After alignment with Silva alignment file modified with my oligos I ran the count and summary.seqs commands and received the following
error message after the summary.seqs command:
[ERROR]: ‘M03580_84_000000000-BWWYH_1_2118_27365_10822’ is not in your name or count file, please correct.
[ERROR]: Your count file contains 3612909 unique sequences, but your fasta file contains 2. File mismatch detected, quitting command.
Here are the commands I used:
align.seqs(fasta=oil_sed.trim.contigs.good.unique.fasta, reference=silva.nr_v132.pcr.align, flip=T) count.seqs(name=oil_sed.trim.contigs.good.names, group=oil_sed.contigs.good.groups) summary.seqs(fasta=oil_sed.trim.contigs.good.unique.align, count=oil_sed.trim.contigs.good.count_table, processors=24)