Tryng to import merged sequences

Hello there, I’m trying to get to my OTU table, but I’m having some problems understanding the workflow (note that I know very little about what I’m doing, so I will be glad with your suggestions). I started with the two .fasta files with which I executed the follow commands:

sudo bbmap/ -Xmx200m in1=SPP1/MP67_1.fastq in2=SPP1/MP67_2.fastq out1=SPP1/MP67_1bbduk.fastq out2=SPP1/MP67_2bbduk.fastq re
f=bbmap/resources/adapters.fa,bbmap/resources/phix174_ill.ref.fa.gz,bbmap/resources/nextera.fa.gz t=20


sickle pe -f SPP1/MP67_1bbduk.fastq -r SPP1/MP67_2bbduk.fastq -t sanger -o MP67_sickle_2.fastq -p MP67_sickle_1.fastq -s MP67_sickle_3.fastq -q 30 -l 50

For the next step I merged them (this is a requirement, but i have no idea if this is the right moment to do it, so correct me with I’m wrong, please) by this command:

sudo bbmap/ in1=MP67_sickle_1 in2=MP67_sickle_2 out=MP67_merged outu1=MP67_unmerged1 outu2=MP67_unmerged2

Now, I understand that I need to import to Qiime2 for the trimming step, and there it gets a bit confusing to me, and I couldn’t find any tutorial for merged sequences yet, so I’m asking for HELP.

The trimming should be no problem.

The following step on my understanding will be the import e further training with my data set of choice, which is the PLanITs, the import i was able to do, but the training of the classifier has been a problem, I’m get a lot of errors, maybe because of previous missteps.