Hi
I am running in to a problem with the pre.cluster step.
I am running it as a batch file and the output in mothur log file is as follows.
mothur > summary.seqs(fasta=current)
Using MethodF2.trim.pcr.trim.good.unique.good.filter.unique.fasta as input file for the fasta parameter.
Using 40 processors.
Start End NBases Ambigs Polymer NumSeqs
Minimum: 1 589 250 0 3 1
2.5%-tile: 3 802 250 0 3 1182
25%-tile: 3 826 250 0 4 11814
Median: 3 831 250 0 4 23627
75%-tile: 3 835 250 0 5 35440
97.5%-tile: 3 854 250 0 6 46072
Maximum: 3 861 250 0 8 47253
Mean: 2 830 250 0 4
# of Seqs: 47253
It took 1 secs to summarize 47253 sequences.
Output File Names:
MethodF2.trim.pcr.trim.good.unique.good.filter.unique.summary
mothur > pre.cluster(fasta=MethodF2.trim.pcr.trim.good.unique.good.filter.unique.fasta, count=MethodF2.trim.pcr.trim.good.unique.good.filter.count_table, diffs=2)
Using 40 processors.
When using running without group information mothur can only use 1 processor, continuing.
0 47164 89
1000 40802 6451
2000 39346 7907
3000 38493 8760
4000 37873 9380
5000 37356 9897
6000 36952 10301
7000 36918 10335
8000 36918 10335
9000 36918 10335
10000 36918 10335
11000 36918 10335
12000 36918 10335
13000 36918 10335
14000 36918 10335
15000 36918 10335
16000 36918 10335
17000 36918 10335
18000 36918 10335
19000 36918 10335
20000 36918 10335
21000 36918 10335
22000 36918 10335
23000 36918 10335
24000 36918 10335
25000 36918 10335
26000 36918 10335
27000 36918 10335
28000 36918 10335
29000 36918 10335
30000 36918 10335
31000 36918 10335
32000 36918 10335
33000 36918 10335
34000 36918 10335
35000 36918 10335
36000 36918 10335
37000 36918 10335
38000 36918 10335
39000 36918 10335
40000 36918 10335
41000 36918 10335
42000 36918 10335
43000 36918 10335
44000 36918 10335
45000 36918 10335
46000 36918 10335
47000 36918 10335
47253 36918 10335
Total number of sequences before precluster was 47253.
pre.cluster removed 10335 sequences.
/******************************************/
[WARNING]: MethodF2.trim.pcr.trim.good.unique.good.filter.unique.fasta does not contain any sequence from the .accnos file.
Selected 0 sequences from MethodF2.trim.pcr.trim.good.unique.good.filter.unique.fasta.
Output File Names:
MethodF2.trim.pcr.trim.good.unique.good.filter.unique.precluster.fasta
/******************************************/
Done.
It took 282 secs to cluster 47253 sequences.
Using 40 processors.
Output File Names:
MethodF2.trim.pcr.trim.good.unique.good.filter.unique.precluster.fasta
MethodF2.trim.pcr.trim.good.unique.good.filter.unique.precluster.count_table
MethodF2.trim.pcr.trim.good.unique.good.filter.unique.precluster.map
The .fasta out put does not contain any sequences after this step.
Can you please help me with this?
Thanks in advance,
Sam