Error: ERROR net.maizegenetics.plugindef.AbstractPlugin - 182 : -FSFHapImputationPlugin

[Sandip Kale]

Hello All,

I get following error while trying to input RIL data.

The command used is : 

/run_pipeline.pl -h PrilC_all_snp_raw_1.hmp.txt -separate -FSFHapImputationPlugin -pedigrees pedigree.txt -logfile log.txt -cluster true -nohets true -merge true -endPLugin -export output.hmp.txt

and the error I got is: 

[pool-1-thread-1] ERROR net.maizegenetics.plugindef.AbstractPlugin - 182

[pool-1-thread-1] INFO net.maizegenetics.plugindef.AbstractPlugin -

Could you please explain the reason

Thank you in advance

With best

Sandip

[Terry Casstevens]

Please run the command this way, and send all output.

./run_pipeline.pl -debug -h Pri...

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[Sandip Kale]

Hello Terry,

Please find attached debug file.

With best

Sandip

[Sandip Kale]

Hello Terry,

Thank you very much for reply.

As suggested, I run the command in debug mode. here is the massages I received:

/mnt/das/ngs/Programs/Tassel5/lib/batik-awt-util.jar:/mnt/das/ngs/Programs/Tassel5/lib/batik-css.jar:/mnt/das/ngs/Programs/Tassel5/lib/batik-dom.jar:/mnt/das/ngs/Programs/Tassel5/lib/batik-ext.jar:/mnt/das/ngs/Programs/Tassel5/lib/batik-gui-util.jar:/mnt/das/ngs/Programs/Tassel5/lib/batik-gvt.jar:/mnt/das/ngs/Programs/Tassel5/lib/batik-parser.jar:/mnt/das/ngs/Programs/Tassel5/lib/batik-svg-dom.jar:/mnt/das/ngs/Programs/Tassel5/lib/batik-svggen.jar:/mnt/das/ngs/Programs/Tassel5/lib/batik-util.jar:/mnt/das/ngs/Programs/Tassel5/lib/batik-xml.jar:/mnt/das/ngs/Programs/Tassel5/lib/biojava3-alignment-4.0.0.jar:/mnt/das/ngs/Programs/Tassel5/lib/biojava3-core-4.0.0.jar:/mnt/das/ngs/Programs/Tassel5/lib/biojava3-phylo-4.0.0.jar:/mnt/das/ngs/Programs/Tassel5/lib/cisd-jhdf5-batteries_included_lin_win_mac.jar:/mnt/das/ngs/Programs/Tassel5/lib/colt.jar:/mnt/das/ngs/Programs/Tassel5/lib/commons-math-2.2.jar:/mnt/das/ngs/Programs/Tassel5/lib/ejml-0.23.jar:/mnt/das/ngs/Programs/Tassel5/lib/forester.jar:/mnt/das/ngs/Programs/Tassel5/lib/geronimo-spec-activation-1.0.2-rc4.jar:/mnt/das/ngs/Programs/Tassel5/lib/guava-14.0.1.jar:/mnt/das/ngs/Programs/Tassel5/lib/itextpdf-5.1.0.jar:/mnt/das/ngs/Programs/Tassel5/lib/jcommon-1.0.6.jar:/mnt/das/ngs/Programs/Tassel5/lib/jfreechart-1.0.3.jar:/mnt/das/ngs/Programs/Tassel5/lib/json-simple-1.1.1.jar:/mnt/das/ngs/Programs/Tassel5/lib/junit-4.10.jar:/mnt/das/ngs/Programs/Tassel5/lib/LiuExt.jar:/mnt/das/ngs/Programs/Tassel5/lib/log4j-1.2.13.jar:/mnt/das/ngs/Programs/Tassel5/lib/mail-1.4.jar:/mnt/das/ngs/Programs/Tassel5/lib/poi-3.0.1-FINAL-20070705.jar:/mnt/das/ngs/Programs/Tassel5/lib/trove-3.0.3.jar:/mnt/das/ngs/Programs/Tassel5/lib/xercesImpl.jar:/mnt/das/ngs/Programs/Tassel5/lib/xml.jar:/mnt/das/ngs/Programs/Tassel5/lib/xmlParserAPIs.jar:/mnt/das/ngs/Programs/Tassel5/sTASSEL.jar

Memory Settings: -Xms512m -Xmx100g

Tassel Pipeline Arguments: -debug -h PrilC_all_snp_raw_1.hmp.txt -separate -FSFHapImputationPlugin -pedigrees pedigree.txt -logfile log.txt -cluster true -merge true -outParents false -endPLugin -export output.hmp.txt

[main] INFO net.maizegenetics.tassel.TasselLogging - Tassel Version: 5.2.0  Date: November 13, 2014

[main] INFO net.maizegenetics.tassel.TasselLogging - Max Available Memory Reported by JVM: 91022 MB

[main] INFO net.maizegenetics.tassel.TasselLogging - Java Version: 1.8.0

[main] INFO net.maizegenetics.tassel.TasselLogging - OS: Linux

[main] INFO net.maizegenetics.pipeline.TasselPipeline - Tassel Pipeline Arguments: [-fork1, -h, PrilC_all_snp_raw_1.hmp.txt, -separate, -FSFHapImputationPlugin, -pedigrees, pedigree.txt, -logfile, log.txt, -cluster, true, -merge, true, -outParents, false, -endPLugin, -export, output.hmp.txt, -runfork1]

[main] INFO net.maizegenetics.pipeline.TasselPipeline - loadFile: PrilC_all_snp_raw_1.hmp.txt

net.maizegenetics.analysis.data.FileLoadPlugin

   net.maizegenetics.analysis.data.SeparatePlugin

      net.maizegenetics.analysis.imputation.FSFHapImputationPlugin

         net.maizegenetics.analysis.data.ExportMultiplePlugin

[pool-1-thread-1] INFO net.maizegenetics.pipeline.TasselPipeline - net.maizegenetics.analysis.data.FileLoadPlugin: progress: 100%

[pool-1-thread-1] 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-1] INFO net.maizegenetics.plugindef.AbstractPlugin - 

FSFHapImputationPlugin Parameters

pedigrees: pedigree.txt

logfile: log.txt

cluster: true

windowLD: false

bc: true

multbc: false

minMaf: 0.1

window: 50

minR: 0.2

maxMissing: 0.8

nohets: false

maxDiff: 0

minHap: 5

overlap: 25

fillgaps: false

phet: 0.07

merge: true

outParents: false

outNuc: true

outIUPAC: true

[pool-1-thread-1] INFO net.maizegenetics.pipeline.TasselPipeline - net.maizegenetics.analysis.imputation.FSFHapImputationPlugin: progress: 10%

[pool-1-thread-1] INFO net.maizegenetics.analysis.imputation.CallParentAllelesPlugin - Calling parent alleles for family fam1, chromosome 1.

[pool-1-thread-1] INFO net.maizegenetics.analysis.imputation.CallParentAllelesPlugin - creating family alignment for family fam1

[pool-1-thread-1] INFO net.maizegenetics.analysis.imputation.CallParentAllelesPlugin - family alignment created

[pool-1-thread-1] INFO net.maizegenetics.pipeline.TasselPipeline - net.maizegenetics.analysis.imputation.FSFHapImputationPlugin: progress: 100%

[pool-1-thread-1] INFO net.maizegenetics.plugindef.AbstractPlugin - net.maizegenetics.analysis.imputation.FSFHapImputationPlugin  Citation: Swarts K, Li H, Romero Navarro JA, Romay-Alvarez MC, Hearne S, Acharya C, Glaubitz JC, Mitchell S, Elshire RJ, Buckler ES, Bradbury PJ (2014) FSFHap (Full-Sib Family Haplotype Imputation) and FILLIN (Fast, Inbred Line Library ImputatioN) optimize genotypic imputation for low-coverage, next-generation sequence data in crop plants. Plant Genome (in review)

[pool-1-thread-1] ERROR net.maizegenetics.plugindef.AbstractPlugin - 67

[pool-1-thread-1] INFO net.maizegenetics.plugindef.AbstractPlugin - 

FSFHapImputationPlugin Description...

The FSFHapImputation Plugin infers parental haplotypes for a full sib family then uses those haplotypes in an HMM to impute variants. It is effective at correctly imputing heterzygotes in GBS data. To use from the command line, use TASSEL's default syntax that passes data from one plugin to another (Note that this creates 2 files, one of just parental calls (A/C) and one of imputed genotypes):

run_pipeline.pl -h input.hmp.txt -FSFHapImputationPlugin [options] -endPLugin -export output.hmp.txt

Usage:

FSFHapImputationPlugin <options>

-pedigrees <Pedigrees> : the pedigree file name (required)

-logfile <Logfile> : the name of a log file for runtime messages

-cluster <true | false> : use the cluster algorithm (Default: false)

-windowLD <true | false> : use the windowLD algorithm (Default: false)

-bc <true | false> : use the single backcross algorithm (Default: true)

-multbc <true | false> : use the multiple backcross algorithm (Default: false)

-minMaf <Min Maf> : filter out sites with less than minimumMinorAlleleFrequency [0.0?1.0] (Default: 0.1)

-window <Window> : filter out sites with less than minimumMinorAlleleFrequency (Default: 50)

-minR <Min R> : filter out sites not correlated with neighboring sites [0.0?1.0] (Default: 0.2)

-maxMissing <Max Missing> : filter out sites with proportion missing > maxMissing [0.0?1.0] (Default: 0.8)

-nohets <true | false> : delete heterozygous calls before imputing (Default: false)

-maxDiff <Max Diff> : use to decide if two haplotypes are equivalent (Default: 0)

-minHap <Min Hap> : haplotype must be observed at least this often (Default: 5)

-overlap <Overlap> : overlap between adjacent windows (Default: 25)

-fillgaps <true | false> : replace missing values with flanking values if equal (Default: false)

-phet <Phet> : proportion of sites that are heterozygous [0.0?1.0] (Default: 0.07)

-merge <true | false> : merge families and chromosomes (Default: false)

-outParents <true | false> : replace missing values with flanking values if equal (Default: true)

-outNuc <true | false> : replace missing values with flanking values if equal (Default: true)

-outIUPAC <true | false> : use IUPAC ambiguity codes for output (Default: true)

[pool-1-thread-1] DEBUG net.maizegenetics.plugindef.AbstractPlugin - 67

java.lang.ArrayIndexOutOfBoundsException: 67

at net.maizegenetics.dna.snp.genotypecall.FilterGenotypeCallTable.translateSite(FilterGenotypeCallTable.java:132)

at net.maizegenetics.dna.snp.genotypecall.FilterGenotypeCallTable.genotype(FilterGenotypeCallTable.java:81)

at net.maizegenetics.dna.snp.genotypecall.AbstractGenotypeCallTable.genotypeRange(AbstractGenotypeCallTable.java:51)

at net.maizegenetics.dna.snp.FilterGenotypeTable.genotypeRange(FilterGenotypeTable.java:467)

at net.maizegenetics.analysis.imputation.NucleotideImputationUtils.clusterWindow(NucleotideImputationUtils.java:1923)

at net.maizegenetics.analysis.imputation.NucleotideImputationUtils.callParentAllelesUsingClusters(NucleotideImputationUtils.java:238)

at net.maizegenetics.analysis.imputation.CallParentAllelesPlugin.performFunction(CallParentAllelesPlugin.java:91)

at net.maizegenetics.analysis.imputation.FSFHapImputationPlugin.processData(FSFHapImputationPlugin.java:108)

at net.maizegenetics.plugindef.AbstractPlugin.performFunction(AbstractPlugin.java:93)

at net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:1407)

at net.maizegenetics.plugindef.AbstractPlugin.fireDataSetReturned(AbstractPlugin.java:1314)

at net.maizegenetics.analysis.data.SeparatePlugin.performFunction(SeparatePlugin.java:83)

at net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:1407)

at net.maizegenetics.plugindef.AbstractPlugin.fireDataSetReturned(AbstractPlugin.java:1314)

at net.maizegenetics.analysis.data.FileLoadPlugin.performFunction(FileLoadPlugin.java:195)

at net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:1407)

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:1142)

at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)

at java.lang.Thread.run(Thread.java:744)

Please suggest

With best

Sandip

On Thursday, November 27, 2014 12:57:22 PM UTC+5:30, Terry wrote:

[Peter Bradbury]

Sanpdip,

The code is failing because it cannot find a window with two distinct haplotypes before it runs out of SNPs. Since it is failing at site 67, it appears that you do not have very many polymorphic SNPs. The data sets for which I have used FSFHap have had at least a few hundred polymorphic SNPs. Also the -cluster option does not work well unless the progeny are inbred at least to S4. If you have a partially inbred family, the default method is better. You could try the cluster or default method with smaller window sizes. With the default method set overlap equal to about half the window size. It is possible that the method will not work well on your data set because it was designed for denser sets. Another thing to check is to filter SNPs using a reasonable minor allele frequency then run LD to make sure SNPs are in LD with their neighbors as expected for a full sib family. 

Peter

[Sandip Kale]

Hello Peter,

Thank you very much for suggestions. We did sequencing at S8 generation so thought to use -cluster method. I will try to filter the data as suggested and then run it again.

With best

Sandip