I am running Mothur MiSeq SOP pipeline on Linux machine. Also, using mock-community (paired), which is in the same directory as my fastq files. While re-running the unique.seqs() after filtering, I am getting an error saying something is missing from the count table.
Command
unique.seqs(fasta=stability.trim.contigs.good.unique.good.filter.fasta, count=stability.trim.contigs.good.good.count_table)
Output/Error
Removing group: 31 because all sequences have been removed.
Removing group: 5 because all sequences have been removed.
Removing group: 57 because all sequences have been removed.
Removing group: 70 because all sequences have been removed.
Removing group: 71 because all sequences have been removed.
Removing group: 72 because all sequences have been removed.
[ERROR]: HWI-M03772_159_000000000-BY9C5_1_2106_19343_5688 is not in your count table. Please correct.
I wonder if this is happening because the mock-community is in the same directory. Do we only use mock-community for error estimation steps as shown in Mothur MiSeq SOP pipeline and not in the previous steps?
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