[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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