[Debian-med-packaging] Bug#997886: prottest: autopkgtest regression: Stats file does not exist
Paul Gevers
elbrus at debian.org
Tue Oct 26 16:02:35 BST 2021
Source: prottest
Version: 3.4.2+dfsg-6
X-Debbugs-CC: debian-ci at lists.debian.org
Severity: serious
User: debian-ci at lists.debian.org
Usertags: regression
Dear maintainer(s),
With a recent upload of prottest the autopkgtest of prottest fails in
testing when that autopkgtest is run with the binary packages of
prottest from unstable. It passes when run with only packages from
testing. In tabular form:
pass fail
prottest from testing 3.4.2+dfsg-6
all others from testing from testing
I copied some of the output at the bottom of this report.
Currently this regression is blocking the migration to testing [1]. Can
you please investigate the situation and fix it?
More information about this bug and the reason for filing it can be found on
https://wiki.debian.org/ContinuousIntegration/RegressionEmailInformation
Paul
[1] https://qa.debian.org/excuses.php?package=prottest
https://ci.debian.net/data/autopkgtest/testing/amd64/p/prottest/16225046/log.gz
-------------------------------------------------------------------------------------------------
Basic usage: - Sequential version: java -jar prottest-3.4.2.jar
-i align_file [OPTIONS]
./prottest3 -i align_file [OPTIONS]
- Parallel version: mpjrun.sh -wdir $PWD/ -np [NUM_PROCS] -jar
prottest-3.4.2.jar -i align_file [OPTIONS]
OPTIONS:
-i alignment_filename
Alignment input file (required)
-t tree_filename
Tree file (optional) [default: NJ tree]
-o output_filename
Output file (optional) [default: standard output]
-log enabled/disabled
Enables / Disables PhyML logging into log directory (see
prottest.properties)
-[matrix]
Include matrix (Amino-acid) = JTT LG DCMut MtREV MtMam MtArt
Dayhoff WAG RtREV CpREV Blosum62 VT
HIVb HIVw FLU If you don't specify any matrix, all
matrices displayed above will
be included.
-I
Include models with a proportion of invariable sites
-G
Include models with rate variation among sites and number of
categories
-IG
include models with both +I and +G properties
-all-distributions
Include models with rate variation among sites, number of
categories and both
-ncat number_of_categories
Define number of categories for +G and +I+G models [default: 4]
-F
Include models with empirical frequency estimation -AIC
Display models sorted by Akaike Information Criterion (AIC)
-BIC
Display models sorted by Bayesian Information Criterion (BIC)
-AICC
Display models sorted by Corrected Akaike Information
Criterion (AICc)
-DT
Display models sorted by Decision Theory Criterion
-all
Displays a 7-framework comparison table
-S optimization_strategy
Optimization strategy mode: [default: 0]
0: Fixed BIONJ JTT
1: BIONJ Tree
2: Maximum Likelihood tree
3: User defined topology
-s moves
Tree search operation for ML search: NNI
(fastest), SPR (slowest), BEST (best of NNI and SPR) [default: NNI]
-t1
Display best-model's newick tree [default: false]
-t2
Display best-model's ASCII tree [default: false]
-tc consensus_threshold Display consensus tree with the
specified threshold, between 0.5 and 1.0
[0.5 = majority rule consensus ; 1.0 = strict consensus]
-threads number_or_threads
Number of threads requested to compute (only if MPJ is not
used) [default: 1]
-verbose
Verbose mode [default: false]
-------------------------------------------------------------------------------------------------
Example: - Sequential version:
java -jar prottest-3.4.2.jar -i align_file -t tree_file -S 0
-all-distributions -F -AIC -BIC -tc 0.5 > output
- Parallel version:
mpjrun.sh -wdir $PWD/ -np 2 -jar prottest-3.4.2.jar -i align_file -t
tree_file -S 0 -all-distributions -F -AIC -BIC -tc 0.5
PHYLIP format detected.MSA read in PHYLIP format (Taxa = 28, Length =
149).MSA successfully converted to PHYLIP format!
No such file or directory
----------------------------------------------------------------------------------------------
ProtTest 3.4.2 Fast selection of the best-fit
models of protein evolution
(c) 2009-2016 Diego Darriba (1,2), Guillermo Taboada (2), Ramón Doallo
(2), David Posada (1)
(1) Facultad de Biologia, Universidad de
Vigo, 36200 Vigo, Spain
(2) Facultade de Informática, Universidade da Coruña,
15071 A Coruña, Spain
----------------------------------------------------------------------------------------------
Manual:
http://darwin.uvigo.es/download/prottest_manual.pdf
Homepage:
http://github.com/ddarriba/prottest3
Discussion group:
https://groups.google.com/group/prottest
Contact:
ddarriba at h-its.org, dposada at uvigo.es
----------------------------------------------------------------------------------------------
Version: 3.4.2 : 8th May 2016
Date: Tue Oct 26 10:11:23 UTC 2021
OS: Linux (4.19.0-18-amd64)
Arch: amd64
Java: 11.0.12 (Debian)
PhyML: /usr/bin/phyml
Citation: Darriba D, Taboada GL, Doallo R, Posada D. ProtTest 3: fast
selection of best-fit models of protein evolution.
Bioinformatics, 27:1164-1165, 2011
ProtTest options
----------------
Alignment file........... : COX2_PF0016/alignment
Tree..................... : COX2_PF0016/tree
StrategyMode............. : User defined topology
Candidate models......... : Matrices............... : JTT LG DCMut
MtREV MtMam MtArt Dayhoff WAG RtREV CpREV Blosum62 VT HIVb HIVw FLU
Distributions.......... : Uniform +G +I +I+G Observed frequencies...
: true
Statistical framework
Sort models according to....: AIC BIC Sample
size.................: 149.0
Other options:
Display best tree in ASCII..: false
Display best tree in Newick.: false
Display consensus tree......: true
Consensus threshold.........: 0.5
Verbose.....................: false
**********************************************************
Observed number of invariant sites: 13
Observed aminoacid frequencies:
A: 0.044 C: 0.018 D: 0.054 E: 0.056 F: 0.049 G: 0.057
H: 0.026 I: 0.086 K: 0.032 L: 0.086 M: 0.039 N: 0.055
P: 0.051 Q: 0.034 R: 0.036 S: 0.086 T: 0.050 V: 0.068
W: 0.028 Y: 0.044
**********************************************************
Model optimization exception: there was an error while executing there
was an error parsing PhyML stats file: Stats file does not exist. Please
check if PhyML is working.
Model................................ : JTT
Number of parameters............... : 53 (0 + 53 branch length estimates)
Model optimization exception: there was an error while executing there
was an error parsing PhyML stats file: Stats file does not exist. Please
check if PhyML is working.
Model................................ : JTT+F
Number of parameters............... : 72 (19 + 53 branch length estimates)
Model optimization exception: there was an error while executing there
was an error parsing PhyML stats file: Stats file does not exist. Please
check if PhyML is working.
Model................................ : JTT+I
Number of parameters............... : 54 (1 + 53 branch length estimates)
Model optimization exception: there was an error while executing there
was an error parsing PhyML stats file: Stats file does not exist. Please
check if PhyML is working.
Model................................ : JTT+I+F
Number of parameters............... : 73 (20 + 53 branch length estimates)
Model optimization exception: there was an error while executing there
was an error parsing PhyML stats file: Stats file does not exist. Please
check if PhyML is working.
Model................................ : JTT+G
Number of parameters............... : 54 (1 + 53 branch length estimates)
Model optimization exception: there was an error while executing there
was an error parsing PhyML stats file: Stats file does not exist. Please
check if PhyML is working.
Model................................ : JTT+G+F
Number of parameters............... : 73 (20 + 53 branch length estimates)
Model optimization exception: there was an error while executing there
was an error parsing PhyML stats file: Stats file does not exist. Please
check if PhyML is working.
Model................................ : JTT+I+G
Number of parameters............... : 55 (2 + 53 branch length estimates)
Model optimization exception: there was an error while executing there
was an error parsing PhyML stats file: Stats file does not exist. Please
check if PhyML is working.
Model................................ : JTT+I+G+F
Number of parameters............... : 74 (21 + 53 branch length estimates)
Model optimization exception: there was an error while executing there
was an error parsing PhyML stats file: Stats file does not exist. Please
check if PhyML is working.
Model................................ : LG
Number of parameters............... : 53 (0 + 53 branch length estimates)
Model optimization exception: there was an error while executing there
was an error parsing PhyML stats file: Stats file does not exist. Please
check if PhyML is working.
Model................................ : LG+F
Number of parameters............... : 72 (19 + 53 branch length estimates)
Model optimization exception: there was an error while executing there
was an error parsing PhyML stats file: Stats file does not exist. Please
check if PhyML is working.
Model................................ : LG+I
Number of parameters............... : 54 (1 + 53 branch length estimates)
Model optimization exception: there was an error while executing there
was an error parsing PhyML stats file: Stats file does not exist. Please
check if PhyML is working.
Model................................ : LG+I+F
Number of parameters............... : 73 (20 + 53 branch length estimates)
Model optimization exception: there was an error while executing there
was an error parsing PhyML stats file: Stats file does not exist. Please
check if PhyML is working.
Model................................ : LG+G
Number of parameters............... : 54 (1 + 53 branch length estimates)
Model optimization exception: there was an error while executing there
was an error parsing PhyML stats file: Stats file does not exist. Please
check if PhyML is working.
Model................................ : LG+G+F
Number of parameters............... : 73 (20 + 53 branch length estimates)
Model optimization exception: there was an error while executing there
was an error parsing PhyML stats file: Stats file does not exist. Please
check if PhyML is working.
Model................................ : LG+I+G
Number of parameters............... : 55 (2 + 53 branch length estimates)
Model optimization exception: there was an error while executing there
was an error parsing PhyML stats file: Stats file does not exist. Please
check if PhyML is working.
Model................................ : LG+I+G+F
Number of parameters............... : 74 (21 + 53 branch length estimates)
Model optimization exception: there was an error while executing there
was an error parsing PhyML stats file: Stats file does not exist. Please
check if PhyML is working.
Model................................ : DCMut
Number of parameters............... : 53 (0 + 53 branch length estimates)
Model optimization exception: there was an error while executing there
was an error parsing PhyML stats file: Stats file does not exist. Please
check if PhyML is working.
Model................................ : DCMut+F
Number of parameters............... : 72 (19 + 53 branch length estimates)
Model optimization exception: there was an error while executing there
was an error parsing PhyML stats file: Stats file does not exist. Please
check if PhyML is working.
Model................................ : DCMut+I
Number of parameters............... : 54 (1 + 53 branch length estimates)
Model optimization exception: there was an error while executing there
was an error parsing PhyML stats file: Stats file does not exist. Please
check if PhyML is working.
Model................................ : DCMut+I+F
Number of parameters............... : 73 (20 + 53 branch length estimates)
Model optimization exception: there was an error while executing there
was an error parsing PhyML stats file: Stats file does not exist. Please
check if PhyML is working.
Model................................ : DCMut+G
Number of parameters............... : 54 (1 + 53 branch length estimates)
Model optimization exception: there was an error while executing there
was an error parsing PhyML stats file: Stats file does not exist. Please
check if PhyML is working.
Model................................ : DCMut+G+F
Number of parameters............... : 73 (20 + 53 branch length estimates)
Model optimization exception: there was an error while executing there
was an error parsing PhyML stats file: Stats file does not exist. Please
check if PhyML is working.
Model................................ : DCMut+I+G
Number of parameters............... : 55 (2 + 53 branch length estimates)
Model optimization exception: there was an error while executing there
was an error parsing PhyML stats file: Stats file does not exist. Please
check if PhyML is working.
Model................................ : DCMut+I+G+F
Number of parameters............... : 74 (21 + 53 branch length estimates)
Model optimization exception: there was an error while executing there
was an error parsing PhyML stats file: Stats file does not exist. Please
check if PhyML is working.
Model................................ : MtREV
Number of parameters............... : 53 (0 + 53 branch length estimates)
Model optimization exception: there was an error while executing there
was an error parsing PhyML stats file: Stats file does not exist. Please
check if PhyML is working.
Model................................ : MtREV+F
Number of parameters............... : 72 (19 + 53 branch length estimates)
Model optimization exception: there was an error while executing there
was an error parsing PhyML stats file: Stats file does not exist. Please
check if PhyML is working.
Model................................ : MtREV+I
Number of parameters............... : 54 (1 + 53 branch length estimates)
Model optimization exception: there was an error while executing there
was an error parsing PhyML stats file: Stats file does not exist. Please
check if PhyML is working.
Model................................ : MtREV+I+F
Number of parameters............... : 73 (20 + 53 branch length estimates)
Model optimization exception: there was an error while executing there
was an error parsing PhyML stats file: Stats file does not exist. Please
check if PhyML is working.
Model................................ : MtREV+G
Number of parameters............... : 54 (1 + 53 branch length estimates)
Model optimization exception: there was an error while executing there
was an error parsing PhyML stats file: Stats file does not exist. Please
check if PhyML is working.
Model................................ : MtREV+G+F
Number of parameters............... : 73 (20 + 53 branch length estimates)
Model optimization exception: there was an error while executing there
was an error parsing PhyML stats file: Stats file does not exist. Please
check if PhyML is working.
Model................................ : MtREV+I+G
Number of parameters............... : 55 (2 + 53 branch length estimates)
Model optimization exception: there was an error while executing there
was an error parsing PhyML stats file: Stats file does not exist. Please
check if PhyML is working.
Model................................ : MtREV+I+G+F
Number of parameters............... : 74 (21 + 53 branch length estimates)
Model optimization exception: there was an error while executing there
was an error parsing PhyML stats file: Stats file does not exist. Please
check if PhyML is working.
Model................................ : MtMam
Number of parameters............... : 53 (0 + 53 branch length estimates)
Model optimization exception: there was an error while executing there
was an error parsing PhyML stats file: Stats file does not exist. Please
check if PhyML is working.
Model................................ : MtMam+F
Number of parameters............... : 72 (19 + 53 branch length estimates)
Model optimization exception: there was an error while executing there
was an error parsing PhyML stats file: Stats file does not exist. Please
check if PhyML is working.
Model................................ : MtMam+I
Number of parameters............... : 54 (1 + 53 branch length estimates)
Model optimization exception: there was an error while executing there
was an error parsing PhyML stats file: Stats file does not exist. Please
check if PhyML is working.
Model................................ : MtMam+I+F
Number of parameters............... : 73 (20 + 53 branch length estimates)
Model optimization exception: there was an error while executing there
was an error parsing PhyML stats file: Stats file does not exist. Please
check if PhyML is working.
Model................................ : MtMam+G
Number of parameters............... : 54 (1 + 53 branch length estimates)
Model optimization exception: there was an error while executing there
was an error parsing PhyML stats file: Stats file does not exist. Please
check if PhyML is working.
Model................................ : MtMam+G+F
Number of parameters............... : 73 (20 + 53 branch length estimates)
Model optimization exception: there was an error while executing there
was an error parsing PhyML stats file: Stats file does not exist. Please
check if PhyML is working.
Model................................ : MtMam+I+G
Number of parameters............... : 55 (2 + 53 branch length estimates)
Model optimization exception: there was an error while executing there
was an error parsing PhyML stats file: Stats file does not exist. Please
check if PhyML is working.
Model................................ : MtMam+I+G+F
Number of parameters............... : 74 (21 + 53 branch length estimates)
Model optimization exception: there was an error while executing there
was an error parsing PhyML stats file: Stats file does not exist. Please
check if PhyML is working.
Model................................ : MtArt
Number of parameters............... : 53 (0 + 53 branch length estimates)
Model optimization exception: there was an error while executing there
was an error parsing PhyML stats file: Stats file does not exist. Please
check if PhyML is working.
Model................................ : MtArt+F
Number of parameters............... : 72 (19 + 53 branch length estimates)
Model optimization exception: there was an error while executing there
was an error parsing PhyML stats file: Stats file does not exist. Please
check if PhyML is working.
Model................................ : MtArt+I
Number of parameters............... : 54 (1 + 53 branch length estimates)
Model optimization exception: there was an error while executing there
was an error parsing PhyML stats file: Stats file does not exist. Please
check if PhyML is working.
Model................................ : MtArt+I+F
Number of parameters............... : 73 (20 + 53 branch length estimates)
Model optimization exception: there was an error while executing there
was an error parsing PhyML stats file: Stats file does not exist. Please
check if PhyML is working.
Model................................ : MtArt+G
Number of parameters............... : 54 (1 + 53 branch length estimates)
Model optimization exception: there was an error while executing there
was an error parsing PhyML stats file: Stats file does not exist. Please
check if PhyML is working.
Model................................ : MtArt+G+F
Number of parameters............... : 73 (20 + 53 branch length estimates)
Model optimization exception: there was an error while executing there
was an error parsing PhyML stats file: Stats file does not exist. Please
check if PhyML is working.
Model................................ : MtArt+I+G
Number of parameters............... : 55 (2 + 53 branch length estimates)
Model optimization exception: there was an error while executing there
was an error parsing PhyML stats file: Stats file does not exist. Please
check if PhyML is working.
Model................................ : MtArt+I+G+F
Number of parameters............... : 74 (21 + 53 branch length estimates)
Model optimization exception: there was an error while executing there
was an error parsing PhyML stats file: Stats file does not exist. Please
check if PhyML is working.
Model................................ : Dayhoff
Number of parameters............... : 53 (0 + 53 branch length estimates)
Model optimization exception: there was an error while executing there
was an error parsing PhyML stats file: Stats file does not exist. Please
check if PhyML is working.
Model................................ : Dayhoff+F
Number of parameters............... : 72 (19 + 53 branch length estimates)
Model optimization exception: there was an error while executing there
was an error parsing PhyML stats file: Stats file does not exist. Please
check if PhyML is working.
Model................................ : Dayhoff+I
Number of parameters............... : 54 (1 + 53 branch length estimates)
Model optimization exception: there was an error while executing there
was an error parsing PhyML stats file: Stats file does not exist. Please
check if PhyML is working.
Model................................ : Dayhoff+I+F
Number of parameters............... : 73 (20 + 53 branch length estimates)
Model optimization exception: there was an error while executing there
was an error parsing PhyML stats file: Stats file does not exist. Please
check if PhyML is working.
Model................................ : Dayhoff+G
Number of parameters............... : 54 (1 + 53 branch length estimates)
Model optimization exception: there was an error while executing there
was an error parsing PhyML stats file: Stats file does not exist. Please
check if PhyML is working.
Model................................ : Dayhoff+G+F
Number of parameters............... : 73 (20 + 53 branch length estimates)
Model optimization exception: there was an error while executing there
was an error parsing PhyML stats file: Stats file does not exist. Please
check if PhyML is working.
Model................................ : Dayhoff+I+G
Number of parameters............... : 55 (2 + 53 branch length estimates)
Model optimization exception: there was an error while executing there
was an error parsing PhyML stats file: Stats file does not exist. Please
check if PhyML is working.
Model................................ : Dayhoff+I+G+F
Number of parameters............... : 74 (21 + 53 branch length estimates)
Model optimization exception: there was an error while executing there
was an error parsing PhyML stats file: Stats file does not exist. Please
check if PhyML is working.
Model................................ : WAG
Number of parameters............... : 53 (0 + 53 branch length estimates)
Model optimization exception: there was an error while executing there
was an error parsing PhyML stats file: Stats file does not exist. Please
check if PhyML is working.
Model................................ : WAG+F
Number of parameters............... : 72 (19 + 53 branch length estimates)
Model optimization exception: there was an error while executing there
was an error parsing PhyML stats file: Stats file does not exist. Please
check if PhyML is working.
Model................................ : WAG+I
Number of parameters............... : 54 (1 + 53 branch length estimates)
Model optimization exception: there was an error while executing there
was an error parsing PhyML stats file: Stats file does not exist. Please
check if PhyML is working.
Model................................ : WAG+I+F
Number of parameters............... : 73 (20 + 53 branch length estimates)
Model optimization exception: there was an error while executing there
was an error parsing PhyML stats file: Stats file does not exist. Please
check if PhyML is working.
Model................................ : WAG+G
Number of parameters............... : 54 (1 + 53 branch length estimates)
Model optimization exception: there was an error while executing there
was an error parsing PhyML stats file: Stats file does not exist. Please
check if PhyML is working.
Model................................ : WAG+G+F
Number of parameters............... : 73 (20 + 53 branch length estimates)
Model optimization exception: there was an error while executing there
was an error parsing PhyML stats file: Stats file does not exist. Please
check if PhyML is working.
Model................................ : WAG+I+G
Number of parameters............... : 55 (2 + 53 branch length estimates)
Model optimization exception: there was an error while executing there
was an error parsing PhyML stats file: Stats file does not exist. Please
check if PhyML is working.
Model................................ : WAG+I+G+F
Number of parameters............... : 74 (21 + 53 branch length estimates)
Model optimization exception: there was an error while executing there
was an error parsing PhyML stats file: Stats file does not exist. Please
check if PhyML is working.
Model................................ : RtREV
Number of parameters............... : 53 (0 + 53 branch length estimates)
Model optimization exception: there was an error while executing there
was an error parsing PhyML stats file: Stats file does not exist. Please
check if PhyML is working.
Model................................ : RtREV+F
Number of parameters............... : 72 (19 + 53 branch length estimates)
Model optimization exception: there was an error while executing there
was an error parsing PhyML stats file: Stats file does not exist. Please
check if PhyML is working.
Model................................ : RtREV+I
Number of parameters............... : 54 (1 + 53 branch length estimates)
Model optimization exception: there was an error while executing there
was an error parsing PhyML stats file: Stats file does not exist. Please
check if PhyML is working.
Model................................ : RtREV+I+F
Number of parameters............... : 73 (20 + 53 branch length estimates)
Model optimization exception: there was an error while executing there
was an error parsing PhyML stats file: Stats file does not exist. Please
check if PhyML is working.
Model................................ : RtREV+G
Number of parameters............... : 54 (1 + 53 branch length estimates)
Model optimization exception: there was an error while executing there
was an error parsing PhyML stats file: Stats file does not exist. Please
check if PhyML is working.
Model................................ : RtREV+G+F
Number of parameters............... : 73 (20 + 53 branch length estimates)
Model optimization exception: there was an error while executing there
was an error parsing PhyML stats file: Stats file does not exist. Please
check if PhyML is working.
Model................................ : RtREV+I+G
Number of parameters............... : 55 (2 + 53 branch length estimates)
Model optimization exception: there was an error while executing there
was an error parsing PhyML stats file: Stats file does not exist. Please
check if PhyML is working.
Model................................ : RtREV+I+G+F
Number of parameters............... : 74 (21 + 53 branch length estimates)
Model optimization exception: there was an error while executing there
was an error parsing PhyML stats file: Stats file does not exist. Please
check if PhyML is working.
Model................................ : CpREV
Number of parameters............... : 53 (0 + 53 branch length estimates)
Model optimization exception: there was an error while executing there
was an error parsing PhyML stats file: Stats file does not exist. Please
check if PhyML is working.
Model................................ : CpREV+F
Number of parameters............... : 72 (19 + 53 branch length estimates)
Model optimization exception: there was an error while executing there
was an error parsing PhyML stats file: Stats file does not exist. Please
check if PhyML is working.
Model................................ : CpREV+I
Number of parameters............... : 54 (1 + 53 branch length estimates)
Model optimization exception: there was an error while executing there
was an error parsing PhyML stats file: Stats file does not exist. Please
check if PhyML is working.
Model................................ : CpREV+I+F
Number of parameters............... : 73 (20 + 53 branch length estimates)
Model optimization exception: there was an error while executing there
was an error parsing PhyML stats file: Stats file does not exist. Please
check if PhyML is working.
Model................................ : CpREV+G
Number of parameters............... : 54 (1 + 53 branch length estimates)
Model optimization exception: there was an error while executing there
was an error parsing PhyML stats file: Stats file does not exist. Please
check if PhyML is working.
Model................................ : CpREV+G+F
Number of parameters............... : 73 (20 + 53 branch length estimates)
Model optimization exception: there was an error while executing there
was an error parsing PhyML stats file: Stats file does not exist. Please
check if PhyML is working.
Model................................ : CpREV+I+G
Number of parameters............... : 55 (2 + 53 branch length estimates)
Model optimization exception: there was an error while executing there
was an error parsing PhyML stats file: Stats file does not exist. Please
check if PhyML is working.
Model................................ : CpREV+I+G+F
Number of parameters............... : 74 (21 + 53 branch length estimates)
Model optimization exception: there was an error while executing there
was an error parsing PhyML stats file: Stats file does not exist. Please
check if PhyML is working.
Model................................ : Blosum62
Number of parameters............... : 53 (0 + 53 branch length estimates)
Model optimization exception: there was an error while executing there
was an error parsing PhyML stats file: Stats file does not exist. Please
check if PhyML is working.
Model................................ : Blosum62+F
Number of parameters............... : 72 (19 + 53 branch length estimates)
Model optimization exception: there was an error while executing there
was an error parsing PhyML stats file: Stats file does not exist. Please
check if PhyML is working.
Model................................ : Blosum62+I
Number of parameters............... : 54 (1 + 53 branch length estimates)
Model optimization exception: there was an error while executing there
was an error parsing PhyML stats file: Stats file does not exist. Please
check if PhyML is working.
Model................................ : Blosum62+I+F
Number of parameters............... : 73 (20 + 53 branch length estimates)
Model optimization exception: there was an error while executing there
was an error parsing PhyML stats file: Stats file does not exist. Please
check if PhyML is working.
Model................................ : Blosum62+G
Number of parameters............... : 54 (1 + 53 branch length estimates)
Model optimization exception: there was an error while executing there
was an error parsing PhyML stats file: Stats file does not exist. Please
check if PhyML is working.
Model................................ : Blosum62+G+F
Number of parameters............... : 73 (20 + 53 branch length estimates)
Model optimization exception: there was an error while executing there
was an error parsing PhyML stats file: Stats file does not exist. Please
check if PhyML is working.
Model................................ : Blosum62+I+G
Number of parameters............... : 55 (2 + 53 branch length estimates)
Model optimization exception: there was an error while executing there
was an error parsing PhyML stats file: Stats file does not exist. Please
check if PhyML is working.
Model................................ : Blosum62+I+G+F
Number of parameters............... : 74 (21 + 53 branch length estimates)
Model optimization exception: there was an error while executing there
was an error parsing PhyML stats file: Stats file does not exist. Please
check if PhyML is working.
Model................................ : VT
Number of parameters............... : 53 (0 + 53 branch length estimates)
Model optimization exception: there was an error while executing there
was an error parsing PhyML stats file: Stats file does not exist. Please
check if PhyML is working.
Model................................ : VT+F
Number of parameters............... : 72 (19 + 53 branch length estimates)
Model optimization exception: there was an error while executing there
was an error parsing PhyML stats file: Stats file does not exist. Please
check if PhyML is working.
Model................................ : VT+I
Number of parameters............... : 54 (1 + 53 branch length estimates)
Model optimization exception: there was an error while executing there
was an error parsing PhyML stats file: Stats file does not exist. Please
check if PhyML is working.
Model................................ : VT+I+F
Number of parameters............... : 73 (20 + 53 branch length estimates)
Model optimization exception: there was an error while executing there
was an error parsing PhyML stats file: Stats file does not exist. Please
check if PhyML is working.
Model................................ : VT+G
Number of parameters............... : 54 (1 + 53 branch length estimates)
Model optimization exception: there was an error while executing there
was an error parsing PhyML stats file: Stats file does not exist. Please
check if PhyML is working.
Model................................ : VT+G+F
Number of parameters............... : 73 (20 + 53 branch length estimates)
Model optimization exception: there was an error while executing there
was an error parsing PhyML stats file: Stats file does not exist. Please
check if PhyML is working.
Model................................ : VT+I+G
Number of parameters............... : 55 (2 + 53 branch length estimates)
Model optimization exception: there was an error while executing there
was an error parsing PhyML stats file: Stats file does not exist. Please
check if PhyML is working.
Model................................ : VT+I+G+F
Number of parameters............... : 74 (21 + 53 branch length estimates)
Model optimization exception: there was an error while executing there
was an error parsing PhyML stats file: Stats file does not exist. Please
check if PhyML is working.
Model................................ : HIVb
Number of parameters............... : 53 (0 + 53 branch length estimates)
Model optimization exception: there was an error while executing there
was an error parsing PhyML stats file: Stats file does not exist. Please
check if PhyML is working.
Model................................ : HIVb+F
Number of parameters............... : 72 (19 + 53 branch length estimates)
Model optimization exception: there was an error while executing there
was an error parsing PhyML stats file: Stats file does not exist. Please
check if PhyML is working.
Model................................ : HIVb+I
Number of parameters............... : 54 (1 + 53 branch length estimates)
Model optimization exception: there was an error while executing there
was an error parsing PhyML stats file: Stats file does not exist. Please
check if PhyML is working.
Model................................ : HIVb+I+F
Number of parameters............... : 73 (20 + 53 branch length estimates)
Model optimization exception: there was an error while executing there
was an error parsing PhyML stats file: Stats file does not exist. Please
check if PhyML is working.
Model................................ : HIVb+G
Number of parameters............... : 54 (1 + 53 branch length estimates)
Model optimization exception: there was an error while executing there
was an error parsing PhyML stats file: Stats file does not exist. Please
check if PhyML is working.
Model................................ : HIVb+G+F
Number of parameters............... : 73 (20 + 53 branch length estimates)
Model optimization exception: there was an error while executing there
was an error parsing PhyML stats file: Stats file does not exist. Please
check if PhyML is working.
Model................................ : HIVb+I+G
Number of parameters............... : 55 (2 + 53 branch length estimates)
Model optimization exception: there was an error while executing there
was an error parsing PhyML stats file: Stats file does not exist. Please
check if PhyML is working.
Model................................ : HIVb+I+G+F
Number of parameters............... : 74 (21 + 53 branch length estimates)
Model optimization exception: there was an error while executing there
was an error parsing PhyML stats file: Stats file does not exist. Please
check if PhyML is working.
Model................................ : HIVw
Number of parameters............... : 53 (0 + 53 branch length estimates)
Model optimization exception: there was an error while executing there
was an error parsing PhyML stats file: Stats file does not exist. Please
check if PhyML is working.
Model................................ : HIVw+F
Number of parameters............... : 72 (19 + 53 branch length estimates)
Model optimization exception: there was an error while executing there
was an error parsing PhyML stats file: Stats file does not exist. Please
check if PhyML is working.
Model................................ : HIVw+I
Number of parameters............... : 54 (1 + 53 branch length estimates)
Model optimization exception: there was an error while executing there
was an error parsing PhyML stats file: Stats file does not exist. Please
check if PhyML is working.
Model................................ : HIVw+I+F
Number of parameters............... : 73 (20 + 53 branch length estimates)
Model optimization exception: there was an error while executing there
was an error parsing PhyML stats file: Stats file does not exist. Please
check if PhyML is working.
Model................................ : HIVw+G
Number of parameters............... : 54 (1 + 53 branch length estimates)
Model optimization exception: there was an error while executing there
was an error parsing PhyML stats file: Stats file does not exist. Please
check if PhyML is working.
Model................................ : HIVw+G+F
Number of parameters............... : 73 (20 + 53 branch length estimates)
Model optimization exception: there was an error while executing there
was an error parsing PhyML stats file: Stats file does not exist. Please
check if PhyML is working.
Model................................ : HIVw+I+G
Number of parameters............... : 55 (2 + 53 branch length estimates)
Model optimization exception: there was an error while executing there
was an error parsing PhyML stats file: Stats file does not exist. Please
check if PhyML is working.
Model................................ : HIVw+I+G+F
Number of parameters............... : 74 (21 + 53 branch length estimates)
Model optimization exception: there was an error while executing there
was an error parsing PhyML stats file: Stats file does not exist. Please
check if PhyML is working.
Model................................ : FLU
Number of parameters............... : 53 (0 + 53 branch length estimates)
Model optimization exception: there was an error while executing there
was an error parsing PhyML stats file: Stats file does not exist. Please
check if PhyML is working.
Model................................ : FLU+F
Number of parameters............... : 72 (19 + 53 branch length estimates)
Model optimization exception: there was an error while executing there
was an error parsing PhyML stats file: Stats file does not exist. Please
check if PhyML is working.
Model................................ : FLU+I
Number of parameters............... : 54 (1 + 53 branch length estimates)
Model optimization exception: there was an error while executing there
was an error parsing PhyML stats file: Stats file does not exist. Please
check if PhyML is working.
Model................................ : FLU+I+F
Number of parameters............... : 73 (20 + 53 branch length estimates)
Model optimization exception: there was an error while executing there
was an error parsing PhyML stats file: Stats file does not exist. Please
check if PhyML is working.
Model................................ : FLU+G
Number of parameters............... : 54 (1 + 53 branch length estimates)
Model optimization exception: there was an error while executing there
was an error parsing PhyML stats file: Stats file does not exist. Please
check if PhyML is working.
Model................................ : FLU+G+F
Number of parameters............... : 73 (20 + 53 branch length estimates)
Model optimization exception: there was an error while executing there
was an error parsing PhyML stats file: Stats file does not exist. Please
check if PhyML is working.
Model................................ : FLU+I+G
Number of parameters............... : 55 (2 + 53 branch length estimates)
Model optimization exception: there was an error while executing there
was an error parsing PhyML stats file: Stats file does not exist. Please
check if PhyML is working.
Model................................ : FLU+I+G+F
Number of parameters............... : 74 (21 + 53 branch length estimates)
************************************************************
Date : Tue Oct 26 10:14:30 UTC 2021
Runtime: 0h:03:07
Lk not initialized
autopkgtest [10:14:30]: test run-unit-test
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