clearcut error and crashes

mothur bugs
1

Trying to use mothur to align and put into a tree a small number of sequences, ran the following:
lign.seqs(fasta=unidentified.blast.hits.fasta, reference=silva.bacteria/silva.bacteria.fasta, flip=T)

filter.seqs(fasta=unidentified.blast.hits.align, vertical=T, trump=.)

dist.seqs(fasta=unidentified.blast.hits.filter.fasta, output=lt)

clearcut(phylip=unidentified.blast.hits.filter.phylip.dist)

Clearcut: Incorrect number of distance values on row.
Clearcut: Syntax error in distance matrix at offset 11539.

And mothur shuts down.

2

If you send your distance matrix to mothur.bugs@gmail.com, I can try to track down the problem for you?

3

Thanks for sending your file. I was able to track down the problem. The clearcut source was written by Initiative for Bioinformatics and Evolutionary Studies (IBEST) at the University of Idaho. The code requires sequence names to be at least 10 characters long. Some of your sequence names are less than 10 characters which is causing the read to get off track. If you modify the sequence names it should run properly. I hope this helps.

4

Hi Sarah and Patrick: I ran into a similar problem with clearcut as Georgia posted in 2012" “Incorrect number of distance values on row” and “Syntax error in distance matrix at offset 3348507401”. After reading your reply, I checked my filenames and found none shorter than 10 characters. Filenames range from 46-48 characters. In case you have time to look at it, I am sending the distance matrix and name file to mothurbugs.

thanks,

Giovanni