I am going through the MiSeq SOP and I think I found a small bug in align.seqs where some characters in the input file name are not allowed. When I try to load the file:
I get the following error:
Unable to open '/data/testdir/results/mothur_test/2016. Trying default /usr/local/bin/mothur/1.36.1/2016
When I change the directory name to one without ‘-’ (e.g. fasta=/data/testdir/results/mothur_test/20160308_120923/stability.trim.contigs.good.unique.fasta) align.seqs runs as expected. This behaviour also doesn’t occur with the ‘reference=’ option which loads files with ‘-’ without any problems. It also didn’t occur in any other function that I used up to now.