I am running through the Schloss_SOP and discovered that I got no output at a certain timepoint when I wanted to try collect.shared on my data. This gave empty outputs for all calculators.
I looked into the log and I noticed that I forgot to include the groups file when subsampling for the first time (OTU based analysis). When I wanted to rerun the sub.sample(shared=final.an.shared,group=final.groups, size=1017) I got the following output:
Group file only valid with listfile or fastafile.
[ERROR]: did not complete sub.sample.
I am running Mothur 1.22.2 on a Ubuntu 10.04 LTS 64 bit machine, Final.groups is not empty (6.0 MB in size), however when I request get.group(shared=final.an.shared) the output file final.an.bootGroups is empty.
Do I need to rerun the entire analysis from scratch or am I overlooking something here (please say yes )?
I re-ran the complete analysis according to the SOP on my data on my server.
I log in via Byobu on a ubuntu 11.10 server.
All goes well untill I try the sub.sample step in which, once again, I obtained the following output: