Every time I have run mothur, I get the typical name progression of $NAME.trim.contigs.fasta (and so on for all other steps). This time I ran mothur (only with 2 samples), and a “paired” was added into the name, such that the file names were now $NAME.paired.trim.contigs.fasta
Setting environment variable OUTPUT_DIR to /home/amichaud/nv_out
mothur > set.dir(output=/home/amichaud/nv_out)
mothur > make.file(inputdir=/home/amichaud/nv_seqs, type=fastq, prefix=nv)
Setting input directory to: /home/amichaud/nv_seqs/
Output File Names:
mothur > make.contigs(file=current, processors=80)
Using /home/amichaud/nv_out/nv.paired.files as input file for the file parameter.
I am trying to make a batch file for our lab and had it working before, but now I need to include “paired” into the batch file or will this be different again next time I run? Just a bit confused.