TASSEL5 standalone: Exception in thread "main" java.lang.IllegalArgumentException

[James Holland]

Sorry to ask what is likely a stupid question, but here is an attempt to run the mlm pipeline using the tutorial data sets on Linux (I moved the data sets into the same folder as run_pipeline.pl):

> ./run_pipeline.pl -fork1 -h mdp_genotype.hmp.txt -fork2 -t mdp_phenotype.txt -fork3  -k mdp_kinship.txt -combine4 -input1 -input2 -intersect -combine5 -input4 -input3 -mlm -mlmCompressionLevel None -export outp -runfork1 -runfork2 -runfork3

Here is result:

./lib/ahocorasick-0.2.4.jar:./lib/batik-parser.jar:./lib/batik-awt-util.jar:./lib/batik-css.jar:./lib/batik-dom.jar:./lib/batik-ext.jar:./lib/batik-gui-util.jar:./lib/batik-gvt.jar:./lib/batik-util.jar:./lib/batik-xml.jar:./lib/batik-svg-dom.jar:./lib/batik-svggen.jar:./lib/biojava-phylo-4.0.0.jar:./lib/biojava-alignment-4.0.0.jar:./lib/biojava-core-4.0.0.jar:./lib/geronimo-spec-activation-1.0.2-rc4.jar:./lib/colt.jar:./lib/cisd-jhdf5-batteries_included_lin_win_mac.jar:./lib/commons-codec-1.10.jar:./lib/commons-math3-3.4.1.jar:./lib/ejml-0.23.jar:./lib/forester.jar:./lib/javax.json-1.0.4.jar:./lib/guava-14.0.1.jar:./lib/htsjdk-1.138.jar:./lib/itextpdf-5.1.0.jar:./lib/json-simple-1.1.1.jar:./lib/jcommon-1.0.6.jar:./lib/jfreechart-1.0.3.jar:./lib/junit-4.10.jar:./lib/slf4j-api-1.7.10.jar:./lib/log4j-1.2.13.jar:./lib/mail-1.4.jar:./lib/poi-3.0.1-FINAL-20070705.jar:./lib/postgresql-9.4-1201.jdbc41.jar:./lib/slf4j-simple-1.7.10.jar:./lib/snappy-java-1.1.1.6.jar:./lib/sqlite-jdbc-3.8.5-pre1.jar:./lib/trove-3.0.3.jar:./lib/xercesImpl.jar:./lib/xml.jar:./lib/xmlParserAPIs.jar:./sTASSEL.jar
Memory Settings: -Xms512m -Xmx1536m
Tassel Pipeline Arguments: -fork1 -h mdp_genotype.hmp.txt -fork2 -t mdp_phenotype.txt -fork3 -k mdp_kinship.txt -combine4 -input1 -input2 -intersect -combine5 -input4 -input3 -mlm -mlmCompressionLevel None -export outp -runfork1 -runfork2 -runfork3
Exception in thread "main" java.lang.IllegalArgumentException
        at java.util.concurrent.ThreadPoolExecutor.<init>(ThreadPoolExecutor.java:1307)
        at java.util.concurrent.ThreadPoolExecutor.<init>(ThreadPoolExecutor.java:1195)
        at java.util.concurrent.Executors.newFixedThreadPool(Executors.java:89)
        at net.maizegenetics.pipeline.TasselPipeline.<init>(TasselPipeline.java:135)
        at net.maizegenetics.pipeline.TasselPipeline.<init>(TasselPipeline.java:118)
        at net.maizegenetics.pipeline.TasselPipeline.main(TasselPipeline.java:263)


For diagnosing, here is some system info:
eos$ java -version
openjdk version "1.8.0_51"
OpenJDK Runtime Environment (build 1.8.0_51-b16)
OpenJDK 64-Bit Server VM (build 25.51-b03, mixed mode)

eos$ lsb_release -a
LSB Version:    :base-4.0-amd64:base-4.0-noarch:core-4.0-amd64:core-4.0-noarch:graphics-4.0-amd64:graphics-4.0-noarch:printing-4.0-amd64:printing-4.0-noarch
Distributor ID: RedHatEnterpriseWorkstation
Description:    Red Hat Enterprise Linux Workstation release 6.7 (Santiago)
Release:        6.7
Codename:       Santiago

eos$ free -m
             total       used       free     shared    buffers     cached
Mem:          1878       1020        857          0        120        571
-/+ buffers/cache:        328       1549
Swap:         4031          0       4031


Lastly, I can make the tassel GUI open using ./start_tassel.pl. I have run very similar pipelines (same/similar arguments) on command line in Windows with success. But baffled by this problem.

Thanks for help. - Jim

[James Holland]

And I am using tassel5 standalone build 9-24-15.

[Terry Casstevens]

Hi Jim,

I can't reproduce this. Can you add -debug flag and send me all the output?

Thank you,

Terry

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[James Holland]

eos$  ./run_pipeline.pl -debug -fork1 -h mdp_genotype.hmp.txt -fork2 -t mdp_phenotype.txt -fork3  -k mdp_kinship.txt -combine4 -input1 -input2 -intersect -combine5 -input4 -input3 -mlm -mlmCompressionLevel None -export outp -runfork1 -runfork2 -runfork3

OUTPUT:
./lib/batik-parser.jar:./lib/batik-awt-util.jar:./lib/batik-css.jar:./lib/batik-dom.jar:./lib/batik-ext.jar:./lib/batik-gui-util.jar:./lib/batik-gvt.jar:./lib/batik-util.jar:./lib/batik-xml.jar:./lib/batik-svg-dom.jar:./lib/batik-svggen.jar:./lib/biojava-phylo-4.0.0.jar:./lib/biojava-alignment-4.0.0.jar:./lib/biojava-core-4.0.0.jar:./lib/geronimo-spec-activation-1.0.2-rc4.jar:./lib/colt.jar:./lib/cisd-jhdf5-batteries_included_lin_win_mac.jar:./lib/commons-codec-1.10.jar:./lib/commons-math3-3.4.1.jar:./lib/ejml-0.23.jar:./lib/forester.jar:./lib/javax.json-1.0.4.jar:./lib/guava-14.0.1.jar:./lib/itextpdf-5.1.0.jar:./lib/json-simple-1.1.1.jar:./lib/jcommon-1.0.6.jar:./lib/jfreechart-1.0.3.jar:./lib/junit-4.10.jar:./lib/mail-1.4.jar:./lib/slf4j-api-1.7.10.jar:./lib/log4j-1.2.13.jar:./lib/poi-3.0.1-FINAL-20070705.jar:./lib/postgresql-9.4-1201.jdbc41.jar:./lib/slf4j-simple-1.7.10.jar:./lib/snappy-java-1.1.1.6.jar:./lib/sqlite-jdbc-3.8.5-pre1.jar:./lib/trove-3.0.3.jar:./lib/xercesImpl.jar:./lib/xml.jar:./lib/xmlParserAPIs.jar:./sTASSEL.jar
Memory Settings: -Xms512m -Xmx1536m
Tassel Pipeline Arguments: -debug -fork1 -h mdp_genotype.hmp.txt -fork2 -t mdp_phenotype.txt -fork3 -k mdp_kinship.txt -combine4 -input1 -input2 -intersect -combine5 -input4 -input3 -mlm -mlmCompressionLevel None -export outp -runfork1 -runfork2 -runfork3

Exception in thread "main" java.lang.IllegalArgumentException
        at java.util.concurrent.ThreadPoolExecutor.<init>(ThreadPoolExecutor.java:1307)
        at java.util.concurrent.ThreadPoolExecutor.<init>(ThreadPoolExecutor.java:1195)
        at java.util.concurrent.Executors.newFixedThreadPool(Executors.java:89)

        at net.maizegenetics.pipeline.TasselPipeline.<init>(TasselPipeline.java:133)
        at net.maizegenetics.pipeline.TasselPipeline.<init>(TasselPipeline.java:116)
        at net.maizegenetics.pipeline.TasselPipeline.main(TasselPipeline.java:259)

[Terry Casstevens]

Hi Jim,

Will you try this sTASSEL.jar? Please send me the output even if it works.

tassel.bitbucket.org/test/sTASSEL.jar

Thank you,

Terry

> https://groups.google.com/d/msgid/tassel/b85ef8bb-7f1d-4fb3-88a3-cbbec9220d9d%40googlegroups.com.

[James Holland]

version 5.2.17 build works, thanks!

outputs are attached - jim