[ensembl-dev] treebest parameter (invalid option -- 'Z')
Jian-Ying Chiu
jychiu at ym.edu.tw
Thu Nov 21 10:23:58 GMT 2013
Dear Dear sir/madam,
I got an error (see below) while running the GeneTree pipeline.
It told me that I gave a invalid option -- 'Z' for treebest.
Does it mean I install a wrong version of treebest?
If so, how can I get the correct one?
Best regards,
Wally
*Treebest version:*
Program: TreeBeST (gene Tree Building guided by Species Tree)
Version: 1.9.2 build 01Jul2013
*Error from 'msg' table:*
--------------------------------------------------- | 1 |
| 54 | njtree_phyml | 4630 | 86553 |
5119 | 2013-11-21 17:53:11 | 1 | RUN | Lowering max_diff_lk
to 0.0001
| 0 |
| 54 | njtree_phyml | 4631 | 86553 |
5119 | 2013-11-21 17:53:11 | 1 | RUN |
-------------------- EXCEPTION --------------------
MSG: error running treebest [cd /tmp/worker_u00wly00.5119/;
/home/u00wly00/ensembl_pipeline/prg/treebest/treebest-1.9.2/treebest best
-f /tmp/worker_u00wly00.5119/spec_tax.nh -p interm -Z 0.000100
/tmp/worker_u00wly00.5119/294.aln]: 1
best: invalid option -- 'Z'
[tr_get_fp] fail to open file 0.000100
STACK
Bio::EnsEMBL::Compara::RunnableDB::GeneTrees::TreeBest::run_treebest_best
/home/u00wly00/ensembl_api/version_71/ensembl-compara/modules/Bio/EnsEMBL/Compara/RunnableDB/GeneTrees/TreeBest.pm:106
STACK
Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::NJTREE_PHYML::run_njtree_phyml
/home/u00wly00/ensembl_api/version_71/ensembl-compara/modules/Bio/EnsEMBL/Compara/RunnableDB/ProteinTrees/NJTREE_PHYML.pm:182
STACK Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::NJTREE_PHYML::run
/home/u00wly00/ensembl_api/version_71/ensembl-compara/modules/Bio/EnsEMBL/Compara/RunnableDB/ProteinTrees/NJTREE_PHYML.pm:93
STACK Bio::EnsEMBL::Hive::Process::life_cycle
/home/u00wly00/ensembl_api/version_71/ensembl-hive/modules/Bio/EnsEMBL/Hive/Process.pm:134
STACK (eval)
/home/u00wly00/ensembl_api/version_71/ensembl-hive/modules/Bio/EnsEMBL/Hive/Worker.pm:695
STACK Bio::EnsEMBL::Hive::Worker::run_one_batch
/home/u00wly00/ensembl_api/version_71/ensembl-hive/modules/Bio/EnsEMBL/Hive/Worker.pm:675
STACK Bio::EnsEMBL::Hive::Worker::run
/home/u00wly00/ensembl_api/version_71/ensembl-hive/modules/Bio/EnsEMBL/Hive/Worker.pm:528
STACK toplevel
/home/u00wly00/ensembl_api/version_71/ensembl-hive/scripts/runWorker.pl:135
Date (localtime) = Thu Nov 21 17:53:11 2013
Ensembl API version = 71
--
======================
Jian-Ying Chiu, R.A.
Institute of Biomedical Informatics
National Yang-Ming University
Taipei, Taiwan
Tel: +886-2-28267000 ext 7359
======================
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