I'm having trouble getting the get_var_length.py script to run with pxrr rooted trees. For example, I typically get the following error:
terminate called after throwing an instance of 'std::bad_alloc'
what(): std::bad_alloc
Error: this really only works with nexus or newick. Exiting.
Aborted (core dumped)
when running
python ~/Phylo-software/SortaDate/src/get_var_length.py gene_trees --flend .part.treefile.rr.txt
--outf var --outg Cladomyrma_petalae_SRR2184127,Euprenolepis_procera_SRR2184132,Lasius_americanus_nr_N232,Lasius_atopus_nr_N220,Lasius_brevicornis_N239,Lasius_brunneus_N224,Lasius_californicus_SRR2184142,Lasius_carniolicus_N231,Lasius_emarginatus_N226,Lasius_flavus_N222,Lasius_fuliginosus_N223,Lasius_latipes_N227,Lasius_myops_N241,Lasius_nearcticus_N234,Lasius_niger_SRR2184143,Lasius_pallitarsis_N221,Lasius_platythorax_N235,Lasius_psammophilus_N236,Lasius_sabularum_N225,Lasius_sonobei_N238,Lasius_spathepus_N237,Lasius_subumbratus_nr_N230,Lasius_turcicus_N233,Metalasius_myrmidon_N240,Myrmecocystus_flaviceps_SRR2184150,Myrmecocystus_mendax_N121,Myrmecocystus_mexicanus_N228,Myrmecocystus_tenuinodis_N229,Paraparatrechina_brunnella_N122,Paraparatrechina_glabra_SRR2184166,Paraparatrechina_oceanica_SRR2184167,Paratrechina_antsingy_SRR2184168,Paratrechina_longicornis_N120,Paratrechina_longicornis_N125,Paratrechina_longicornis_PPP036,Paratrechina_longicornis_SRR2184169,Paratrechina_zanjensis_SRR2184170,Prenolepis_imparis_SRR2184180,Prenolepis_shanialena_PPP226,Pseudolasius_australis_SRR2184183,Zatania_albimaculata_SRR2184196,Zatania_cisipa_PPP203,Zatania_gloriosa_PPP201
uce_9.part.treefile.rr.txt
I'm having trouble getting the get_var_length.py script to run with pxrr rooted trees. For example, I typically get the following error:
terminate called after throwing an instance of 'std::bad_alloc'
what(): std::bad_alloc
Error: this really only works with nexus or newick. Exiting.
Aborted (core dumped)
when running
python ~/Phylo-software/SortaDate/src/get_var_length.py gene_trees --flend .part.treefile.rr.txt
--outf var --outg Cladomyrma_petalae_SRR2184127,Euprenolepis_procera_SRR2184132,Lasius_americanus_nr_N232,Lasius_atopus_nr_N220,Lasius_brevicornis_N239,Lasius_brunneus_N224,Lasius_californicus_SRR2184142,Lasius_carniolicus_N231,Lasius_emarginatus_N226,Lasius_flavus_N222,Lasius_fuliginosus_N223,Lasius_latipes_N227,Lasius_myops_N241,Lasius_nearcticus_N234,Lasius_niger_SRR2184143,Lasius_pallitarsis_N221,Lasius_platythorax_N235,Lasius_psammophilus_N236,Lasius_sabularum_N225,Lasius_sonobei_N238,Lasius_spathepus_N237,Lasius_subumbratus_nr_N230,Lasius_turcicus_N233,Metalasius_myrmidon_N240,Myrmecocystus_flaviceps_SRR2184150,Myrmecocystus_mendax_N121,Myrmecocystus_mexicanus_N228,Myrmecocystus_tenuinodis_N229,Paraparatrechina_brunnella_N122,Paraparatrechina_glabra_SRR2184166,Paraparatrechina_oceanica_SRR2184167,Paratrechina_antsingy_SRR2184168,Paratrechina_longicornis_N120,Paratrechina_longicornis_N125,Paratrechina_longicornis_PPP036,Paratrechina_longicornis_SRR2184169,Paratrechina_zanjensis_SRR2184170,Prenolepis_imparis_SRR2184180,Prenolepis_shanialena_PPP226,Pseudolasius_australis_SRR2184183,Zatania_albimaculata_SRR2184196,Zatania_cisipa_PPP203,Zatania_gloriosa_PPP201
uce_9.part.treefile.rr.txt