i have followed the analysis tutorial in the Esophageal community analysis but keep running into a problem with trying to execute make.shared in that it only outputs the uniques in the .shared file. I feel that this is a bug as the same commands were run in a previous version with many of the same sequences with out this problem.
Any help would be appreciated
Thanks!!
here is what i have run with the output files shown:
mothur > align.seqs(fasta=sample_sequences_all.fas, reference=core_set_aligned.imputed.fasta, flip=T)
Output File Names:
sample_sequences_all.align
sample_sequences_all.align.report
sample_sequences_all.flip.accnos
mothur > dist.seqs(fasta=sample_sequences_all.align, output=lt, processors=2)
Output File Name:
sample_sequences_all.phylip.dist
mothur > cluster(phylip=sample_sequences_all.phylip.dist, cutoff=0.10)
Output File Names:
sample_sequences_all.phylip.an.sabund
sample_sequences_all.phylip.an.rabund
sample_sequences_all.phylip.an.list
mothur > make.shared(list=sample_sequences_all.phylip.an.list, group=sample_sequences_all.groups, label=unique-0.03-0.05-0.10)
unique
Output File Names:
sample_sequences_all.phylip.an.ESP_200m.rabund
sample_sequences_all.phylip.an.ESP_450m.rabund
sample_sequences_all.phylip.an.ESP_60m.rabund
sample_sequences_all.phylip.an.HOT_4000.rabund
sample_sequences_all.phylip.an.HOT_500.rabund
sample_sequences_all.phylip.an.J8_P4_1000m.rabund
sample_sequences_all.phylip.an.NAM119m.rabund
sample_sequences_all.phylip.an.NAM130m.rabund
sample_sequences_all.phylip.an.NAM90m.rabund
sample_sequences_all.phylip.an.P1210.rabund
sample_sequences_all.phylip.an.P121000.rabund
sample_sequences_all.phylip.an.P122000.rabund
sample_sequences_all.phylip.an.P12500.rabund
sample_sequences_all.phylip.an.P2610.rabund
sample_sequences_all.phylip.an.P261000.rabund
sample_sequences_all.phylip.an.P262000.rabund
sample_sequences_all.phylip.an.P26500.rabund
sample_sequences_all.phylip.an.P410.rabund
sample_sequences_all.phylip.an.P41000.rabund
sample_sequences_all.phylip.an.P41300.rabund
sample_sequences_all.phylip.an.P4500.rabund
sample_sequences_all.phylip.an.SI060_100.rabund
sample_sequences_all.phylip.an.SI060_150.rabund
sample_sequences_all.phylip.an.SI060_185.rabund
sample_sequences_all.phylip.an.SI_Apr07_100m.rabund
sample_sequences_all.phylip.an.SI_Apr07_10m.rabund
sample_sequences_all.phylip.an.SI_Apr07_120m.rabund
sample_sequences_all.phylip.an.SI_Apr07_200m.rabund
sample_sequences_all.phylip.an.SI_Apr08_100m.rabund
sample_sequences_all.phylip.an.SI_Apr08_120m.rabund
sample_sequences_all.phylip.an.SI_Apr08_200m.rabund
sample_sequences_all.phylip.an.SI_Feb06_100m.rabund
sample_sequences_all.phylip.an.SI_Feb06_10m.rabund
sample_sequences_all.phylip.an.SI_Feb06_125m.rabund
sample_sequences_all.phylip.an.SI_Feb06_215m.rabund
sample_sequences_all.phylip.an.SI_Jul06_100m.rabund
sample_sequences_all.phylip.an.SI_Jul06_10m.rabund
sample_sequences_all.phylip.an.SI_Jul06_120m.rabund
sample_sequences_all.phylip.an.SI_Jul06_200m.rabund
sample_sequences_all.phylip.an.SI_Nov06_100m.rabund
sample_sequences_all.phylip.an.SI_Nov06_10m.rabund
sample_sequences_all.phylip.an.SI_Nov06_120m.rabund
sample_sequences_all.phylip.an.SI_Nov06_200m.rabund
sample_sequences_all.phylip.an.shared
mothur > quit()