Hi all I am trying to use cluster or cluster.seq on my data and It has worked before but I keep getting duplicates of otu’s in my data output so I was trying to see where I made an error and It keeps saying this for all my samples.
**** Exceeded maximum allowed command errors, quitting ****
[ERROR]: cannot convert F24NPR1_2S to an integer.
Any help would be great!
What version of mothur are you using? Could you post the commands you ran?
Hi I am using Mothur v.1.48.2
Here is the commands I wrote. I also can’t find the file it spits out at the end on my computer so I am assuming it did not actually make one.
Thanks for providing the screen shot. It looks like there is an issue reading the count file. Could you post the first few lines of the count file?
The count file looks like it was modified outside of mothur which is causing an issue. For the compressed count table format, mothur expects the first 2 lines to look like:
#Compressed Format: groupIndex,abundance. For example 1,6 would mean the read has an abundance of 6 for group F3D0.
#1,F3D0 2,F3D1 3,F3D141 4,F3D142 5,F3D143 6,F3D144 7,F3D145 8,F3D146 9,F3D147 10,F3D148 11,F3D149 12,F3D150 13,F3D2 14,F3D3 15,F3D5 16,F3D6 17,F3D7 18,F3D8 19,F3D9 20,Mock
Your file is missing the first line.
oh my gosh! I probably did edit it when i was playing with it in R studio, thank you!!