[ensembl-dev] treebest parameter (invalid option -- 'Z')

[Matthieu Muffato]

Dear Wally

We have indeed added some new options in TreeBest. The latest version 
can be found on github: https://github.com/muffato/treebest

Please note that the location of the repository will probably move in 
December to join the new Ensembl organisation (still on github)

Best regards,
Matthieu

On 21/11/13 10:23, Jian-Ying Chiu wrote:
> 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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>


-- 
Matthieu Muffato, Ph.D.
Ensembl Developer and Ensembl Compara Manager
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus, Hinxton
Cambridge, CB10 1SD, United Kingdom
Room  A3-145
Phone + 44 (0) 1223 49 4631
Fax   + 44 (0) 1223 49 4468