CRITICAL: No target sequence remained after merging structure files

xinehc / args_oap

ARGs-OAP: Online Analysis Pipeline for Antibiotic Resistance Genes Detection from Metagenomic Data Using an Integrated Structured ARG Database

MIT License

43 stars 11 forks source link

CRITICAL: No target sequence remained after merging structure files #37

Open Yixiangzhang1996 opened 1 year ago

Yixiangzhang1996 commented 1 year ago

Hello The error message, "CRITICAL: No target sequence remained after merging structure files, no further normalization will be made," indicates that there is an issue related to merging structure files and normalization in your analysis. This error occurs both with self-built databases and default databases.

Is it the data itself, or are the environment variables not configured properly?

xinehc commented 1 year ago

Hi,

it means no sequence passes the filter in step 2:

  --e FLOAT             E-value cutoff for target sequences. [1e-7]
  --id FLOAT            Identity cutoff (in percentage) for target sequences. [80]
  --qcov FLOAT          Query cover cutoff (in percentage) for target sequences. [75]
  --length INT          Aligned length cutoff (in amino acid) for target sequences. [25]

If your sequences are very short (below 25 aa or 75 bp), then using the default value of --length will lead to a removal or all sequences.

linki11 commented 10 months ago

Hi Chen, I have encountered a similar issue with my sequences. In my case, I have 150-base pair paired-end (PE) sequences, and even after quality trimming, I still have sequences longer than 100 base pairs. Any suggestions or solutions you can provide for this problem. thank you for your patient.

linki11 commented 10 months ago

<img width="641" alt="Screenshot 2024-01-04 at 8 30 21 P

M" src="https://github.com/xinehc/args_oap/assets/89136993/03d3ce0a-b954-486d-94f3-336953822b97"> (extracted fa) More information for you