ERROR - null key in entry

[PTyagi]

Hi,

1) I am trying to use -ref flag in  DiscoverySNPCallerV2 Plugin in Tassel version: 5.2.23 but its showing this error

ERROR net.maizegenetics.plugindef.AbstractPlugin - null key in entry: null=TaxaDist{taxaWithRead=0, totalDepth=0, maxTaxa=13, []} 

Here is the complete log for DiscoverySNPCallerV2 Plugin:

/TASSEL/tassel5/lib/commons-codec-1.10.jar:/TASSEL/tassel5/lib/ahocorasick-0.2.4.jar:/TASSEL/tassel5/lib/batik-awt-util.jar:/TASSEL/tassel5/lib/batik-css.jar:/TASSEL/tassel5/lib/batik-dom.jar:/TASSEL/tassel5/lib/batik-ext.jar:/TASSEL/tassel5/lib/batik-gui-util.jar:/TASSEL/tassel5/lib/batik-gvt.jar:/TASSEL/tassel5/lib/batik-parser.jar:/TASSEL/tassel5/lib/batik-svg-dom.jar:/TASSEL/tassel5/lib/batik-svggen.jar:/TASSEL/tassel5/lib/batik-util.jar:/TASSEL/tassel5/lib/batik-xml.jar:/TASSEL/tassel5/lib/biojava-alignment-4.0.0.jar:/TASSEL/tassel5/lib/biojava-core-4.0.0.jar:/TASSEL/tassel5/lib/biojava-phylo-4.0.0.jar:/TASSEL/tassel5/lib/cisd-jhdf5-batteries_included_lin_win_mac.jar:/TASSEL/tassel5/lib/colt.jar:/TASSEL/tassel5/lib/commons-math3-3.4.1.jar:/TASSEL/tassel5/lib/ejml-0.23.jar:/TASSEL/tassel5/lib/forester.jar:/TASSEL/tassel5/lib/geronimo-spec-activation-1.0.2-rc4.jar:/TASSEL/tassel5/lib/guava-14.0.1.jar:/TASSEL/tassel5/lib/htsjdk-1.138.jar:/TASSEL/tassel5/lib/itextpdf-5.1.0.jar:/TASSEL/tassel5/lib/javax.json-1.0.4.jar:/TASSEL/tassel5/lib/jcommon-1.0.6.jar:/TASSEL/tassel5/lib/jfreechart-1.0.3.jar:/TASSEL/tassel5/lib/json-simple-1.1.1.jar:/TASSEL/tassel5/lib/junit-4.10.jar:/TASSEL/tassel5/lib/log4j-1.2.13.jar:/TASSEL/tassel5/lib/mail-1.4.jar:/TASSEL/tassel5/lib/poi-3.0.1-FINAL-20070705.jar:/TASSEL/tassel5/lib/postgresql-9.4-1201.jdbc41.jar:/TASSEL/tassel5/lib/slf4j-api-1.7.10.jar:/TASSEL/tassel5/lib/slf4j-simple-1.7.10.jar:/TASSEL/tassel5/lib/snappy-java-1.1.1.6.jar:/TASSEL/tassel5/lib/sqlite-jdbc-3.8.5-pre1.jar:/TASSEL/tassel5/lib/trove-3.0.3.jar:/TASSEL/tassel5/lib/xercesImpl.jar:/TASSEL/tassel5/lib/xml.jar:/TASSEL/tassel5/lib/xmlParserAPIs.jar:/TASSEL/tassel5/sTASSEL.jar

Memory Settings: -Xms512m -Xmx175g

Tassel Pipeline Arguments: -fork1 -DiscoverySNPCallerPluginV2 -db database/T23.db -mnMAF 0.01 -mnLCov 0.05 -ref /home/Genome.fa -deleteOldData true -endPlugin -runfork1

[main] INFO net.maizegenetics.tassel.TasselLogging - Tassel Version: 5.2.23  Date: March 31, 2016

[main] INFO net.maizegenetics.tassel.TasselLogging - Max Available Memory Reported by JVM: 159289 MB

[main] INFO net.maizegenetics.tassel.TasselLogging - Java Version: 1.8.0_45

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

[main] INFO net.maizegenetics.tassel.TasselLogging - Number of Processors: 16

[main] INFO net.maizegenetics.pipeline.TasselPipeline - Tassel Pipeline Arguments: [-fork1, -DiscoverySNPCallerPluginV2, -db, database/T23.db, -mnMAF, 0.01, -mnLCov, 0.05, -ref, /home/Genome.fa, -deleteOldData, true, -endPlugin, -runfork1]

net.maizegenetics.analysis.gbs.v2.DiscoverySNPCallerPluginV2

[pool-1-thread-1] INFO net.maizegenetics.plugindef.AbstractPlugin - Starting net.maizegenetics.analysis.gbs.v2.DiscoverySNPCallerPluginV2: time: Apr 7, 2016 13:44:6

Genome FASTA character conversion: ACGTNacgtn to ACGTNacgtn

[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.DiscoverySNPCallerPluginV2 - MinMAF:0.0100000 

[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.DiscoverySNPCallerPluginV2 - includeRare:false includeGaps:false 

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

DiscoverySNPCallerPluginV2 Parameters

db: database/T23.db

mnMAF: 0.01

mnLCov: 0.05

ref: /home/Genome.fa

sC: null

eC: null

inclRare: false

inclGaps: false

callBiSNPsWGap: false

gapAlignRatio: 1.0

maxTagsCutSite: 64

deleteOldData: true

[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.DiscoverySNPCallerPluginV2 - Finding SNPs in database/T23.db.

[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.DiscoverySNPCallerPluginV2 - StartChr:null EndChr:null 

size of all tags in tag table=928159

size of all tissues in tissue table=0

size of all tags in mappingApproach table=2

size of all taxa in taxa table=13

[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.DiscoverySNPCallerPluginV2 - deleteOldData is TRUE: Clearing previous Discovery and SNPQuality data

[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.DiscoverySNPCallerPluginV2 - Start processing chromosome 1A

[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.DiscoverySNPCallerPluginV2 - Calling getCutPosForStrand FORWARD strands...

size of all positions in cutPosition table=596215

positionTagTaxaMap size, forwardStrand, true size:10912 totalTagsAdded:15475

[pool-1-thread-1] ERROR net.maizegenetics.plugindef.AbstractPlugin - null key in entry: null=TaxaDist{taxaWithRead=0, totalDepth=0, maxTaxa=13, []}

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

Usage:

DiscoverySNPCallerPluginV2 <options>

-db <Input GBS Database> : Input Database file if using SQLite (required)

-mnMAF <Min Minor Allele Freq> : Minimum minor allele frequency (Default: 0.01)

-mnLCov <Min Locus Coverage> : Minimum locus coverage (proportion of Taxa with a genotype) (Default: 0.1)

-ref <Reference Genome File> : Path to reference genome in fasta format. Ensures that a tag from the reference genome is always included when the tags at a locus are aligned against each other to call SNPs. The reference allele for each site is then provided in the output HapMap files, under the taxon name "REFERENCE_GENOME" (first taxon). DEFAULT: Don't use reference genome.

-sC <Start Chromosome> : Start Chromosome

-eC <End Chromosome> : End Chromosome

-inclRare <true | false> : Include the rare alleles at site (3 or 4th states) (Default: false)

-inclGaps <true | false> : Include sites where major or minor allele is a GAP (Default: false)

-callBiSNPsWGap <true | false> : Include sites where the third allele is a GAP (mutually exclusive with inclGaps) (Default: false)

-gapAlignRatio <Gap Alignment Threshold> : Gap alignment threshold ratio of indel contrasts to non indel contrasts: IC/(IC + NC). Any loci with a tag alignment value above this threshold will be excluded from the pool. (Default: 1.0)

-maxTagsCutSite <Max Number of Cut Sites> : Maximum number of tags per cut site (Default: 64)

-deleteOldData <true | false> : Delete existing SNP data from tables (Default: false)

2) Also, recently there was a post regarding the issue of SNP positions being occasionally wrong in version 22. I have run a couple of big projects using version 22 so I am concerned about the quality of data. Would you recommend re-running the pipelines again with the version 23 or is there any adjustment that I can use to correct the positions?

Your help would be truly appreciated.

Thanks 

Priyanka

[Lynn Carol Johnson]

Please send us the debug data as per the link below.  I would like to see the full stack trace:

https://bytebucket.org/tasseladmin/tassel-5-source/wiki/docs/ReportingTassel5Issues.pdf?rev=4572ff1eae9bf46ee975690b15abc8c8459da5c5

Thanks - lynn

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[PTyagi]

Hi Lynn,

Here is the debug data generated using the command:

/TASSEL/tassel5/run_pipeline.pl -debug ./logs/Reftag_debug.txt -fork1 -DiscoverySNPCallerPluginV2 -db database/T23.db -mnMAF 0.01 -mnLCov 0.05 -ref ~/GBS_Analyses/GBS_Reference_Genomes/Wheat_Genome.fa -deleteOldData true -endPlugin -runfork1 

Debug output:

[main] INFO net.maizegenetics.tassel.TasselLogging - Tassel Version: 5.2.23  Date: March 31, 2016

[main] INFO net.maizegenetics.tassel.TasselLogging - Max Available Memory Reported by JVM: 159289 MB

[main] INFO net.maizegenetics.tassel.TasselLogging - Java Version: 1.8.0_45

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

[main] INFO net.maizegenetics.tassel.TasselLogging - Number of Processors: 16

[main] INFO net.maizegenetics.pipeline.TasselPipeline - Tassel Pipeline Arguments: [-fork1, -DiscoverySNPCallerPluginV2, -db, database/T23.db, -mnMAF, 0.01, -mnLCov, 0.05, -ref, /home/gbg_lab_admin/GBS_Analyses/GBS_Reference_Genomes/Wheat_Genome.fa, -deleteOldData, true, -endPlugin, -runfork1]

net.maizegenetics.analysis.gbs.v2.DiscoverySNPCallerPluginV2

[pool-1-thread-1] INFO net.maizegenetics.plugindef.AbstractPlugin - Starting net.maizegenetics.analysis.gbs.v2.DiscoverySNPCallerPluginV2: time: Apr 7, 2016 15:14:4

Genome FASTA character conversion: ACGTNacgtn to ACGTNacgtn

[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.DiscoverySNPCallerPluginV2 - MinMAF:0.0100000 

[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.DiscoverySNPCallerPluginV2 - includeRare:false includeGaps:false 

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

DiscoverySNPCallerPluginV2 Parameters

db: database/T23.db

mnMAF: 0.01

mnLCov: 0.05

ref: /home/gbg_lab_admin/GBS_Analyses/GBS_Reference_Genomes/Wheat_Genome.fa

[pool-1-thread-1] DEBUG net.maizegenetics.plugindef.AbstractPlugin - null key in entry: null=TaxaDist{taxaWithRead=0, totalDepth=0, maxTaxa=13, []}

java.lang.NullPointerException: null key in entry: null=TaxaDist{taxaWithRead=0, totalDepth=0, maxTaxa=13, []}

at com.google.common.base.Preconditions.checkNotNull(Preconditions.java:235)

at com.google.common.collect.ImmutableMap.entryOf(ImmutableMap.java:143)

at com.google.common.collect.ImmutableMap$Builder.put(ImmutableMap.java:182)

at net.maizegenetics.analysis.gbs.v2.DiscoverySNPCallerPluginV2.createReferenceTag(DiscoverySNPCallerPluginV2.java:385)

at net.maizegenetics.analysis.gbs.v2.DiscoverySNPCallerPluginV2.findAlleleByAlignment(DiscoverySNPCallerPluginV2.java:266)

at net.maizegenetics.analysis.gbs.v2.DiscoverySNPCallerPluginV2.lambda$null$65(DiscoverySNPCallerPluginV2.java:179)

at net.maizegenetics.analysis.gbs.v2.DiscoverySNPCallerPluginV2$$Lambda$33/214232000.accept(Unknown Source)

at java.util.HashMap$EntrySpliterator.forEachRemaining(HashMap.java:1683)

at java.util.stream.ReferencePipeline$Head.forEach(ReferencePipeline.java:580)

at net.maizegenetics.analysis.gbs.v2.DiscoverySNPCallerPluginV2.lambda$processData$67(DiscoverySNPCallerPluginV2.java:178)

at net.maizegenetics.analysis.gbs.v2.DiscoverySNPCallerPluginV2$$Lambda$30/2017032318.accept(Unknown Source)

at java.util.ArrayList$ArrayListSpliterator.forEachRemaining(ArrayList.java:1374)

at java.util.stream.ReferencePipeline$Head.forEach(ReferencePipeline.java:580)

at net.maizegenetics.analysis.gbs.v2.DiscoverySNPCallerPluginV2.processData(DiscoverySNPCallerPluginV2.java:165)

at net.maizegenetics.plugindef.AbstractPlugin.performFunction(AbstractPlugin.java:110)

at net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:1631)

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:745)

[Lynn Carol Johnson]

HI Priyanka -

Can you verify the reference genome you are using is the same reference genome that was used by your aligner?

Regarding your question about previous SNPs called.  Tassel version 5.2.23 has a fix for reference genomes.   If you used a reference genome in the DiscoverySNPCallerPluginV2 step in an earlier version then yes, you should re-run these files. While the SNPs were called correctly in that version, the build Terry will make tomorrow will have a fix relating to the reverse strand cut position.  I would advise waiting for tomorrow’s build, then re-running.

I will send a google group message specific to this code change.

Thanks - Lynn

To view this discussion on the web visit https://groups.google.com/d/msgid/tassel/8195d443-1a9c-497f-8ad5-dd9abc6443cb%40googlegroups.com.

[PTyagi]

Hi Lynn,

Yes, I used the same reference genome fasta file for aligning tags to the reference sequence. 

Thanks for your help

Priyanka

[Jeff Glaubitz]

My best wild guess is that you have either a blank FullSampleName or blank trailing lines in your keyfile.

Best,

Jeff

To view this discussion on the web visit https://groups.google.com/d/msgid/tassel/73b2511b-959d-43c4-97e3-3bd7123fd7fa%40googlegroups.com.

[Priyanka Tyagi]

Hi Jeff,

I have tried running 3 different datasets and none of the keyfiles contained blanks in FullSampleName column or blank trailing lines. However, in all three cases I get the same error message. I am attaching one of the keyfiles here.

Thanks 

Priyanka

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--

Priyanka Tyagi

Postdoctoral research scholar

Eastern Regional Small Grains Genotyping Lab

4203 Williams Hall, NCSU

Raleigh, 27695

[Lynn Carol Johnson]

HI Priyanka -

The stack trace shows the error coming from code related to the reference genome.  The tassel build Terry will release later today has code changes relative to the GBSv2 pipeline.  I would download the new version when it is released and try the pipeline again.  You’ll want to re-run from the beginning steps to ensure consistency.  Let us know after that if you’re still having problems.

Thanks - Lynn

To view this discussion on the web visit https://groups.google.com/d/msgid/tassel/CAPyfyWWHd5eDo463SbaYnm0bhWzHs%2BaXFHr%3Diq8mMA_r8WuLsA%40mail.gmail.com.

[PTyagi]

Hi Lynn

I updated Tassel to version 24 today and ran two different SNP calling projects. I am still getting the same error as with Tassel version 23. Also, this error shows up only if -ref flag is used in DiscoverySNPCallerPluginV2. Here is the debug data:

Command:
/TASSEL/tassel5/run_pipeline.pl -debug ./logs/Reftag_debug.txt -fork1 -DiscoverySNPCallerPluginV2 -db database/HF_T24.db -mnMAF 0.01 -mnLCov 0.05 -ref ~/GBS_Analyses/GBS_Reference_Genomes/Wheat_IWGSC1_popseq_30/Wheat_Genome.fa -deleteOldData true -endPlugin -runfork1

[main] INFO net.maizegenetics.tassel.TasselLogging - Tassel Version: 5.2.24  Date: April 7, 2016

[main] INFO net.maizegenetics.tassel.TasselLogging - Max Available Memory Reported by JVM: 159289 MB
[main] INFO net.maizegenetics.tassel.TasselLogging - Java Version: 1.8.0_45
[main] INFO net.maizegenetics.tassel.TasselLogging - OS: Linux
[main] INFO net.maizegenetics.tassel.TasselLogging - Number of Processors: 16

[main] INFO net.maizegenetics.pipeline.TasselPipeline - Tassel Pipeline Arguments: [-fork1, -DiscoverySNPCallerPluginV2, -db, database/HF_T24.db, -mnMAF, 0.01, -mnLCov, 0.05, -ref, /home/gbg_lab_admin/GBS_Analyses/GBS_Reference_Genomes/Wheat_IWGSC1_popseq_30/Wheat_Genome.fa, -deleteOldData, true, -endPlugin, -runfork1]
net.maizegenetics.analysis.gbs.v2.DiscoverySNPCallerPluginV2
[pool-1-thread-1] INFO net.maizegenetics.plugindef.AbstractPlugin - Starting net.maizegenetics.analysis.gbs.v2.DiscoverySNPCallerPluginV2: time: Apr 11, 2016 11:38:15

Genome FASTA character conversion: ACGTNacgtn to ACGTNacgtn
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.DiscoverySNPCallerPluginV2 - MinMAF:0.0100000

[pool-1-thread-1] INFO net.maizegenetics.plugindef.AbstractPlugin -
DiscoverySNPCallerPluginV2 Parameters

db: database/HF_T24.db
mnMAF: 0.01
mnLCov: 0.05
ref: /home/gbg_lab_admin/GBS_Analyses/GBS_Reference_Genomes/Wheat_IWGSC1_popseq_30/Wheat_Genome.fa
sC: null
eC: null
inclGaps: false

gapAlignRatio: 1.0
maxTagsCutSite: 64
deleteOldData: true

[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.DiscoverySNPCallerPluginV2 - Finding SNPs in database/HF_T24.db.

[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.DiscoverySNPCallerPluginV2 - StartChr:null EndChr:null

size of all tags in tag table=928159
size of all tissues in tissue table=0
size of all tags in mappingApproach table=2
size of all taxa in taxa table=13
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.DiscoverySNPCallerPluginV2 - deleteOldData is TRUE: Clearing previous Discovery and SNPQuality data
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.DiscoverySNPCallerPluginV2 - Start processing chromosome 1A

[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.DiscoverySNPCallerPluginV2 - Calling getCutPosForStrand FORWARD strands...

size of all positions in cutPosition table=587486

positionTagTaxaMap size, forwardStrand, true size:10912 totalTagsAdded:15475
[pool-1-thread-1] ERROR net.maizegenetics.plugindef.AbstractPlugin - null key in entry: null=TaxaDist{taxaWithRead=0, totalDepth=0, maxTaxa=13, []}
[pool-1-thread-1] INFO net.maizegenetics.plugindef.AbstractPlugin -
Usage:
DiscoverySNPCallerPluginV2 <options>
-db <Input GBS Database> : Input Database file if using SQLite (required)
-mnMAF <Min Minor Allele Freq> : Minimum minor allele frequency (Default: 0.01)
-mnLCov <Min Locus Coverage> : Minimum locus coverage (proportion of Taxa with a genotype) (Default: 0.1)
-ref <Reference Genome File> : Path to reference genome in fasta format. Ensures that a tag from the reference genome is always included when the tags at a locus are aligned against each other to call SNPs. The reference allele for each site is then provided in the output HapMap files, under the taxon name "REFERENCE_GENOME" (first taxon). DEFAULT: Don't use reference genome.
-sC <Start Chromosome> : Start Chromosome
-eC <End Chromosome> : End Chromosome

-inclGaps <true | false> : Include sites where major or minor allele is a GAP (Default: false)

-gapAlignRatio <Gap Alignment Threshold> : Gap alignment threshold ratio of indel contrasts to non indel contrasts: IC/(IC + NC). Any loci with a tag alignment value above this threshold will be excluded from the pool. (Default: 1.0)
-maxTagsCutSite <Max Number of Cut Sites> : Maximum number of tags per cut site (Default: 64)

-deleteOldData <true | false> : Delete existing SNP data from tables (Default: true)

[pool-1-thread-1] DEBUG net.maizegenetics.plugindef.AbstractPlugin - null key in entry: null=TaxaDist{taxaWithRead=0, totalDepth=0, maxTaxa=13, []}
java.lang.NullPointerException: null key in entry: null=TaxaDist{taxaWithRead=0, totalDepth=0, maxTaxa=13, []}
    at com.google.common.base.Preconditions.checkNotNull(Preconditions.java:235)
    at com.google.common.collect.ImmutableMap.entryOf(ImmutableMap.java:143)
    at com.google.common.collect.ImmutableMap$Builder.put(ImmutableMap.java:182)

    at net.maizegenetics.analysis.gbs.v2.DiscoverySNPCallerPluginV2.createReferenceTag(DiscoverySNPCallerPluginV2.java:400)
    at net.maizegenetics.analysis.gbs.v2.DiscoverySNPCallerPluginV2.findAlleleByAlignment(DiscoverySNPCallerPluginV2.java:266)
    at net.maizegenetics.analysis.gbs.v2.DiscoverySNPCallerPluginV2.lambda$null$64(DiscoverySNPCallerPluginV2.java:179)
    at net.maizegenetics.analysis.gbs.v2.DiscoverySNPCallerPluginV2$$Lambda$33/182606418.accept(Unknown Source)

    at java.util.HashMap$EntrySpliterator.forEachRemaining(HashMap.java:1683)
    at java.util.stream.ReferencePipeline$Head.forEach(ReferencePipeline.java:580)

    at net.maizegenetics.analysis.gbs.v2.DiscoverySNPCallerPluginV2.lambda$processData$66(DiscoverySNPCallerPluginV2.java:178)
    at net.maizegenetics.analysis.gbs.v2.DiscoverySNPCallerPluginV2$$Lambda$30/1780891682.accept(Unknown Source)

    at java.util.ArrayList$ArrayListSpliterator.forEachRemaining(ArrayList.java:1374)
    at java.util.stream.ReferencePipeline$Head.forEach(ReferencePipeline.java:580)
    at net.maizegenetics.analysis.gbs.v2.DiscoverySNPCallerPluginV2.processData(DiscoverySNPCallerPluginV2.java:165)
    at net.maizegenetics.plugindef.AbstractPlugin.performFunction(AbstractPlugin.java:110)
    at net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:1631)
    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:745)

Thanks
Priyanka

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Priyanka Tyagi

Postdoctoral research scholar

Eastern Regional Small Grains Genotyping Lab

4203 Williams Hall, NCSU

Raleigh, 27695

[Lynn Carol Johnson]

I seems to be something strange in your reference genome file.  What crop are you using?

Can you send me your command line, your existing DB (up to the Discovery stage) and your reference genome.   You’ll probably need to put them in a dropbox somewhere that I can pull.

Thanks - Lynn

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[Lynn Carol Johnson]

Priyanka -

Please respond to me privately at lc...@cornell.edu with the files.

Thanks - Lynn

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