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Bio::Root::Exception error #6

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frederic-foucault opened this issue Dec 9, 2014 · 0 comments
Open

Bio::Root::Exception error #6

frederic-foucault opened this issue Dec 9, 2014 · 0 comments

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@frederic-foucault
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Here is an example of multiple messages of error like the one below.
Is there a solutions?
Thank you

2014/12/09 10:30:55> Working on /repos/MicrobeDB/share/Bacteria_2014-12-08/Arthrobacter_chlorophenolicus_A6_uid58969/
/repos/MicrobeDB/share/Bacteria_2014-12-08/Arthrobacter_chlorophenolicus_A6_uid58969/NC_011879.gbk
/repos/MicrobeDB/share/Bacteria_2014-12-08/Arthrobacter_chlorophenolicus_A6_uid58969/NC_011881.gbk
/repos/MicrobeDB/share/Bacteria_2014-12-08/Arthrobacter_chlorophenolicus_A6_uid58969/NC_011886.gbk2014/12/09 10:30:55> Parsing file: /repos/MicrobeDB/share/Bacteria_2014-12-08/Arthrobacter_chlorophenolicus_A6_uid58969/NC_011879.gbk
2014/12/09 10:30:56> Couldn't add the following to microbedb: /repos/MicrobeDB/share/Bacteria_2014-12-08/Arthrobacter_chlorophenolicus_A6_uid58969/ ! Reason:
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: start [426645] is greater than end [617].
If you want to truncated and reverse complement,
you must call trunc followed by revcom. Sorry.
STACK: Error::throw
STACK: Bio::Root::Root::throw /Library/Perl/5.18/Bio/Root/Root.pm:449
STACK: Bio::PrimarySeqI::trunc /Library/Perl/5.18/Bio/PrimarySeqI.pm:456
STACK: Bio::SeqFeature::Generic::seq /Library/Perl/5.18/Bio/SeqFeature/Generic.pm:705
STACK: MicrobeDB::Parse::parse_gbk ../../MicrobeDB/Parse.pm:232
STACK: MicrobeDB::Parse::parse_genome ../../MicrobeDB/Parse.pm:94
STACK: main::load_microbedb /Users/frederic.foucault/repos/MicrobeDB/scripts/load_version.pl:119
STACK: /Users/frederic.foucault/repos/MicrobeDB/scripts/load_version.pl:95

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