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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比对结束第一步,然后第二步,显示这个,如何解决 #63

Open pl19940314 opened 2 months ago

pl19940314 commented 2 months ago

Error: Unknown argument: "mt_mode" Error: (CArgException::eInvalidArg) Unknown argument: "mt_mode" Traceback (most recent call last): File "/home/meta/miniconda3/envs/args_oap/bin/args_oap", line 10, in sys.exit(main()) ^^^^^^ File "/home/meta/miniconda3/envs/args_oap/lib/python3.11/site-packages/args_oap/args_oap.py", line 97, in main options.func(options) File "/home/meta/miniconda3/envs/args_oap/lib/python3.11/site-packages/args_oap/stage_two.py", line 190, in run_stage_two StageTwo(vars(options)).run() File "/home/meta/miniconda3/envs/args_oap/lib/python3.11/site-packages/args_oap/stage_two.py", line 185, in run self.extract_seqs() File "/home/meta/miniconda3/envs/args_oap/lib/python3.11/site-packages/args_oap/stage_two.py", line 115, in extract_seqs subprocess.run(cmd, check=True) File "/home/meta/miniconda3/envs/args_oap/lib/python3.11/subprocess.py", line 571, in run raise CalledProcessError(retcode, process.args, subprocess.CalledProcessError: Command '['blastx', '-db', '/home/meta/miniconda3/envs/args_oap/lib/python3.11/site-packages/args_oap/db/sarg.fasta', '-query', '/home/meta/mdisk/pl/soil/soil_fasta/L1HHK01/L1HHK01_args/extracted.fa', '-out', '/home/meta/mdisk/pl/soil/soil_fasta/L1HHK01/L1HHK01_args/blastout.txt', '-outfmt', '6 qseqid sseqid pident length qlen slen evalue bitscore', '-evalue', '1e-07', '-max_target_seqs', '5', '-num_threads', '5', '-mt_mode', '0']' returned non-zero exit status 1.

xinehc commented 2 months ago

Hi,

you may consider upgrading blast to >=2.12.

Reference: https://blast.ncbi.nlm.nih.gov/doc/blast-news/2021-BLAST-News.html