issue with genes.to.kronaTable.py to get COG.tab file

[smeeta]

Hi,

I tried to run the COG from the script :

genes.to.kronaTable.py -i PROKKA.$SAMPLE.cog -m ~/mg-workshop/reference_db/cog/cog.to.cat -H ~/mg-workshop/reference_db/cog/cat.hierarchy -n $SAMPLE -c $SAMPLE.coverage -o $SAMPLE.krona.COG.tab

I get the following error :

$ python genes.to.kronaTable.py \

--infile ~/GROUP/sm/PROKKA.sm.cog
--mapfile ~/GROUP/sm/metagenomics-workshop-master/reference_db/cog/cog.to.cat
--hierarchy ~/GROUP/sm/metagenomics-workshop-master/reference_db/cog/cat.hierarchy
--outfile ~/GROUP/sm/sm.krona.COG.tab
Traceback (most recent call last):
File "genes.to.kronaTable.py", line 200, in
if name == "main": main()
File "genes.to.kronaTable.py", line 157, in main
annotations = ReadMap(args.infile) ## Read annotations the same way as above, then get length of the list for counts
File "genes.to.kronaTable.py", line 30, in ReadMap
ann = row[1]
IndexError: list index out of range

Any help could be really appreciated.

regards
Smeeta