error when convert hmp to VCF using tassel4.0

[Xiaofei Zhang]

Hi,

   I obtained *hmp.txt file using UNEAK. And I am able to convert the raw *hmp.txt to VCF format.

   I matched all the markers with the markers in a genetic map. I sampled the matched marker data from *hmp.txt, saved as "*hmp.matched.txt". I sorted all the markers based on the chromosome and position. When I run the command below, I got an error.

command:  perl run_pipeline.pl -Xmx5g -fork1 -h hmp.hmc.test.v1.txt -export -exportType VCF -runfork1    (see details below)

The test data (hmp.hmc.test.v1.txt ) were attached. Can anyone help to figure it out? How should I format the *hmp.new.txt file? Thank you.

===============

zhangx8@labq03 [~/tassel-tassel4-standalone] % perl run_pipeline.pl -Xmx5g -fork1 -h hmp.hmc.test.v1.txt -export -exportType VCF -runfork1            ./lib/LiuExt.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-parser.jar:./lib/batik-svg-dom.jar:./lib/batik-svggen.jar:./lib/batik-util.jar:./lib/batik-xml.jar:./lib/biojava3-alignment-3.0.jar:./lib/biojava3-core-3.0.jar:./lib/biojava3-phylo-3.0.jar:./lib/cisd-jhdf5-batteries_included_lin_win_mac.jar:./lib/colt.jar:./lib/commons-math-2.2.jar:./lib/ejml-0.23.jar:./lib/forester.jar:./lib/geronimo-spec-activation-1.0.2-rc4.jar:./lib/guava-14.0.1.jar:./lib/itextpdf-5.1.0.jar:./lib/jcommon-1.0.6.jar:./lib/jfreechart-1.0.3.jar:./lib/junit-4.1.jar:./lib/log4j-1.2.13.jar:./lib/mail-1.4.jar:./lib/poi-3.0.1-FINAL-20070705.jar:./lib/xercesImpl.jar:./lib/xml.jar:./lib/xmlParserAPIs.jar:./sTASSEL.jar
Memory Settings: -Xms512m -Xmx5g
Tassel Pipeline Arguments: -fork1 -h hmp.hmc.test.v1.txt -export -exportType VCF -runfork1
[main] INFO net.maizegenetics.pipeline.TasselPipeline - Tassel Version: 4.3.13  Date: December 18, 2014
[main] INFO net.maizegenetics.pipeline.TasselPipeline - Max Available Memory Reported by JVM: 4551 MB
[main] INFO net.maizegenetics.pipeline.TasselPipeline - loadFile: hmp.hmc.test.v1.txt
net.maizegenetics.baseplugins.FileLoadPlugin
   net.maizegenetics.baseplugins.ExportMultiplePlugin
[Thread-0] INFO net.maizegenetics.pal.alignment.ImportUtils - readFromHapmap: Number of Sites: 101
[Thread-0] INFO net.maizegenetics.pal.alignment.ImportUtils - readFromHapmap: Time to count lines: 0
java.lang.NumberFormatException: For input string: "11.093"
        at java.lang.NumberFormatException.forInputString(NumberFormatException.java:65)
        at java.lang.Integer.parseInt(Integer.java:492)
        at java.lang.Integer.parseInt(Integer.java:527)
        at net.maizegenetics.pal.alignment.ImportUtils.readFromHapmap(ImportUtils.java:441)
        at net.maizegenetics.baseplugins.FileLoadPlugin.processDatum(FileLoadPlugin.java:328)
        at net.maizegenetics.baseplugins.FileLoadPlugin.performFunction(FileLoadPlugin.java:176)
        at net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
        at net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
java.lang.IllegalArgumentException: ImportUtils: readFromHapmap: Problem creating Alignment: hmp.hmc.test.v1.txt: For input string: "11.093"
        at net.maizegenetics.pal.alignment.ImportUtils.readFromHapmap(ImportUtils.java:515)
        at net.maizegenetics.baseplugins.FileLoadPlugin.processDatum(FileLoadPlugin.java:328)
        at net.maizegenetics.baseplugins.FileLoadPlugin.performFunction(FileLoadPlugin.java:176)
        at net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:201)
        at net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
[Thread-0] ERROR net.maizegenetics.baseplugins.FileLoadPlugin - Error loading: hmp.hmc.test.v1.txt
ImportUtils: readFromHapmap: Problem creating Alignment:
hmp.hmc.test.v1.txt: For input string: "11.093"

=============================================================

Best,

Xiaofei

[Terry Casstevens]

Please use Tassel 5.

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[Xiaofei Zhang]

Hi, Terry,

    I used Tassel5, but got another error, labeled with red. Thank you.

    I do not have the right Java version to run this program? Or any other reason?

=====

zhangx8@labq01 [~/tassel-5-standalone] % perl run_pipeline.pl -Xmx5g -fork1 -h hmp.hmc.test.v1.txt -export -exportType VCF -runfork1                       ./lib/LiuExt.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-parser.jar:./lib/batik-svg-dom.jar:./lib/batik-svggen.jar:./lib/batik-util.jar:./lib/batik-xml.jar:./lib/biojava3-alignment-4.0.0.jar:./lib/biojava3-core-4.0.0.jar:./lib/biojava3-phylo-4.0.0.jar:./lib/cisd-jhdf5-batteries_included_lin_win_mac.jar:./lib/colt.jar:./lib/commons-codec-1.10.jar:./lib/commons-math3-3.4.1.jar:./lib/ejml-0.23.jar:./lib/forester.jar:./lib/geronimo-spec-activation-1.0.2-rc4.jar:./lib/guava-14.0.1.jar:./lib/itextpdf-5.1.0.jar:./lib/jcommon-1.0.6.jar:./lib/jfreechart-1.0.3.jar:./lib/json-simple-1.1.1.jar:./lib/junit-4.10.jar:./lib/log4j-1.2.13.jar:./lib/mail-1.4.jar:./lib/poi-3.0.1-FINAL-20070705.jar:./lib/snappy-java-1.1.1.6.jar:./lib/sqlite-jdbc-3.8.4.3-SNAPSHOT.jar:./lib/trove-3.0.3.jar:./lib/xercesImpl.jar:./lib/xml.jar:./lib/xmlParserAPIs.jar:./sTASSEL.jar

Memory Settings: -Xms512m -Xmx5g
Tassel Pipeline Arguments: -fork1 -h hmp.hmc.test.v1.txt -export -exportType VCF -runfork1

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)

=====

[Terry Casstevens]

That's right, you need Java 8 for Tassel 5

> https://groups.google.com/d/msgid/tassel/0de2afa8-3099-4470-b9bb-7eac3e40670d%40googlegroups.com.

[Terry Casstevens]

This is a text output of image. I can't see image.

On Wed, Feb 25, 2015 at 12:13 PM, Xiaofei Zhang <xfzha...@gmail.com> wrote:
> Hi, Terry,
>
> I run Tassel 5 using my own computer with Java 8. I still got an error
> shown in the figure. Can you please help? Thanks.

> https://groups.google.com/d/msgid/tassel/7e1b9ef0-de61-42ca-9c20-655c97d57333%40googlegroups.com.

[Xiaofei Zhang]

Hi, Terry,

   Sorry. This is the image. Thank you.

[Terry Casstevens]

Is sTASSEL.jar in the directory?  How was this installed?

On Wed, Feb 25, 2015 at 12:22 PM, Xiaofei Zhang <xfzha...@gmail.com> wrote:

Hi, Terry,

   Sorry. This is the image. Thank you.

On Wednesday, February 25, 2015 at 11:17:11 AM UTC-6, Terry wrote:

This is a text output of image.  I can't see image.

On Wed, Feb 25, 2015 at 12:13 PM, Xiaofei Zhang <xfzha...@gmail.com> wrote:
> Hi, Terry,
>
>    I run Tassel 5 using my own computer with Java 8. I still got an error
> shown in the figure. Can you please help? Thanks.
>
>

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[Xiaofei Zhang]

Hi, Terry,

   sTASSEL.jar is in the directory (see the image). I did not install it. I just downloaded  tassel 5,  and ran the command in Command Prompt.

   I checked the Java version is 8 (1.8.0_31-b13)

[Terry Casstevens]

Please run this in the bash shell.  If you are already, see the last troubleshooting tip in this document.

https://bytebucket.org/tasseladmin/tassel-5-source/wiki/docs/ExecutingTassel.pdf

On Wed, Feb 25, 2015 at 12:45 PM, Xiaofei Zhang <xfzha...@gmail.com> wrote:

Hi, Terry,

   sTASSEL.jar is in the directory (see the image). I did not install it. I just downloaded  tassel 5,  and ran the command in Command Prompt.

   I checked the Java version is 8 (1.8.0_31-b13)

On Wednesday, February 25, 2015 at 11:34:29 AM UTC-6, Terry wrote:

Is sTASSEL.jar in the directory?  How was this installed?

On Wed, Feb 25, 2015 at 12:22 PM, Xiaofei Zhang <xfzha...@gmail.com> wrote:

Hi, Terry,

   Sorry. This is the image. Thank you.

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[Xiaofei Zhang]

Terry,

   I followed your suggestions. I can run tassel 5 with raw *hmp.txt file. But I still got error when I run my test file attached. I checked the format. The raw *hmp.txt  and my test file are the same. I would be appreciated it if you can have a look at the test data file attached.

[Terry Casstevens]

Position values should be physical position (not genetic).  You could multiple those by 1000 or 10000 to eliminate the decimal.

To view this discussion on the web visit https://groups.google.com/d/msgid/tassel/7dce53fb-0c47-4a0f-b3bb-1517e5c4fff5%40googlegroups.com.

[Xiaofei Zhang]

Hi, Terry,

   Thank you so much. That's the reason [physical position (not genetic)].

Have a good week,

Xiaofei