error

[Nannuru Vinay]

Hello,

Following is the error message when running pipeline for tagslist
"Found 1 files to process
Error in Reading Annotated Taxon File:keyfile/barcodes.txt
java.lang.IndexOutOfBoundsException: Index: 1, Size: 0
    at java.util.ArrayList.rangeCheck(ArrayList.java:657)
    at java.util.ArrayList.get(ArrayList.java:433)
    at net.maizegenetics.taxa.TaxaListIOUtils.readTaxaAnnotationFileAL(TaxaListIOUtils.java:295)
    at net.maizegenetics.taxa.TaxaListIOUtils.readTaxaAnnotationFile(TaxaListIOUtils.java:243)
    at net.maizegenetics.analysis.gbs.v2.GBSSeqToTagDBPlugin.processData(GBSSeqToTagDBPlugin.java:180)
    at net.maizegenetics.plugindef.AbstractPlugin.performFunction(AbstractPlugin.java:112)
    at net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:1837)
    at net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
    at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
    at java.util.concurrent.FutureTask.run(FutureTask.java:266)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
    at java.lang.Thread.run(Thread.java:748)
size of all tags in tag table=0
size of all tissues in tissue table=0
size of all tags in mappingApproach table=0
size of all taxa in taxa table=0"

i checked and correctedthe barcode file many times, still the same error appears again and again.

thanks,

vinay kumar reddy nannuru.
 

[Lynn Carol Johnson]

Please follow the instructions at the site below to report an error.  I need to see the commands and log output.

 

https://bytebucket.org/tasseladmin/tassel-5-source/wiki/docs/ReportingTassel5Issues.pdf

 

Thanks - Lynn

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[Nannuru Vinay]

Hello Lynn,

Again there appears the same error with no files in keyfile, though there is one.

'vinay410@server230:mthesis > tassel-5-standalone/run_pipeline.pl -Xmx200g -fork1 -GBSSeqToTagDBPlugin -i reads -k keyfile/hm_barcodes.txt -e ApeKI -db db/mthesis.db -kmerLength 64 -mnQS 20 -endPlugin -runfork1
tassel-5-standalone/lib/commons-codec-1.10.jar:tassel-5-standalone/lib/junit-4.10.jar:tassel-5-standalone/lib/slf4j-simple-1.7.10.jar:tassel-5-standalone/lib/postgresql-9.4-1201.jdbc41.jar:tassel-5-standalone/lib/javax.json-1.0.4.jar:tassel-5-standalone/lib/biojava-core-4.0.0.jar:tassel-5-standalone/lib/slf4j-api-1.7.10.jar:tassel-5-standalone/lib/sqlite-jdbc-3.8.5-pre1.jar:tassel-5-standalone/lib/snappy-java-1.1.1.6.jar:tassel-5-standalone/lib/jfreechart-1.0.19.jar:tassel-5-standalone/lib/commons-math3-3.4.1.jar:tassel-5-standalone/lib/json-simple-1.1.1.jar:tassel-5-standalone/lib/htsjdk-2.14.0.jar:tassel-5-standalone/lib/forester-1.038.jar:tassel-5-standalone/lib/mail-1.4.jar:tassel-5-standalone/lib/ejml-0.23.jar:tassel-5-standalone/lib/jcommon-1.0.23.jar:tassel-5-standalone/lib/jhdf5-14.12.5.jar:tassel-5-standalone/lib/jfreesvg-3.2.jar:tassel-5-standalone/lib/biojava-phylo-4.0.0.jar:tassel-5-standalone/lib/log4j-1.2.13.jar:tassel-5-standalone/lib/trove-3.0.3.jar:tassel-5-standalone/lib/itextpdf-5.1.0.jar:tassel-5-standalone/lib/ahocorasick-0.2.4.jar:tassel-5-standalone/lib/biojava-alignment-4.0.0.jar:tassel-5-standalone/lib/colt-1.2.0.jar:tassel-5-standalone/lib/guava-22.0.jar:tassel-5-standalone/sTASSEL.jar
Memory Settings: -Xms512m -Xmx200g
Tassel Pipeline Arguments: -fork1 -GBSSeqToTagDBPlugin -i reads -k keyfile/hm_barcodes.txt -e ApeKI -db db/mthesis.db -kmerLength 64 -mnQS 20 -endPlugin -runfork1
[main] INFO net.maizegenetics.tassel.TasselLogging - Tassel Version: 5.2.43  Date: February 22, 2018
[main] INFO net.maizegenetics.tassel.TasselLogging - Max Available Memory Reported by JVM: 182044 MB
[main] INFO net.maizegenetics.tassel.TasselLogging - Java Version: 1.8.0_161
[main] INFO net.maizegenetics.tassel.TasselLogging - OS: Linux
[main] INFO net.maizegenetics.tassel.TasselLogging - Number of Processors: 32
[main] INFO net.maizegenetics.pipeline.TasselPipeline - Tassel Pipeline Arguments: [-fork1, -GBSSeqToTagDBPlugin, -i, reads, -k, keyfile/hm_barcodes.txt, -e, ApeKI, -db, db/mthesis.db, -kmerLength, 64, -mnQS, 20, -endPlugin, -runfork1]
net.maizegenetics.analysis.gbs.v2.GBSSeqToTagDBPlugin
[pool-1-thread-1] INFO net.maizegenetics.plugindef.AbstractPlugin - Starting net.maizegenetics.analysis.gbs.v2.GBSSeqToTagDBPlugin: time: May 24, 2018 14:29:38
Enzyme: ApeKI
[pool-1-thread-1] INFO net.maizegenetics.plugindef.AbstractPlugin -
GBSSeqToTagDBPlugin Parameters
i: reads
k: keyfile/hm_barcodes.txt
e: ApeKI
kmerLength: 64
minKmerL: 20
c: 10
db: db/mthesis.db
mnQS: 20
mxKmerNum: 50000000
batchSize: 8
deleteOldData: true

GBSSeqToTagDBPlugin:processData - found NO files represented in key file.
Please verify your file names are formatted correctly and that your key file contains the required headers.
[pool-1-thread-1] INFO net.maizegenetics.plugindef.AbstractPlugin - Finished net.maizegenetics.analysis.gbs.v2.GBSSeqToTagDBPlugin: time: May 24, 2018 14:29:38
[pool-1-thread-1] INFO net.maizegenetics.pipeline.TasselPipeline - net.maizegenetics.analysis.gbs.v2.GBSSeqToTagDBPlugin: time: May 24, 2018 14:29:38: progress: 100%
[pool-1-thread-1] INFO net.maizegenetics.plugindef.AbstractPlugin - net.maizegenetics.analysis.gbs.v2.GBSSeqToTagDBPlugin  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.
vinay410@server230:mthesis > cd..
-bash: cd..: command not found
vinay410@server230:mthesis > cd ..
vinay410@server230:nvinay > cd mthesis
vinay410@server230:mthesis > cd tassel-5-standalone/
vinay410@server230:tassel-5-standalone > ./run_pipeline.pl -debug [<keyfile>]
-bash: keyfile: No such file or directory
vinay410@server230:tassel-5-standalone > ./run_pipeline.pl -debug [<keyfile/hm_barcodes.txt>]
-bash: keyfile/hm_barcodes.txt: No such file or directory
vinay410@server230:tassel-5-standalone > cd ..
vinay410@server230:mthesis > ./run_pipeline.pl -debug [<keyfile/hm_barcodes.txt>]
-bash: ./run_pipeline.pl: No such file or directory

vinay410@server230:mthesis > ./tassel-5-standalone/run_pipeline.pl -debug [<keyfile/hm_barcodes.txt>]"

Thanks,

Vinay.

[Lynn Carol Johnson]

Send me privately your keyfile and the list of file names that exist in your “reads” directory.

 

From: <tas...@googlegroups.com> on behalf of Nannuru Vinay <vinayred...@gmail.com>
Reply-To: "tas...@googlegroups.com" <tas...@googlegroups.com>
Date: Thursday, May 24, 2018 at 8:54 AM
To: "tas...@googlegroups.com" <tas...@googlegroups.com>
Subject: [TASSEL-Group] error

 

Hello Lynn,

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