Problems with distance matrix

mothur bugs
1

I am trying to conduct a phylogenetic analysis of MiSeq data using the commands outlined in the MiSeq SOP.

I have been running into issues with the clearcut command. Mothur will successfully complete the dist.seq command and produce a phylip formatted matrix that is needed for the clearcut command, however when I try and run clearcut I get errors that look like this:

Clearcut: Incorrect number of values in the distance matrix. Expected 162945179, and found 1029876420.
Clearcut: Syntax error in distance matrix at offset 1122910206.

then mothur crashes. I have tried running dist.seqs with 1 or 2 processors as I thought it might be caused by splitting the operation between too many processors but I continue running into the issue.

If anyone has experienced this before or has any advice on how to fix this problem it would be greatly appreciated,

Thank you,

Mike H.

2

This error occurs when mothur finds an error in the distance file. Too many distances on a line, not enough lines in the file, ect. Most often when this occurs it is caused by a corruption of the file or a problem when the file was created like insufficient disk space to write the entire file.