*.files vs *.paired.files


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

Batch Mode

Setting environment variable OUTPUT_DIR to /home/amichaud/nv_out

mothur > set.dir(output=/home/amichaud/nv_out)
Mothur’s directories:

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.


The make.file command searches the input directory for *.fastq files and then tries to pair them based on the names of the files. If mothur is able to pair all the fastq files, then the output file is names nv.files. If mothur is able to pair some of the fastq files but others remain unpaired, then 2 output files are created: nv.paired.files and nv.single.files.

Thanks, Sarah! I understand now.

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