args_oap
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xinehc
ARGs-OAP: Online Analysis Pipeline for Antibiotic Resistance Genes Detection from Metagenomic Data Using an Integrated Structured ARG Database
“-t” parameter lose efficacy in stage two sometimes , for example: I used "-t 8" parameter in stage two, and info shows that: INFO: BLAST settings: 21401791 bps, 232757 reads,...
I installed the latest version via git clone. And I ran arg_oap -v, args_oap stage_one -h, args-oap, stage_two -h, and the above three commands all showed that the installation was...
Hi, I wanted to download the results of the "Risk Ranking Version 3.0", but the web was 404. Can you solve it please? Thanks.
Could you add a documentation of the pipeline (maybe a wiki) that describes which programs and algorithms are being used in each step? For example, on step one diamond is...
Dear Xi Chen, The n16S and nCell in the metadata.txt for paired sample are the mean of _1.fq and _2.fq? Or calculated in some special method?
I want to use binned protein sequences to predict ARG. I downloaded the SARG v3.2.1-L (version for long read annotation) and successfully built it using "args_oap make_db -i Long_subdatabase_V3.2.1/Long_subdatabase/3.SARG_v3.2_20220917_Long_subdatabase.fasta". However,...
Hello There, 1. I have little doubt about normalized_16s.gene.txt/normalised_16s.subtype.txt/normalised_16s.type.txt The gene names which I can are ARG genes, so, can u just breif me about the 16s files. I thought...
Hi! I'm having some problems when I run the stage_two step. The input files number is 27 but in the output result I onlt got 25 samples. The command I...
I ran ARGs_OAP on 200 sequences (paired end). The step one ran smoothly and gave me two files as output (metadata.txt and extracted.fa) but when I ran stage two, it...
首先，十分感谢贵课题组的ARGs-OAP给我们这种生信刚入门的小白提供了研究ARG的便利工具，我最近在尝试使用Desktop版本（windows）进行个性化数据库分析，已经成功使用Ncyc等多种数据库进行分析，但是当使用同样的方法进行Nature文章中所提供的MGEs数据库进行分析时，总是会出现如下错误，恳请您们帮忙指点迷津，十分感谢 [2023-07-25 00:13:06,443] [INFO] Calling args_oap/stage_one with ['stage_one', '--indir', 'D:\\Metagenomics\\ARGs-OAP\\input\\test_P', '--outdir', 'D:\\Metagenomics\\ARGs-OAP\\input\\test', '--thread', '2', '--format', 'fa', '--skip', '--database', 'D:\\Metagenomics\\ARGs-OAP\\MGEs\\MobileGeneticElementDatabase-master\\MGEs_FINAL_99perc_trim.fasta'] [2023-07-25 00:13:06,457] [INFO] Building databases ... [2023-07-25 00:13:20,312] [INFO] Processing (1/1)...
