how to run batch mode?

Commands in mothur
1

Hi! I’m new to Mothur! I just finished my first runthrough with the MiSeq SOP. For some reason, I am unable to run the batch file for that sop. At the prompt, I enter the file name “stability.batch” and get an error message, as follows:

mothur > stability.batch

[ERROR]: You are missing (
Invalid.

What am I doing wrong?

Thank you!

2

Before you even start mothur you want to run:


mothur stability.batch
3

How do I do so? What command do I need to give? I changed directories, so I’m in the folder containing all of the necessary items. I get the prompt, and enter the file name, as follows:

localhost:MiSeq_SOP michaelfriedman$ stability.batch
-bash: stability.batch: command not found

And, nada. Same on Windows. I’m missing some command or something after the prompt.

Thank you,
Mike

4

at the prompt outside of mothur type:

mothur stability.batch

or

./mothur stability.batch

5

sarahsWork$ ./mothur batchfile

6

Thanks, folks. It worked! :mrgreen:

7

Hi,

I was trying to run the batch mode, but got into a similar problem. All the fastq.gz files and the test2.stability.files file is in the folder mothur_data_batch.

Details:

mothur_data_batch pca$ head -n 3 test2.stability.files
1 428_S5_L001_R1_001.fastq.gz 428_S5_L001_R2_001.fastq.gz
2 431_S1_L001_R1_001.fastq.gz 431_S1_L001_R2_001.fastq.gz
3 436_S83_L001_R1_001.fastq.gz 436_S83_L001_R2_001.fastq.gz


mothur_data_batch pca$ mothur test2.stability.files mothur > 1 428_S5_L001_R1_001.fastq.gz 428_S5_L001_R2_001.fastq.gz [ERROR]: You are missing ( Invalid.

mothur > 2 1431_S1_L001_R1_001.fastq.gz 431_S1_L001_R2_001.fastq.gz
[ERROR]: You are missing (
Invalid.
.
.
mothur > quit()
mothur_data_batch pca$

should I be doing something else?

thanks!

8

you need to give mother the batchfile which is the list of commands. You can look at mine https://github.com/krmaas/bioinformatics/blob/master/mothur.batch

9

Thanks !!