Tired of creating the input files for make.contigs? Let mothur do that for you! The make.file command takes a input directory and creates a file containing the fastq or gz files in the directory. Need to make a count file that associates your fasta files with samples? The make.file and make.count commands can do that!

Default Settings

The make.fastq command parameters are inputdir, numcols, type and prefix. Inputdir is required.

mothur > make.file(inputdir=fastqTest)

The resulting stability.files looks like:

F8D0     F8D0_S345_L001_R1_001.fastq     F8D0_S345_L001_R2_001.fastq  
F8D125   F8D125_S358_L001_R1_001.fastq   F8D125_S358_L001_R2_001.fastq    
F8D141   F8D141_S359_L001_R1_001.fastq   F8D141_S359_L001_R2_001.fastq    
F8D142   F8D142_S360_L001_R1_001.fastq   F8D142_S360_L001_R2_001.fastq    
F8D143   F8D143_S361_L001_R1_001.fastq   F8D143_S361_L001_R2_001.fastq    



The type parameter is used to indicate what file type you would like mothur to look for. Options are fasta, gz or fastq. Default=fastq.

 mothur > make.file(inputdir=gzTest, type=gz)

The resulting stability.files looks like:

F8D0     F8D0_S345_L001_R1_001.fastq.gz     F8D0_S345_L001_R2_001.fastq.gz  
F8D125   F8D125_S358_L001_R1_001.fastq.gz   F8D125_S358_L001_R2_001.fastq.gz    
F8D141   F8D141_S359_L001_R1_001.fastq.gz   F8D141_S359_L001_R2_001.fastq.gz    
F8D142   F8D142_S360_L001_R1_001.fastq.gz   F8D142_S360_L001_R2_001.fastq.gz    
F8D143   F8D143_S361_L001_R1_001.fastq.gz   F8D143_S361_L001_R2_001.fastq.gz       

Let’s make a file file we can use with make.count.

mothur > make.file(inputdir=fastaTest, type=fasta)

The resulting stability.files will look like:

testfile.DN1576.CAD	    testfile.DN1576.CAD_705.fasta	
testfile.DN1576.EF1a	testfile.DN1576.EF1a_771.fasta	
testfile.DN1576.MDH	    testfile.DN1576.MDH_498.fasta	
testfile.DN1576.RpS5	testfile.DN1576.RpS5_597.fasta	
testfile.DN1577.EF1a	testfile.DN1577.EF1a_771.fasta	
testfile.DN1577.MDH	    testfile.DN1577.MDH_498.fasta	
testfile.DN1577.RpS5	testfile.DN1577.RpS5_597.fasta	
testfile.DN1578.CAD	    testfile.DN1578.CAD_705.fasta	
testfile.DN1578.EF1a	testfile.DN1578.EF1a_771.fasta	

You can use this file as an input for the make.count command:

mothur > make.count(file=stability.files)


The numcols parameter allows you to set number of columns you mothur to make in the file. Options 2 or 3. Default=3 for type=fastq and type=gz, meaning groupName forwardFastq reverseFastq. The groupName is made from the beginning part of the forwardFastq file. Everything up to the first ‘’ or if no ‘’ is found then the root of the forwardFastq filename. The default is 2 for type=fasta, meaning groupName fastaFile.


The prefix parameter allows you to enter your own prefix for the output filename. Default=stability.

 mothur > make.file(inputdir=gzTest, type=gz, prefix=myReallyAwesomeData)

Would create a file containing the list of gz files in gzTest named myReallyAwesomeData.files.


  • 1.36.0 - First Introduced
  • 1.37.0 Adds numcols parameter #162
  • 1.38.1 Adds more flexibility to input file names. #243
  • 1.38.1 Adds prefix parameter. #251
  • 1.39.0 Fixes Windows bug - unable to find files
  • 1.39.0 Creates unique group names for 3 column format
  • 1.39.0 Fixes bug with “find” command for Linux user
  • 1.40.0 Bug Fix: Fixes group names.
  • 1.48.1 Adds fasta type.