Stage_one WARNING: Duplicated sequences

[HuangLoong]

I generated a warning message while running ARGs OAP stage_one on the server. The metagenomic data is sourced from NCBI and has gone through the kneaddata process. However, when I used my own sequencing data, no warning message was generated. What is the reason and will it affect subsequent analysis? Thanks very much for your answer！ WARNING: Duplicated sequences in sequence extraction. WARNING: Duplicated sequences in 16S copy number calculation. WARNING: Duplicated sequences in cell number calculation.

[xinehc]

This likely means some of your sequences have exactly identical sequence id. You can check the duplication using e.g. seqkit rmdup.

[HuangLoong]

This likely means some of your sequences have exactly identical sequence id. You can check the duplication using e.g. seqkit rmdup.

We renamed the sequence after downloading the raw data from NCBI, and no duplicate sequence IDs were detected using seqkit rmdup.

[xinehc]

Hi,

do you mind sharing a minimal reproducible example? Does your _1 and _2 files have identical sequence id?

cat _1.fa _2.fa > seq.fa
seqkit rmdup seq.fa -D dup.fa

[HuangLoong]

Hi,

do you mind sharing a minimal reproducible example? Does your _1 and _2 files have identical sequence id?

cat _1.fa _2.fa > seq.fa
seqkit rmdup seq.fa -D dup.fa

Thank you. Based on the command you provided, I did detect some duplicated sequences. I then extracted the previously retrieved duplicate IDs from the paired-end sequencing file. Duplicate IDs were found only in one of the pairwise sequence files. I wonder if this error will affect the final result output.

[xinehc]

Only the first detected sequence will be counted. This will lead to an underestimation of either ARG/16S/genome copies.