Dear Sir,
I am new user to mothur, I got stuck at command dist.shared in MiSeq_SOP. It is showing that i have not provided enough valid groups. Please help me to sort the problem- I am mentioning the programme file which i got from command count.groups.
Thanking you.
mothur > count.groups(shared=stability.an.shared)
mice contains 114769.
Total seqs: 114769.
Output File Names:
stability.an.count.summary
mothur > sub.sample(shared=stability.an.shared, size=2241) Sampling 2241 from each group. 0.03
Output File Names:
stability.an.0.03.subsample.shared
mothur > collect.single(shared=stability.an.shared, calc=chao-invsimpson, freq=100) 0.03
Output File Names:
stability.an.mice.chao
stability.an.mice.invsimpson
mothur > rarefaction.single(shared=stability.an.shared, calc=sobs, freq=100)
Using 8 processors.
0.03
Output File Names:
stability.an.groups.rarefaction
mothur > summary.single(shared=stability.an.shared, calc=nseqs-coverage-sobs-invsimpson, subsample=2441) 0.03
Output File Names:
stability.an.groups.ave-std.summary
stability.an.groups.summary
mothur > heatmap.bin(shared=stability.an.0.03.subsample.shared, scale=log2, numotu=50) 0.03
Output File Names:
stability.an.0.03.subsample.0.03.heatmap.bin.svg
mothur > dist.shared(shared=stability.an.shared, calc=thetayc-jclass, subsample=2241)
Using 8 processors.
You have not provided enough valid groups. I cannot run the command.
With Regards! Dr Ch Mashhood Alam Postdoctoral fellow, Dr Alan Schulmann Group, Plant Genomics Lab, Institute of Biotechnology, University of Helsinki, Finland.