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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

taxize fails #37

Closed rvosa closed 9 years ago

rvosa commented 9 years ago 
vagrant@supersmart:~/piperaceae$ smrt taxize -i names.txt 
INFO Bio::SUPERSMART::App::smrt::Command::Taxize::run [/home/vagrant/SUPERSMART/src/supersmart/lib/Bio/SUPERSMART/App/smrt/Command/Taxize.pm: 91] - read 88 species names from names.txt
INFO Bio::Phylo::PhyLoTA::Service::ParallelService::pmap_pthreads [/home/vagrant/SUPERSMART/src/supersmart/lib/Bio/Phylo/PhyLoTA/Service/ParallelService.pm: 116] - pmap pthreads has 3 nodes available
INFO Bio::Phylo::PhyLoTA::Service::ParallelService::pmap_pthreads [/home/vagrant/SUPERSMART/src/supersmart/lib/Bio/Phylo/PhyLoTA/Service/ParallelService.pm: 123] - Detaching 30 items to thread # 1
INFO Bio::Phylo::PhyLoTA::Service::ParallelService::pmap_pthreads [/home/vagrant/SUPERSMART/src/supersmart/lib/Bio/Phylo/PhyLoTA/Service/ParallelService.pm: 123] - Detaching 30 items to thread # 2
INFO Bio::Phylo::PhyLoTA::Service::ParallelService::__ANON__ [/home/vagrant/SUPERSMART/src/supersmart/lib/Bio/Phylo/PhyLoTA/Service/ParallelService.pm: 129] - Thread 1 is processing item # 1 / 30
Thread 1 terminated abnormally: main=HASH(0x7f271c44fa70) at /home/vagrant/SUPERSMART/src/supersmart/lib/Bio/Phylo/PhyLoTA/Service/ParallelService.pm line 137.
INFO Bio::Phylo::PhyLoTA::Service::ParallelService::pmap_pthreads [/home/vagrant/SUPERSMART/src/supersmart/lib/Bio/Phylo/PhyLoTA/Service/ParallelService.pm: 123] - Detaching 28 items to thread # 3
INFO Bio::Phylo::PhyLoTA::Service::ParallelService::__ANON__ [/home/vagrant/SUPERSMART/src/supersmart/lib/Bio/Phylo/PhyLoTA/Service/ParallelService.pm: 129] - Thread 2 is processing item # 1 / 30
Thread 2 terminated abnormally: main=HASH(0x7f2714285f90) at /home/vagrant/SUPERSMART/src/supersmart/lib/Bio/Phylo/PhyLoTA/Service/ParallelService.pm line 137.
INFO Bio::Phylo::PhyLoTA::Service::ParallelService::__ANON__ [/home/vagrant/SUPERSMART/src/supersmart/lib/Bio/Phylo/PhyLoTA/Service/ParallelService.pm: 129] - Thread 3 is processing item # 1 / 28
Thread 3 terminated abnormally: main=HASH(0x7f2718285930) at /home/vagrant/SUPERSMART/src/supersmart/lib/Bio/Phylo/PhyLoTA/Service/ParallelService.pm line 137.
INFO Bio::SUPERSMART::App::smrt::Command::Taxize::run [/home/vagrant/SUPERSMART/src/supersmart/lib/Bio/SUPERSMART/App/smrt/Command/Taxize.pm: 150] - Data received, writing outfile!
INFO Bio::SUPERSMART::App::smrt::Command::Taxize::run [/home/vagrant/SUPERSMART/src/supersmart/lib/Bio/SUPERSMART/App/smrt/Command/Taxize.pm: 188] - DONE, results written to ./species.tsv
hettling commented 9 years ago

I cannot reproduce this using a fresh vm. This bug was fixed in a previous version. Does 'git pull' on the vm fix this?