/site-packages/mag_annotator/database_processing.py", line 391, in download_genome_summary_form
download_file('https://raw.githubusercontent.com/WrightonLabCSU/DRAM/%s/data/genome_summary_form.tsv' % branch,
File "/data5/baidefeng/miniconda3/envs/DRAM/lib/python3.10/site-packages/mag_annotator/utils.py", line 33, in download_file
raise URLError("DRAM whas not able to download a key database, check the logg for details")
urllib.error.URLError: <urlopen error DRAM whas not able to download a key database, check the logg for details>

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