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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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wrong in stage_two #73

Closed hemingwang closed 1 month ago

hemingwang commented 1 month ago

I have problem in stage two, their is my code:

args_oap stage_one -i raw_data/ -o output -f fastq -t 8 [2024-10-16 15:10:12] WARNING: Output folder contains and/or , they/it will be overwritten. [2024-10-16 15:10:12] INFO: Processing <raw_data/MDL001-01D2236263T-DNA-B38-20220903.nonhuman.fastq> (1/4) ... [2024-10-16 15:10:15] INFO: Processing <raw_data/MDL001-01D2237199Z-DNA-C11-20220910.nonhuman.fastq> (2/4) ... [2024-10-16 15:10:22] INFO: Processing <raw_data/MDL001-04C2244072L-DNA-A21-20221028.nonhuman.fastq> (3/4) ... [2024-10-16 15:10:25] INFO: Processing <raw_data/MDL001-04D2244023L-DNA-C41-20221025.nonhuman.fastq> (4/4) ... [2024-10-16 15:10:27] INFO: Finished. (args_oap) @DESKTOP-LCP2OM4:~/data$ args_oap stage_two -i output -t 8 [2024-10-16 15:12:12] WARNING: Output folder contains and/or <.filtered.>, they/it will be overwritten. [2024-10-16 15:12:12] INFO: Processing <output/extracted.fa> ... [2024-10-16 15:12:12] INFO: Extracting target sequences using BLAST ... [2024-10-16 15:12:12] INFO: BLAST settings: 52900 bps, 1058 reads, 8 threads, mt_mode 0. [2024-10-16 15:12:13] INFO: Merging files ... [2024-10-16 15:12:13] CRITICAL: No target sequence remained after merging structure files, no further normalization will be made.

xinehc commented 1 month ago

it likely means no ARGs were detected in your 1058 reads using the default cutoffs.

hemingwang commented 1 month ago

Thank you！ I solve my problem.