UNEAK to generate vcf files - StringIndexOutOfBounds error

Rebecca Bloomer

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Sep 8, 2014, 8:46:02 PM9/8/14

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I'm currently working through the following modification of the UNEAK pipeline, as recommended by Katie Hyma (thanks Katie!) to get vcf files from the non-reference pipeline.

1) FastqToTagCountPlugin

2) MergeMultipleTagCountPlugin - if there are multiple lanes of data

3) TagCountToFastqPlugin

4) UTagCountToTagPairPlugin

5) UExportTagPairPlugin

6) FastqToTBTPlugin

7) MergeTagsByTaxaFilesPlugin - if there are multiple lanes of data

8) tbt2vcfPlugin

9) MergeDuplicateSNP_vcf_Plugin

At the MergeTagsByTaxaFilesPlugin step, using the following arguments

-MergeTagsByTaxaFilesPlugin -i UNEAK/tagsByTaxa -o UNEAK/tagsByTaxa/mergedTagsByTaxa -s 300000000 -h hapmap -endPlugin -runfork1

I'm getting the following error:

ERROR net.maizegenetics.pipeline.TasselPipeline - java.lang.StringIndexOutOfBoundsException: String index out of range: -1

java.lang.IllegalArgumentException: TasselPipeline: parseArgs: Unknown parameter: -MergeTagsByTaxaFilesPlugin

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)

Presumably this is an issue with the TBT files generated at theFastqToTBTPlugin step - I get the same error during the subsequent merging whether I use the master tag count file or the topm to generate the TBT files. Any advice on what I'm doing wrong would be appreciated!

Rebecca

Rebecca Bloomer

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Sep 11, 2014, 11:34:23 PM9/11/14

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Got that bit figured out - but now I'm running into a new problem which, interestingly, looks to be the same issue whether I use the TASSEL3 pipeline outlined above or the TASSEL5 UNEAK diversion.

When I try to call SNPs with either the tbt2vcfPlugin in TASSEL3 or the DiscoverySNPCallerPlugin in TASSEL5, I get a similar error: I begin getting an output, the first five tags are shown, it says "begin processing chromosome 1" and then I get java.lang.ExceptionInInitializerError and a whole host of other error messages including NullPointerException and NoClassDef messages (happy to share if they're diagnostically useful).

Anyone have any idea what's going wrong?

Terry Casstevens

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Sep 12, 2014, 11:53:17 AM9/12/14

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Please send command and all output.

Best,

Terry

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Rebecca Bloomer

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Sep 14, 2014, 4:02:22 PM9/14/14

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Hi Terry,

See below - I've removed the list of numbers for SNP likelihood ratio for length reasons. Any help appreciated!

Tassel Pipeline Arguments: -fork1 -DiscoverySNPCallerPlugin -i UNEAK_T5/05_TagsByTaxa/TBT_HDF5_pivot.h5 -m UNEAK_T5/04_TOPM/topm.bin -o UNEAK_T5/04_TOPM/topm_variants.bin -log UNEAK_T5/07_VCF/logDSCP.log -mnMAF 0.01 -mnLCov 0.1 -sC 1 -eC 1 -endPlugin -runfork1

[main] INFO net.maizegenetics.pipeline.TasselPipeline - Tassel Version: 5.1.0 Date: August 28, 2014

[main] INFO net.maizegenetics.pipeline.TasselPipeline - Max Available Memory Reported by JVM: 21845 MB

[main] INFO net.maizegenetics.pipeline.TasselPipeline - Java Version: 1.8.0_20

[main] INFO net.maizegenetics.pipeline.TasselPipeline - Tassel Pipeline Arguments: [-fork1, -DiscoverySNPCallerPlugin, -i, UNEAK_T5/05_TagsByTaxa/TBT_HDF5_pivot.h5, -m, UNEAK_T5/04_TOPM/topm.bin, -o, UNEAK_T5/04_TOPM/topm_variants.bin, -log, UNEAK_T5/07_VCF/logDSCP.log, -mnMAF, 0.01, -mnLCov, 0.1, -sC, 1, -eC, 1, -endPlugin, -runfork1]

net.maizegenetics.analysis.gbs.DiscoverySNPCallerPlugin

File = UNEAK_T5/04_TOPM/topm.bin

TagMapFile Row Read:0

Count of Tags=335572

initPhysicalSort

Position index sort begin.

Position index sort end.

[Thread-0] INFO net.maizegenetics.analysis.gbs.DiscoverySNPCallerPlugin - minTaxaWithLocus:58 MinF:-2.00000 MinMAF:0.0100000 MinMAC:10

[Thread-0] INFO net.maizegenetics.analysis.gbs.DiscoverySNPCallerPlugin - includeRare:false includeGaps:false

[Thread-0] INFO net.maizegenetics.plugindef.AbstractPlugin -

DiscoverySNPCallerPlugin Parameters

i: UNEAK_T5/05_TagsByTaxa/TBT_HDF5_pivot.h5

y: false

m: UNEAK_T5/04_TOPM/topm.bin

o: UNEAK_T5/04_TOPM/topm_variants.bin

log: UNEAK_T5/07_VCF/logDSCP.log

mnF: -2.0

p: null

mnMAF: 0.01

mnMAC: 10

mnLCov: 0.1

eR: 0.01

ref: null

sC: 1

eC: 1

inclRare: false

inclGaps: false

callBiSNPsWGap: false

[Thread-0] INFO net.maizegenetics.analysis.gbs.DiscoverySNPCallerPlugin - Finding SNPs in UNEAK_T5/05_TagsByTaxa/TBT_HDF5_pivot.h5.

[Thread-0] INFO net.maizegenetics.analysis.gbs.DiscoverySNPCallerPlugin - StartChr:1 EndChr:1

Starting Read Table Sort ...Done in 135ms

initPhysicalSort

Position index sort begin.

Position index sort end.

[Thread-0] INFO net.maizegenetics.analysis.gbs.DiscoverySNPCallerPlugin -

As a check, here are the first 5 tags in the TOPM (sorted by position):

TGCAGAAAAAAAAAAAAATTGGTCGGTACCTCCCCCCCAGCCTCCGCCCGTGCGCTTAGAGTCC 64 64 0 * * * * * * * * *

TGCAGAAAAAAAAAAAAATTGGTCGGTACCTCCGCCCCAGCCTCCGCCCGTGCGCTTAGAGTCC 64 64 0 * * * * * * * * *

TGCAGAAAAAAAAAAAACGTTCTTTCAGGCCGGCGGGATGTGCTTGGGGATCTCCGCTGAAGCG 64 1001 1064 0 * * * * * * * *

TGCAGAAAAAAAAAAAACGTTCTTTCAGGCCGGCGGGATGTGCTTGGTGATCTCCGCTGAAGCG 64 1001 1064 0 * * * * * * * *

TGCAGAAAAAAAAAAAACTATGAAATGAAGTGAAGACTTGATCGCTAGGACAAGCAAGATTTGA 64 2001 2064 0 * * * * * * * *

[Thread-0] INFO net.maizegenetics.analysis.gbs.DiscoverySNPCallerPlugin -

Processing chromosome 1...

Initializing the cutoffs for quantitative SNP calling likelihood ratio (pHet/pErr) >1

totalReadsForSNPInIndiv minLessTaggedAlleleCountForHet

...

java.util.concurrent.ExecutionException: java.lang.ExceptionInInitializerError

at java.util.concurrent.FutureTask.report(FutureTask.java:122)

at java.util.concurrent.FutureTask.get(FutureTask.java:192)

at org.biojava3.alignment.Alignments.getListFromFutures(Alignments.java:282)

at org.biojava3.alignment.Alignments.runPairwiseScorers(Alignments.java:602)

at org.biojava3.alignment.Alignments.getMultipleSequenceAlignment(Alignments.java:173)

at net.maizegenetics.dna.map.TagLocus.getVariableSites(TagLocus.java:501)

at net.maizegenetics.dna.map.TagLocus.getSNPCallsQuant(TagLocus.java:297)

at net.maizegenetics.analysis.gbs.DiscoverySNPCallerPlugin.findSNPsInTagLocus(DiscoverySNPCallerPlugin.java:689)

at net.maizegenetics.analysis.gbs.DiscoverySNPCallerPlugin.discoverSNPsOnChromosome(DiscoverySNPCallerPlugin.java:632)

at net.maizegenetics.analysis.gbs.DiscoverySNPCallerPlugin.processData(DiscoverySNPCallerPlugin.java:131)

at net.maizegenetics.plugindef.AbstractPlugin.performFunction(AbstractPlugin.java:83)

at net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:1164)

at net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)

Caused by: java.lang.ExceptionInInitializerError

at org.biojava3.alignment.SimpleAlignedSequence.setLocation(SimpleAlignedSequence.java:358)

at org.biojava3.alignment.SimpleAlignedSequence.<init>(SimpleAlignedSequence.java:88)

at org.biojava3.alignment.SimpleProfile.<init>(SimpleProfile.java:118)

at org.biojava3.alignment.SimpleSequencePair.<init>(SimpleSequencePair.java:86)

at org.biojava3.alignment.SimpleSequencePair.<init>(SimpleSequencePair.java:69)

at org.biojava3.alignment.NeedlemanWunsch.setProfile(NeedlemanWunsch.java:71)

at org.biojava3.alignment.template.AbstractMatrixAligner.align(AbstractMatrixAligner.java:342)

at org.biojava3.alignment.template.AbstractPairwiseSequenceAligner.getPair(AbstractPairwiseSequenceAligner.java:112)

at org.biojava3.alignment.FractionalIdentityScorer.align(FractionalIdentityScorer.java:112)

at org.biojava3.alignment.FractionalIdentityScorer.getScore(FractionalIdentityScorer.java:105)

at org.biojava3.alignment.template.CallablePairwiseSequenceScorer.call(CallablePairwiseSequenceScorer.java:53)

at org.biojava3.alignment.template.CallablePairwiseSequenceScorer.call(CallablePairwiseSequenceScorer.java:38)

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)

Caused by: java.lang.NullPointerException

at java.util.Collections$UnmodifiableCollection.<init>(Collections.java:1026)

at java.util.Collections$UnmodifiableList.<init>(Collections.java:1302)

at java.util.Collections.unmodifiableList(Collections.java:1287)

at org.biojava3.core.sequence.location.template.AbstractLocation.<init>(AbstractLocation.java:111)

at org.biojava3.core.sequence.location.template.AbstractLocation.<init>(AbstractLocation.java:85)

at org.biojava3.core.sequence.location.SimpleLocation.<init>(SimpleLocation.java:57)

at org.biojava3.core.sequence.location.SimpleLocation.<init>(SimpleLocation.java:53)

at org.biojava3.core.sequence.location.template.Location.<clinit>(Location.java:48)

... 16 more

[Thread-0] INFO net.maizegenetics.pipeline.TasselPipeline - net.maizegenetics.analysis.gbs.DiscoverySNPCallerPlugin: progress: 100%

[Thread-0] INFO net.maizegenetics.plugindef.AbstractPlugin - net.maizegenetics.analysis.gbs.DiscoverySNPCallerPlugin 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.

Exception in thread "Thread-0" java.lang.NoClassDefFoundError: Could not initialize class org.biojava3.core.sequence.location.SimpleLocation