Error during run

[christellesawaya]

Hi, I am trying to run the Tax4FUN2 pipeline on R and get this error after some time: Warning: cannot open file '/Users/..../Tax4FUN2/Tax4Fun2_ReferenceData_v2/KEGG/ko.txt': No such file or directoryError in file(file, "rt") : cannot open the connection

Could you please help me with this issue?

Thank you, Christelle

[songweizhi]

Hi Christelle,

Have you downloaded the referende dataser Tax4Fun2_ReferenceData_v2 on your computer and provided the corrected path to this folder?

Weizhi

[christellesawaya]

I downloaded it again and rerun the code. Are output files correct? (image attached)

Thank you! Christelle

[songweizhi]

Looks good to me (by their names), there are also some example input/output files included in this repo: https://github.com/songweizhi/Tax4Fun2_short_tutorial/blob/master/example_input_files/outputs.zip

[christellesawaya]

Thank you for validating, the content is correct (I was using the tutorial files as well). I am trying now to run it with my actual data I obtained from mothur SOP. For .fasta, i am using a representative sequences .fasta file. I am not sure what _table.txt file to use, I have a .shared file that contains counts , and it caused the following error: "Using minimum idenity cutoff of 97% to nearest neighbor Error in read.table(file = file, header = header, sep = sep, quote = quote, : more columns than column names"

[songweizhi]

the table file contains the abundance information of OTUs across your samples.