I’m currently working on a Debian Linux (Lenny) system, with oodles of memory. I have compiled mothur for 64 bit linux, but without mpi. I ran the dist.seqs command to generate a distance matrix, but when I try to read it back in using read.dist, I get a message saying that mothur is unable to open my distance file. I have checked numerous times, and the problem is not that I am mistyping the filename.
I have copied the relevant bits of the mothur logfile below. I tried to attach it to this message, but the extension “logfile” is not allowed. I tried changing to end in .txt, but apparently that is not allowed either.
Can you please let me know if I’m missing something obvious that is keeping me from being able to read my distance matrix back in? (In case, it’s relevant: the distance matrix file is very large: 751 Mb)
Bits of the mothur logfile:
mothur v.1.13.0 Last updated: 9/17/2010 mothur > dist.seqs(fasta=hendrik_mothur_pick.fasta, output=lt)
mothur > dist.seqs(fasta=hendrik_mothur_pick.fasta, output=lt)
…and so on, until:
Output File Name:
It took 1139 to calculate the distances for 15125 sequences.
mothur > read.dist(phylip=hendrik_mothur_pick.phylip.dist , name=hendrik_mothur_pick.names, cutoff=0.25)
Unable to open hendrik_mothur_pick.phylip.dist
mothur > quit