Cookbook index
Composing custom workflows¶
This recipe shows how to combine applications to create custom workflows in ete-build.
It shows how to explore the list of available applications and used them in a custom way.
Requirement¶
- ete3
- ete3_external_apps
- Basic concepts regarding ete-build
In [3]:
%%bash
ete3 build apps
---------------------------------------------------------------------------------------------------------------------
tree builders
---------------------------------------------------------------------------------------------------------------------
name | app type | desc.
======================= | ======== | ================================================================================
bionj_default | phyml | BioNJ tree inferred with Phyml. default models JTT/GTR
fasttree_default | fasttree | Fasttree with default parameters
fasttree_full | fasttree | Fasttree with slow NNI and MLACC=3
phyml_default | phyml | Phyml tree using +G+I+F, 4 classes and aLRT branch supports. Default models JTT/
| | GTR
phyml_default_bootstrap | phyml | Phyml tree using +G+I+F, 4 classes and 100 bootstraps. Default models JTT/GTR
raxml_default | raxml | RAxML with default parameters, GAMMA JTT/GTR and aLRT branch supports.
raxml_default_bootstrap | raxml | RAxML with default parameters, GAMMA JTT/GTR and 100 boostrap replicates
treebest_ensembl | phyml | (EXPERIMENTAL)
--------------------------------------------------------------------------------------------------------------------
aligners
--------------------------------------------------------------------------------------------------------------------
name | app type | desc.
==================== | ========== | ================================================================================
metaligner_phylomedb | metaligner | Meta-aligning based on head/tail alignments produced by muscle, mafft and dialig
| | n-tx, scanned with M-Coffee. Unconsistent columns are removed and final alignmen
| | t is cleaned with trimAl
metaligner_trimmed | metaligner | Meta-aligning based on head/tail alignments produced by muscle, mafft and clusta
| | lomega, scanned with M-Coffee. Unconsistent columns are removed and final alignm
| | ent is cleaned with trimAl
metaligner_default | metaligner | Meta-aligning based on head/tail alignments produced by muscle, mafft and clusta
| | lomega, scanned with M-Coffee. Unconsistent columns are removed
tcoffee_default | tcoffee | (EXPERIMENTAL) tcoffee alignment with default paramerters
mcoffee_ensembl | tcoffee | (EXPERIMENTAL) mcoffee alignment as used in the Ensembl database
muscle_default | muscle | muscle alignment with default parameters
mafft_default | mafft | mafft alignment with default parameters
mafft_einsi | mafft | mafft alignment using the E-INS-i mode
mafft_linsi | mafft | mafft alignment using the L-INS-i mode
mafft_ginsi | mafft | mafft alignment using the G-INS-i mode
clustalo_default | clustalo | clustalo with default parameters
------------------------------------------------------------------------------------------------
COG selectors
------------------------------------------------------------------------------------------------
name | app type | desc.
============= | =========== | ==================================================================
brh_cog_dummy | cogselector | Only 4 genes are selected. Just for testing purposes
brh_cog_all | cogselector | all clusters of orthologous groups (COGs) will be used
brh_cog_100 | cogselector | only COGs including 100% of the target species will be used
brh_cog_95 | cogselector | all COGs including at least 95% of the target species will be used
brh_cog_90 | cogselector | all COGs including at least 90% of the target species will be used
brh_cog_85 | cogselector | all COGs including at least 85% of the target species will be used
--------------------------------------
alg concatenators
--------------------------------------
name | app type | desc.
================== | ========= | =====
alg_concat_default | concatalg |
-------------------------------------------------------------------------------------------------------------------------
model testers
-------------------------------------------------------------------------------------------------------------------------
name | app type | desc.
========================= | ========== | ================================================================================
prottest_default | prottest | Uses BioNJ trees to select best protein model from: JTT, WAG, VT, LG and MtREV.
| | Fixed parameters: +G+I+F
pmodeltest_full_ultrafast | pmodeltest | Test all models using NJ tree inference and skipping gamma, invariant sites, and
| | frequency site checks
pmodeltest_full_fast | pmodeltest | Test all models using NJ tree inference
pmodeltest_full_slow | pmodeltest | Test all models using ML tree inference
pmodeltest_soft_ultrafast | pmodeltest | Test JTT,WAG,VT,LG,MtREV models using NJ tree inference and skipping gamma, inva
| | riant sites, and frequency site checks
pmodeltest_soft_fast | pmodeltest | Test JTT,WAG,VT,LG,MtREV models using NJ tree inference
pmodeltest_soft_slow | pmodeltest | Test JTT,WAG,VT,LG,MtREV models using ML tree inference
--------------------------------------------------------------------------------------
alg cleaners
--------------------------------------------------------------------------------------
name | app type | desc.
=============== | ======== | =========================================================
trimal001 | trimal | trimal alignment cleaning removing columns with >1% gaps
trimal01 | trimal | trimal alignment cleaning removing columns with >10% gaps
trimal02 | trimal | trimal alignment cleaning removing columns with >20% gaps
trimal03 | trimal | trimal alignment cleaning removing columns with >30% gaps
trimal05 | trimal | trimal alignment cleaning removing columns with >50% gaps
trimal_gappyout | trimal | trimal alignment cleaning using gappyout algorithm
application can also be looked up by group name: "aligners", "alg cleaners", etc...
In [21]:
%%bash
ete3 build apps "model testers" "alg cleaners"
---------------------------------------------------------------------------------------------------------------
model testers
---------------------------------------------------------------------------------------------------------------
name | app type | desc.
========================= | ========== | ======================================================================
prottest_default | prottest | Uses BioNJ trees to select best protein model from: JTT, WAG, VT, LG a
| | nd MtREV. Fixed parameters: +G+I+F
pmodeltest_full_ultrafast | pmodeltest | Test all models using NJ tree inference and skipping gamma, invariant
| | sites, and frequency site estimations (!G!I!F)
pmodeltest_full_fast | pmodeltest | Test all models using NJ tree inference
pmodeltest_full_slow | pmodeltest | Test all models using ML tree inference
pmodeltest_soft_ultrafast | pmodeltest | Test JTT,WAG,VT,LG,MtREV models using NJ tree inference and skipping g
| | amma, invariant sites, and frequency site estimation (!G!I!F)
pmodeltest_soft_fast | pmodeltest | Test JTT,WAG,VT,LG,MtREV models using NJ tree inference
pmodeltest_soft_slow | pmodeltest | Test JTT,WAG,VT,LG,MtREV models using ML tree inference
--------------------------------------------------------------------------------------
alg cleaners
--------------------------------------------------------------------------------------
name | app type | desc.
=============== | ======== | =========================================================
trimal001 | trimal | trimal alignment cleaning removing columns with >1% gaps
trimal01 | trimal | trimal alignment cleaning removing columns with >10% gaps
trimal02 | trimal | trimal alignment cleaning removing columns with >20% gaps
trimal03 | trimal | trimal alignment cleaning removing columns with >30% gaps
trimal05 | trimal | trimal alignment cleaning removing columns with >50% gaps
trimal_gappyout | trimal | trimal alignment cleaning using gappyout algorithm
2. Understanding workflow names¶
There are currently 4 types of applications that can be used to create a workflow: aligners, alignment trimmers, model testers and tree builders.
A custom workflow name can be created using the following format:
aligner-trimmer-tester-builderWhere each word separated by "-" represents a valid name from the list of available application bindings. For instance, a valid workflow names would be:
mafft_linsi-trimal01-pmodeltest_soft_ultrafast-raxml_defaultThe word none is also allowed to indicate that a step should be ignored.
Any workflow name following such format can be passed with the -w option to ete-build. The list of available workflows produced by ete3 build workflows is in fact a list of aliases to real workflow names. For instance,
standard_fasttree, translates into clustalo_default-none-none-fasttree_default
3. Run your preferred workflow¶
Once you understand how workflow names, you can compose your own pipeline of programs and run it through ete-build.
In [26]:
%%bash
ete3 build -a data/NUP62.aa.fa -o custom/ --clearall -w mafft_linsi-trimal01-pmodeltest_soft_ultrafast-raxml_default
Toolchain path: /Users/jhc/anaconda/bin/ete3_apps
Toolchain version: 2.0.3
--------------------------------------------------------------------------------
ETE build - reproducible phylogenetic workflows
unknown, unknown.
If you use ETE in a published work, please cite:
Jaime Huerta-Cepas, Joaquín Dopazo and Toni Gabaldón. ETE: a python
Environment for Tree Exploration. BMC Bioinformatics 2010,
11:24. doi:10.1186/1471-2105-11-24
(Note that a list of the external programs used to complete all necessary
computations will be also shown after execution. Those programs should
also be cited.)
--------------------------------------------------------------------------------
INFO - Testing x86-64 portable applications...
clustalo: OK - 1.2.1
Dialign-tx not supported in OS X
fasttree: OK - FastTree Version 2.1.8 Double precision (No SSE3), OpenMP (1 threads)
kalign: OK - Kalign version 2.04, Copyright (C) 2004, 2005, 2006 Timo Lassmann
mafft: OK - MAFFT v6.861b (2011/09/24)
muscle: OK - MUSCLE v3.8.31 by Robert C. Edgar
phyml: OK - . This is PhyML version 20160115.
pmodeltest: OK - pmodeltest.py v1.4
prank: OK - prank v.100802. Minimal usage: 'prank sequence_file'
probcons: OK - PROBCONS version 1.12 - align multiple protein sequences and print to standard output
raxml: OK - This is RAxML version 8.1.20 released by Alexandros Stamatakis on April 18 2015.
raxml-pthreads: OK - This is RAxML version 8.1.20 released by Alexandros Stamatakis on April 18 2015.
readal: OK - readAl v1.4.rev6 build[2012-02-02]
statal: OK - statAl v1.4.rev6 build[2012-02-02]
tcoffee: OK - PROGRAM: T-COFFEE Version_11.00.8cbe486 (2014-08-12 22:05:29 - Revision 8cbe486 - Build 477)
trimal: OK - trimAl v1.4.rev6 build[2012-02-02]
INFO - Starting ETE-build execution at Fri Feb 5 21:44:14 2016
INFO - Output directory /Users/jhc/_Devel/cookbook/recipes/custom
INFO - Erasing all existing npr data...
WRNG - Using existing dir: /Users/jhc/_Devel/cookbook/recipes/custom/db
INFO - Reading aa sequences from data/NUP62.aa.fa...
WRNG - 25 target sequences
INFO - ETE build starts now!
INFO - Updating tasks status: (Fri Feb 5 21:44:14 2016)
INFO - Thread mafft_linsi-trimal01-pmodeltest_soft_ultrafast-raxml_default: pending tasks: 1 of sizes: 25
INFO - (W) MultiSeqTask (25 aa seqs, MSF, /mafft_lins...ml_default)
INFO - (D) MultiSeqTask (25 aa seqs, MSF, /mafft_lins...ml_default)
INFO - Waiting 2 seconds
INFO - Updating tasks status: (Fri Feb 5 21:44:16 2016)
INFO - Thread mafft_linsi-trimal01-pmodeltest_soft_ultrafast-raxml_default: pending tasks: 1 of sizes: 25
INFO - (W) AlgTask (25 aa seqs, Mafft, /mafft_lins...ml_default)
INFO - Waiting 2 seconds
INFO - Updating tasks status: (Fri Feb 5 21:44:18 2016)
INFO - Thread mafft_linsi-trimal01-pmodeltest_soft_ultrafast-raxml_default: pending tasks: 1 of sizes: 25
INFO - (W) AlgTask (25 aa seqs, Mafft, /mafft_lins...ml_default)
INFO - Waiting 2 seconds
INFO - Updating tasks status: (Fri Feb 5 21:44:20 2016)
INFO - Thread mafft_linsi-trimal01-pmodeltest_soft_ultrafast-raxml_default: pending tasks: 1 of sizes: 25
INFO - (R) AlgTask (25 aa seqs, Mafft, /mafft_lins...ml_default)
INFO - (D) AlgTask (25 aa seqs, Mafft, /mafft_lins...ml_default)
INFO - Waiting 2 seconds
INFO - Updating tasks status: (Fri Feb 5 21:44:22 2016)
INFO - Thread mafft_linsi-trimal01-pmodeltest_soft_ultrafast-raxml_default: pending tasks: 1 of sizes: 25
INFO - (W) AlgCleanerTask (25 aa seqs, Trimal, /mafft_lins...ml_default)
INFO - Waiting 2 seconds
INFO - Updating tasks status: (Fri Feb 5 21:44:24 2016)
INFO - Thread mafft_linsi-trimal01-pmodeltest_soft_ultrafast-raxml_default: pending tasks: 1 of sizes: 25
INFO - (W) AlgCleanerTask (25 aa seqs, Trimal, /mafft_lins...ml_default)
INFO - Waiting 2 seconds
INFO - Updating tasks status: (Fri Feb 5 21:44:26 2016)
INFO - Thread mafft_linsi-trimal01-pmodeltest_soft_ultrafast-raxml_default: pending tasks: 1 of sizes: 25
INFO - (Q) AlgCleanerTask (25 aa seqs, Trimal, /mafft_lins...ml_default)
INFO - (D) AlgCleanerTask (25 aa seqs, Trimal, /mafft_lins...ml_default)
INFO - Waiting 2 seconds
INFO - Updating tasks status: (Fri Feb 5 21:44:28 2016)
INFO - Thread mafft_linsi-trimal01-pmodeltest_soft_ultrafast-raxml_default: pending tasks: 1 of sizes: 25
INFO - (W) ModelTesterTask (25 aa seqs, PModelTest-[JTT,WAG,VT,LG,MtREV], /mafft_lins...ml_default)
INFO - Waiting 2 seconds
INFO - Updating tasks status: (Fri Feb 5 21:44:30 2016)
INFO - Thread mafft_linsi-trimal01-pmodeltest_soft_ultrafast-raxml_default: pending tasks: 1 of sizes: 25
INFO - (W) ModelTesterTask (25 aa seqs, PModelTest-[JTT,WAG,VT,LG,MtREV], /mafft_lins...ml_default)
INFO - Waiting 2 seconds
INFO - Updating tasks status: (Fri Feb 5 21:44:32 2016)
INFO - Thread mafft_linsi-trimal01-pmodeltest_soft_ultrafast-raxml_default: pending tasks: 1 of sizes: 25
INFO - (Q) ModelTesterTask (25 aa seqs, PModelTest-[JTT,WAG,VT,LG,MtREV], /mafft_lins...ml_default)
INFO - Waiting 2 seconds
INFO - Updating tasks status: (Fri Feb 5 21:44:34 2016)
INFO - Thread mafft_linsi-trimal01-pmodeltest_soft_ultrafast-raxml_default: pending tasks: 1 of sizes: 25
INFO - (R) ModelTesterTask (25 aa seqs, PModelTest-[JTT,WAG,VT,LG,MtREV], /mafft_lins...ml_default)
INFO - Waiting 2 seconds
INFO - Updating tasks status: (Fri Feb 5 21:44:36 2016)
INFO - Thread mafft_linsi-trimal01-pmodeltest_soft_ultrafast-raxml_default: pending tasks: 1 of sizes: 25
INFO - (R) ModelTesterTask (25 aa seqs, PModelTest-[JTT,WAG,VT,LG,MtREV], /mafft_lins...ml_default)
INFO - Waiting 2 seconds
INFO - Updating tasks status: (Fri Feb 5 21:44:38 2016)
INFO - Thread mafft_linsi-trimal01-pmodeltest_soft_ultrafast-raxml_default: pending tasks: 1 of sizes: 25
INFO - (R) ModelTesterTask (25 aa seqs, PModelTest-[JTT,WAG,VT,LG,MtREV], /mafft_lins...ml_default)
INFO - Waiting 2 seconds
INFO - Updating tasks status: (Fri Feb 5 21:44:40 2016)
INFO - Thread mafft_linsi-trimal01-pmodeltest_soft_ultrafast-raxml_default: pending tasks: 1 of sizes: 25
INFO - (R) ModelTesterTask (25 aa seqs, PModelTest-[JTT,WAG,VT,LG,MtREV], /mafft_lins...ml_default)
INFO - Waiting 2 seconds
INFO - Updating tasks status: (Fri Feb 5 21:44:42 2016)
INFO - Thread mafft_linsi-trimal01-pmodeltest_soft_ultrafast-raxml_default: pending tasks: 1 of sizes: 25
INFO - (R) ModelTesterTask (25 aa seqs, PModelTest-[JTT,WAG,VT,LG,MtREV], /mafft_lins...ml_default)
INFO - Waiting 2 seconds
INFO - Updating tasks status: (Fri Feb 5 21:44:44 2016)
INFO - Thread mafft_linsi-trimal01-pmodeltest_soft_ultrafast-raxml_default: pending tasks: 1 of sizes: 25
INFO - (R) ModelTesterTask (25 aa seqs, PModelTest-[JTT,WAG,VT,LG,MtREV], /mafft_lins...ml_default)
INFO - (D) ModelTesterTask (25 aa seqs, PModelTest-[JTT,WAG,VT,LG,MtREV], /mafft_lins...ml_default)
INFO - Waiting 2 seconds
INFO - Updating tasks status: (Fri Feb 5 21:44:46 2016)
INFO - Thread mafft_linsi-trimal01-pmodeltest_soft_ultrafast-raxml_default: pending tasks: 1 of sizes: 25
INFO - (W) TreeTask (25 aa seqs, RaxML, /mafft_lins...ml_default)
INFO - Waiting 2 seconds
INFO - Updating tasks status: (Fri Feb 5 21:44:48 2016)
INFO - Thread mafft_linsi-trimal01-pmodeltest_soft_ultrafast-raxml_default: pending tasks: 1 of sizes: 25
INFO - (W) TreeTask (25 aa seqs, RaxML, /mafft_lins...ml_default)
INFO - Waiting 2 seconds
INFO - Updating tasks status: (Fri Feb 5 21:44:50 2016)
INFO - Thread mafft_linsi-trimal01-pmodeltest_soft_ultrafast-raxml_default: pending tasks: 1 of sizes: 25
INFO - (Q) TreeTask (25 aa seqs, RaxML, /mafft_lins...ml_default)
INFO - Waiting 2 seconds
INFO - Updating tasks status: (Fri Feb 5 21:44:52 2016)
INFO - Thread mafft_linsi-trimal01-pmodeltest_soft_ultrafast-raxml_default: pending tasks: 1 of sizes: 25
INFO - (R) TreeTask (25 aa seqs, RaxML, /mafft_lins...ml_default)
INFO - Waiting 2 seconds
INFO - Updating tasks status: (Fri Feb 5 21:44:54 2016)
INFO - Thread mafft_linsi-trimal01-pmodeltest_soft_ultrafast-raxml_default: pending tasks: 1 of sizes: 25
INFO - (R) TreeTask (25 aa seqs, RaxML, /mafft_lins...ml_default)
INFO - Waiting 2 seconds
INFO - Updating tasks status: (Fri Feb 5 21:44:56 2016)
INFO - Thread mafft_linsi-trimal01-pmodeltest_soft_ultrafast-raxml_default: pending tasks: 1 of sizes: 25
INFO - (R) TreeTask (25 aa seqs, RaxML, /mafft_lins...ml_default)
INFO - Waiting 2 seconds
INFO - Updating tasks status: (Fri Feb 5 21:44:58 2016)
INFO - Thread mafft_linsi-trimal01-pmodeltest_soft_ultrafast-raxml_default: pending tasks: 1 of sizes: 25
INFO - (R) TreeTask (25 aa seqs, RaxML, /mafft_lins...ml_default)
INFO - Waiting 2 seconds
INFO - Updating tasks status: (Fri Feb 5 21:45:00 2016)
INFO - Thread mafft_linsi-trimal01-pmodeltest_soft_ultrafast-raxml_default: pending tasks: 1 of sizes: 25
INFO - (R) TreeTask (25 aa seqs, RaxML, /mafft_lins...ml_default)
INFO - Waiting 2 seconds
INFO - Updating tasks status: (Fri Feb 5 21:45:02 2016)
INFO - Thread mafft_linsi-trimal01-pmodeltest_soft_ultrafast-raxml_default: pending tasks: 1 of sizes: 25
INFO - (R) TreeTask (25 aa seqs, RaxML, /mafft_lins...ml_default)
INFO - Waiting 2 seconds
INFO - Updating tasks status: (Fri Feb 5 21:45:04 2016)
INFO - Thread mafft_linsi-trimal01-pmodeltest_soft_ultrafast-raxml_default: pending tasks: 1 of sizes: 25
INFO - (R) TreeTask (25 aa seqs, RaxML, /mafft_lins...ml_default)
INFO - Waiting 2 seconds
INFO - Updating tasks status: (Fri Feb 5 21:45:06 2016)
INFO - Thread mafft_linsi-trimal01-pmodeltest_soft_ultrafast-raxml_default: pending tasks: 1 of sizes: 25
INFO - (R) TreeTask (25 aa seqs, RaxML, /mafft_lins...ml_default)
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INFO - Thread mafft_linsi-trimal01-pmodeltest_soft_ultrafast-raxml_default: pending tasks: 1 of sizes: 25
INFO - (R) TreeTask (25 aa seqs, RaxML, /mafft_lins...ml_default)
INFO - Waiting 2 seconds
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INFO - Thread mafft_linsi-trimal01-pmodeltest_soft_ultrafast-raxml_default: pending tasks: 1 of sizes: 25
INFO - (R) TreeTask (25 aa seqs, RaxML, /mafft_lins...ml_default)
INFO - Waiting 2 seconds
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INFO - Thread mafft_linsi-trimal01-pmodeltest_soft_ultrafast-raxml_default: pending tasks: 1 of sizes: 25
INFO - (R) TreeTask (25 aa seqs, RaxML, /mafft_lins...ml_default)
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INFO - Thread mafft_linsi-trimal01-pmodeltest_soft_ultrafast-raxml_default: pending tasks: 1 of sizes: 25
INFO - (R) TreeTask (25 aa seqs, RaxML, /mafft_lins...ml_default)
INFO - Waiting 2 seconds
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INFO - Thread mafft_linsi-trimal01-pmodeltest_soft_ultrafast-raxml_default: pending tasks: 1 of sizes: 25
INFO - (R) TreeTask (25 aa seqs, RaxML, /mafft_lins...ml_default)
INFO - Waiting 2 seconds
INFO - Updating tasks status: (Fri Feb 5 21:45:18 2016)
INFO - Thread mafft_linsi-trimal01-pmodeltest_soft_ultrafast-raxml_default: pending tasks: 1 of sizes: 25
INFO - (R) TreeTask (25 aa seqs, RaxML, /mafft_lins...ml_default)
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INFO - (R) TreeTask (25 aa seqs, RaxML, /mafft_lins...ml_default)
INFO - Waiting 2 seconds
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INFO - Thread mafft_linsi-trimal01-pmodeltest_soft_ultrafast-raxml_default: pending tasks: 1 of sizes: 25
INFO - (R) TreeTask (25 aa seqs, RaxML, /mafft_lins...ml_default)
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INFO - (R) TreeTask (25 aa seqs, RaxML, /mafft_lins...ml_default)
INFO - Waiting 2 seconds
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INFO - (R) TreeTask (25 aa seqs, RaxML, /mafft_lins...ml_default)
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INFO - (R) TreeTask (25 aa seqs, RaxML, /mafft_lins...ml_default)
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INFO - (R) TreeTask (25 aa seqs, RaxML, /mafft_lins...ml_default)
INFO - Waiting 2 seconds
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INFO - (R) TreeTask (25 aa seqs, RaxML, /mafft_lins...ml_default)
INFO - Waiting 2 seconds
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INFO - (R) TreeTask (25 aa seqs, RaxML, /mafft_lins...ml_default)
INFO - Waiting 2 seconds
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INFO - (R) TreeTask (25 aa seqs, RaxML, /mafft_lins...ml_default)
INFO - Waiting 2 seconds
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INFO - (R) TreeTask (25 aa seqs, RaxML, /mafft_lins...ml_default)
INFO - Waiting 2 seconds
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INFO - (R) TreeTask (25 aa seqs, RaxML, /mafft_lins...ml_default)
INFO - Waiting 2 seconds
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INFO - (R) TreeTask (25 aa seqs, RaxML, /mafft_lins...ml_default)
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INFO - (R) TreeTask (25 aa seqs, RaxML, /mafft_lins...ml_default)
INFO - Waiting 2 seconds
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INFO - (R) TreeTask (25 aa seqs, RaxML, /mafft_lins...ml_default)
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INFO - Thread mafft_linsi-trimal01-pmodeltest_soft_ultrafast-raxml_default: pending tasks: 1 of sizes: 25
INFO - (R) TreeTask (25 aa seqs, RaxML, /mafft_lins...ml_default)
INFO - Waiting 2 seconds
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INFO - (R) TreeTask (25 aa seqs, RaxML, /mafft_lins...ml_default)
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INFO - (R) TreeTask (25 aa seqs, RaxML, /mafft_lins...ml_default)
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INFO - Updating tasks status: (Fri Feb 5 21:45:54 2016)
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INFO - (R) TreeTask (25 aa seqs, RaxML, /mafft_lins...ml_default)
INFO - Waiting 2 seconds
INFO - Updating tasks status: (Fri Feb 5 21:45:56 2016)
INFO - Thread mafft_linsi-trimal01-pmodeltest_soft_ultrafast-raxml_default: pending tasks: 1 of sizes: 25
INFO - (R) TreeTask (25 aa seqs, RaxML, /mafft_lins...ml_default)
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INFO - Updating tasks status: (Fri Feb 5 21:45:58 2016)
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INFO - (R) TreeTask (25 aa seqs, RaxML, /mafft_lins...ml_default)
INFO - Waiting 2 seconds
INFO - Updating tasks status: (Fri Feb 5 21:46:00 2016)
INFO - Thread mafft_linsi-trimal01-pmodeltest_soft_ultrafast-raxml_default: pending tasks: 1 of sizes: 25
INFO - (R) TreeTask (25 aa seqs, RaxML, /mafft_lins...ml_default)
INFO - Waiting 2 seconds
INFO - Updating tasks status: (Fri Feb 5 21:46:02 2016)
INFO - Thread mafft_linsi-trimal01-pmodeltest_soft_ultrafast-raxml_default: pending tasks: 1 of sizes: 25
INFO - (R) TreeTask (25 aa seqs, RaxML, /mafft_lins...ml_default)
INFO - Waiting 2 seconds
INFO - Updating tasks status: (Fri Feb 5 21:46:04 2016)
INFO - Thread mafft_linsi-trimal01-pmodeltest_soft_ultrafast-raxml_default: pending tasks: 1 of sizes: 25
INFO - (R) TreeTask (25 aa seqs, RaxML, /mafft_lins...ml_default)
INFO - Waiting 2 seconds
INFO - Updating tasks status: (Fri Feb 5 21:46:06 2016)
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INFO - (R) TreeTask (25 aa seqs, RaxML, /mafft_lins...ml_default)
INFO - Waiting 2 seconds
INFO - Updating tasks status: (Fri Feb 5 21:46:08 2016)
INFO - Thread mafft_linsi-trimal01-pmodeltest_soft_ultrafast-raxml_default: pending tasks: 1 of sizes: 25
INFO - (R) TreeTask (25 aa seqs, RaxML, /mafft_lins...ml_default)
INFO - Waiting 2 seconds
INFO - Updating tasks status: (Fri Feb 5 21:46:10 2016)
INFO - Thread mafft_linsi-trimal01-pmodeltest_soft_ultrafast-raxml_default: pending tasks: 1 of sizes: 25
INFO - (R) TreeTask (25 aa seqs, RaxML, /mafft_lins...ml_default)
INFO - Waiting 2 seconds
INFO - Updating tasks status: (Fri Feb 5 21:46:12 2016)
INFO - Thread mafft_linsi-trimal01-pmodeltest_soft_ultrafast-raxml_default: pending tasks: 1 of sizes: 25
INFO - (R) TreeTask (25 aa seqs, RaxML, /mafft_lins...ml_default)
INFO - Waiting 2 seconds
INFO - Updating tasks status: (Fri Feb 5 21:46:14 2016)
INFO - Thread mafft_linsi-trimal01-pmodeltest_soft_ultrafast-raxml_default: pending tasks: 1 of sizes: 25
INFO - (R) TreeTask (25 aa seqs, RaxML, /mafft_lins...ml_default)
INFO - Waiting 2 seconds
INFO - Updating tasks status: (Fri Feb 5 21:46:16 2016)
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INFO - (R) TreeTask (25 aa seqs, RaxML, /mafft_lins...ml_default)
INFO - Waiting 2 seconds
INFO - Updating tasks status: (Fri Feb 5 21:46:18 2016)
INFO - Thread mafft_linsi-trimal01-pmodeltest_soft_ultrafast-raxml_default: pending tasks: 1 of sizes: 25
INFO - (R) TreeTask (25 aa seqs, RaxML, /mafft_lins...ml_default)
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INFO - Updating tasks status: (Fri Feb 5 21:46:20 2016)
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INFO - (R) TreeTask (25 aa seqs, RaxML, /mafft_lins...ml_default)
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INFO - Updating tasks status: (Fri Feb 5 21:46:22 2016)
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INFO - (R) TreeTask (25 aa seqs, RaxML, /mafft_lins...ml_default)
INFO - Waiting 2 seconds
INFO - Updating tasks status: (Fri Feb 5 21:46:24 2016)
INFO - Thread mafft_linsi-trimal01-pmodeltest_soft_ultrafast-raxml_default: pending tasks: 1 of sizes: 25
INFO - (R) TreeTask (25 aa seqs, RaxML, /mafft_lins...ml_default)
INFO - Waiting 2 seconds
INFO - Updating tasks status: (Fri Feb 5 21:46:26 2016)
INFO - Thread mafft_linsi-trimal01-pmodeltest_soft_ultrafast-raxml_default: pending tasks: 1 of sizes: 25
INFO - (R) TreeTask (25 aa seqs, RaxML, /mafft_lins...ml_default)
INFO - Waiting 2 seconds
INFO - Updating tasks status: (Fri Feb 5 21:46:28 2016)
INFO - Thread mafft_linsi-trimal01-pmodeltest_soft_ultrafast-raxml_default: pending tasks: 1 of sizes: 25
INFO - (R) TreeTask (25 aa seqs, RaxML, /mafft_lins...ml_default)
INFO - Waiting 2 seconds
INFO - Updating tasks status: (Fri Feb 5 21:46:30 2016)
INFO - Thread mafft_linsi-trimal01-pmodeltest_soft_ultrafast-raxml_default: pending tasks: 1 of sizes: 25
INFO - (R) TreeTask (25 aa seqs, RaxML, /mafft_lins...ml_default)
INFO - Waiting 2 seconds
INFO - Updating tasks status: (Fri Feb 5 21:46:32 2016)
INFO - Thread mafft_linsi-trimal01-pmodeltest_soft_ultrafast-raxml_default: pending tasks: 1 of sizes: 25
INFO - (R) TreeTask (25 aa seqs, RaxML, /mafft_lins...ml_default)
INFO - Waiting 2 seconds
INFO - Updating tasks status: (Fri Feb 5 21:46:34 2016)
INFO - Thread mafft_linsi-trimal01-pmodeltest_soft_ultrafast-raxml_default: pending tasks: 1 of sizes: 25
INFO - (R) TreeTask (25 aa seqs, RaxML, /mafft_lins...ml_default)
INFO - Waiting 2 seconds
INFO - Updating tasks status: (Fri Feb 5 21:46:36 2016)
INFO - Thread mafft_linsi-trimal01-pmodeltest_soft_ultrafast-raxml_default: pending tasks: 1 of sizes: 25
INFO - (R) TreeTask (25 aa seqs, RaxML, /mafft_lins...ml_default)
INFO - Waiting 2 seconds
INFO - Updating tasks status: (Fri Feb 5 21:46:38 2016)
INFO - Thread mafft_linsi-trimal01-pmodeltest_soft_ultrafast-raxml_default: pending tasks: 1 of sizes: 25
INFO - (R) TreeTask (25 aa seqs, RaxML, /mafft_lins...ml_default)
INFO - Waiting 2 seconds
INFO - Updating tasks status: (Fri Feb 5 21:46:40 2016)
INFO - Thread mafft_linsi-trimal01-pmodeltest_soft_ultrafast-raxml_default: pending tasks: 1 of sizes: 25
INFO - (R) TreeTask (25 aa seqs, RaxML, /mafft_lins...ml_default)
INFO - Waiting 2 seconds
INFO - Updating tasks status: (Fri Feb 5 21:46:42 2016)
INFO - Thread mafft_linsi-trimal01-pmodeltest_soft_ultrafast-raxml_default: pending tasks: 1 of sizes: 25
INFO - (R) TreeTask (25 aa seqs, RaxML, /mafft_lins...ml_default)
INFO - Waiting 2 seconds
INFO - Updating tasks status: (Fri Feb 5 21:46:44 2016)
INFO - Thread mafft_linsi-trimal01-pmodeltest_soft_ultrafast-raxml_default: pending tasks: 1 of sizes: 25
INFO - (W) TreeTask (25 aa seqs, RaxML, /mafft_lins...ml_default)
INFO - Waiting 2 seconds
INFO - Updating tasks status: (Fri Feb 5 21:46:46 2016)
INFO - Thread mafft_linsi-trimal01-pmodeltest_soft_ultrafast-raxml_default: pending tasks: 1 of sizes: 25
INFO - (Q) TreeTask (25 aa seqs, RaxML, /mafft_lins...ml_default)
INFO - Waiting 2 seconds
INFO - Updating tasks status: (Fri Feb 5 21:46:48 2016)
INFO - Thread mafft_linsi-trimal01-pmodeltest_soft_ultrafast-raxml_default: pending tasks: 1 of sizes: 25
INFO - (R) TreeTask (25 aa seqs, RaxML, /mafft_lins...ml_default)
INFO - (D) TreeTask (25 aa seqs, RaxML, /mafft_lins...ml_default)
INFO - Waiting 2 seconds
INFO - Updating tasks status: (Fri Feb 5 21:46:50 2016)
INFO - Thread mafft_linsi-trimal01-pmodeltest_soft_ultrafast-raxml_default: pending tasks: 1 of sizes: 25
INFO - (W) TreeMergeTask (25 aa seqs, TreeMerger, /mafft_lins...ml_default)
INFO - (D) TreeMergeTask (25 aa seqs, TreeMerger, /mafft_lins...ml_default)
INFO - Waiting 2 seconds
INFO - Assembling final tree...
INFO - Done thread mafft_linsi-trimal01-pmodeltest_soft_ultrafast-raxml_default in 1 iteration(s)
INFO - Writing final tree for mafft_linsi-trimal01-pmodeltest_soft_ultrafast-raxml_default
/Users/jhc/_Devel/cookbook/recipes/custom/mafft_linsi-trimal01-pmodeltest_soft_ultrafast-raxml_default/NUP62.aa.fa.final_tree.nw
/Users/jhc/_Devel/cookbook/recipes/custom/mafft_linsi-trimal01-pmodeltest_soft_ultrafast-raxml_default/NUP62.aa.fa.final_tree.nwx (newick extended)
INFO - Writing final tree alignment mafft_linsi-trimal01-pmodeltest_soft_ultrafast-raxml_default
/Users/jhc/_Devel/cookbook/recipes/custom/mafft_linsi-trimal01-pmodeltest_soft_ultrafast-raxml_default/NUP62.aa.fa.final_tree.used_alg.fa
INFO - Writing root node alignment mafft_linsi-trimal01-pmodeltest_soft_ultrafast-raxml_default
/Users/jhc/_Devel/cookbook/recipes/custom/mafft_linsi-trimal01-pmodeltest_soft_ultrafast-raxml_default/NUP62.aa.fa.final_tree.fa
INFO - Writing root node trimmed alignment mafft_linsi-trimal01-pmodeltest_soft_ultrafast-raxml_default
/Users/jhc/_Devel/cookbook/recipes/custom/mafft_linsi-trimal01-pmodeltest_soft_ultrafast-raxml_default/NUP62.aa.fa.final_tree.trimmed.fa
INFO - Generating tree image for mafft_linsi-trimal01-pmodeltest_soft_ultrafast-raxml_default
/Users/jhc/_Devel/cookbook/recipes/custom/mafft_linsi-trimal01-pmodeltest_soft_ultrafast-raxml_default/NUP62.aa.fa.final_tree.png
INFO - Done
INFO - Deleting temporal data...
========================================================================
The following published software and/or methods were used.
*** Please, do not forget to cite them! ***
========================================================================
Capella-Gutiérrez S, Silla-Martínez JM, Gabaldón T. trimAl: a tool for
automated alignment trimming in large-scale phylogenetic analyses.
Bioinformatics. 2009 Aug 1;25(15):1972-3.
Guindon S, Dufayard JF, Lefort V, Anisimova M, Hordijk W, Gascuel O. New
algorithms and methods to estimate maximum-likelihood phylogenies:
assessing the performance of PhyML 3.0. Syst Biol. 2010
May;59(3):307-21.
Huerta-Cepas J, Dopazo J, Gabaldón T. ETE: a python Environment for Tree
Exploration. BMC Bioinformatics. 2010 Jan 13;11:24.
Katoh K, Kuma K, Toh H, Miyata T. MAFFT version 5: improvement in
accuracy of multiple sequence alignment. Nucleic Acids Res. 2005 Jan
20;33(2):511-8.
Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and
post-analysis of large phylogenies Bioinformatics (2014) 30 (9):
1312-1313.
In [29]:
from IPython.display import Image
Image(filename='custom/mafft_linsi-trimal01-pmodeltest_soft_ultrafast-raxml_default//NUP62.aa.fa.final_tree.png')
Out[29]:
