How to make Galaxy identify an adaptor when it doesn't? What is the possible source of errors?

Question

[Sanjukta]

This post is a continuation of my previous discussion here. I tried Galaxy to analyse miRNA-seq data and not miRdeep2 as was suggested, due to some temporary issues of internet at my campus.

My miRNA fastq files read as follows:

>SRR1658346.1 HISEQ1:187:D0NWFACXX:3:1101:2565:2050 length=51
ATCATACAAGGACAATTTCTTTTAACGTCGTATGCCGTCTTCTGCTTGNAA
>SRR1658346.2 HISEQ1:187:D0NWFACXX:3:1101:2654:2232 length=51 
TCGAGGAGCTCACAGTCTAGTATAACGTCGTATGCCGTCTTCTGCTTGAAA
>SRR1658346.3 HISEQ1:187:D0NWFACXX:3:1101:2870:2103 length=51 
TTCAAGTAATCCAGGATAGGCTAACGTCGTATGCCGTCTTCTGCTTGAAAA
>SRR1658346.4 HISEQ1:187:D0NWFACXX:3:1101:3001:2147 length=51 
TAGCACCATCCGAAATCAGTTTAACGTCGTATGCCGGCTTCTGCTTGAAAA

The second sequence is probably my adaptor sequence:

ATCATACAAGGACAATTTCTTT  TAACGTCGTATGCCGTCTTCTGCTTGNAA

TCGAGGAGCTCACAGTCTAGTA  TAACGTCGTATGCCGTCTTCTGCTTGAAA 

TTCAAGTAATCCAGGATAGGC  TAACGTCGTATGCCGTCTTCTGCTTGAAAA 

TAGCACCATCCGAAATCAGTT  TAACGTCGTATGCCGGCTTCTGCTTGAAAA

But on doing FastQC and MultiQC, "No samples found with any adapter contamination > 0.1%" this message is displayed.

The individual FASTQC file however predicted the occurrence of Adaptor:

Is the alignment of the sequence wrong? Is it supposed to start with the adaptor sequence? So should I rewrite the fastq files?

[GenoMax]

Galaxy specific questions are best asked on their help forum: https://help.galaxyproject.org/

Here are some past threads there that may be of help: https://help.galaxyproject.org/tag/mirna