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...@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% [================ ] 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....................: 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=1WARNING!!! Parameter YN98.123_Full.theta not specified. Default used instead: 0.5
Parameter found........................: YN98.123_Full.theta_1=0.5WARNING!!! Parameter YN98.123_Full.theta1 not specified. Default used instead: 0.5
Parameter found........................: YN98.123_Full.theta1_1=0.5WARNING!!! 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=1WARNING!!! Parameter YN98.123_Full.theta not specified. Default used instead: 0.5
Parameter found........................: YN98.123_Full.theta_2=0.5WARNING!!! Parameter YN98.123_Full.theta1 not specified. Default used instead: 0.5
Parameter found........................: YN98.123_Full.theta1_2=0.5WARNING!!! 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% [================ ] 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....................: 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% [============= ] 34% [============== ] 36% [=============== ] 39% [================ ] 42% [================= ] 44% [================== ] 47% [=================== ] 50% [==================== ] 52% [===================== ] 55% [====================== ] 57% [======================= ] 60% [======================== ] 63% [========================= ] 65% [========================== ] 68% [=========================== ] 71% [============================ ] 73% [============================= ] 76% [============================== ] 79% [=============================== ] 81% [================================ ] 84% [================================= ] 86% [================================== ] 89% [=================================== ] 92% [==================================== ] 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............................: 0.437628WARNING!!! 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.................: [ ] 0% [ ] 0% [ ] 0% [ ] 0% [ ] 0% [ ] 0% [ ] 0% [ ] 0% [ ] 0% [ ] 0% [ ] 0% [ ] 0% [ ] 0% [ ] 0% [ ] 0% [ ] 0% [ ] 0% [ ] 0% [ ] 0% [ ] 0% [ ] 0% [ ] 0% [ ] 0% [= ] 2% [== ] 5% [=== ] 8% [==== ] 11% [===== ] 14% [====== ] 16% [======= ] 20% [======== ] 23% [========= ] 26% [=========== ] 29% [============ ] 31% [============ ] 31% [============ ] 31% [============ ] 31% [============ ] 31% [============ ] 32% [============ ] 32% [============ ] 32% [============ ] 32% [============ ] 32% [============ ] 32% [============ ] 32% [============ ] 32% [============ ] 32% [============ ] 32% [============ ] 33% [============ ] 33% [============ ] 33% [============ ] 33% [============ ] 33% [============ ] 33% [============ ] 33% [============ ] 33% [============ ] 33% [============ ] 33% [============ ] 34% [============ ] 34% [============= ] 34% [============= ] 34% [============= ] 34% [============= ] 34% [============== ] 37% [=============== ] 40% [================ ] 43% [================= ] 46% [================== ] 49% [================== ] 49% [================== ] 49% [=================== ] 50% [=================== ] 50% [======================================] 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
OpenPGP_signature
Description: OpenPGP digital signature
