Running a script from command line

Hi all,

I have a txt file of commands that I want Mothur to run. Im having some trouble getting mothur to open the txt file and run the commands inside. I am running Mothur from the command line. The first line contains the initial commands with the input file I want to use. I have everything in the correct directory. I feel like this should be simple but I am missing something. Any advice? Thanks in advance

Please explain a little bit more. What is your command, what is the result etc…
Maybe have a look at this documentation

So I looked around that link some. I think what I want to do is run Mothur in Batch mode with the txt file I created that has my commands in it. Im just not sure how to get mothur to do that.

These are the commands in my text file which is called mothurscript

make.contigs(ffastq=10_S11_L001_R1_001.fastq, rfastq=10_S11_L001_R2_001.fastq, processors=10)
screen.seqs(fasta=current, maxambig=0, maxlength=300)
count.seqs(name=current, group=current)
align.seq candidate=current,template=/home/cputonti/bacteria_reads/Silva/silva.nr_v119.align)
summary.seqs(fasta=current, count=current, processors=10)

I want to tell Mothur to use this text file to run those commands.


To run mothur in batch file mode you need to open a command prompt. From the command line, it will look like this:

commandPrompt pathTomothur nameOfBatchFile


TARGET_BUILD_DIRTARGET_BUILD_DIR sarahwestcott$ ./mothur “myBatchFile.txt”

Thanks. I figured it out finally. I was trying to run the batch file from inside of Mothur. You need to run the file from outside of Mothur like in your example. Thanks again