Hello Everyone,
Currently I am Woking on the pipeline of GBSv2 and my query is regarding the same.
AS I am new to this field.
Currently I am facing problem with UNEAK pipeline on GBSv2.
So could you please tell me that how to solve this.
as from the site of Tassel. I got to know it is only working with Tassel3. After that
I tried it on my system but I am not able to do so.
Please Suggest me some option for this part..
Currently I am Woking on the pipeline of GBSv2 and my query is regarding the same.
AS I am new to this field.
Currently I am facing problem with UNEAK pipeline on GBSv2.
So could you please tell me that how to solve this.
as from the site of Tassel. I got to know it is only working with Tassel3. After that
I tried it on my system but I am not able to do so.
Please Suggest me some option for this part..
Code:
bash-4.2$ /mnt/bioinfo3/TASSEL5/run_pipeline.pl -fork1 -UCreatWorkingDirPlugin -w UNEAK/ -endPlugin -runfork1 /mnt/bioinfo3/TASSEL5/lib/sTASSEL.jar:/mnt/bioinfo3/TASSEL5/lib/slf4j-api-1.7.10.jar:/mnt/bioinfo3/TASSEL5/lib/snappy-java-1.1.1.6.jar:/mnt/bioinfo3/TASSEL5/lib/forester.jar:/mnt/bioinfo3/TASSEL5/lib/batik-parser.jar:/mnt/bioinfo3/TASSEL5/lib/batik-dom.jar:/mnt/bioinfo3/TASSEL5/lib/slf4j-simple-1.7.10.jar:/mnt/bioinfo3/TASSEL5/lib/mail-1.4.jar:/mnt/bioinfo3/TASSEL5/lib/xmlParserAPIs.jar:/mnt/bioinfo3/TASSEL5/lib/jcommon-1.0.6.jar:/mnt/bioinfo3/TASSEL5/lib/cisd-jhdf5-batteries_included_lin_win_mac.jar:/mnt/bioinfo3/TASSEL5/lib/batik-svg-dom.jar:/mnt/bioinfo3/TASSEL5/lib/javax.json-1.0.4.jar:/mnt/bioinfo3/TASSEL5/lib/poi-3.0.1-FINAL-20070705.jar:/mnt/bioinfo3/TASSEL5/lib/junit-4.10.jar:/mnt/bioinfo3/TASSEL5/lib/batik-xml.jar:/mnt/bioinfo3/TASSEL5/lib/log4j-1.2.13.jar:/mnt/bioinfo3/TASSEL5/lib/itextpdf-5.1.0.jar:/mnt/bioinfo3/TASSEL5/lib/xml.jar:/mnt/bioinfo3/TASSEL5/lib/xercesImpl.jar:/mnt/bioinfo3/TASSEL5/lib/trove-3.0.3.jar:/mnt/bioinfo3/TASSEL5/lib/batik-gui-util.jar:/mnt/bioinfo3/TASSEL5/lib/biojava-phylo-4.0.0.jar:/mnt/bioinfo3/TASSEL5/lib/commons-codec-1.10.jar:/mnt/bioinfo3/TASSEL5/lib/batik-css.jar:/mnt/bioinfo3/TASSEL5/lib/colt.jar:/mnt/bioinfo3/TASSEL5/lib/json-simple-1.1.1.jar:/mnt/bioinfo3/TASSEL5/lib/batik-util.jar:/mnt/bioinfo3/TASSEL5/lib/jfreechart-1.0.3.jar:/mnt/bioinfo3/TASSEL5/lib/postgresql-9.4-1201.jdbc41.jar:/mnt/bioinfo3/TASSEL5/lib/batik-gvt.jar:/mnt/bioinfo3/TASSEL5/lib/guava-19.0.jar:/mnt/bioinfo3/TASSEL5/lib/geronimo-spec-activation-1.0.2-rc4.jar:/mnt/bioinfo3/TASSEL5/lib/batik-ext.jar:/mnt/bioinfo3/TASSEL5/lib/batik-svggen.jar:/mnt/bioinfo3/TASSEL5/lib/batik-awt-util.jar:/mnt/bioinfo3/TASSEL5/lib/sqlite-jdbc-3.8.5-pre1.jar:/mnt/bioinfo3/TASSEL5/lib/biojava-core-4.0.0.jar:/mnt/bioinfo3/TASSEL5/lib/ejml-0.23.jar:/mnt/bioinfo3/TASSEL5/lib/guava-14.0.1.jar:/mnt/bioinfo3/TASSEL5/lib/biojava-alignment-4.0.0.jar:/mnt/bioinfo3/TASSEL5/lib/htsjdk-1.138.jar:/mnt/bioinfo3/TASSEL5/lib/commons-math3-3.4.1.jar:/mnt/bioinfo3/TASSEL5/lib/ahocorasick-0.2.4.jar:/mnt/bioinfo3/TASSEL5/sTASSEL.jar Memory Settings: -Xms512m -Xmx1536m Tassel Pipeline Arguments: -fork1 -UCreatWorkingDirPlugin -w UNEAK/ -endPlugin -runfork1 [main] INFO net.maizegenetics.tassel.TasselLogging - Tassel Version: 5.2.30 Date: September 1, 2016 [main] INFO net.maizegenetics.tassel.TasselLogging - Max Available Memory Reported by JVM: 1365 MB [main] INFO net.maizegenetics.tassel.TasselLogging - Java Version: 1.8.0_91 [main] INFO net.maizegenetics.tassel.TasselLogging - OS: Linux [main] INFO net.maizegenetics.tassel.TasselLogging - Number of Processors: 8 [main] INFO net.maizegenetics.pipeline.TasselPipeline - Tassel Pipeline Arguments: [-fork1, -UCreatWorkingDirPlugin, -w, UNEAK/, -endPlugin, -runfork1] [main] ERROR net.maizegenetics.pipeline.TasselPipeline - TasselPipeline: parseArgs: Unknown parameter: -UCreatWorkingDirPlugin