lmrodriguezr
commented
1 year ago @cruizperez Hi Carlos! Any ideas? Looks to me like a network issue, but I'm not familiar enough with the code.
Open saras224 opened 1 year ago
lmrodriguezr
commented
1 year ago @cruizperez Hi Carlos! Any ideas? Looks to me like a network issue, but I'm not familiar enough with the code.
Hi @lmrodriguezr I am getting this error while trying to download the MicrobeAnnotator database: (microbeannotator) microbeannotator_db_builder -d MicrobeAnnotator_DB -m [blast,diamond,sword] -t 40 2023-02-20 14:16:22,892 [INFO]: This is MicrobeAnnotator v2.0.5 2023-02-20 14:16:22,893 [INFO]: I will download and format the databases I use. 2023-02-20 14:16:22,893 [INFO]: Creating database folders 2023-02-20 14:16:22,894 [INFO]: Step 1 2023-02-20 14:16:22,894 [INFO]: Downloading KOfam data 100% [............................................................................] 823196 / 823196gzip: MicrobeAnnotator_DB/kofam_data/ko_list already exists; do you wish to overwrite (y or n)? n not overwritten 100% [....................................................................] 1403716982 / 14037169822023-02-20 15:41:15,994 [INFO]: Extracting profiles 2023-02-20 15:43:06,573 [INFO]: Finished 2023-02-20 15:43:06,574 [INFO]: Step 2 2023-02-20 15:43:06,574 [INFO]: Formatting KOfam profiles 2023-02-20 15:44:00,315 [INFO]: Finished 2023-02-20 15:44:00,319 [INFO]: Step 3 2023-02-20 15:44:04,119 [INFO]: Downloading SwissProt Fasta files 100% [........................................................................] 91432446 / 914324462023-02-20 15:49:20,717 [INFO]: Finished 2023-02-20 15:49:20,718 [INFO]: Step 4 2023-02-20 15:49:20,720 [INFO]: Downloading Swissprot .dat files 100% [......................................................................] 644647457 / 6446474572023-02-20 16:17:21,559 [INFO]: Finished 2023-02-20 16:17:21,559 [INFO]: Step 5 2023-02-20 16:17:21,559 [INFO]: Parsing MicrobeAnnotator_DB/temp_swissprot_dat_files/uniprot_sprot.dat.gz and storing in MicrobeAnnotator_DB/uniprot_swissprot.table 2023-02-20 16:18:58,543 [INFO]: Finished 2023-02-20 16:18:58,543 [INFO]: Step 6 2023-02-20 16:19:01,685 [INFO]: Downloading TrEMBL Fasta files
24% [................ ] 13970448384 / 57043853550Traceback (most recent call last): File "/home/rsharma/anaconda3/envs/microbeannotator/bin/microbeannotator_db_builder", line 445, in
main()
File "/home/rsharma/anaconda3/envs/microbeannotator/bin/microbeannotator_db_builder", line 437, in main
single_step, aspera, keep_temp, bin_path)
File "/home/rsharma/anaconda3/envs/microbeannotator/bin/microbeannotator_db_builder", line 141, in database_duilder
trembl_fasta = uniprot.trembl_fasta_downloader(database_directory)
File "/home/rsharma/anaconda3/envs/microbeannotator/lib/python3.7/site-packages/microbeannotator/database/uniprot_data_downloader.py", line 148, in trembl_fasta_downloader
wget.download(fasta_url, out=str(output_fasta))
File "/home/rsharma/anaconda3/envs/microbeannotator/lib/python3.7/site-packages/wget.py", line 526, in download
(tmpfile, headers) = ulib.urlretrieve(binurl, tmpfile, callback)
File "/home/rsharma/anaconda3/envs/microbeannotator/lib/python3.7/urllib/request.py", line 276, in urlretrieve
block = fp.read(bs)
File "/home/rsharma/anaconda3/envs/microbeannotator/lib/python3.7/tempfile.py", line 481, in func_wrapper
return func(*args, *kwargs)
File "/home/rsharma/anaconda3/envs/microbeannotator/lib/python3.7/tempfile.py", line 481, in func_wrapper
return func(args, **kwargs)
File "/home/rsharma/anaconda3/envs/microbeannotator/lib/python3.7/socket.py", line 589, in readinto
return self._sock.recv_into(b)
ConnectionResetError: [Errno 104] Connection reset by peer
Kindly help me resolve the error.
Thanks in Advance!! :)