how to launch batch file in mothur

Hi all,

I’ve been trying to launch batch file in mothur for several time but it keeps telling “you are missing (”. Does anyone know how to successfully get mothur running batch file?

I tried “./mothur stability.batch” from MiSeq SOP but cant get it working.

when you use a batch file you launch from the command line not within mothur.

$mothur mothur.batch

Can you show us the contents of the batch file?

Thank you for pointing it out! But i’ve tried in command line, still not working. says"‘stability.batch’ is not recognized as an internal or external command, operable program or batch file." after i entered.

It is the file from the SOP zip downloaded from the mothur website. I just wanna try the batch mode and see how it works. then try to see if i can replicate it to my own data. but keep failing.

I just downloaded the SOP files and ran the script without issues. Are you sure it hasn’t been modified in some way?

I finally got it running. i have to set the working directory to my samples right from C:, not like put sample folders into mothur. it won’t recognized properly, which caused the failure.

i dont know exactly why it failed with my samples in the first place. it ran ok with SOP. but when i copied the mothur into my sample sets and ran the batch file, it kept failing. so i looked into the log file today and figured i needed to set the directory from C:, not like “mothur\samples”.