Hi,
I have an issue when running pre.cluster as it leads to an empty output file. I looked at the other topics about this which state that it is most likely a missing counts file but I checked my commands and unless I’m overlooking something, I think they are correct. The biggest difference is that I’m starting from a single sample so there is no counts file generated by make.contigs and only after I run unique.seqs for the first time. When I run the same analysis with Mothur v1.43.0, pre.cluster works without issues although it does seem to run a command get.seqs automatically which the one in v1.48.0 doesn’t.
Do you have any idea what is going on or what I’m missing?
The commands that I ran before pre.cluster are:
make.contigs(ffastq=SAMPLE.trimmed_reads_1P.fastq, rfastq=SAMPLE.trimmed_reads_2P.fastq, processors=8)
summary.seqs(fasta=current)
screen.seqs(fasta=current, processors=1, maxambig=5, maxhomop=15, maxlength=600)
unique.seqs(fasta=current)
pcr.seqs(fasta=silva.db.fasta, processors=8, keepdots=F, keepprimer=T, start=11895, end=25318)
align.seqs(fasta=SAMPLE.trimmed_reads_1P.trim.contigs.good.unique.fasta, reference=silva.db.pcr.fasta, processors=8)
summary.seqs(fasta=current, count=current)
screen.seqs(fasta=current, count=current, processors=1, start=1968, end=11550)
summary.seqs(fasta=current, count=current)
filter.seqs(fasta=current, processors=8, trump=., vertical=T)
unique.seqs(fasta=current, count=current)
And the output from pre.cluster:
mothur > pre.cluster(fasta=current, count=current, processors=1, diffs=2)
Using SAMPLE.trimmed_reads_1P.trim.contigs.good.unique.good.filter.count_table as input file for the count parameter.
Using SAMPLE.trimmed_reads_1P.trim.contigs.good.unique.good.filter.unique.fasta as input file for the fasta parameter.
Using 1 processors.
1774 710 1064
Total number of sequences before precluster was 1774.
pre.cluster removed 1064 sequences.
/******************************************/
[WARNING]: SAMPLE.trimmed_reads_1P.trim.contigs.good.unique.good.filter.unique.fasta does not contain any sequence from the .accnos file.
Selected 0 sequences from SAMPLE.trimmed_reads_1P.trim.contigs.good.unique.good.filter.unique.fasta.
Output File Names:
SAMPLE.trimmed_reads_1P.trim.contigs.good.unique.good.filter.unique.precluster.fasta
/******************************************/
Done.
It took 0 secs to cluster 1774 sequences.
Using 1 processors.
Output File Names:
SAMPLE.trimmed_reads_1P.trim.contigs.good.unique.good.filter.unique.precluster.fasta
SAMPLE.trimmed_reads_1P.trim.contigs.good.unique.good.filter.unique.precluster.count_table
SAMPLE.trimmed_reads_1P.trim.contigs.good.unique.good.filter.unique.precluster.map