UNEAK and installing tassel3

[GD]

Hi there,

I would like to use the UNEAK pipeline on a GBS run that I have. If I understood correctly, to do so I need to install tassel 3, am I right? I went to sourceforge (http://sourceforge.net/projects/tassel/files/Tassel%203.0/2013-04-25/) to download the 2 zip files that I've unzipped on my linux server (Once unzipped I have 3 files:       javadoc        __MACOSX         tassel3-src)

I'm following the TASSEL 3.0 UNEAK pipeline documentation to run it but I'm quite lost here. Do I need to do anything else with these files? I tried to run the "run pipeline.pl" as it is shown in the documentation but I obtained the result pasted at the end of this email..

I'm still pretty new to linux so any help would be greatly appreciated.

Thanks,
G

P.S. I started the perl script with "perl" because It would not detect the file otherwise..

jimp@jimp:~/Desktop/tassel_3$ perl ./tassel3-src/run_pipeline.pl -fork1 -UCreatWorkingDirPlugin -w /home/jimp/Cranberry_GBS -endPlugin -runfork1

./tassel3-src/lib/jfreechart-1.0.3.jar:./tassel3-src/lib/junit-4.1.jar:./tassel3-src/lib/batik-ext.jar:./tassel3-src/lib/mail-1.4.jar:./tassel3-src/lib/batik-xml.jar:./tassel3-src/lib/commons-logging-1.1.jar:./tassel3-src/lib/commons-dbcp-1.2.1.jar:./tassel3-src/lib/mysql-connector-java-3.1.13-bin.jar:./tassel3-src/lib/axiom-impl-1.2.4.jar:./tassel3-src/lib/batik-awt-util.jar:./tassel3-src/lib/batik-gui-util.jar:./tassel3-src/lib/xmlParserAPIs.jar:./tassel3-src/lib/commons-httpclient-3.0.1.jar:./tassel3-src/lib/batik-css.jar:./tassel3-src/lib/ejml-0.13.jar:./tassel3-src/lib/batik-svg-dom.jar:./tassel3-src/lib/commons-lang-2.1.jar:./tassel3-src/lib/cisd-jhdf5-batteries_included_lin_win_mac.jar:./tassel3-src/lib/commons-pool-1.3.jar:./tassel3-src/lib/commons-codec-1.3.jar:./tassel3-src/lib/commons-math-2.2.jar:./tassel3-src/lib/jung-1.7.5.jar:./tassel3-src/lib/batik-svggen.jar:./tassel3-src/lib/batik-gvt.jar:./tassel3-src/lib/XmlSchema-1.3.1.jar:./tassel3-src/lib/log4j-1.2.13.jar:./tassel3-src/lib/commons-configuration-1.2.jar:./tassel3-src/lib/gdpc.jar:./tassel3-src/lib/geronimo-spec-activation-1.0.2-rc4.jar:./tassel3-src/lib/poi-3.0.1-FINAL-20070705.jar:./tassel3-src/lib/jgrapht-0.5.3.jar:./tassel3-src/lib/batik-util.jar:./tassel3-src/lib/wsdl4j-1.6.2.jar:./tassel3-src/lib/jcommon-1.0.6.jar:./tassel3-src/lib/crimson-parser.jar:./tassel3-src/lib/batik-parser.jar:./tassel3-src/lib/LiuExt.jar:./tassel3-src/lib/xml.jar:./tassel3-src/lib/biojava3-core-3.0.jar:./tassel3-src/lib/colt.jar:./tassel3-src/lib/batik-dom.jar:./tassel3-src/lib/axis2-kernel-1.2.jar:./tassel3-src/lib/commons-discovery.jar:./tassel3-src/lib/ssj.jar:./tassel3-src/lib/forester.jar:./tassel3-src/lib/lzma-4.63-jio-0.93.jar:./tassel3-src/lib/biojava3-alignment-3.0.jar:./tassel3-src/lib/commons-collections-3.1.jar:./tassel3-src/lib/xercesImpl.jar:./tassel3-src/lib/axiom-api-1.2.4.jar:./tassel3-src/lib/biojava3-phylo-3.0.jar:./tassel3-src/dist/sTASSEL.jar
Memory Settings: -Xms2g -Xmx10g
Tassel Pipeline Arguments: -fork1 -UCreatWorkingDirPlugin -w /home/jimp/Cranberry_GBS -endPlugin -runfork1
Error: Could not find or load main class net.maizegenetics.pipeline.TasselPipeline

[Terry Casstevens]

Yes, Tassel 3.

Click on "Download Snapshot"

http://sourceforge.net/p/tassel/tassel3-standalone/ci/master/tree/

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[guillaume daverdin]

Hi Thierry,

Thank you for your response, I was able to go a little further and to run the first plugin UCreatWorkingDirPlugin.

However, when I tried the second plugin UFastqToTagCountPlugin I got an error.

[main] ERROR net.maizegenetics.pipeline.TasselPipeline - java.lang.IllegalArgumentException: Please specify the working directory

Do you have an idea of what this is about? I have seen that a lot of problems for new users are linked to Java and I suppose it's the same here..

Thanks,

G

--> command line and result:

jimp@jimp:~/Cranberry_GBS/tassel3$ ./run_pipeline.pl -fork1 -UFastqToTagCountPlugin –w /home/jimp/Cranberry_GBS/fastq -e EcoT22I -endPlugin -runfork1 

 ./lib/jfreechart-1.0.3.jar:./lib/junit-4.1.jar:./lib/batik-ext.jar:./lib/mail-1.4.jar:./lib/batik-xml.jar:./lib/commons-logging-1.1.jar:./lib/commons-dbcp-1.2.1.jar:./lib/mysql-connector-java-3.1.13-bin.jar:./lib/axiom-impl-1.2.4.jar:./lib/batik-awt-util.jar:./lib/batik-gui-util.jar:./lib/xmlParserAPIs.jar:./lib/commons-httpclient-3.0.1.jar:./lib/batik-css.jar:./lib/ejml-0.13.jar:./lib/batik-svg-dom.jar:./lib/commons-lang-2.1.jar:./lib/cisd-jhdf5-batteries_included_lin_win_mac.jar:./lib/commons-pool-1.3.jar:./lib/commons-codec-1.3.jar:./lib/commons-math-2.2.jar:./lib/jung-1.7.5.jar:./lib/batik-svggen.jar:./lib/batik-gvt.jar:./lib/XmlSchema-1.3.1.jar:./lib/log4j-1.2.13.jar:./lib/commons-configuration-1.2.jar:./lib/gdpc.jar:./lib/geronimo-spec-activation-1.0.2-rc4.jar:./lib/poi-3.0.1-FINAL-20070705.jar:./lib/jgrapht-0.5.3.jar:./lib/batik-util.jar:./lib/wsdl4j-1.6.2.jar:./lib/jcommon-1.0.6.jar:./lib/crimson-parser.jar:./lib/batik-parser.jar:./lib/LiuExt.jar:./lib/xml.jar:./lib/biojava3-core-3.0.jar:./lib/colt.jar:./lib/batik-dom.jar:./lib/axis2-kernel-1.2.jar:./lib/commons-discovery.jar:./lib/ssj.jar:./lib/forester.jar:./lib/lzma-4.63-jio-0.93.jar:./lib/biojava3-alignment-3.0.jar:./lib/commons-collections-3.1.jar:./lib/xercesImpl.jar:./lib/axiom-api-1.2.4.jar:./lib/biojava3-phylo-3.0.jar:./sTASSEL.jar
Memory Settings: -Xms10g -Xmx40g
Tassel Pipeline Arguments: -fork1 -UFastqToTagCountPlugin –w /home/jimp/Cranberry_GBS/fastq -e EcoT22I -endPlugin -runfork1
[main] INFO net.maizegenetics.pipeline.TasselPipeline - Tassel Version: 3.0.171  Date: December 18, 2014
[main] INFO net.maizegenetics.gbs.pipeline.UFastqToTagCountPlugin -

Usage is as follows:
 -w  Working directory to contain subdirectories
 -e  Enzyme used to create the GBS library
 -s  Maximum number of good, barcoded reads per lane. Default: 200,000,000
 -c  Minimum number of tags seen to output to file, Default: 1
[main] ERROR net.maizegenetics.pipeline.TasselPipeline - java.lang.IllegalArgumentException: Please specify the working directory.
java.lang.IllegalArgumentException: TasselPipeline: parseArgs: Unknown parameter: -UFastqToTagCountPlugin
        at net.maizegenetics.pipeline.TasselPipeline.parseArgs(TasselPipeline.java:1233)
        at net.maizegenetics.pipeline.TasselPipeline.<init>(TasselPipeline.java:121)
        at net.maizegenetics.pipeline.TasselPipeline.main(TasselPipeline.java:161)

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[Terry Casstevens]

I don't know.  Please review the documentation or maybe someone else can help.

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

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[guillaume daverdin]

Thank you anyway Thierry!

I actually found why in case someone has the same problem.. Basically the problem is due to a copy past problem from the pdf file...  you will find a more detail response on this thread https://groups.google.com/forum/#!topic/tassel/2jV8Nikg_6M

G

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[Marcel Brun]

Hi GD, we were able to run UNEAK on Tassel 5, using the new GBS library. We uploaded an small perl script that run, as an example, the UNEAK pipeline on the 200K GBS tutorial data (you need to download it from the GBS tutorial page). You may give a try, adapting it to your custom folder structure (you may need to change the string in the COMMAND variable to point to run_pipeline.pl)

https://github.com/txgen/txgen-tassel

Marcel

[guillaume daverdin]

Hi there,

Sorry for the slow reply... Thanks Marcel, I'll try that soon!

One more question that you may be able to answer, do you know if UNEAK/TASSEL can "use" 300bp reads? I read earlier in a forum that it was limited at 64bp but this forum discussion has been written a long time ago so I wonder if there has been any evolution about that!

Thanks,

GD

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[Edward S. Buckler]

The GBSv2 pipeline that is in testing does.

Cheers-

Ed

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