summary.tax 1.39.4 missing taxonomy causes huge log

mothur bugs
1

Hi Sarah

another one. I’m having trouble getting a particular set of samples through my normal process (see classify.seqs error in 1.39.2) so I went ahead without that. But I forgot to comment out summary.tax later in my batch. And got this error enough times that the file was 3tb when the sys admin noticed and killed it.

mothur > summary.tax(taxonomy=current, count=current)
Using JARFSoilFfu.trim.contigs.good.unique.good.filter.precluster.pick.opti_mcc.0.03.rep.count_table as input file for the count parameter.
[WARNING]: no file was saved for taxonomy parameter.
You have no current taxonomy file and the taxonomy parameter is required.
[ERROR]: Could not open
[ERROR]:  is already in your taxonomy file, names must be unique./n[ERROR]:  is already in your taxonomy file, names must be unique./n[ERROR
]:  is already in your taxonomy file, names must be unique./n[ERROR]:  is already in your taxonomy file, names must be unique./n[ERROR]:  is
already in your taxonomy file, names must be unique./n[ERROR]:  is already in your taxonomy file, names must be unique./n[ERROR]:  is alrea
dy in your taxonomy file, names must be unique./n[ERROR]:  is already in your taxonomy file, names must be
2

Mothur should have aborted the command. I will fix that. Without the taxonomy parameter provided, the command is trying to open and read a file with no name.