make.contigs - number of seqs in fasta does not match .groups file

Commands in mothur
1

Hey,
Thanks again for this wonderful software and the work and support your are doing! Great!
We are facing a problem in analysing Illumina seqs right after the first command (make.contigs). The total number of seqs in the .groups file is higher than in the .fasta file? We did the command twince now, but always less seqs in the fasta compared to the .groups. Why is that?
Now of course, we are facing downstream problems.
Thanks a lot in advance! Looking very much forward to your response/discussion.

Kind regards,
Maraike

Here´s a summary of the output:

After make.contig:
…
Total of all groups is 4537734

Output File Names:
bacteria.trim.contigs.fasta
bacteria.trim.contigs.qual
bacteria.contigs.report
bacteria.scrap.contigs.fasta
bacteria.scrap.contigs.qual
bacteria.contigs.groups

mothur >
summary.seqs(fasta=bacteria.trim.contigs.fasta)
Start End NBases Ambigs Polymer NumSeqs
Minimum: 1 35 35 0 3 1
2.5%-tile: 1 440 440 0 4 113442
25%-tile: 1 443 443 0 5 1134414
Median: 1 448 448 0 5 2268828
75%-tile: 1 467 467 0 6 3403242
97.5%-tile: 1 470 470 2 6 4424214
Maximum: 1 500 500 72 249 4537655
Mean: 1 453.41 453.41 0.150312 5.35023

of Seqs: 4537655

Output File Names:
bacteria.trim.contigs.summary

2

Hmmm… That’s weird. How many processors are you using to run this? Could you possibly try running it with fewer processors (or even just 1) and tell us what happens?

Pat

3

What version of mothur are you using?

4

Thanks Pat, for the fast answer. I rerun the command on my laptop now using 8 processors and on the computer I used before using only one processor. Both was fine and the seqs number matches. Thanks a lot - your suggestion solved the problem.
Does this mean I should use only one processor for further analyses on the computer?
All the best, maraike

5

Hi again, the version of mothur I used is v.1.36.1 (last update 7/27/2015).
Thanks for the great support!
Kind regards,
maraike