Solved! Groups missing in sequence and name files

mothur bugs
1

Hi

Have a strange problem, v1.25. Start with trim.flows with an oligo file and get out 8 flow files. Then shhh.flows and trim.seqs. After trim.seqs I saw that something was wrong. The shhh.flows gave out 8 sets of qual, fasta, names, counts, groups. But when I did trim.seqs on the main fasta and name file, It only gave med 6 sets (2 missing). I have two different datasets with 8 each, and in both only 6 sets was left after trim.seqs. I saw that these sets where missing in the main fasta and name file after shhh.flows, even if all the individual files where there for all 8 sets. The missing ones where located next to each other on the oligo file, on the first dataset on barcode 5 and 6, and in the second dataset on barcode 3 and 4.

Could this be a bug?

Best
Erik

2

How many sequences were in the 8 shhh.fasta files? Are you using the same pdiffs and bdiffs settings in trim.flows and trim.seqs?

3

I used the same settings pdiffs=2, bdiffs=1 in both trim.flows and trim.seqs. The number of sequences in the eight files are from 6197 to 10521.

4

Hi

This was probably a bug in v.1.25. Got 8 sets in v.1.26

Erik