[Bioperl-l] Error while using bp_genbank2gff3.pl script

Dave Messina David.Messina at sbc.su.se
Wed Jan 28 03:19:13 EST 2009

Hi Shafeeq,

The error messages that you got provide a clue:

Possible gene unflattening error withNT_011512: consult STDERR

> MSG: seq_id must be set

Perhaps there is an improperly formed or missing identifier in that record
I would open up the genbank file you are trying to process and look at
NT_011512 (and even the record before it -- sometimes an error isn't caught
right away).

Then I would extract that single record from the file and try to run the
script on it alone. If doing that produced the same error, then I would run
the script again on the main file (with that record having been removed) and
see if there's still a problem.


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