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Metagenomics Workshop
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issue with genes.to.kronaTable.py to get COG.tab file #18

Open smeeta opened 2 years ago

smeeta commented 2 years ago

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