Trouble with Miseq SOP Example Analysis

1

Hello,

Going through the Miseq SOP example (MiSeq SOP) and am having issues with a step:

After running this step:

mothur > screen.seqs(fasta=stability.trim.contigs.unique.align, count=stability.trim.contigs.count_table, start=1969, end=11551)

The results that I should have seen are:

mothur > summary.seqs(fasta=current, count=current)

Using stability.trim.contigs.good.count_table as input file for the count parameter.
Using stability.trim.contigs.unique.good.align as input file for the fasta parameter.

Using 16 processors.
 
       Start	End	NBases	Ambigs	Polymer	NumSeqs
Minimum:	1966	11551	250	0	3	1
2.5%-tile:	1969	11551	252	0	3	3217
25%-tile:	1969	11551	252	0	4	32165
Median: 	1969	11551	252	0	4	64329
75%-tile:	1969	11551	253	0	5	96493
97.5%-tile:	1969	11551	253	0	6	125440
Maximum:	1969	13401	270	0	8	128656
Mean:	1968	11551	252	0	4
# of unique seqs:	16299
total # of seqs:	128656

Instead, I saw:

mothur > summary.seqs(fasta=current, count=current)
Using stability.trim.contigs.good.count_table as input file for the count parameter.
Using stability.trim.contigs.unique.good.align as input file for the fasta parameter.

Using 16 processors.

                Start   End     NBases  Ambigs  Polymer NumSeqs
Minimum:        1965    11552   251     0       3       1
2.5%-tile:      1965    11552   251     0       3       1
25%-tile:       1967    11552   252     0       4       7
Median:         1967    11552   252     0       4       13
75%-tile:       1968    11552   253     0       5       19
97.5%-tile:     1968    13400   270     0       8       24
Maximum:        1968    13400   270     0       8       24
Mean:   1967   11629   252     0       4
# of unique seqs:       23
total # of seqs:        24

Don’t know what went wrong in this step, as everything I had before was matching up with the example.

Specifically, what went wrong was that the unique seqs decreased immensely:

# of unique seqs:       23
total # of seqs:        24

Thanks for any help.

2

This isn’t anythign to worry about. There are subtle differences between versions of mothur and the output from running mothur on different operating systems. I don’t always have the time to update the output of the SOP.

pat