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xinehc / args_oap

ARGs-OAP: Online Analysis Pipeline for Antibiotic Resistance Genes Detection from Metagenomic Data Using an Integrated Structured ARG Database
MIT License
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UnboundLocalError: local variable 'dbtype' referenced before assignment #66

Open tenethe opened 1 month ago

tenethe commented 1 month ago

Hei,

Many thanks to the developers. I installed args_oap in a container environment (tykky). When I ran stage_one for the example fasta files, an issue occurred. Was the error due to the environment? May I ask if there is any solution for this? Thank you.

$ args_oap stage_one -i input -o output -f fa -t 8 [2024-06-03 15:44:15] INFO: Building databases ... Traceback (most recent call last): File "//tykky-env/bin/args_oap", line 10, in sys.exit(main()) File "//python3.10/site-packages/args_oap/args_oap.py", line 232, in main options.func(options) File "//python3.10/site-packages/args_oap/stage_one.py", line 229, in run_stage_one StageOne(vars(options)).run() File "//python3.10/site-packages/args_oap/stage_one.py", line 62, in init make_db(file) File "/*/python3.10/site-packages/args_oap/make_db.py", line 42, in make_db '-dbtype', dbtype, UnboundLocalError: local variable 'dbtype' referenced before assignment

xinehc commented 1 month ago

Hi,

it is likely you do not have the write permission to path /*/python3.10/site-packages/args_oap/.

tenethe commented 1 month ago

Hi,

it is likely you do not have the write permission to path /*/python3.10/site-packages/args_oap/.

Thanks so much for your reply. It seems that the path has been hidden in the container, and we don't have the access permission. I will contact the admin soon. Alternatively, I tried the windows version, but there are also some issues:

[2024-06-06 12:17:53,494] [INFO] Calling args_oap/stage_one with ['stage_one', '--indir', 'C:\Users\Downloads\example.tar\example\example\input', '--outdir', 'C:\Users\AppData\Roaming\args-desktop\output\args_oap_edf5', '--thread', '4', '--format', 'fa', '--e2', '3'] [2024-06-06 12:17:53,504] [INFO] Processing <C:\Users\Downloads\example.tar\example\example\input\STAS_1.fa> (1/4) ... [2024-06-06 12:18:10,491] [WARNING] No 16S-like sequences found in file <C:\Users\Downloads\example.tar\example\example\input\STAS_1.fa>. [2024-06-06 12:18:22,613] [INFO] Processing <C:\Users\Downloads\example.tar\example\example\input\STAS_2.fa> (2/4) ... [2024-06-06 12:18:40,484] [ERROR] C:\Users\AppData\Local\Temp\ONEFIL~1\interface.py 474 CalledProcessError(1, ['bwa', 'mem', '-t', '4', 'C:\Users\AppData\Local\Temp\onefile_22260_133621389485638375\resources\args_oap\db\gg85.fasta', 'C:\Users\Downloads\example.tar\example\example\input\STAS_2.fa'])

[2024-06-06 12:16:34,466] [INFO] Calling args_oap/stage_one with ['stage_one', '--indir', 'C:\Users\Downloads\example.tar\example\example\input', '--outdir', 'C:\Users\AppData\Roaming\args-desktop\output\args_oap_IGXv', '--thread', '4', '--format', 'fa', '--e2', '3'] [2024-06-06 12:16:34,478] [INFO] Building databases ... [2024-06-06 12:16:40,675] [INFO] Processing <C:\Users\Downloads\example.tar\example\example\input\STAS_1.fa> (1/4) ... [2024-06-06 12:16:55,061] [ERROR] C:\Users\AppData\Local\Temp\ONEFIL~1\interface.py 519 CalledProcessError(1, ['bwa', 'mem', '-t', '4', 'C:\Users\AppData\Local\Temp\onefile_22260_133621389485638375\resources\args_oap\db\gg85.fasta', 'C:\Users\Downloads\example.tar\example\example\input\STAS_1.fa'])

Did you see these issues before? Thank you.