Quntify Antibiotic resistance gene abundence

Question

[raju.koorakula]

Dear all

I wanted to quantify the Antibiotic resistance gene abundance in metatranscriptomic data (RNA-seq) using MEGARes database with USEARCH global. But I am confused because 100.0% Searching input.fastq 0.0% matched so if anyone have experience in resistance gene abundance, please suggest. here is my command and output

usearch/usearch -usearch_global input.fastq -db megares.udb -id 0.9 -maxaccepts 1 -threads 20 -alnout out.aln -strand plus

**output**
00:00 19Mb    100.0% Rows
00:00 19Mb   Reading pointers...done.
00:00 19Mb   Reading db seqs...done.
19:27 316Mb   100.0% Searching input.fastq, 0.0% matched


Query >A00700:50:HF7LGDRXX:1:1101:18638:16391#GACGCATCGAGGCTGC
 %Id   TLen  Target
 90%   1195  CARD|pvgb|NC_002516|4767810-4769004|ARO:3001312|elfamycin|Elfamycins|EF-Tu_inhibition|TUFAB|RequiresSNPConfirmation

 Query   63nt >A00700:50:HF7LGDRXX:1:1101:18638:16391#GACGCATCGAGGCTGC
Target 1195nt >CARD|pvgb|NC_002516|4767810-4769004|ARO:3001312|elfamycin|Elfamycins|EF-Tu_inhibition|TUFAB|RequiresSNPConfirmation

Qry    1 + GGTGATAGCAGCGGTCAGAGTGGTCTTGCCGTGGTCAACGTGGCCGATGGTGCCGATGTTGAC 63
           ||| |  ||||||||||||||||||||||| ||||||||||| ||||||||||||| ||||||
Tgt 1096 + GGTCAGTGCAGCGGTCAGAGTGGTCTTGCCATGGTCAACGTGACCGATGGTGCCGACGTTGAC 1158

63 cols, 57 ids (90.5%), 0 gaps (0.0%)

Query >A00700:50:HF7LGDRXX:1:1101:26675:33348#GACGCATCGAGGCTGC
 %Id   TLen  Target
 93%   1230  CARD|pvgb|AE014075|3901532-3902762|ARO:3003438|Escherichia|Elfamycins|EF-Tu_inhibition|TUFAB|RequiresSNPConfirmation

 Query  100nt >A00700:50:HF7LGDRXX:1:1101:26675:33348#GACGCATCGAGGCTGC
Target 1230nt >CARD|pvgb|AE014075|3901532-3902762|ARO:3003438|Escherichia|Elfamycins|EF-Tu_inhibition|TUFAB|RequiresSNPConfirmation

Qry    1 + CTCTTCGTCATCAACCATGTCGCACTTGTTCAGGAATACGACGATGTACGGTACACCTACCTGACGAGCGAGCAGGATGT 80
           |||||||||||||||||||||||| ||||||||||| |||| ||||||||| || |||||||||||| | ||||||||||
Tgt  751 + CTCTTCGTCATCAACCATGTCGCATTTGTTCAGGAACACGATGATGTACGGAACGCCTACCTGACGACCCAGCAGGATGT 830

[GenoMax]

100.0% Searching input.fastq 0.0% matched

But the example you are showing above seems to be aligning reasonably well (90% identity).