tassel-5-standalone does not start

[jahn...@gmail.com]

Hello,

I am trying to get Tassel running on my ubuntu computer. When I do

"./start_tassel.pl -Xmx6g -importGuess TASStutorialData/data/mdp_genotype.hmp.txt -filterAlign -filterAlignMinFreq 0.05"

from the linux prompt, the Tassel GUI does not show up. The only result I see is the following:

./start_tassel.pl -Xmx6g -importGuess TASStutorialData/data/mdp_genotype.hmp.txt -filterAlign -filterAlignMinFreq 0.05
./lib/jhdf5-14.12.5.jar:./lib/mail-1.4.jar:./lib/kotlin-stdlib-1.4.32.jar:./lib/postgresql-9.4-1201.jdbc41.jar:./lib/scala-library-2.10.1.jar:./lib/log4j-1.2.13.jar:./lib/jfreesvg-3.2.jar:./lib/kotlin-stdlib-jdk8-1.4.32.jar:./lib/kotlin-stdlib-jdk7-1.4.32.jar:./lib/slf4j-api-1.7.10.jar:./lib/gs-core-1.3.jar:./lib/snappy-java-1.1.1.6.jar:./lib/ejml-ddense-0.41.jar:./lib/guava-22.0.jar:./lib/biojava-phylo-4.2.12.jar:./lib/json-simple-1.1.1.jar:./lib/commons-codec-1.10.jar:./lib/colt-1.2.0.jar:./lib/trove-3.0.3.jar:./lib/slf4j-simple-1.7.10.jar:./lib/biojava-alignment-6.0.4.jar:./lib/sqlite-jdbc-3.8.5-pre1.jar:./lib/forester-1.039.jar:./lib/ejml-core-0.41.jar:./lib/phg.jar:./lib/junit-4.10.jar:./lib/jcommon-1.0.23.jar:./lib/javax.json-1.0.4.jar:./lib/commons-math3-3.4.1.jar:./lib/itextpdf-5.1.0.jar:./lib/kotlinx-coroutines-core-jvm-1.4.3.jar:./lib/ini4j-0.5.4.jar:./lib/fastutil-8.2.2.jar:./lib/ahocorasick-0.2.4.jar:./lib/htsjdk-2.23.0.jar:./lib/jfreechart-1.0.19.jar:./lib/gs-ui-1.3.jar:./lib/biojava-core-6.0.4.jar:./sTASSEL.jar
Memory Settings: -Xms512m -Xmx6g
Tassel Pipeline Arguments: -importGuess TASStutorialData/data/mdp_genotype.hmp.txt -filterAlign -filterAlignMinFreq 0.05
[main] INFO net.maizegenetics.tassel.PreferencesDialog - TasselPrefs: default locale set: English (United States)
[main] INFO net.maizegenetics.tassel.TASSELMainFrame - TASSELMainFrame: addThirdPartyMenus: adding: /phg/tassel_menu.xml
[main] INFO net.maizegenetics.tassel.TasselLogging - Tassel Version: 5.2.80  Date: February 17, 2022
[main] INFO net.maizegenetics.tassel.TasselLogging - Max Available Memory Reported by JVM: 6144 MB
[main] INFO net.maizegenetics.tassel.TasselLogging - Java Version: 11.0.14.1
[main] INFO net.maizegenetics.tassel.TasselLogging - OS: Linux
[main] INFO net.maizegenetics.tassel.TasselLogging - Number of Processors: 8

Help is appreciated.

jahn

[Terry Casstevens]

Please add -debug to get more information.

./start_tassel.pl -Xmx6g -debug ...

Best,

Terry

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[jahn...@gmail.com]

Thanks for responding. Here is what the -debug results in:

./start_tassel.pl -Xmx6g -debug -importGuess TASStutorialData/data/mdp_genotype.hmp.txt -filterAlign -filterAlignMinFreq 0.05

./lib/jhdf5-14.12.5.jar:./lib/mail-1.4.jar:./lib/kotlin-stdlib-1.4.32.jar:./lib/postgresql-9.4-1201.jdbc41.jar:./lib/scala-library-2.10.1.jar:./lib/log4j-1.2.13.jar:./lib/jfreesvg-3.2.jar:./lib/kotlin-stdlib-jdk8-1.4.32.jar:./lib/kotlin-stdlib-jdk7-1.4.32.jar:./lib/slf4j-api-1.7.10.jar:./lib/gs-core-1.3.jar:./lib/snappy-java-1.1.1.6.jar:./lib/ejml-ddense-0.41.jar:./lib/guava-22.0.jar:./lib/biojava-phylo-4.2.12.jar:./lib/json-simple-1.1.1.jar:./lib/commons-codec-1.10.jar:./lib/colt-1.2.0.jar:./lib/trove-3.0.3.jar:./lib/slf4j-simple-1.7.10.jar:./lib/biojava-alignment-6.0.4.jar:./lib/sqlite-jdbc-3.8.5-pre1.jar:./lib/forester-1.039.jar:./lib/ejml-core-0.41.jar:./lib/phg.jar:./lib/junit-4.10.jar:./lib/jcommon-1.0.23.jar:./lib/javax.json-1.0.4.jar:./lib/commons-math3-3.4.1.jar:./lib/itextpdf-5.1.0.jar:./lib/kotlinx-coroutines-core-jvm-1.4.3.jar:./lib/ini4j-0.5.4.jar:./lib/fastutil-8.2.2.jar:./lib/ahocorasick-0.2.4.jar:./lib/htsjdk-2.23.0.jar:./lib/jfreechart-1.0.19.jar:./lib/gs-ui-1.3.jar:./lib/biojava-core-6.0.4.jar:./sTASSEL.jar
Memory Settings: -Xms512m -Xmx6g

Tassel Pipeline Arguments: -debug -importGuess TASStutorialData/data/mdp_genotype.hmp.txt -filterAlign -filterAlignMinFreq 0.05

[main] INFO net.maizegenetics.tassel.PreferencesDialog - TasselPrefs: default locale set: English (United States)
[main] INFO net.maizegenetics.tassel.TASSELMainFrame - TASSELMainFrame: addThirdPartyMenus: adding: /phg/tassel_menu.xml
[main] INFO net.maizegenetics.tassel.TasselLogging - Tassel Version: 5.2.80  Date: February 17, 2022
[main] INFO net.maizegenetics.tassel.TasselLogging - Max Available Memory Reported by JVM: 6144 MB
[main] INFO net.maizegenetics.tassel.TasselLogging - Java Version: 11.0.14.1
[main] INFO net.maizegenetics.tassel.TasselLogging - OS: Linux
[main] INFO net.maizegenetics.tassel.TasselLogging - Number of Processors: 8

[Terry Casstevens]

This is working for me. Is your directory for the file correct?
Should it be TASSELTutorialData5?

> To view this discussion on the web visit https://groups.google.com/d/msgid/tassel/bc134789-ce3b-444f-9e23-e4aec152e217n%40googlegroups.com.

[jahn...@gmail.com]

Thanks. Error identified.