new user's problems

[yuanyuan chen]

Hi everyone,

I'm a new user of tassel-5-standalone.

I met some problems which I really need your help.

Actually I tried to use "-homozygous" in tassel-3-standalone. But it failed forever, reporting "unknown parameter: -homozygous". I thought that might because tassel 3 does not include this usage. Therefore, I change to use tassel-5-standalone.
I am trying to run tassel 5 pipeline. Unfortunately, I met another trouble. I have no idea how to fix it.

Another question is how to use "-homozygous" correctly? I'm not sure if there is something wrong with my script.

 Any suggestion or solution, I would appreciate.
Thanks a lot!  You have a good one!

Here is my script and the error information.

 perl /public/home/yychen/software/tassel-5-standalone/run_pipeline.pl \
    -Xms5g -Xmx15g \
    -fork1 -h ./chr$chr.75.hmp.gz -homozygous \
    -includeTaxaInFile ./taxalist.txt -filterAlign -filterAlignMinFreq 0.05 \
    -fork2 -r ./pheno/${trait}.txt \
    -fork3 -q ./PopStructure.txt \
    -fork4 -k  ./Kinship.txt -combine5 -input1 -input2 -input3 -intersect -combine6 -input5 -input4 -mlm -mlmVarCompEst P3D -mlmCompressionLevel None \
    -mlmOutputFile ./res/mlmOut_homozygous${trait}_${chr} \
    -runfork1 -runfork2 -runfork3 -runfork4 \
    > log_${trait}_chr${chr}

Exception in thread "main" java.lang.UnsupportedClassVersionError: net/maizegenetics/pipeline/TasselPipeline : Unsupported major.minor version 52.0
    at java.lang.ClassLoader.defineClass1(Native Method)
    at java.lang.ClassLoader.defineClass(ClassLoader.java:800)
    at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:142)
    at java.net.URLClassLoader.defineClass(URLClassLoader.java:449)
    at java.net.URLClassLoader.access$100(URLClassLoader.java:71)
    at java.net.URLClassLoader$1.run(URLClassLoader.java:361)
    at java.net.URLClassLoader$1.run(URLClassLoader.java:355)
    at java.security.AccessController.doPrivileged(Native Method)
    at java.net.URLClassLoader.findClass(URLClassLoader.java:354)
    at java.lang.ClassLoader.loadClass(ClassLoader.java:425)
    at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:308)
    at java.lang.ClassLoader.loadClass(ClassLoader.java:358)
    at sun.launcher.LauncherHelper.checkAndLoadMain(LauncherHelper.java:482)

[Iris]

Hello everybody in the group,

I just figured out the error is due to the low version of java. I updated java to 1.8.0_121, and the error disappeared. That's so exciting.
However, I'm still not sure about the usage "-homozygous". Here is attached the information I got. The programing is still running. Is this all right? Am I on the right track?
Thanks a lot for your advice and help.

[pool-1-thread-3] INFO net.maizegenetics.plugindef.AbstractPlugin - Starting net.maizegenetics.analysis.data.FileLoadPlugin: time: Mar 27, 2017 20:12:45
[pool-1-thread-4] INFO net.maizegenetics.plugindef.AbstractPlugin - Starting net.maizegenetics.analysis.data.FileLoadPlugin: time: Mar 27, 2017 20:12:45
[pool-1-thread-1] INFO net.maizegenetics.plugindef.AbstractPlugin - Starting net.maizegenetics.analysis.data.FileLoadPlugin: time: Mar 27, 2017 20:12:45
[pool-1-thread-2] INFO net.maizegenetics.plugindef.AbstractPlugin - Starting net.maizegenetics.analysis.data.FileLoadPlugin: time: Mar 27, 2017 20:12:45
[pool-1-thread-4] INFO net.maizegenetics.plugindef.AbstractPlugin -
FileLoadPlugin Parameters
format: Square Matrix
sortPositions: false

[pool-1-thread-2] INFO net.maizegenetics.plugindef.AbstractPlugin -
FileLoadPlugin Parameters
format: Phenotype
sortPositions: false

[pool-1-thread-3] INFO net.maizegenetics.plugindef.AbstractPlugin -
FileLoadPlugin Parameters
format: Phenotype
sortPositions: false

[pool-1-thread-1] INFO net.maizegenetics.plugindef.AbstractPlugin -
FileLoadPlugin Parameters
format: Hapmap
sortPositions: false

[pool-1-thread-4] INFO net.maizegenetics.analysis.data.FileLoadPlugin - Start Loading File: /home/Chenyuanyuan/1404_magic_Kinship.txt time: Mar 27, 2017 20:12:45
[pool-1-thread-2] INFO net.maizegenetics.analysis.data.FileLoadPlugin - Start Loading File: ./pheno/As.txt time: Mar 27, 2017 20:12:45
[pool-1-thread-3] INFO net.maizegenetics.analysis.data.FileLoadPlugin - Start Loading File: /home/Chenyuanyuan/1404_magic_PopStructure.txt time: Mar 27, 2017 20:12:45
[pool-1-thread-1] INFO net.maizegenetics.analysis.data.FileLoadPlugin - Start Loading File: /Maizego/MAGIC_Public/Original_SNPs/chr10.75.hmp time: Mar 27, 2017 20:12:45
[pool-1-thread-2] INFO net.maizegenetics.analysis.data.FileLoadPlugin - Finished Loading File: ./pheno/As.txt time: Mar 27, 2017 20:12:45
[pool-1-thread-2] INFO net.maizegenetics.plugindef.AbstractPlugin - Finished net.maizegenetics.analysis.data.FileLoadPlugin: time: Mar 27, 2017 20:12:45
[pool-1-thread-2] INFO net.maizegenetics.pipeline.TasselPipeline - net.maizegenetics.analysis.data.FileLoadPlugin: time: Mar 27, 2017 20:12:45: progress: 100%
[pool-1-thread-2] INFO net.maizegenetics.plugindef.AbstractPlugin - net.maizegenetics.analysis.data.FileLoadPlugin  Citation: Bradbury PJ, Zhang Z, Kroon DE, Casstevens TM, Ramdoss Y, Buckler ES. (2007) TASSEL: Software for association mapping of complex traits in diverse samples. Bioinformatics 23:2633-2635.
[pool-1-thread-3] INFO net.maizegenetics.analysis.data.FileLoadPlugin - Finished Loading File: /home/Chenyuanyuan/1404_magic_PopStructure.txt time: Mar 27, 2017 20:12:45
[pool-1-thread-3] INFO net.maizegenetics.plugindef.AbstractPlugin - Finished net.maizegenetics.analysis.data.FileLoadPlugin: time: Mar 27, 2017 20:12:45
[pool-1-thread-3] INFO net.maizegenetics.pipeline.TasselPipeline - net.maizegenetics.analysis.data.FileLoadPlugin: time: Mar 27, 2017 20:12:45: progress: 100%
[pool-1-thread-4] INFO net.maizegenetics.analysis.data.FileLoadPlugin - Finished Loading File: /home/Chenyuanyuan/1404_magic_Kinship.txt time: Mar 27, 2017 20:12:46
[pool-1-thread-4] INFO net.maizegenetics.plugindef.AbstractPlugin - Finished net.maizegenetics.analysis.data.FileLoadPlugin: time: Mar 27, 2017 20:12:46
[pool-1-thread-4] INFO net.maizegenetics.pipeline.TasselPipeline - net.maizegenetics.analysis.data.FileLoadPlugin: time: Mar 27, 2017 20:12:46: progress: 100%
[pool-1-thread-1] INFO net.maizegenetics.pipeline.TasselPipeline - net.maizegenetics.analysis.data.FileLoadPlugin: time: Mar 27, 2017 20:14:25: progress: 0%
[pool-1-thread-1] INFO net.maizegenetics.pipeline.TasselPipeline - net.maizegenetics.analysis.data.FileLoadPlugin: time: Mar 27, 2017 20:14:27: progress: 10%
[pool-1-thread-1] INFO net.maizegenetics.pipeline.TasselPipeline - net.maizegenetics.analysis.data.FileLoadPlugin: time: Mar 27, 2017 20:14:28: progress: 20%
[pool-1-thread-1] INFO net.maizegenetics.pipeline.TasselPipeline - net.maizegenetics.analysis.data.FileLoadPlugin: time: Mar 27, 2017 20:14:29: progress: 30%
[pool-1-thread-1] INFO net.maizegenetics.pipeline.TasselPipeline - net.maizegenetics.analysis.data.FileLoadPlugin: time: Mar 27, 2017 20:14:30: progress: 40%
[pool-1-thread-1] INFO net.maizegenetics.pipeline.TasselPipeline - net.maizegenetics.analysis.data.FileLoadPlugin: time: Mar 27, 2017 20:14:32: progress: 50%
[pool-1-thread-1] INFO net.maizegenetics.pipeline.TasselPipeline - net.maizegenetics.analysis.data.FileLoadPlugin: time: Mar 27, 2017 20:14:33: progress: 60%
[pool-1-thread-1] INFO net.maizegenetics.pipeline.TasselPipeline - net.maizegenetics.analysis.data.FileLoadPlugin: time: Mar 27, 2017 20:14:34: progress: 70%
[pool-1-thread-1] INFO net.maizegenetics.pipeline.TasselPipeline - net.maizegenetics.analysis.data.FileLoadPlugin: time: Mar 27, 2017 20:14:35: progress: 80%
[pool-1-thread-1] INFO net.maizegenetics.pipeline.TasselPipeline - net.maizegenetics.analysis.data.FileLoadPlugin: time: Mar 27, 2017 20:14:37: progress: 90%
[pool-1-thread-1] INFO net.maizegenetics.pipeline.TasselPipeline - net.maizegenetics.analysis.data.FileLoadPlugin: time: Mar 27, 2017 20:14:38: progress: 100%

[Terry Casstevens]

Your usage of -homozygous looks good

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[Iris]

Thank you, Terry.  I really appreciate all the questions and answers in this group, which is very helpful.