sub.sample error: group file only valid with listfile (...)

Dear all,

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 :wink: )?

Kind regards,

Frederiek - Maarten Kerckhof

Did you try running sub.sample(list=yourListFile, group=yourGroupFile), then make.group(list=subsampledList, group=subsampledGroup)?

I did and got the following output:

make.group(list=final2.an.subsample.list, groups=final2.subsample.groups )

list is not a valid parameter.
The valid parameters are: fasta, groups, inputdir, and outputdir.
Using final2.fasta as input file for the fasta parameter.
[ERROR]: did not complete make.group.

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:

sub.sample(shared=final2.an.shared, group=final2.groups, size=2000)

Group file only valid with listfile or fastafile.
[ERROR]: did not complete sub.sample.

I see no reason why this doesn’t work. I ran the data trough a previous version of mothur without any problems. No that I try to redo the analysis on mothur 1.22.2 it fails.

Please help.

Kind regards,

FM

With another dataset I got the same error, does anyone has the same problem as me here?

Kind regards,

FM

Sorry, I meant make.shared(list=subsampledList, group=subsampledGroup).

This worked very well.
Thanks!
However I still don’t understand why it wouldn’t work initially for it is exactly the way the tutorial was written.

Kind regards,

FM