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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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Stage_two error #61

Open HuangLoong opened 2 months ago

HuangLoong commented 2 months ago

image Hello! We used MGEdb as the custom database(https://github.com/KatariinaParnanen/MobileGeneticElementDatabase). However, an error occurred when we ran the second phase. Can you tell us how to solve this problem?

HuangLoong commented 2 months ago

Warning: Not all extracted target sequences can be found in structure files.

HuangLoong commented 2 months ago

After several minutes, we still achieved the corresponding results. But is this trustworthy? image

xinehc commented 2 months ago

It seems your metadata files have a third column called "unnamed: 3", please remove the space in the header. It may cause the error.

HuangLoong commented 2 months ago

Thank you. Following your suggestion, we have recompiled the annotation file of the MGEdb database. But the warning still exists. Will this affect the final output? image image

xinehc commented 1 month ago

Sry I missed this.

This warning means some sequences IDs in your .fasta file cannot be found in the structure file. You may write a simple script to check the existence of the IDs.