I am running into an error following my align sequences command with the silva.v4 database between my aligned fasta file and my most recent count table.
The error I keep getting is: [ERROR]: Your count file contains 3538449 unique sequences, but your fasta file contains 249941. File mismatch detected, quitting command.
I’ve re-started my run right from make.contigs to ensure that files haven’t somehow gotten mis-aligned. However, I still seem to be coming up with this error… could I have the wrong silva.v4.fasta file perhaps??
The workflow I’ve used and output are as follows:
mothur >
make.contigs(file=stability.file, processors=16)
It took 39 secs to assemble 242886 reads.
Total of all groups is 12486425
mothur >
summary.seqs(fasta=stability.trim.contigs.fasta)
It took 65 secs to summarize 12247832 sequences.
screen.seqs(fasta=stability.trim.contigs.fasta, group=stability.contigs.groups, maxambig=0, minlength=291, maxlength=293)
It took 54 secs to screen 12247832 sequences, removed 2453909.
mothur >
summary.seqs(fasta=stability.trim.contigs.good.fasta, processors=16)
It took 52 secs to summarize 9793923 sequences.
mothur >
unique.seqs(fasta=stability.trim.contigs.good.fasta)
mothur >
count.seqs(name=stability.trim.contigs.good.names, group=stability.contigs.good.groups)
mothur >
summary.seqs(count=stability.trim.contigs.good.count_table)
It took 52 secs to summarize 9793923 sequences.
mothur >
align.seqs(fasta=stability.trim.contigs.good.unique.fasta, reference= silva.v4.fasta)
Reading in the silva.v4.fasta template sequences… DONE.
It took 3 to read 14956 sequences.
It took 656 secs to align 3538449 sequences.
mothur >
summary.seqs(fasta=stability.trim.contigs.good.unique.align, count=stability.trim.contigs.good.count_table)
[ERROR]: Your count file contains 3538449 unique sequences, but your fasta file contains 447516. File mismatch detected, quitting command.
Any insight into code errors would be greatly appreciated.
JM