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naturalis / supersmart

Self-Updating Platform for the Estimation of Rates of Speciation, Migration And Relationships of Taxa
MIT License
17 stars 5 forks source link

Serious bug in bbdecompose #80

Closed rvosa closed 9 years ago

rvosa commented 9 years ago

Also, the body of bbedcompose::run() is still way too big, so now it is very hard to understand what is actually happening on line 126.

SUPERSMART v0.1.22 - c7e7337591 ~/testcase2 $ smrt bbdecompose
INFO: This is SUPERSMART release v0.1.22
INFO: Going to read backbone tree /home/vagrant/testcase2/consensus.nex
INFO: Going to read taxa mapping /home/vagrant/testcase2/species.tsv
INFO: Going to read list of alignments /home/vagrant/testcase2/aligned.txt
INFO: Extracted 1 clades
-------------------------- EXCEPTION ----------------------------
Message: Can't search on name 'ARRAY(0x5674c08)'
An exception of type Bio::Phylo::Util::Exceptions::BadString
was thrown.
This kind of error happens when an unsafe string argument is
provided.
Refer to the Bio::Phylo::Util::Exceptions documentation for more
information.
------------------------- STACK TRACE ---------------------------
STACK: Bio::Phylo::ListableRole::get_by_name('Bio::Phylo::Forest::Tree=SCALAR(0x69c49c0)', 'ARRAY(0x5674c08)') called at /home/vagrant/SUPERSMART/src/supersmart/lib/Bio/SUPERSMART/App/smrt/Command/BBdecompose.pm line 126
STACK: Bio::SUPERSMART::App::smrt::Command::BBdecompose::run('Bio::SUPERSMART::App::smrt::Command::BBdecompose=HASH(0x6633490)', 'Getopt::Long::Descriptive::Opts::__OPT__::2=HASH(0x67b3c88)', 'ARRAY(0x20138a8)') called at /home/vagrant/SUPERSMART/src/supersmart/lib/Bio/SUPERSMART/App/SubCommand.pm line 119
STACK: Bio::SUPERSMART::App::SubCommand::execute('Bio::SUPERSMART::App::smrt::Command::BBdecompose=HASH(0x6633490)', 'Getopt::Long::Descriptive::Opts::__OPT__::2=HASH(0x67b3c88)', 'ARRAY(0x20138a8)') called at /usr/local/share/perl/5.18.2/App/Cmd.pm line 445
STACK: App::Cmd::execute_command('Bio::SUPERSMART::App::smrt=HASH(0x555c5a8)', 'Bio::SUPERSMART::App::smrt::Command::BBdecompose=HASH(0x6633490)', 'Getopt::Long::Descriptive::Opts::__OPT__::2=HASH(0x67b3c88)') called at /usr/local/share/perl/5.18.2/App/Cmd.pm line 312
STACK: App::Cmd::run('Bio::SUPERSMART::App::smrt') called at /home/vagrant/SUPERSMART/src/supersmart/script/smrt line 4
-----------------------------------------------------------------
SUPERSMART v0.1.22 - c7e7337591 ~/testcase2 $ 
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