[Biopython] KOBAS - KEGG Orthology Based Annotation System XML file empty problem

[Laszlo Kun]

Dear All,

I am trying to install for a user the KOBAS software, which is done apparently, but after about 3 hours is felt over with
the error message:

======================
[rossh at tango Ov_KOBAS]$ cat NY.e789941
Traceback (most recent call last):
File "/usr/local/python/2.6.2-gcc/bin/blast2ko.py", line 90, in <module>
annots = dict([ (i.query, i) for i in annotator.annotate() ])
File
"/usr/local/python/2.6.2-gcc/lib/python2.6/site-packages/kobas/annot.py",
line 151, in annotate
for record in self.reader:
File
"/usr/local/python/2.6.2-gcc/lib/python2.6/site-packages/Bio/Blast/NCBIXML.py",
line 605, in parse
raise ValueError("Your XML file was empty")
ValueError: Your XML file was empty

=============================


The script appears to have completed the blast section against the KOBAS
database, but has fallen over on the annotation pass.

I haven't come across this error before.

Thanks again for your help.

cheers,
Laszlo