[Debian-med-packaging] Bug#1026328: libbpp-core breaks bppsuite autopkgtest
Paul Gevers
elbrus at debian.org
Sun Dec 18 16:52:07 GMT 2022
Source: libbpp-core, bppsuite
Control: found -1 libbpp-core/2.4.1-9
Control: found -1 bppsuite/2.4.1-5
Severity: serious
Tags: sid bookworm
User: debian-ci at lists.debian.org
Usertags: breaks needs-update
Dear maintainer(s),
With a recent upload of libbpp-core the autopkgtest of bppsuite fails in
testing when that autopkgtest is run with the binary packages of
libbpp-core from unstable. It passes when run with only packages from
testing. In tabular form:
pass fail
libbpp-core from testing 2.4.1-9
bppsuite from testing 2.4.1-5
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 of libbpp-core to
testing [1]. Due to the nature of this issue, I filed this bug report
against both packages. Can you please investigate the situation and
reassign the bug to the right package?
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=libbpp-core
https://ci.debian.net/data/autopkgtest/testing/arm64/b/bppsuite/29470275/log.gz
Test 1
******************************************************************
* Bio++ Maximum Likelihood Computation, version 2.4.0 *
* *
* Authors: J. Dutheil Last Modif. 19/02/18 *
* B. Boussau *
* L. Guéguen *
* M. Groussin *
******************************************************************
Parsing options:
Parsing file ML.bpp for options.
Alphabet type .........................: Codon(letter=DNA)
Genetic Code...........................: Standard
Sequence file .........................: ../../../Data/lysozymeLarge.fasta
Sequence format .......................: FASTA file
Sites to use...........................: all
Remove sites with gaps.................:
[ ] 0%
[= ] 3%
[== ] 6%
[=== ] 9%
[==== ] 12%
[===== ] 15%
[======= ] 18%
[======== ] 21%
[========= ] 24%
[========== ] 27%
[=========== ] 31%
[============ ] 34%
[============== ] 37%
[=============== ] 40%
[================ ] 43%
[================= ] 46%
[================== ] 49%
[==================== ] 52%
[===================== ] 55%
[====================== ] 58%
[======================= ] 62%
[======================== ] 65%
[========================= ] 68%
[=========================== ] 71%
[============================ ] 74%
[============================= ] 77%
[============================== ] 80%
[=============================== ] 83%
[================================ ] 86%
[================================== ] 89%
[=================================== ] 93%
[==================================== ] 96%
[===================================== ] 99%
[======================================] 100%Done.
Remove Stop Codons.....................: yes
Number of sequences....................: 19
Number of sites........................: 130
Input tree.............................: user
Input tree file .......................: ../../../Data/lysozymeLarge.dnd
Input tree format .....................: Newick
Number of leaves.......................: 19
Output tree file ......................: lysozymeLarge.ML.dnd
Output tree format ....................: Newick
Branch lengths.........................: Input
Heterogeneous model....................: one_per_branch
StopCodon frequencies distribution ....: quadratic
Substitution model.....................: YN98
External frequencies initialization for: None
Parameter found........................: YN98.kappa=1
Parameter found........................: YN98.omega=1
Parameter found........................: YN98.123_Full.theta=0.5
Parameter found........................: YN98.123_Full.theta1=0.5
Parameter found........................: YN98.123_Full.theta2=0.5
Distribution...........................: Constant
Number of classes......................: 1
- Category 0 (Pr = 1) rate.............: 1
Rate distribution......................: Constant
Number of classes......................: 1
Stationarity assumed...................: yes
Global parameter.......................: YN98.kappa
Global parameter.......................: YN98.123_*
Likelihood recursion...................: simple
Initializing data structure............: Done.
Number of distinct sites...............: 86
WARNING!!! Branch length 1 is too small: 0. Value is set to 1e-06
WARNING!!! Branch length 9 is too small: 0. Value is set to 1e-06
WARNING!!! Branch length 10 is too small: 0. Value is set to 1e-06
WARNING!!! Branch length 12 is too small: 0. Value is set to 1e-06
WARNING!!! Branch length 22 is too small: 0. Value is set to 1e-06
WARNING!!! Branch length 24 is too small: 0. Value is set to 1e-06
WARNING!!! Branch length 31 is too small: 0. Value is set to 1e-06
Initial log likelihood.................: -1083.53965420421
Message handler........................: lysozymeLarge.messages
Profiler...............................: lysozymeLarge.profile
Max # ML evaluations...................: 10000
Tolerance..............................: 1e-06
Optimize topology......................: no
Optimization method....................: FullD
Algorithm used for derivable parameters: Newton
Reparametrization......................: no
Molecular clock........................: None
Optimizing... / 1
Optimizing... - 2
Optimizing... \ 3
Optimizing... - 4
Optimizing... / 5
Optimizing... - 6
Optimizing... \ 7
Optimizing... - 8
Optimizing... / 9
Optimizing... - 10
Optimizing... \ 11
Optimizing... - 12
Optimizing... / 13
Optimizing... - 14
Optimizing... \ 15
Optimizing... - 16
Optimizing... / 17
Optimizing... - 18
Optimizing... \ 19
Performed..............................: 20 function evaluations.
Output tree file ......................: lysozymeLarge.ML.dnd
Output tree format ....................: Newick
Log likelihood.........................: -1025.19727691627
YN98.kappa_1...........................: 4.53742
YN98.omega_1...........................: 0.001
YN98.123_Full.theta_1..................: 0.445215
YN98.123_Full.theta1_1.................: 0.537621
YN98.123_Full.theta2_1.................: 0.580786
YN98.omega_2...........................: 0.001
YN98.omega_3...........................: 0.195682
YN98.omega_4...........................: 999
YN98.omega_5...........................: 0.001
YN98.omega_6...........................: 0.933468
YN98.omega_7...........................: 1.42369
YN98.omega_8...........................: 3.70967
YN98.omega_9...........................: 0.001
YN98.omega_10..........................: 0.001
YN98.omega_11..........................: 0.001
YN98.omega_12..........................: 999
YN98.omega_13..........................: 0.001
YN98.omega_14..........................: 999
YN98.omega_15..........................: 0.385806
YN98.omega_16..........................: 0.001
YN98.omega_17..........................: 0.001
YN98.omega_18..........................: 999
YN98.omega_19..........................: 999
YN98.omega_20..........................: 0.475048
YN98.omega_21..........................: 1.56053
YN98.omega_22..........................: 0.001
YN98.omega_23..........................: 0.001
YN98.omega_24..........................: 999
YN98.omega_25..........................: 0.001
YN98.omega_26..........................: 999
YN98.omega_27..........................: 0.394757
YN98.omega_28..........................: 999
YN98.omega_29..........................: 0.640665
YN98.omega_30..........................: 0.140303
YN98.omega_31..........................: 0.0844713
YN98.omega_32..........................: 5.54658
YN98.omega_33..........................: 0.38067
WARNING!!! This parameter has a value close to the boundary: BrLen1(1e-06).
WARNING!!! This parameter has a value close to the boundary: BrLen9(1e-06).
WARNING!!! This parameter has a value close to the boundary: BrLen10(1e-06).
WARNING!!! This parameter has a value close to the boundary: BrLen12(1e-06).
WARNING!!! This parameter has a value close to the boundary: BrLen22(1e-06).
WARNING!!! This parameter has a value close to the boundary: BrLen24(1e-06).
WARNING!!! This parameter has a value close to the boundary: BrLen31(1e-06).
WARNING!!! This parameter has a value close to the boundary:
YN98.omega_1(0.001).
WARNING!!! This parameter has a value close to the boundary:
YN98.omega_2(0.001).
WARNING!!! This parameter has a value close to the boundary:
YN98.omega_4(999).
WARNING!!! This parameter has a value close to the boundary:
YN98.omega_5(0.001).
WARNING!!! This parameter has a value close to the boundary:
YN98.omega_9(0.001).
WARNING!!! This parameter has a value close to the boundary:
YN98.omega_10(0.001).
WARNING!!! This parameter has a value close to the boundary:
YN98.omega_11(0.001).
WARNING!!! This parameter has a value close to the boundary:
YN98.omega_12(999).
WARNING!!! This parameter has a value close to the boundary:
YN98.omega_13(0.001).
WARNING!!! This parameter has a value close to the boundary:
YN98.omega_14(999).
WARNING!!! This parameter has a value close to the boundary:
YN98.omega_16(0.001).
WARNING!!! This parameter has a value close to the boundary:
YN98.omega_17(0.001).
WARNING!!! This parameter has a value close to the boundary:
YN98.omega_18(999).
WARNING!!! This parameter has a value close to the boundary:
YN98.omega_19(999).
WARNING!!! This parameter has a value close to the boundary:
YN98.omega_22(0.001).
WARNING!!! This parameter has a value close to the boundary:
YN98.omega_23(0.001).
WARNING!!! This parameter has a value close to the boundary:
YN98.omega_24(999).
WARNING!!! This parameter has a value close to the boundary:
YN98.omega_25(0.001).
WARNING!!! This parameter has a value close to the boundary:
YN98.omega_26(999).
WARNING!!! This parameter has a value close to the boundary:
YN98.omega_28(999).
WARNING!!! Parameter output.estimates.alias not specified. Default used
instead: 1
Output estimates to file...............: lysozymeLarge.params.txt
Posterior rate distribution for dataset:
Pr(1.000000) = 1.000000
Alignment information logfile..........: lysozymeLarge.infos
BppML's done. Bye.
Total execution time: 0.000000d, 0.000000h, 2.000000m, 34.000000s.
Passed
Test 2
******************************************************************
* Bio++ Maximum Likelihood Computation, version 2.4.0 *
* *
* Authors: J. Dutheil Last Modif. 19/02/18 *
* B. Boussau *
* L. Guéguen *
* M. Groussin *
******************************************************************
Parsing options:
Parsing file ML.bpp for options.
Alphabet type .........................: Codon(letter=DNA)
Genetic Code...........................: Standard
Sequence file .........................: ../../../Data/lysozymeLarge.fasta
Sequence format .......................: FASTA file
Sites to use...........................: all
Remove sites with gaps.................:
[ ] 0%
[= ] 3%
[== ] 6%
[=== ] 9%
[==== ] 12%
[===== ] 15%
[======= ] 18%
[======== ] 21%
[========= ] 24%
[========== ] 27%
[=========== ] 31%
[============ ] 34%
[============== ] 37%
[=============== ] 40%
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[================= ] 46%
[================== ] 49%
[==================== ] 52%
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[====================== ] 58%
[======================= ] 62%
[======================== ] 65%
[========================= ] 68%
[=========================== ] 71%
[============================ ] 74%
[============================= ] 77%
[============================== ] 80%
[=============================== ] 83%
[================================ ] 86%
[================================== ] 89%
[=================================== ] 93%
[==================================== ] 96%
[===================================== ] 99%
[======================================] 100%Done.
Remove Stop Codons.....................: yes
Number of sequences....................: 19
Number of sites........................: 130
Input tree.............................: user
Input tree file .......................: ../../../Data/lysozymeLarge.dnd
Input tree format .....................: Newick
Number of leaves.......................: 19
Output tree file ......................: lysozymeLarge.ML.dnd
Output tree format ....................: Newick
Branch lengths.........................: Input
Heterogeneous model....................: general
Number of distinct models..............: 2
StopCodon frequencies distribution ....: quadratic
Stationarity assumed...................: yes
StopCodon frequencies distribution ....: quadratic
Substitution model.....................: YN98
Frequencies Initialization for model...: None
Parameter found........................: YN98.kappa_1=1
Parameter found........................: YN98.omega_1=1
WARNING!!! Parameter YN98.123_Full.theta not specified. Default used
instead: 0.5
Parameter found........................: YN98.123_Full.theta_1=0.5
WARNING!!! Parameter YN98.123_Full.theta1 not specified. Default used
instead: 0.5
Parameter found........................: YN98.123_Full.theta1_1=0.5
WARNING!!! Parameter YN98.123_Full.theta2 not specified. Default used
instead: 0.5
Parameter found........................: YN98.123_Full.theta2_1=0.5
Model1 is associated to................: 21 node(s).
StopCodon frequencies distribution ....: quadratic
Substitution model.....................: YN98
Frequencies Initialization for model...: None
Parameter found........................: YN98.omega_2=1
WARNING!!! Parameter YN98.123_Full.theta not specified. Default used
instead: 0.5
Parameter found........................: YN98.123_Full.theta_2=0.5
WARNING!!! Parameter YN98.123_Full.theta1 not specified. Default used
instead: 0.5
Parameter found........................: YN98.123_Full.theta1_2=0.5
WARNING!!! Parameter YN98.123_Full.theta2 not specified. Default used
instead: 0.5
Parameter found........................: YN98.123_Full.theta2_2=0.5
Model2 is associated to................: 12 node(s).
Parameter alias found..................: YN98.kappa_2 -> YN98.kappa_1 = 1
Distribution...........................: Constant
Number of classes......................: 1
- Category 0 (Pr = 1) rate.............: 1
Rate distribution......................: Constant
Number of classes......................: 1
Likelihood recursion...................: simple
Initializing data structure............: Done.
Number of distinct sites...............: 86
WARNING!!! Branch length 1 is too small: 0. Value is set to 1e-06
WARNING!!! Branch length 9 is too small: 0. Value is set to 1e-06
WARNING!!! Branch length 10 is too small: 0. Value is set to 1e-06
WARNING!!! Branch length 12 is too small: 0. Value is set to 1e-06
WARNING!!! Branch length 22 is too small: 0. Value is set to 1e-06
WARNING!!! Branch length 24 is too small: 0. Value is set to 1e-06
WARNING!!! Branch length 31 is too small: 0. Value is set to 1e-06
Initial log likelihood.................: -1083.53965420421
Message handler........................: lysozymeLarge.messages
Profiler...............................: lysozymeLarge.profile
Max # ML evaluations...................: 10000
Tolerance..............................: 1e-06
Optimize topology......................: no
Optimization method....................: FullD
Algorithm used for derivable parameters: Newton
Reparametrization......................: no
Molecular clock........................: None
Optimizing... / 1
Optimizing... - 2
Optimizing... \ 3
Optimizing... - 4
Optimizing... / 5
Optimizing... - 6
Optimizing... \ 7
Optimizing... - 8
Optimizing... / 9
Optimizing... - 10
Optimizing... \ 11
Optimizing... - 12
Optimizing... / 13
Optimizing... - 14
Optimizing... \ 15
Optimizing... - 16
Optimizing... / 17
Optimizing... - 18
Optimizing... \ 19
Optimizing... - 20
Optimizing... / 21
Optimizing... - 22
Performed..............................: 23 function evaluations.
Output tree file ......................: lysozymeLarge.ML.dnd
Output tree format ....................: Newick
Log likelihood.........................: -1042.24079503814
YN98.kappa_1...........................: 4.59093
YN98.omega_1...........................: 0.781376
YN98.123_Full.theta_1..................: 0.441884
YN98.123_Full.theta1_1.................: 0.557934
YN98.123_Full.theta2_1.................: 0.604597
YN98.omega_2...........................: 0.465205
YN98.123_Full.theta_2..................: 0.464083
YN98.123_Full.theta1_2.................: 0.434315
YN98.123_Full.theta2_2.................: 0.455226
WARNING!!! This parameter has a value close to the boundary: BrLen1(1e-06).
WARNING!!! This parameter has a value close to the boundary: BrLen9(1e-06).
WARNING!!! This parameter has a value close to the boundary: BrLen10(1e-06).
WARNING!!! This parameter has a value close to the boundary: BrLen12(1e-06).
WARNING!!! This parameter has a value close to the boundary: BrLen22(1e-06).
WARNING!!! This parameter has a value close to the boundary: BrLen24(1e-06).
WARNING!!! This parameter has a value close to the boundary: BrLen31(1e-06).
WARNING!!! Parameter output.estimates.alias not specified. Default used
instead: 1
Output estimates to file...............: lysozymeLarge.params.txt
Posterior rate distribution for dataset:
Pr(1.000000) = 1.000000
Alignment information logfile..........: lysozymeLarge.infos
BppML's done. Bye.
Total execution time: 0.000000d, 0.000000h, 1.000000m, 1.000000s.
Passed
Test 3
******************************************************************
* Bio++ Maximum Likelihood Computation, version 2.4.0 *
* *
* Authors: J. Dutheil Last Modif. 19/02/18 *
* B. Boussau *
* L. Guéguen *
* M. Groussin *
******************************************************************
Parsing options:
Parsing file ML.bpp for options.
Alphabet type .........................: Codon(letter=DNA)
Genetic Code...........................: Standard
Sequence file .........................: ../../../Data/lysozymeLarge.fasta
Sequence format .......................: FASTA file
Sites to use...........................: all
Remove sites with gaps.................:
[ ] 0%
[= ] 3%
[== ] 6%
[=== ] 9%
[==== ] 12%
[===== ] 15%
[======= ] 18%
[======== ] 21%
[========= ] 24%
[========== ] 27%
[=========== ] 31%
[============ ] 34%
[============== ] 37%
[=============== ] 40%
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[=========================== ] 71%
[============================ ] 74%
[============================= ] 77%
[============================== ] 80%
[=============================== ] 83%
[================================ ] 86%
[================================== ] 89%
[=================================== ] 93%
[==================================== ] 96%
[===================================== ] 99%
[======================================] 100%Done.
Remove Stop Codons.....................: yes
Number of sequences....................: 19
Number of sites........................: 130
Input tree.............................: user
Input tree file .......................: ../../../Data/lysozymeLarge.dnd
Input tree format .....................: Newick
Number of leaves.......................: 19
Output tree file ......................: lysozymeLarge.ML.dnd
Output tree format ....................: Newick
Branch lengths.........................: Input
Heterogeneous model....................: no
Substitution model.....................: YN98
External frequencies initialization for: None
Parameter found........................: YN98.kappa=1
Parameter found........................: YN98.omega=1
Distribution...........................: Constant
Number of classes......................: 1
- Category 0 (Pr = 1) rate.............: 1
Rate distribution......................: Constant
Number of classes......................: 1
Likelihood recursion...................: simple
Likelihood data compression............: recursive
Initializing data structure............: Done.
Number of distinct sites...............: 86
WARNING!!! Branch length 1 is too small: 0. Value is set to 1e-06
WARNING!!! Branch length 9 is too small: 0. Value is set to 1e-06
WARNING!!! Branch length 10 is too small: 0. Value is set to 1e-06
WARNING!!! Branch length 12 is too small: 0. Value is set to 1e-06
WARNING!!! Branch length 22 is too small: 0. Value is set to 1e-06
WARNING!!! Branch length 24 is too small: 0. Value is set to 1e-06
WARNING!!! Branch length 31 is too small: 0. Value is set to 1e-06
Initial log likelihood.................: -1084.23740828788
Message handler........................: lysozymeLarge.messages
Profiler...............................: lysozymeLarge.profile
Max # ML evaluations...................: 10000
Tolerance..............................: 1e-06
Optimize topology......................: no
Optimization method....................: FullD
Algorithm used for derivable parameters: Newton
Reparametrization......................: no
Molecular clock........................: None
Optimizing... / 1
Optimizing... - 2
Optimizing... \ 3
Optimizing... - 4
Optimizing... / 5
Optimizing... - 6
Optimizing... \ 7
Optimizing... - 8
Optimizing... / 9
Optimizing... - 10
Optimizing... \ 11
Performed..............................: 12 function evaluations.
Output tree file ......................: lysozymeLarge.ML.dnd
Output tree format ....................: Newick
Log likelihood.........................: -1056.00142355909
YN98.kappa.............................: 4.67827
YN98.omega.............................: 0.624942
WARNING!!! This parameter has a value close to the boundary: BrLen1(1e-06).
WARNING!!! This parameter has a value close to the boundary: BrLen9(1e-06).
WARNING!!! This parameter has a value close to the boundary: BrLen10(1e-06).
WARNING!!! This parameter has a value close to the boundary: BrLen12(1e-06).
WARNING!!! This parameter has a value close to the boundary: BrLen22(1e-06).
WARNING!!! This parameter has a value close to the boundary: BrLen24(1e-06).
WARNING!!! This parameter has a value close to the boundary: BrLen31(1e-06).
WARNING!!! Parameter output.estimates.alias not specified. Default used
instead: 1
Output estimates to file...............: lysozymeLarge.params.txt
Posterior rate distribution for dataset:
Pr(1.000000) = 1.000000
Alignment information logfile..........: lysozymeLarge.infos
BppML's done. Bye.
Total execution time: 0.000000d, 0.000000h, 0.000000m, 19.000000s.
Passed
Test 4
******************************************************************
* Bio++ Maximum Likelihood Computation, version 2.4.0 *
* *
* Authors: J. Dutheil Last Modif. 19/02/18 *
* B. Boussau *
* L. Guéguen *
* M. Groussin *
******************************************************************
Parsing options:
Parsing file ML.bpp for options.
Alphabet type .........................: DNA
Sequence file .........................: ../../../Data/LSU.phy
Sequence format .......................: Phylip file, extended,sequential
Sites to use...........................: all
Remove sites with gaps.................:
[ ] 0%
[= ] 2%
[== ] 5%
[=== ] 7%
[==== ] 10%
[===== ] 13%
[====== ] 15%
[======= ] 18%
[======== ] 21%
[========= ] 23%
[========== ] 26%
[=========== ] 28%
[============ ] 31%
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[================================== ] 89%
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[==================================== ] 94%
[===================================== ] 97%
[======================================] 100%Done.
Number of sequences....................: 79
Number of sites........................: 2353
Input tree.............................: user
Input tree file .......................: ../../../Data/LSU.dnd
Input tree format .....................: Newick
Number of leaves.......................: 79
Output tree file ......................: LSU.ML.dnd
Output tree format ....................: Newick
Branch lengths.........................: Input
Heterogeneous model....................: no
Substitution model.....................: HKY85
External frequencies initialization for: observed
Parameter found........................: HKY85.kappa=2.843
Parameter found........................: HKY85.theta=0.532167
Parameter found........................: HKY85.theta1=0.57134
Parameter found........................: HKY85.theta2=0.584364
Distribution...........................: Gamma
Number of classes......................: 4
Parameter found........................: Gamma.alpha=0.358
- Category 0 (Pr = 0.25) rate..........: 0.0111505
- Category 1 (Pr = 0.25) rate..........: 0.149763
- Category 2 (Pr = 0.25) rate..........: 0.681517
- Category 3 (Pr = 0.25) rate..........: 3.15757
Rate distribution......................: Gamma
Number of classes......................: 4
Initializing data structure............: Done.
Number of distinct sites...............: 1522
Initial log likelihood.................: -65826.8851880443
Message handler........................: LSU.messages
Profiler...............................: LSU.profile
Max # ML evaluations...................: 10000
Tolerance..............................: 1e-06
Optimize topology......................: yes
Optimization method....................: FullD
Algorithm used for derivable parameters: Newton
Reparametrization......................: no
Molecular clock........................: None
Trying to perform 5 NNI(s).
Current value.......................: 65805.15327
Trying to perform 1 NNI(s).
Current value.......................: 65803.47083
Optimizing... / 1
Optimizing... - 2
Optimizing... \ 3
Optimizing... - 4
Optimizing... / 5
Optimizing... - 6
Optimizing... \ 7
Optimizing... - 8
Optimizing... / 9
Optimizing... - 10
Optimizing... \ 11
Optimizing... - 12
Optimizing... / 13
Optimizing... - 14
Optimizing... \ 15
Optimizing... - 16
Optimizing... / 17
Optimizing... - 18
Optimizing... \ 19
Optimizing... - 20
Optimizing... / 21
Optimizing... - 22
Optimizing... \ 23
Optimizing... - 24
Optimizing... / 25
Optimizing... - 26
Optimizing... \ 27
Optimizing... - 28
Performed..............................: 29 function evaluations.
Output tree file ......................: LSU.ML.dnd
Output tree format ....................: Newick
Log likelihood.........................: -65428.4472842493
HKY85.kappa............................: 2.63455
HKY85.theta............................: 0.494128
HKY85.theta1...........................: 0.473663
HKY85.theta2...........................: 0.528379
Gamma.alpha............................: 0.437628
WARNING!!! Parameter output.estimates.alias not specified. Default used
instead: 1
Output estimates to file...............: LSU.params.txt
Posterior rate distribution for dataset:
Pr(0.022496) = 0.328517
Pr(0.209264) = 0.217595
Pr(0.768987) = 0.240969
Pr(2.999253) = 0.212920
Alignment information logfile..........: LSU.infos
BppML's done. Bye.
Total execution time: 0.000000d, 0.000000h, 2.000000m, 15.000000s.
Passed
Test 5
******************************************************************
* Bio++ Maximum Likelihood Computation, version 2.4.0 *
* *
* Authors: J. Dutheil Last Modif. 19/02/18 *
* B. Boussau *
* L. Guéguen *
* M. Groussin *
******************************************************************
Parsing options:
Parsing file ML.bpp for options.
Alphabet type .........................: Proteic
Sequence file .........................: ../../../Data/Myo.mase
Sequence format .......................: MASE file
Sites to use...........................: all
Remove sites with gaps.................:
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[======================================] 100%Done.
Number of sequences....................: 100
Number of sites........................: 153
Input tree.............................: user
Input tree file .......................: ../../../Data/Myo.dnd
Input tree format .....................: Newick
Number of leaves.......................: 100
Output tree file ......................: Myo.ML.dnd
Output tree format ....................: Newick
Branch lengths.........................: Input
Heterogeneous model....................: no
Substitution model.....................: JTT92
External frequencies initialization for: None
Distribution...........................: Gamma
Number of classes......................: 4
Parameter found........................: Gamma.alpha=0.5
- Category 0 (Pr = 0.25) rate..........: 0.0333878
- Category 1 (Pr = 0.25) rate..........: 0.251916
- Category 2 (Pr = 0.25) rate..........: 0.820268
- Category 3 (Pr = 0.25) rate..........: 2.89443
Rate distribution......................: Gamma
Number of classes......................: 4
Initializing data structure............: Done.
Number of distinct sites...............: 148
Initial log likelihood.................: -5172.32804563857
Message handler........................: Myo.messages
Profiler...............................: Myo.profile
Max # ML evaluations...................: 10000
Tolerance..............................: 1e-06
Optimize topology......................: yes
Optimization method....................: FullD
Algorithm used for derivable parameters: Newton
Reparametrization......................: no
Molecular clock........................: None
Trying to perform 14 NNI(s).
Current value.......................: 5138.691253
Trying to perform 10 NNI(s).
Current value.......................: 5115.13294
Trying to perform 3 NNI(s).
Current value.......................: 5099.807407
Trying to perform 4 NNI(s).
Current value.......................: 5095.515277
Optimizing... / 1
Trying to perform 3 NNI(s).
Current value.......................: 5088.452859
Trying to perform 3 NNI(s).
Current value.......................: 5082.250586
Trying to perform 3 NNI(s).
Current value.......................: 5080.008793
Trying to perform 2 NNI(s).
Current value.......................: 5079.627776
Optimizing... / 1
Trying to perform 3 NNI(s).
Current value.......................: 5072.042006
Trying to perform 4 NNI(s).
Current value.......................: 5072.041936
Optimizing... / 1
Optimizing... - 2
Optimizing... \ 3
Optimizing... - 4
Optimizing... / 5
Optimizing... - 6
Optimizing... \ 7
Optimizing... - 8
Optimizing... / 9
Optimizing... - 10
Optimizing... \ 11
Optimizing... - 12
Optimizing... / 13
Optimizing... - 14
Optimizing... \ 15
Optimizing... - 16
Optimizing... / 17
Optimizing... - 18
Optimizing... \ 19
Optimizing... - 20
Optimizing... / 21
Optimizing... - 22
Optimizing... \ 23
Optimizing... - 24
Optimizing... / 25
Performed..............................: 26 function evaluations.
Output tree file ......................: Myo.ML.dnd
Output tree format ....................: Newick
Log likelihood.........................: -5032.52152323802
Gamma.alpha............................: 1.03575
WARNING!!! This parameter has a value close to the boundary: BrLen9(1e-06).
WARNING!!! This parameter has a value close to the boundary: BrLen10(1e-06).
WARNING!!! This parameter has a value close to the boundary: BrLen11(1e-06).
WARNING!!! This parameter has a value close to the boundary: BrLen12(1e-06).
WARNING!!! This parameter has a value close to the boundary: BrLen13(1e-06).
WARNING!!! This parameter has a value close to the boundary: BrLen24(1e-06).
WARNING!!! This parameter has a value close to the boundary: BrLen36(1e-06).
WARNING!!! This parameter has a value close to the boundary: BrLen49(1e-06).
WARNING!!! This parameter has a value close to the boundary: BrLen54(1e-06).
WARNING!!! This parameter has a value close to the boundary: BrLen55(1e-06).
WARNING!!! This parameter has a value close to the boundary: BrLen58(1e-06).
WARNING!!! This parameter has a value close to the boundary: BrLen63(1e-06).
WARNING!!! This parameter has a value close to the boundary: BrLen64(1e-06).
WARNING!!! This parameter has a value close to the boundary: BrLen70(1e-06).
WARNING!!! This parameter has a value close to the boundary: BrLen77(1e-06).
WARNING!!! This parameter has a value close to the boundary: BrLen78(1e-06).
WARNING!!! This parameter has a value close to the boundary: BrLen79(1e-06).
WARNING!!! This parameter has a value close to the boundary: BrLen80(1e-06).
WARNING!!! This parameter has a value close to the boundary: BrLen81(1e-06).
WARNING!!! This parameter has a value close to the boundary: BrLen85(1e-06).
WARNING!!! This parameter has a value close to the boundary: BrLen86(1e-06).
WARNING!!! This parameter has a value close to the boundary: BrLen97(1e-06).
WARNING!!! This parameter has a value close to the boundary: BrLen99(1e-06).
WARNING!!! This parameter has a value close to the boundary:
BrLen100(1e-06).
WARNING!!! This parameter has a value close to the boundary:
BrLen101(1e-06).
WARNING!!! This parameter has a value close to the boundary:
BrLen108(1e-06).
WARNING!!! This parameter has a value close to the boundary:
BrLen109(1e-06).
WARNING!!! This parameter has a value close to the boundary:
BrLen110(1e-06).
WARNING!!! This parameter has a value close to the boundary:
BrLen116(1e-06).
WARNING!!! This parameter has a value close to the boundary:
BrLen120(1e-06).
WARNING!!! This parameter has a value close to the boundary:
BrLen122(1e-06).
WARNING!!! This parameter has a value close to the boundary:
BrLen141(1e-06).
WARNING!!! This parameter has a value close to the boundary:
BrLen142(1e-06).
WARNING!!! This parameter has a value close to the boundary:
BrLen145(1e-06).
WARNING!!! This parameter has a value close to the boundary:
BrLen147(1e-06).
WARNING!!! This parameter has a value close to the boundary:
BrLen148(1e-06).
WARNING!!! This parameter has a value close to the boundary:
BrLen149(1e-06).
WARNING!!! This parameter has a value close to the boundary:
BrLen152(1e-06).
WARNING!!! This parameter has a value close to the boundary:
BrLen153(1e-06).
WARNING!!! This parameter has a value close to the boundary:
BrLen154(1e-06).
WARNING!!! This parameter has a value close to the boundary:
BrLen155(1e-06).
WARNING!!! This parameter has a value close to the boundary:
BrLen156(1e-06).
WARNING!!! This parameter has a value close to the boundary:
BrLen161(1e-06).
WARNING!!! This parameter has a value close to the boundary:
BrLen164(1e-06).
WARNING!!! This parameter has a value close to the boundary:
BrLen165(1e-06).
WARNING!!! This parameter has a value close to the boundary:
BrLen178(1e-06).
WARNING!!! Parameter output.estimates.alias not specified. Default used
instead: 1
Output estimates to file...............: Myo.params.txt
Posterior rate distribution for dataset:
Pr(0.144031) = 0.294118
Pr(0.487239) = 0.254902
Pr(1.005679) = 0.281046
Pr(2.363052) = 0.169935
Alignment information logfile..........: Myo.infos
BppML's done. Bye.
Total execution time: 0.000000d, 0.000000h, 2.000000m, 41.000000s.
1c1
<
(MYG_HETPO:0.3681,(MYG_MUSAN:0.0235,(MYG_GALJA:0.0287,MYG_GALGA:0.0446):0.0701):0.5651,(((MYG_CYPCA:0.1660,MYG_BRARE:0.1473):0.1709,(((((MYG_THUOB:1e-06,MYG_THUTO:1e-06):1e-06,MYG_THUTH:1e-06):1e-06,MYG_THUAL:0.0155):0.0590,MYG_AUXRO:0.1247):0.0432,((MYG_NOTCO:0.0079,((MYG_PSEGE:0.0238,MYG_GOBGI:0.0078):1e-06,(MYG_CRYAN:0.0237,MYG_CHIRA:0.0078):0.0234):0.0078):0.1597,MYG_TETNG:0.1453):0.0525):0.0706):0.7284,((((MYG_ANAPO:0.0023,MYG_APTFO:0.2034):0.0090,(((MYG_URILO:0.0234,(MYG_CERMN:1e-06,MYG_AETPY:0.0075):0.0231):0.0186,MYG_CHICK:0.0360):0.0069,MYG_PHAFI:0.0341):0.0093):0.1226,((((((MYG_ORYAF:0.0508,(MYG_LOXAF:0.0157,MYG_ELEMA:0.0091):0.1453):0.0290,(MYG_ROUAE:0.0172,MYG_ERIEU:0.0569):0.0158):1e-06,((((((((MYG_MOUSE:0.1268,MYG_SPAEH:0.0220):0.0180,(MYG_OCHPR:1e-06,MYG_OCHCU:0.0158):0.0398):0.0165,((((MYG_PERPO:0.0152,MYG_NYCCO:0.0078):0.0237,MYG_GALCR:0.0554):0.0248,MYG_LEPMU:0.0959):0.0308,MYG_TUPGL:0.0224):0.0093):0.0078,((MYG_ONDZI:0.0570,MYG_CASFI:0.0455):0.0308,MYG_RABIT:0.0593):0.0077):0.0080,((MYG_LUTLU:0.0173,(((MYG_HALGR:1e-06,MYG_PHOVI:1e-06):1e-06,MYG_PHOSI:0.0233):0.0823,MYG_ZALCA:0.0576):0.0249):0.0075,((MYG_VULCH:1e-06,(MYG_LYCPI:0.0076,(MYG_OTOME:1e-06,MYG_CANFA:1e-06):1e-06):0.0076):0.0859,MYG_MELME:0.0425):0.0077):0.0168):1e-06,(MYG_CTEGU:0.0415,(MYG_PROGU:0.0240,MYG_LAGMA:0.0163):0.0247):0.0329):0.0077,MYG_PIG:0.0183):1e-06,((((MYG_SHEEP:0.0075,MYG_CEREL:1e-06):0.0069,MYG_BOVIN:0.0157):0.0925,(MYG_HORSE:1e-06,MYG_EQUBU:1e-06):0.0398):0.0145,(((MYG_PHYCA:1e-06,MYG_KOGSI:0.0391):0.0608,(MYG_ESCGI:1e-06,(MYG_MEGNO:1e-06,(MYG_BALPH:0.0150,MYG_BALAC:0.0073):0.0075):0.0075):0.0283):0.0262,(((MYG_DELLE:1e-06,(((MYG_TURTR:1e-06,MYG_DELDE:1e-06):1e-06,(MYG_ORCOR:1e-06,MYG_GLOME:0.0076):0.0076):0.0235,(MYG_PHOPH:1e-06,MYG_PHODA:1e-06):0.0078):0.0079):0.0098,(MYG_ZIPCA:0.0074,MYG_MESCA:0.0078):0.0906):0.0162,MYG_INIGE:0.0142):0.0162):0.0363):0.0406):0.0222):0.0113,((((((MYG_PANTR:0.0078,MYG_GORBE:0.0078):1e-06,MYG_HUMAN:1e-06):0.0078,(MYG_HYLSY:1e-06,MYG_HYLAG:1e-06):1e-06):0.0077,MYG_PONPY:1e-06):0.0235,(((MYG_ERYPA:1e-06,MYG_PREEN:1e-06):1e-06,MYG_PAPAN:1e-06):1e-06,MYG_MACFA:0.0077):0.0078):0.0175,((MYG_CALJA:1e-06,MYG_AOTTR:0.0079):1e-06,(MYG_LAGLA:0.0240,(MYG_SAISC:0.0239,MYG_CEBAP:1e-06):0.0079):0.0079):0.0655):0.0127):0.0398,(MYG_TACAC:0.0450,MYG_ORNAN:0.0322):0.1019):0.0088,(MYG_MACRU:0.1098,MYG_DIDMA:0.0407):0.0090):0.2378):0.0389,(MYG_ALLMI:0.2278,(MYG_VARVA:0.1822,(MYG_GRAGE:0.0214,(MYG_CHEMY:0.0149,MYG_CARCR:1e-06):0.0401):0.1270):0.0462):0.0238):0.5338):0.5120);
---
> (MYG_HETPO:0.3681,(MYG_MUSAN:0.0235,(MYG_GALJA:0.0287,MYG_GALGA:0.0446):0.0701):0.5651,(((MYG_CYPCA:0.1660,MYG_BRARE:0.1473):0.1709,((((MYG_THUTO:1e-06,(MYG_THUTH:1e-06,MYG_THUOB:1e-06):1e-06):1e-06,MYG_THUAL:0.0155):0.0590,MYG_AUXRO:0.1247):0.0432,((MYG_NOTCO:0.0079,((MYG_PSEGE:0.0238,MYG_GOBGI:0.0078):1e-06,(MYG_CRYAN:0.0237,MYG_CHIRA:0.0078):0.0234):0.0078):0.1597,MYG_TETNG:0.1453):0.0525):0.0706):0.7284,((((MYG_ANAPO:0.0023,MYG_APTFO:0.2034):0.0090,(((MYG_URILO:0.0234,(MYG_CERMN:1e-06,MYG_AETPY:0.0075):0.0231):0.0186,MYG_CHICK:0.0360):0.0069,MYG_PHAFI:0.0341):0.0093):0.1226,((((((MYG_ORYAF:0.0508,(MYG_LOXAF:0.0157,MYG_ELEMA:0.0091):0.1453):0.0290,(MYG_ROUAE:0.0172,MYG_ERIEU:0.0569):0.0158):1e-06,((((((((MYG_MOUSE:0.1268,MYG_SPAEH:0.0220):0.0180,(MYG_OCHPR:1e-06,MYG_OCHCU:0.0158):0.0398):0.0165,((((MYG_PERPO:0.0152,MYG_NYCCO:0.0078):0.0237,MYG_GALCR:0.0554):0.0248,MYG_LEPMU:0.0959):0.0308,MYG_TUPGL:0.0224):0.0093):0.0078,((MYG_ONDZI:0.0570,MYG_CASFI:0.0455):0.0308,MYG_RABIT:0.0593):0.0077):0.0080,((MYG_LUTLU:0.0173,(((MYG_HALGR:1e-06,MYG_PHOVI:1e-06):1e-06,MYG_PHOSI:0.0233):0.0823,MYG_ZALCA:0.0576):0.0249):0.0075,((MYG_VULCH:1e-06,(MYG_LYCPI:0.0076,(MYG_OTOME:1e-06,MYG_CANFA:1e-06):1e-06):0.0076):0.0859,MYG_MELME:0.0425):0.0077):0.0168):1e-06,(MYG_CTEGU:0.0415,(MYG_PROGU:0.0240,MYG_LAGMA:0.0163):0.0247):0.0329):0.0077,MYG_PIG:0.0183):1e-06,((((MYG_SHEEP:0.0075,MYG_CEREL:1e-06):0.0069,MYG_BOVIN:0.0157):0.0925,(MYG_HORSE:1e-06,MYG_EQUBU:1e-06):0.0398):0.0145,(((MYG_PHYCA:1e-06,MYG_KOGSI:0.0391):0.0608,(MYG_ESCGI:1e-06,(MYG_MEGNO:1e-06,(MYG_BALPH:0.0150,MYG_BALAC:0.0073):0.0075):0.0075):0.0283):0.0262,(((MYG_DELLE:1e-06,(((MYG_TURTR:1e-06,MYG_DELDE:1e-06):1e-06,(MYG_ORCOR:1e-06,MYG_GLOME:0.0076):0.0076):0.0235,(MYG_PHOPH:1e-06,MYG_PHODA:1e-06):0.0078):0.0079):0.0098,(MYG_ZIPCA:0.0074,MYG_MESCA:0.0078):0.0906):0.0162,MYG_INIGE:0.0142):0.0162):0.0363):0.0406):0.0222):0.0113,((((((MYG_PANTR:0.0078,MYG_GORBE:0.0078):1e-06,MYG_HUMAN:1e-06):0.0078,(MYG_HYLSY:1e-06,MYG_HYLAG:1e-06):1e-06):0.0077,MYG_PONPY:1e-06):0.0235,((MYG_PREEN:1e-06,(MYG_PAPAN:1e-06,MYG_ERYPA:1e-06):1e-06):1e-06,MYG_MACFA:0.0077):0.0078):0.0175,((MYG_CALJA:1e-06,MYG_AOTTR:0.0079):1e-06,(MYG_LAGLA:0.0240,(MYG_SAISC:0.0239,MYG_CEBAP:1e-06):0.0079):0.0079):0.0655):0.0127):0.0398,(MYG_TACAC:0.0450,MYG_ORNAN:0.0322):0.1019):0.0088,(MYG_MACRU:0.1098,MYG_DIDMA:0.0407):0.0090):0.2378):0.0389,(MYG_ALLMI:0.2278,(MYG_VARVA:0.1822,(MYG_GRAGE:0.0214,(MYG_CHEMY:0.0149,MYG_CARCR:1e-06):0.0401):0.1270):0.0462):0.0238):0.5338):0.5120);
autopkgtest [22:24:35]: test run-unit-test
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