Resistance Gene Identifier (RGI). Software to predict resistomes from protein or nucleotide data, including metagenomics data, based on homology and SNP models.
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RGI auto_load not working properly system wide #235
INFO 2022-10-17 13:16:49,025 : {
"local_database": false,
"clean": true,
"debug": true
}
INFO 2022-10-17 13:16:49,026 : card cannonical version: 3.2.5
INFO 2022-10-17 13:16:49,026 : card variants version: 4.0.0
Redirecting output to ‘wget-log’.
Redirecting output to ‘wget-log.1’.
INtar: Error opening archive: Failed to open '/Users/amos/Desktop/test_rgi600/rgi_autoload_sl6a65l4/variants'
gunzip: can't stat: /Users/amos/Desktop/test_rgi600/rgi_autoload_sl6a65l4/card_variants/*.gz (/Users/amos/Desktop/test_rgi600/rgi_autoload_sl6a65l4/card_variants/*.gz.gz): No such file or directory
Traceback (most recent call last):
File "/Users/amos/miniconda3/envs/rgi600/bin/rgi", line 4, in <module>
MainBase()
File "/Users/amos/miniconda3/envs/rgi600/lib/python3.7/site-packages/app/MainBase.py", line 83, in __init__
getattr(self, args.command)()
File "/Users/amos/miniconda3/envs/rgi600/lib/python3.7/site-packages/app/MainBase.py", line 223, in card_annotation
self.card_annotation_run(args)
File "/Users/amos/miniconda3/envs/rgi600/lib/python3.7/site-packages/app/MainBase.py", line 230, in card_annotation_run
app.card_annotation.main(args)
File "/Users/amos/miniconda3/envs/rgi600/lib/python3.7/site-packages/app/card_annotation.py", line 14, in main
with open(os.path.join(args.input), 'r') as jfile:
FileNotFoundError: [Errno 2] No such file or directory: '/Users/amos/Desktop/test_rgi600/rgi_autoload_sl6a65l4/card_data/card.json'
Traceback (most recent call last):
File "/Users/amos/miniconda3/envs/rgi600/bin/rgi", line 4, in <module>
MainBase()
File "/Users/amos/miniconda3/envs/rgi600/lib/python3.7/site-packages/app/MainBase.py", line 83, in __init__
getattr(self, args.command)()
File "/Users/amos/miniconda3/envs/rgi600/lib/python3.7/site-packages/app/MainBase.py", line 235, in wildcard_annotation
self.wildcard_annotation_run(args)
File "/Users/amos/miniconda3/envs/rgi600/lib/python3.7/site-packages/app/MainBase.py", line 242, in wildcard_annotation_run
app.wildcard_annotation.main(args)
File "/Users/amos/miniconda3/envs/rgi600/lib/python3.7/site-packages/app/wildcard_annotation.py", line 32, in main
prev_models = get_model(args.input_directory)
File "/Users/amos/miniconda3/envs/rgi600/lib/python3.7/site-packages/app/wildcard_annotation.py", line 48, in get_model
raise e
File "/Users/amos/miniconda3/envs/rgi600/lib/python3.7/site-packages/app/wildcard_annotation.py", line 42, in get_model
with open(os.path.join(input_directory, "index-for-model-sequences.txt"), 'r') as ifile:
FileNotFoundError: [Errno 2] No such file or directory: '/Users/amos/Desktop/test_rgi600/rgi_autoload_sl6a65l4/card_variants/index-for-model-sequences.txt'
INFO 2022-10-17 13:24:04,388 : Remove: /Users/amos/miniconda3/envs/rgi600/lib/python3.7/site-packages/app/_data/index-for-model-sequences.txt
INFO 2022-10-17 13:24:04,389 : Remove: /Users/amos/miniconda3/envs/rgi600/lib/python3.7/site-packages/app/_data/card_wildcard_reference_all.fasta
INFO 2022-10-17 13:24:04,390 : Remove: /Users/amos/miniconda3/envs/rgi600/lib/python3.7/site-packages/app/_data/card_wildcard_reference.fasta
INFO 2022-10-17 13:24:04,415 : Remove: /Users/amos/miniconda3/envs/rgi600/lib/python3.7/site-packages/app/_data/61mer_database.json
INFO 2022-10-17 13:24:04,455 : Remove: /Users/amos/miniconda3/envs/rgi600/lib/python3.7/site-packages/app/_data/card_reference.fasta
INFO 2022-10-17 13:24:04,455 : Remove: /Users/amos/miniconda3/envs/rgi600/lib/python3.7/site-packages/app/_data/amr_61mer.txt
INFO 2022-10-17 13:24:04,582 : Remove: /Users/amos/miniconda3/envs/rgi600/lib/python3.7/site-packages/app/_data/card_reference_all.fasta
INFO 2022-10-17 13:24:04,583 : Cleaned directory: /Users/amos/miniconda3/envs/rgi600/lib/python3.7/site-packages/app/_data/
INFO 2022-10-17 13:24:04,583 : Cleaned directory: /Users/amos/miniconda3/envs/rgi600/lib/python3.7/site-packages/app/_db/
INFO 2022-10-17 13:24:06,248 : file /Users/amos/miniconda3/envs/rgi600/lib/python3.7/site-packages/app/_data/loaded_databases.json exists load
INFO 2022-10-17 13:24:06,248 : {
"card_json": "/Users/amos/Desktop/test_rgi600/rgi_autoload_sl6a65l4/card_data/card.json",
"card_annotation": "card_database_v3.2.5.fasta",
"card_annotation_all_models": "card_database_v3.2.5_all.fasta",
"wildcard_annotation": "wildcard_database_v4.0.0.fasta",
"wildcard_annotation_all_models": "wildcard_database_v4.0.0_all.fasta",
"wildcard_index": "/Users/amos/Desktop/test_rgi600/rgi_autoload_sl6a65l4/card_variants/index-for-model-sequences.txt",
"wildcard_version": "4.0.0",
"baits_annotation": null,
"baits_index": null,
"kmer_database": "/Users/amos/Desktop/test_rgi600/rgi_autoload_sl6a65l4/card_variants/61_kmer_db.json",
"amr_kmers": "/Users/amos/Desktop/test_rgi600/rgi_autoload_sl6a65l4/card_variants/all_amr_61mers.txt",
"kmer_size": "61",
"local_database": false,
"debug": true
}
Traceback (most recent call last):
File "/Users/amos/miniconda3/envs/rgi600/bin/rgi", line 4, in <module>
MainBase()
File "/Users/amos/miniconda3/envs/rgi600/lib/python3.7/site-packages/app/MainBase.py", line 83, in __init__
getattr(self, args.command)()
File "/Users/amos/miniconda3/envs/rgi600/lib/python3.7/site-packages/app/MainBase.py", line 154, in load
self.load_run(args)
File "/Users/amos/miniconda3/envs/rgi600/lib/python3.7/site-packages/app/MainBase.py", line 161, in load_run
app.load.main(args)
File "/Users/amos/miniconda3/envs/rgi600/lib/python3.7/site-packages/app/load.py", line 113, in main
if validate_file(args.card_json) == False:
File "/Users/amos/miniconda3/envs/rgi600/lib/python3.7/site-packages/app/load.py", line 59, in validate_file
with open(filename) as f:
FileNotFoundError: [Errno 2] No such file or directory: '/Users/amos/Desktop/test_rgi600/rgi_autoload_sl6a65l4/card_data/card.json'
card_canonical: 3.2.5 | card_canonical_model_type_used: homolog;variant;rRNA;overexpression;knockout | card_variants: 4.0.0 | card_variants_model_type_used: homolog;variant;rRNA;overexpression;knockout | kmer_sizes: 61
rm: /Users/amos/Desktop/test_rgi600/rgi_autoload_sl6a65l4/data: No such file or directory
rm: /Users/amos/Desktop/test_rgi600/rgi_autoload_sl6a65l4/variants: No such file or directory
rm: /Users/amos/Desktop/test_rgi600/rgi_autoload_sl6a65l4/card_data/*: No such file or directory
rm: /Users/amos/Desktop/test_rgi600/rgi_autoload_sl6a65l4/card_variants/*: No such file or directory
rm: /Users/amos/Desktop/test_rgi600/rgi_autoload_sl6a65l4/card_data: No such file or directory
rm: card_database_v3.2.5.fasta: No such file or directory
rm: card_database_v3.2.5_all.fasta: No such file or directory
rm: wildcard_database_v4.0.0.fasta: No such file or directory
rm: wildcard_database_v4.0.0_all.fasta: No such file or directory
Directory '/Users/amos/Desktop/test_rgi600/rgi_autoload_sl6a65l4' created
=================================== DOWNLOAD CARD CANONICAL DATA ===================================
=================================== DOWNLOAD CARD VARIANTS DATA ===================================
=================================== CARD CANONICAL ANNOTATIONS ===================================
=================================== CARD VARIANTS ANNOTATIONS ===================================
=================================== CLEAN OLD DATABASES ===================================
=================================== LOAD DATABASES ===================================
=================================== CHECK LOADED DATABASES ===================================
=================================== CLEAN UP ===================================
=================================== DONE ===================================
Results
Data directory (system wide):
ls /Users/amos/miniconda3/envs/rgi600/lib/python3.7/site-packages/app/_data
__init__.py __pycache__ card.json loaded_databases.json
Command used:
rgi auto_load --debug --clean
Log:
Results
Data directory (system wide):
Data directory (local):
These should contain same files after
rgi auto_load