sub.sample won't write names file

mothur bugs
1

Hi All,

Using latest mothur version (1.26.0) on OS X mountain lion). While trying to create a normalized data set (after cleaning up sequences according to SOP+removing singletons), I’ve tryind running sub.sample on fasta, name, group and shared. Mothur has been able to write all files, except names. Any idea why? Am I doing something wrong?

Thanks,
Gil

** - it seems to be trying to run a rename command, and there is a syntax error… ?

mothur > sub.sample(fasta=current,name=current, group=current, size=5710)
Using /Users/gils/documents/seqanalysis/ccf.redo.abund.fasta as input file for the fasta parameter.
Using /Users/gils/documents/seqanalysis/ccf.redo.abund.groups as input file for the group parameter.
Using /Users/gils/documents/seqanalysis/ccf.redo.abund.names as input file for the name parameter.
Sampling 5710 from 424426.
Deconvoluting subsampled fasta file…
/******************************************/
Running command: unique.seqs(fasta=/Users/gils/documents/seqanalysis/output/ccf.redo.abund.subsample.fasta)
1000 1
2000 5
3000 16
4000 29
5000 178
5710 408

Output File Names:
/Users/gils/documents/seqanalysis/output/ccf.redo.abund.subsample.unique.fasta
/Users/gils/documents/seqanalysis/output/ccf.redo.abund.subsample.names

mv: rename /Users/gils/documents/seqanalysis/output/ccf.redo.abund.subsample.names to /Users/gils/documents/seqanalysis/output/ccf.redo.abund.subsample.names: No such file or directory
/******************************************/
Done.

Output File Names:
/Users/gils/documents/seqanalysis/output/ccf.redo.abund.subsample.names
/Users/gils/documents/seqanalysis/output/ccf.redo.abund.subsample.fasta
/Users/gils/documents/seqanalysis/output/ccf.redo.abund.subsample.groups


mothur >
2

Hi again,

I guess this is a known issue - I couldn’t find the executable for 1.25 for Mac (hoping it’ll work well with 10.8).

Thanks
Gil

3

This is fixed in version 1.27.0, releasing today.

4

Thanks! works well.