Hi All,
I am working to align 16s v4 rRNA gene ASVs. I have successfully done pcr.seqs as described below. I have also read in my ASVs.fa file to ensure that it seems reasonable (using summary.seqs) as described below. This is not my first time processing data this way, but for whatever reason, when I do the align.seqs it starts to read in the reference sequences then quits. I have tried adjusting the number of processors (2 to 16) but that did not solve the issue. I was wondering what else I could do to determine the issue. I am wondering if it is a memory/RAM issue?
input:
pcr.seqs(fasta=silva.nr_v138_2.align, start=11894, end=25319, keepdots=F, processors=16)
output:
\[NOTE\]: no sequences were bad, removing silva.nr_v138_2.bad.accnos
It took 11 secs to screen 164296 sequences.
Output File Names:
silva.nr_v138_2.pcr.align
input:
summary.seqs(fasta=silva.nr_v138_2.pcr.align )
output:
Start End NBases Ambigs Polymer NumSeqs
Minimum: 1 9876 85 0 3 1
2.5%-tile: 1 13425 291 0 3 4108
25%-tile: 1 13425 293 0 4 41075
Median: 1 13425 293 0 5 82149
75%-tile: 1 13425 293 0 5 123223
97.5%-tile: 1 13425 460 1 6 160189
Maximum: 4227 13425 1521 5 20 164296
Mean: 1 13424 308 0 4
# of Seqs: 164296
It took 3 secs to summarize 164296 sequences.
input:
summary.seqs(fasta = ./Analysis/ASVs.fa)
output:
Start End NBases Ambigs Polymer NumSeqs
Minimum: 1 220 220 0 3 1
2.5%-tile: 1 220 220 0 3 157
25%-tile: 1 252 252 0 4 1568
Median: 1 253 253 0 5 3135
75%-tile: 1 253 253 0 6 4702
97.5%-tile: 1 254 254 0 8 6113
Maximum: 1 257 257 0 220 6269
Mean: 1 246 246 0 5
# of Seqs: 6269
It took 0 secs to summarize 6269 sequences.
input:
align.seqs(fasta = ./Analysis/ASVs.fa, reference= silva.nr_v138_2.pcr.align, processors =2)
output:
Using 2 processors.
Reading in the silva.nr_v138_2.pcr.align template sequences… Killed