dist.seqs outputs files aren't output

I just ran dist.seq on some data and mothur reported the following

Output File Name:

It took 7992 to calculate the distances for 34797 sequences.

but the file doesn’t seem to exist:
andrew@andrew-desktop:~/Documents/SEQ_DATA/linum_tags/bac$ ls
bissett08-10-10LabeledparseTH bissett_bac.processed_chim.filter.fasta.summary bissett_bac.processed_good.filter.fasta.summary
bissett_bac.filter bissett_bac.processed_chim.names bissett_bac.processed_good.names
bissett_bac.processed_chim.fasta bissett_bac.processed_good.fasta seq_processing
bissett_bac.processed_chim.filter.fasta bissett_bac.processed_good.filter.fasta

I ran it again on another dataset:

Output File Name:

It took 538 to calculate the distances for 9978 sequences.

and again no output file appeared.

Any suggestions as to where they might be would be appreciated

Thanks again,


Could you run the find command to see if mothur mistakenly put the file somewhere else?

did that, they don’t seem to be anywhere

I noticed you have ~ in the file name, I am wondering if mothur did not resolve that properly in the path name. Could you try running the dist.seqs command with full path names?

Sorry for the delayed response, I’ve been on leave. I was a bit skeptical but using the full path name did indeed fix the problem. This seems a bit strange given that ~ just signifies the home directory and this works with all other mothur commands used so far. Thanks for your help