Problems with distance matrix

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.

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.