However, I am quite interested in using codon models, but I got many errors while trying:
with -sm UNIFORMCODON:
ERROR: null
Use option -h or --help to show usage.
See .info file for more information.
Content of the info file:
# =========================================================================
# || PRE-RUN INFO ||
# =========================================================================
# DELIRIOUS
# Arguments: [../../../../taxon_data/Rodentia.timetree.nointernal.nozero.dots.nwk, RodentiaENSGT00760000118824.d.b.a.a.b.a.a.b_backtrans.mfa, RodentiaENSGT00760000118824.d.b.a.a.b.a.a.b_gsmap.tsv, -i, 100000, -o, DLRS_default100k-3, -lout, -sm, UNIFORMCODON]
# Current time: 2018-01-04 04:53:06
# Host tree rescaling factor: 0.013721810598397183
# Run failed. Reason:
java.lang.NullPointerException
at se.cbb.jprime.math.AdditionalEJMLOps.getEigensystemSolution(AdditionalEJMLOps.java:30)
at se.cbb.jprime.seqevo.SubstitutionMatrixHandler.update(SubstitutionMatrixHandler.java:185)
at se.cbb.jprime.seqevo.SubstitutionMatrixHandler.<init>(SubstitutionMatrixHandler.java:109)
at se.cbb.jprime.seqevo.UniformCodon.createUniformCodon(UniformCodon.java:30)
at se.cbb.jprime.seqevo.SubstitutionMatrixHandlerFactory.create(SubstitutionMatrixHandlerFactory.java:48)
at se.cbb.jprime.apps.dlrs.Delirious.main(Delirious.java:123)
at se.cbb.jprime.apps.JPrIMEStarter.main(JPrIMEStarter.java:88)
with -sm ARVECODON
ERROR: 62
Use option -h or --help to show usage.
See .info file for more information.
info file:
# =========================================================================
# || PRE-RUN INFO ||
# =========================================================================
# DELIRIOUS
# Arguments: [../../../../taxon_data/Rodentia.timetree.nointernal.nozero.dots.nwk, RodentiaENSGT00760000118824.d.b.a.a.b.a.a.b_backtrans.mfa, RodentiaENSGT00760000118824.d.b.a.a.b.a.a.b_gsmap.tsv, -i, 100000, -o, DLRS_default100k-3, -lout, -sm, ARVECODON]
# Current time: 2018-01-04 05:09:19
# Host tree rescaling factor: 0.013721810598397183
# Initial guest tree: Produced with NJ on sequence identity (arbitrarily rooted).
# Run failed. Reason:
java.lang.ArrayIndexOutOfBoundsException: 62
at se.cbb.jprime.seqevo.SequenceType.getLeafLikelihood(SequenceType.java:200)
at se.cbb.jprime.seqevo.SubstitutionMatrixHandler.getLeafLikelihood(SubstitutionMatrixHandler.java:249)
at se.cbb.jprime.seqevo.SubstitutionModel.updateLeafLikelihood(SubstitutionModel.java:294)
at se.cbb.jprime.seqevo.SubstitutionModel.updateLikelihood(SubstitutionModel.java:217)
at se.cbb.jprime.seqevo.SubstitutionModel.updateLikelihood(SubstitutionModel.java:222)
at se.cbb.jprime.seqevo.SubstitutionModel.updateLikelihood(SubstitutionModel.java:222)
at se.cbb.jprime.seqevo.SubstitutionModel.updateLikelihood(SubstitutionModel.java:222)
at se.cbb.jprime.seqevo.SubstitutionModel.<init>(SubstitutionModel.java:114)
at se.cbb.jprime.apps.dlrs.Delirious.main(Delirious.java:177)
at se.cbb.jprime.apps.JPrIMEStarter.main(JPrIMEStarter.java:88)
with USERDEFINED
I went into the code to copy the arvecodon matrix into a text file with the correct format, and ran with the following option: -sm USERDEFINED="$(cat arvecodon.txt)"
This resulted in a stackoverflow error:
Exception in thread "main" java.lang.StackOverflowError
at java.util.regex.Pattern$Loop.match(Pattern.java:4785)
at java.util.regex.Pattern$GroupTail.match(Pattern.java:4717)
at java.util.regex.Pattern$Curly.match0(Pattern.java:4272)
at java.util.regex.Pattern$Curly.match(Pattern.java:4234)
at java.util.regex.Pattern$BmpCharProperty.match(Pattern.java:3798)
at java.util.regex.Pattern$GroupHead.match(Pattern.java:4658)
(repeated many times)
Would you mind helping me on that? I'm a bit lost. Also I have never developped in java, but with some help I could maybe use the source code in this github repository instead of the dropbox jar file.
Let me know if you want to test using my input files, I will send you a zip.
Hi,
I downloaded the jar file from the dropbox link, and am able to run jprime Delirious with default parameters, for example:
However, I am quite interested in using codon models, but I got many errors while trying:
with
-sm UNIFORMCODON
:Content of the info file:
with
-sm ARVECODON
info file:
with
USERDEFINED
I went into the code to copy the arvecodon matrix into a text file with the correct format, and ran with the following option:
-sm USERDEFINED="$(cat arvecodon.txt)"
This resulted in a stackoverflow error:
(repeated many times)
Would you mind helping me on that? I'm a bit lost. Also I have never developped in java, but with some help I could maybe use the source code in this github repository instead of the dropbox jar file.
Let me know if you want to test using my input files, I will send you a zip.
Thanks a lot! :)