<div dir="ltr"><p style="font-family:arial,sans-serif;font-size:13px">Dear Dear sir/madam,</p><p style="font-family:arial,sans-serif;font-size:13px">I got an error (see below) while running the GeneTree pipeline. </p><p style="font-family:arial,sans-serif;font-size:13px">
It told me that I gave a invalid option -- 'Z' for treebest. </p><p style="font-family:arial,sans-serif;font-size:13px">Does it mean I install a wrong version of treebest? </p><p style="font-family:arial,sans-serif;font-size:13px">
If so, how can I get the correct one?</p><p style="font-family:arial,sans-serif;font-size:13px"><br></p><p style="font-family:arial,sans-serif;font-size:13px">Best regards,</p><p style="font-family:arial,sans-serif;font-size:13px">
Wally</p><p style="font-family:arial,sans-serif;font-size:13px"><br></p><p style="font-family:arial,sans-serif;font-size:13px"><b>Treebest version:</b></p><p style="font-family:arial,sans-serif;font-size:13px">Program: TreeBeST (gene Tree Building guided by Species Tree)</p>
<p style="font-family:arial,sans-serif;font-size:13px">Version: 1.9.2 build 01Jul2013 <br></p><p style="font-family:arial,sans-serif;font-size:13px"><br></p><p style="font-family:arial,sans-serif;font-size:13px"><b>Error from 'msg' table:</b></p>
<p style="font-family:arial,sans-serif;font-size:13px">--------------------------------------------------- |        1 | </p><p style="font-family:arial,sans-serif;font-size:13px">|          54 | njtree_phyml              |           4630 |  86553 |      5119 | 2013-11-21 17:53:11 |     1 | RUN            | Lowering max_diff_lk to 0.0001                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   |        0 | </p>
<p style="font-family:arial,sans-serif;font-size:13px">|          54 | njtree_phyml              |           4631 |  86553 |      5119 | 2013-11-21 17:53:11 |     1 | RUN            | </p><p style="font-family:arial,sans-serif;font-size:13px">
-------------------- EXCEPTION --------------------</p><p style="font-family:arial,sans-serif;font-size:13px">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</p>
<p style="font-family:arial,sans-serif;font-size:13px"><font color="#ff0000">best: invalid option -- 'Z'</font></p><p style="font-family:arial,sans-serif;font-size:13px">[tr_get_fp] fail to open file 0.000100</p><p style="font-family:arial,sans-serif;font-size:13px">
<br></p><p style="font-family:arial,sans-serif;font-size:13px">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</p>
<p style="font-family:arial,sans-serif;font-size:13px">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</p>
<p style="font-family:arial,sans-serif;font-size:13px">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</p>
<p style="font-family:arial,sans-serif;font-size:13px">STACK Bio::EnsEMBL::Hive::Process::life_cycle /home/u00wly00/ensembl_api/version_71/ensembl-hive/modules/Bio/EnsEMBL/Hive/Process.pm:134</p><p style="font-family:arial,sans-serif;font-size:13px">
STACK (eval) /home/u00wly00/ensembl_api/version_71/ensembl-hive/modules/Bio/EnsEMBL/Hive/Worker.pm:695</p><p style="font-family:arial,sans-serif;font-size:13px">STACK Bio::EnsEMBL::Hive::Worker::run_one_batch /home/u00wly00/ensembl_api/version_71/ensembl-hive/modules/Bio/EnsEMBL/Hive/Worker.pm:675</p>
<p style="font-family:arial,sans-serif;font-size:13px">STACK Bio::EnsEMBL::Hive::Worker::run /home/u00wly00/ensembl_api/version_71/ensembl-hive/modules/Bio/EnsEMBL/Hive/Worker.pm:528</p><p style="font-family:arial,sans-serif;font-size:13px">
STACK toplevel /home/u00wly00/ensembl_api/version_71/ensembl-hive/scripts/runWorker.pl:135</p><p style="font-family:arial,sans-serif;font-size:13px">Date (localtime)    = Thu Nov 21 17:53:11 2013</p><p style="font-family:arial,sans-serif;font-size:13px">
Ensembl API version = 71</p><br clear="all"><div><br></div>-- <br><div dir="ltr">======================<br>Jian-Ying Chiu, R.A.<br>Institute of Biomedical Informatics<br>National Yang-Ming University<br>Taipei, Taiwan<br>
Tel: <a value="+886228267000" style="color:rgb(17,85,204)">+886-2-28267000 ext 7359</a><br>======================<br></div></div>