Make.file issue

Commands in mothur
#1

Hello
I am trying to go through the MiSeq SOP with the F3D0_S188_L001_R1_001.fastq and F3D0_S188_L001_R2_001.fastq files and I can’t get past the make.file step.

When I run

make.file(inputdir=mothurhome, type=fastq, prefix=stability)

the application just shuts down with no other result

and when I run
make.file(inputdir=., type=fastq, prefix=stability)

or when I specify the exact location of the files in inputdir, I get a stability files but with only headers:

F3D0 F3D0_S188_L001_R1_001.fastq F3D0_S188_L001_R2_001.fastq

Please let me know if I did something the wrong way
Thanks!

#2

Hi dporco,

The correct output from make.file will have multiple lines that look like this…

F3D0 F3D0_S188_L001_R1_001.fastq F3D0_S188_L001_R2_001.fastq

There should be one line per sample. So it looks like you’re getting the right output when you specify the correct location.

Pat

#3

Hi Pat
Thanks for your answer.
Sorry I was not clear - I meant that I only get one single line in the stability file:
F3D0 F3D0_S188_L001_R1_001.fastq F3D0_S188_L001_R2_001.fastq

When I should have several lines:

F3D0 F3D0_S188_L001_R1_001.fastq F3D0_S188_L001_R2_001.fastq
F3D141 F3D141_S207_L001_R1_001.fastq F3D141_S207_L001_R2_001.fastq
F3D142 F3D142_S208_L001_R1_001.fastq F3D142_S208_L001_R2_001.fastq
…

dp

#4

Are you sure you see all of the other fastq files in that directory?

#5

yes that was why… sorry about that!
Thanks

#6

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