One of the commands, regarding the "phylotype" is not running

1

Hi, I’ve just started using Mothur for genomic analysis. Every command ran smoothly until the OTUs analysis. When I give the command:
make.shared(list=final.tx.list, count=final.count_table, label=1), it gives an error stating:
Unable to open final.count_table. Trying input directory C:\Users\eeman\OneDrive\Desktop\miseqsopdata\MiSeq_SOP\final.count_table.
Unable to open C:\Users\eeman\OneDrive\Desktop\miseqsopdata\MiSeq_SOP\final.count_table. Trying MOTHUR_FILES directory C:\Users\eeman\OneDrive\Desktop\miseqsopdata\MiSeq_SOP\final.count_table.
Unable to open C:\Users\eeman\OneDrive\Desktop\miseqsopdata\MiSeq_SOP\final.count_table. Trying mothur’s executable directory C:\Users\eeman\OneDrive\Desktop\miseqsopdata\MiSeq_SOP\final.count_table.
Unable to open C:\Users\eeman\OneDrive\Desktop\miseqsopdata\MiSeq_SOP\final.count_table.
Unable to open final.count_table
Using final.count_table as input file for the count parameter.
[ERROR]: did not complete make.shared.
Kindly assist me in this regard! @pschloss

2

Hi,

Are you sure you didn’t get any error messages earlier in the pipeline? Can you confirm that you see final.count_table in the same directory as final.tx.list?

Pat

3

Hey,
I didn’t get any error messages earlier in the pipeline, and my final count table is in the same directory as final.tx.list with the name final.full!
One thing that confused me is whether the issues arises because my final count table is in excel form? I’m not sure, however
Thank you for your response @pschloss

4

Nothing should be in excel format :slight_smile: Can you regenerate the count_table file without opening the files in excel? I wonder if opening it into excel is corrupting the file.

Pat

5

Got your point, Pat
Thanks a lot!

6

Hey Pat,
I rer-un the commands that are provided in the ‘Miseq SOP’ but the count tables are only appearing in the excel format, what may be the possible reason?
Can you kindly guide me through?
Thank you in anticipation

7

Maybe I don’t know what you mean by excel format? Everything generated by mothur is a text file. There are no excel formatted files generated by mothur.

Can you confirm that you see final.count_table in the same directory as final.tx.list? Your original error makes me think that you’re not in the same location when running mothur as your files

Pat

8

I think I’ve solved the issue
Thank you!