Hi Sarah
I’m running my normal batch (pretty much the miseq sop). The last sequence is getting duplicated when making the *trim.contigs.good.good.count_table using 1.36.1. I thought that this might be related to calling for a group file when there isn’t one (this time I’m processing a single sample), so removed all the “group=” from the batch, but it still duplicated the last line of the count_table when screen.seqs
grep "M00618_6_000000000-AKVA8_1_2114_15906_28552" CowSaliva.paired.trim.contigs.good.count_table
M00618_6_000000000-AKVA8_1_2114_15906_28552 1
grep "M00618_6_000000000-AKVA8_1_2114_15906_28552" CowSaliva.paired.trim.contigs.good.good.count_table
M00618_6_000000000-AKVA8_1_2114_15906_28552 1
M00618_6_000000000-AKVA8_1_2114_15906_28552 1
Here’s the logfile generating those 2 files:
mothur > count.seqs(name=current, group=current)
[WARNING]: no file was saved for group parameter.
Using CowSaliva.paired.trim.contigs.good.names as input file for the name parameter.
Using 16 processors.
It took 0 secs to create a table for 121530 sequences.
Total number of sequences: 121530
Output File Names:
CowSaliva.paired.trim.contigs.good.count_table
mothur > align.seqs(fasta=current, reference=silva.nr_v119.v4.align) Using CowSaliva.paired.trim.contigs.good.unique.fasta as input file for the fasta parameter.
Using 16 processors.
Reading in the silva.nr_v119.v4.align template sequences… DONE.
It took 64 to read 153307 sequences.
Aligning sequences from CowSaliva.paired.trim.contigs.good.unique.fasta …
Some of you sequences generated alignments that eliminated too many bases, a list is provided in CowSaliva.paired.trim.contigs.good.unique.flip.accnos. If you set the flip parameter to true mothur will try aligning the reverse compliment as well.
It took 17 secs to align 5055 sequences.
Output File Names: CowSaliva.paired.trim.contigs.good.unique.align CowSaliva.paired.trim.contigs.good.unique.align.report CowSaliva.paired.trim.contigs.good.unique.flip.accnos
mothur > summary.seqs(fasta=current, count=current) Using CowSaliva.paired.trim.contigs.good.count_table as input file for the count parameter. Using CowSaliva.paired.trim.contigs.good.unique.align as input file for the fasta parameter.
Using 16 processors.
Start End NBases Ambigs Polymer NumSeqs
Minimum: 1 1231 3 0 1 1
2.5%-tile: 1968 11550 253 0 4 3039
25%-tile: 1968 11550 253 0 4 30383
Median: 1968 11550 253 0 6 60766
75%-tile: 1968 11550 253 0 6 91148
97.5%-tile: 1968 11550 253 0 6 118492
Maximum: 3803 11553 263 0 8 121530
Mean: 1969.85 11549.5 252.999 0 5.12357of unique seqs: 5055
total # of seqs: 121530
Output File Names:
CowSaliva.paired.trim.contigs.good.unique.summary
It took 1 secs to summarize 121530 sequences.
mothur > screen.seqs(fasta=current, count=current, summary=current, start=1968, end=11550, maxhomop=8)
Using CowSaliva.paired.trim.contigs.good.count_table as input file for the count parameter.
Using CowSaliva.paired.trim.contigs.good.unique.align as input file for the fasta parameter.
Using CowSaliva.paired.trim.contigs.good.unique.summary as input file for the summary parameter.
Using 16 processors.
Output File Names:
CowSaliva.paired.trim.contigs.good.unique.good.summary
CowSaliva.paired.trim.contigs.good.unique.good.align
CowSaliva.paired.trim.contigs.good.unique.bad.accnos
CowSaliva.paired.trim.contigs.good.good.count_table
It took 2 secs to screen 5055 sequences.
mothur > filter.seqs(fasta=current, vertical=T)
Using CowSaliva.paired.trim.contigs.good.unique.good.align as input file for the fasta parameter.
Using 16 processors.
Creating Filter…
Running Filter...
Length of filtered alignment: 374 Number of columns removed: 13051 Length of the original alignment: 13425 Number of sequences used to construct filter: 5002
Output File Names:
CowSaliva.filter
CowSaliva.paired.trim.contigs.good.unique.good.filter.fasta
mothur > summary.seqs(fasta=current, count=current) Using CowSaliva.paired.trim.contigs.good.good.count_table as input file for the count parameter. Using CowSaliva.paired.trim.contigs.good.unique.good.filter.fasta as input file for the fasta parameter.
Using 16 processors.
[ERROR]: Your count table contains more than 1 sequence named M00618_6_000000000-AKVA8_1_2114_15906_28552, sequence names must be unique. Please correct.