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arpcard / rgi

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

Closed raphenya closed 11 months ago

raphenya commented 1 year ago

Command used: rgi auto_load --debug --clean

Log:

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

Data directory (local):

ls localDB 
16s_rRNA.txt                amr_61mer.txt               card_reference_all.fasta        index-for-model-sequences.txt       protein.db.phr              proteindb.fsa
23s_rRNA.txt                card.json               card_wildcard_reference.fasta       loaded_databases.json           protein.db.pin              rnadb.fsa
61mer_database.json         card_reference.fasta            card_wildcard_reference_all.fasta   protein.db.dmnd             protein.db.psq

These should contain same files after rgi auto_load

raphenya commented 11 months ago

Tested the rgi auto_load using rgi version 6.0.3 (mamba version 1.4.2, conda version 23.3.1, Ubuntu 18.04.6) and it works fine.

raphenya commented 11 months ago

Also, tested on MacOS with no issues both running python version 3.8.