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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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Run stage_two yielded no results #59

Open theboy97 opened 4 months ago

theboy97 commented 4 months ago

Hello. I am using version 3.2.4. I have about 900 sets of bipartite macro genomic data all reporting the following message when running stage_two: "No target sequence detected in file <output/extracted.fa>, no further normalisation will be made."Or the following message is reported when stage_two is in progress:"Found zero reads/16s/cells in metadata file <output/metadata.txt>. These samples will be ignored." But when the output file is opened, there is data and content in it: 微信图片_20240309110506 (My metadata.txt format is default, no changes were made) 微信图片_20240309110511 I'd like to ask the author what might be wrong with this.

With all due respect Respectfully!

xinehc commented 4 months ago

The ID of your samples (e.g. SRR15330304) indicates some of your data are likely amplicons of ITS/16S, which should not contain any universal single copy marker genes of bacteria/archaea, or 16S. That's why you see many 0s in your 3th/4th columns.

Please note ARGs-OAP only works with metagenomics.

theboy97 commented 4 months ago

First of all, thanks for your reply. I also have a question, for example, if 8 groups out of 10 metagenomic data do not review the specification, will the analysis results of the remaining 2 groups be displayed? With regards Respect!

xinehc commented 4 months ago

no, only the detected ARG types will be shown