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CompEvol / beast2

Bayesian Evolutionary Analysis by Sampling Trees
www.beast2.org
GNU Lesser General Public License v2.1
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Stack size error #676

Closed ViralExanthemata closed 7 years ago

ViralExanthemata commented 7 years ago

For about one week I cannot run BEAST.

I used the parameters that Veronika and I had worked out the the Taming the BEAST workshop. It worked for 5 different alignments of WGS. Now I want to perform analysis for a smaller region of the same pathogen but a different outbreak. I also need to include outgroups. At the first attempt to run BEAST, the error is about tree height. I changed the starting value for origin in BEAUti (as I had not closed the file yet). Running the corrected file, the error is stack size # (various numbers: 3, 10, 11, and many more) (screenshot attached).

Additionally, BEAUti acts funny. When setting up BEASTModelTest, strict clock, and BirthDeathSkylineSerial, the prior window shows parameters without descriptor (screenshot attached). I get the expected window after switching back and forth between the prior models. It remains to be determined if this contributes to the error.

major difference in BEAUti file.pdf parameters without descriptors.pdf

and BEAST output: Random number seed: 1489260057713

JN635404.MVi/Virginia.USA/15.09_2009-04-06_2009.2630: 1180 4 JN635407.MVi/Texas.USA/4.07_2007-01-22_2007.0603: 1180 4 MVs/AbreuLima.PE.BRA/19.13_2013-05-06_2013.3425: 1180 4 MVs/AbreuLima.PE.BRA/49.13/2_2013-12-01_2013.9151: 1180 4 MVs/Alianca.PE.BRA/28.13/2_2013-07-09_2013.5178: 1180 4 MVs/Camaragibe.PE.BRA/18.13/5_2013-05-02_2013.3315: 1180 4 MVs/Caucaia.CE.BRA/48.14/3_2014-11-29_2014.9096: 1180 4 MVs/Forquilha.CE.BRA/31.14_2014-07-31_2014.5780: 1180 4 MVs/Forquilha.CE.BRA/32.14/2_D8_2014-08-09_2014.6027: 1180 4 MVs/Fortaleza.CE.BRA/50.14/4_2014-12-08_2014.9343: 1180 4 MVs/Fortaleza.CE.BRA/53.14/2_2015-01-01_2015.0: 1180 4 MVs/Fortazela.CE.BRA/21.14_2014-05-21_2014.3836: 1180 4 MVs/Goiana.PE.BRA/45.13/6_2013-11-25_2013.8986: 1180 4 MVs/Goiana.PE.BRA/50.13/3_2013-12-09_2013.9397: 1180 4 MVs/Goiana.PE.BRA/50.13/5_2013-12-10_2013.9429: 1180 4 MVs/Groairas.CE.BRA/44.14_2014-10-30_2014.8274: 1180 4 MVs/Maracanau.CE.BRA/53.14/4_2014-12-29_2014.9918: 1180 4 MVs/Olinda.PE.BRA/13.13_2013-04-03_2013.2521: 1180 4 MVs/Paulista.PE.BRA/16.13/4_2013-04-16_2013.2877: 1180 4 MVs/Recife.PE.BRA/47.13/2_2013-11-19_2013.8822: 1180 4 MVs/SenadorSa.CE.BRA/46.14_2014-11-11_2014.8603: 1180 4 MVs/Trairi.CE.BRA/5.14/11_2014-01-27_2014.0712: 1180 4 MVs/Uruburetama.CE.BRA/8.14/2_2014-02-22_2014.1425: 1180 4 MVs/VitSntAntao.PE.BRA/17.13/2_2013-04-28_2013.3206: 1180 4 Alignment(24 strains) 24 taxa 1180 sites 51 patterns

JN635404.MVi/Virginia.USA/15.09_2009-04-06_2009.2630 = 2009.263 (5.73700000000008) JN635407.MVi/Texas.USA/4.07_2007-01-22_2007.0603 = 2007.0603 (7.9396999999999025) MVs/AbreuLima.PE.BRA/19.13_2013-05-06_2013.3425 = 2013.3425 (1.6575000000000273) MVs/AbreuLima.PE.BRA/49.13/2_2013-12-01_2013.9151 = 2013.9151 (1.0849000000000615) MVs/Alianca.PE.BRA/28.13/2_2013-07-09_2013.5178 = 2013.5178 (1.4821999999999207) MVs/Camaragibe.PE.BRA/18.13/5_2013-05-02_2013.3315 = 2013.3315 (1.6684999999999945) MVs/Caucaia.CE.BRA/48.14/3_2014-11-29_2014.9096 = 2014.9096 (0.09040000000004511) MVs/Forquilha.CE.BRA/31.14_2014-07-31_2014.5780 = 2014.578 (0.42200000000002547) MVs/Forquilha.CE.BRA/32.14/2_D8_2014-08-09_2014.6027 = 2014.6027 (0.3973000000000866) MVs/Fortaleza.CE.BRA/50.14/4_2014-12-08_2014.9343 = 2014.9343 (0.06570000000010623) MVs/Fortaleza.CE.BRA/53.14/2_2015-01-01_2015.0 = 2015.0 (0.0) MVs/Fortazela.CE.BRA/21.14_2014-05-21_2014.3836 = 2014.3836 (0.6164000000001124) MVs/Goiana.PE.BRA/45.13/6_2013-11-25_2013.8986 = 2013.8986 (1.1014000000000124) MVs/Goiana.PE.BRA/50.13/3_2013-12-09_2013.9397 = 2013.9397 (1.0603000000000975) MVs/Goiana.PE.BRA/50.13/5_2013-12-10_2013.9429 = 2013.9429 (1.0570999999999913) MVs/Groairas.CE.BRA/44.14_2014-10-30_2014.8274 = 2014.8274 (0.17260000000010223) MVs/Maracanau.CE.BRA/53.14/4_2014-12-29_2014.9918 = 2014.9918 (0.008199999999987995) MVs/Olinda.PE.BRA/13.13_2013-04-03_2013.2521 = 2013.2521 (1.7479000000000724) MVs/Paulista.PE.BRA/16.13/4_2013-04-16_2013.2877 = 2013.2877 (1.7122999999999138) MVs/Recife.PE.BRA/47.13/2_2013-11-19_2013.8822 = 2013.8822 (1.1177999999999884) MVs/SenadorSa.CE.BRA/46.14_2014-11-11_2014.8603 = 2014.8603 (0.13969999999994798) MVs/Trairi.CE.BRA/5.14/11_2014-01-27_2014.0712 = 2014.0712 (0.9287999999999101) MVs/Uruburetama.CE.BRA/8.14/2_2014-02-22_2014.1425 = 2014.1425 (0.8575000000000728) MVs/VitSntAntao.PE.BRA/17.13/2_2013-04-28_2013.3206 = 2013.3206 (1.679399999999987) Starting frequencies: [0.2952683615819209, 0.39413841807909605, 0.2028954802259887, 0.10769774011299435] TreeLikelihood(treeLikelihood.24 strains0) uses BeerLikelihoodCore4 Alignment(24 strains): [taxa, patterns, sites] = [24, 51, 1180] Failed to load BEAGLE library: no hmsbeagle-jni in java.library.path with (Math) { function f(BMT_ProportionInvariable, hasInvariableSites) { return BMT_ProportionInvariable hasInvariableSites;} } with (Math) { function f(BMT_gammaShape, hasGammaRates) { return BMT_gammaShape hasGammaRates;} }

Error 110 parsing the xml input file

validate and intialize error: Error in expression: Stack size 3 ( != 1 ) at end of expression evaluation

Error detected about here:

java.lang.RuntimeException: Error in expression: Stack size 3 ( != 1 ) at end of expression evaluation at beast.math.statistic.RPNcalculator.initAndValidate(Unknown Source) at beast.util.XMLParser.initBEASTObjects(Unknown Source) at beast.util.XMLParser.parse(Unknown Source) at beast.util.XMLParser.parseFile(Unknown Source) at beast.app.BeastMCMC.parseArgs(Unknown Source) at beast.app.beastapp.BeastMain.main(Unknown Source) at beast.app.beastapp.BeastLauncher.main(Unknown Source)
rbouckaert commented 7 years ago

Hi Helene,

At first glance, this looks like a problem with the RPNcalculator, which can happen when there are spaces or other special characters in variable names (see #369). When that happens, the RPN calculator throws an exception and this may also explain the weird behaviour of BEAUti.

Is it possible that you used quite different names for the alignment that contain spaces?

If not, would you mind emailing the XML so I can investigate what is going wrong? Cheers, Remco

ViralExanthemata commented 7 years ago

Hello Remco,

I have shortened the name (and there are no spaces in the name), but the error remains. Attached please find a small data set. Hopefully it is not going to be too complicated. Please treat the data confidentially.

Cheers,

Helene

On Mar 12, 2017, at 14:31, Remco Bouckaert notifications@github.com wrote:

Hi Helene,

At first glance, this looks like a problem with the RPNcalculator, which can happen when there are spaces or other special characters in variable names (see #369 https://github.com/CompEvol/beast2/issues/369). When that happens, the RPN calculator throws an exception and this may also explain the weird behaviour of BEAUti.

Is it possible that you used quite different names for the alignment that contain spaces?

If not, would you mind emailing the XML so I can investigate what is going wrong? Cheers, Remco

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/CompEvol/beast2/issues/676#issuecomment-285968924, or mute the thread https://github.com/notifications/unsubscribe-auth/AQSKJMLTtEvegRqBEZXoShDXLg0k74dxks5rlEf7gaJpZM4MaUEj.

rbouckaert commented 7 years ago

It was indeed a space in the file name “24 strains” that caused the hiccup. Replacing every “24 strains” with “24_strains” solves the problem (though #369 is still open).

ViralExanthemata commented 7 years ago

Thank you. I was looking for spaces in the strain names and overlooked the file name.

On Mar 12, 2017, at 19:51, Remco Bouckaert notifications@github.com wrote:

It was indeed a space in the file name “24 strains” that caused the hiccup. Replacing every “24 strains” with “24_strains” solves the problem (though #369 https://github.com/CompEvol/beast2/issues/369 is still open).

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/CompEvol/beast2/issues/676#issuecomment-285992340, or mute the thread https://github.com/notifications/unsubscribe-auth/AQSKJO9HBtLqqun6fjHxE8oEotZVh3ahks5rlJMIgaJpZM4MaUEj.