Error Processing VCF block: Mismatch of alleles.
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Ryan Disney
Mar 15, 2024, 12:59:03 PMMar 15
to TASSEL - Trait Analysis by Association, Evolution and Linkage
Hello,
I'm attempting to get this protocol for using SVs in GWAS to work, and have succeeded with the dummy data. I have a custom script that formats my VCF in the same manner as the dummy data (which leaves my header alone; not sure if that's pertinent), and then when I try to run TASSEL 5 to create the Hapmap from my VCF, I get the following. Any suggestions are appreciated.
Thanks,
Ryan
# Using TASSEL to convert to diploid Hapmap format
/Applications/TASSEL\ 5/run_pipeline.pl -debug -vcf Supplemental_SV_dataset_1of7_reformatted.vcf -sortPositions -export Supplemental_SV_dataset_1of7_reformatted.hmp.txt -exportType HapmapDiploid
/Applications/TASSEL 5/lib/sTASSEL.jar:/Applications/TASSEL 5/lib/biojava-genome-6.0.4.jar:/Applications/TASSEL 5/lib/htsjdk-2.24.1.jar:/Applications/TASSEL 5/lib/protobuf-kotlin-3.23.0.jar:/Applications/TASSEL 5/lib/jhdf5-14.12.5.jar:/Applications/TASSEL 5/lib/kotlin-stdlib-jdk7-1.6.10.jar:/Applications/TASSEL 5/lib/snappy-java-1.1.8.4.jar:/Applications/TASSEL 5/lib/ini4j-0.5.4.jar:/Applications/TASSEL 5/lib/scala-library-2.10.1.jar:/Applications/TASSEL 5/lib/javax.json-1.0.4.jar:/Applications/TASSEL 5/lib/biojava-alignment-6.0.4.jar:/Applications/TASSEL 5/lib/junit-4.10.jar:/Applications/TASSEL 5/lib/gs-ui-1.3.jar:/Applications/TASSEL 5/lib/commons-io-2.11.0.jar:/Applications/TASSEL 5/lib/guava-22.0.jar:/Applications/TASSEL 5/lib/sshj-0.32.0.jar:/Applications/TASSEL 5/lib/kotlin-stdlib-jdk8-1.6.10.jar:/Applications/TASSEL 5/lib/ahocorasick-0.2.4.jar:/Applications/TASSEL 5/lib/kotlin-stdlib-1.6.10.jar:/Applications/TASSEL 5/lib/jfreechart-1.0.19.jar:/Applications/TASSEL 5/lib/forester-1.039.jar:/Applications/TASSEL 5/lib/postgresql-42.6.0.jar:/Applications/TASSEL 5/lib/jackson-core-2.13.2.jar:/Applications/TASSEL 5/lib/kotlin-reflect-1.6.10.jar:/Applications/TASSEL 5/lib/colt-1.2.0.jar:/Applications/TASSEL 5/lib/jackson-databind-2.13.2.2.jar:/Applications/TASSEL 5/lib/biojava-core-6.0.4.jar:/Applications/TASSEL 5/lib/jackson-module-kotlin-2.13.2.jar:/Applications/TASSEL 5/lib/json-simple-1.1.1.jar:/Applications/TASSEL 5/lib/commons-math3-3.4.1.jar:/Applications/TASSEL 5/lib/ejml-core-0.41.jar:/Applications/TASSEL 5/lib/mail-1.4.jar:/Applications/TASSEL 5/lib/kotlinx-coroutines-core-jvm-1.6.0.jar:/Applications/TASSEL 5/lib/commons-codec-1.10.jar:/Applications/TASSEL 5/lib/log4j-api-2.21.1.jar:/Applications/TASSEL 5/lib/protobuf-java-3.23.0.jar:/Applications/TASSEL 5/lib/jackson-annotations-2.13.2.jar:/Applications/TASSEL 5/lib/jfreesvg-3.2.jar:/Applications/TASSEL 5/lib/itextpdf-5.1.0.jar:/Applications/TASSEL 5/lib/ejml-ddense-0.41.jar:/Applications/TASSEL 5/lib/slf4j-simple-1.7.10.jar:/Applications/TASSEL 5/lib/protobuf-java-util-3.23.0.jar:/Applications/TASSEL 5/lib/gs-core-1.3.jar:/Applications/TASSEL 5/lib/jcommon-1.0.23.jar:/Applications/TASSEL 5/lib/log4j-core-2.21.1.jar:/Applications/TASSEL 5/lib/sqlite-jdbc-3.39.2.1.jar:/Applications/TASSEL 5/lib/biojava-phylo-4.2.12.jar:/Applications/TASSEL 5/lib/error_prone_annotations-2.19.1.jar:/Applications/TASSEL 5/lib/fastutil-8.2.2.jar:/Applications/TASSEL 5/lib/slf4j-api-1.7.10.jar:/Applications/TASSEL 5/lib/phg.jar:/Applications/TASSEL 5/lib/trove-3.0.3.jar:/Applications/TASSEL 5/sTASSEL.jar
Memory Settings: -Xms512m -Xmx1536m
Tassel Pipeline Arguments: -debug -vcf Supplemental_SV_dataset_1of7_reformatted.vcf -sortPositions -export Supplemental_SV_dataset_1of7_reformatted.hmp.txt -exportType HapmapDiploid
[main] INFO net.maizegenetics.tassel.TasselLogging - Tassel Version: 5.2.93 Date: December 21, 2023
[main] INFO net.maizegenetics.tassel.TasselLogging - Max Available Memory Reported by JVM: 1536 MB
[main] INFO net.maizegenetics.tassel.TasselLogging - Java Version: 21.0.2
[main] INFO net.maizegenetics.tassel.TasselLogging - OS: Mac OS X
[main] INFO net.maizegenetics.tassel.TasselLogging - Number of Processors: 8
[main] INFO net.maizegenetics.tassel.TasselLogging - Tassel 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.
[main] INFO net.maizegenetics.tassel.TasselLogging -
[main] INFO net.maizegenetics.tassel.TasselLogging - Tassel Using Library: Practical Haplotype Graph (PHG): Version: 1.9 Date: December 21, 2023
[main] INFO net.maizegenetics.tassel.TasselLogging - PHG Citation: Bradbury PJ, Casstevens T, Jensen SE, Johnson LC, Miller ZR, Monier B, Romay MC, Song B, Buckler ES. The Practical Haplotype Graph, a platform for storing and using pangenomes for imputation. Bioinformatics. 2022 Aug 2;38(15):3698-3702. doi: 10.1093/bioinformatics/btac410. PMID: 35748708; PMCID: PMC9344836.
[main] INFO net.maizegenetics.pipeline.TasselPipeline - Tassel Pipeline Arguments: [-fork1, -vcf, Supplemental_SV_dataset_1of7_reformatted.vcf, -sortPositions, -export, Supplemental_SV_dataset_1of7_reformatted.hmp.txt, -exportType, HapmapDiploid, -runfork1]
net.maizegenetics.analysis.data.FileLoadPlugin
net.maizegenetics.analysis.data.ExportMultiplePlugin
[pool-2-thread-1] INFO net.maizegenetics.plugindef.AbstractPlugin - Starting net.maizegenetics.analysis.data.FileLoadPlugin: time: Mar 15, 2024 11:09:24
[pool-2-thread-1] INFO net.maizegenetics.plugindef.AbstractPlugin -
FileLoadPlugin Parameters
format: VCF
sortPositions: true
keepDepth: false
[pool-2-thread-1] INFO net.maizegenetics.analysis.data.FileLoadPlugin - Start Loading File: Supplemental_SV_dataset_1of7_reformatted.vcf time: Mar 15, 2024 11:09:24
java.lang.IllegalStateException:
Error Processing VCF block: Mismatch of alleles.
At Chromosome 1, Position 208787.
Allele ID larger than number of alleles
at net.maizegenetics.dna.snp.io.ProcessVCFBlock.call(BuilderFromVCF.java:635)
at net.maizegenetics.dna.snp.io.ProcessVCFBlock.call(BuilderFromVCF.java:428)
at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:317)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1144)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:642)
at java.base/java.lang.Thread.run(Thread.java:1583)
java.lang.IllegalStateException:
Error Processing VCF block: Mismatch of alleles.
At Chromosome 1, Position 3912448.
Allele ID larger than number of alleles
at net.maizegenetics.dna.snp.io.ProcessVCFBlock.call(BuilderFromVCF.java:635)
at net.maizegenetics.dna.snp.io.ProcessVCFBlock.call(BuilderFromVCF.java:428)
at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:317)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1144)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:642)
at java.base/java.lang.Thread.run(Thread.java:1583)
java.lang.IllegalStateException:
Error Processing VCF block: Mismatch of alleles.
At Chromosome 1, Position 7781289.
Allele ID larger than number of alleles
at net.maizegenetics.dna.snp.io.ProcessVCFBlock.call(BuilderFromVCF.java:635)
at net.maizegenetics.dna.snp.io.ProcessVCFBlock.call(BuilderFromVCF.java:428)
at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:317)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1144)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:642)
at java.base/java.lang.Thread.run(Thread.java:1583)
[pool-2-thread-1] DEBUG net.maizegenetics.dna.snp.io.BuilderFromVCF - java.lang.IllegalStateException:
Error Processing VCF block: Mismatch of alleles.
At Chromosome 1, Position 208787.
Allele ID larger than number of alleles
java.util.concurrent.ExecutionException: java.lang.IllegalStateException:
Error Processing VCF block: Mismatch of alleles.
At Chromosome 1, Position 208787.
Allele ID larger than number of alleles
at java.base/java.util.concurrent.FutureTask.report(FutureTask.java:122)
at java.base/java.util.concurrent.FutureTask.get(FutureTask.java:191)
at net.maizegenetics.dna.snp.io.BuilderFromVCF.buildEngine(BuilderFromVCF.java:212)
at net.maizegenetics.dna.snp.io.BuilderFromVCF.buildAndSortInMemory(BuilderFromVCF.java:111)
at net.maizegenetics.dna.snp.ImportUtils.readFromVCF(ImportUtils.java:132)
at net.maizegenetics.analysis.data.FileLoadPlugin.processDatum(FileLoadPlugin.java:542)
at net.maizegenetics.analysis.data.FileLoadPlugin.processData(FileLoadPlugin.java:347)
at net.maizegenetics.plugindef.AbstractPlugin.performFunction(AbstractPlugin.java:112)
at net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:2018)
at net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:30)
at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:572)
at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:317)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1144)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:642)
at java.base/java.lang.Thread.run(Thread.java:1583)
Caused by: java.lang.IllegalStateException:
Error Processing VCF block: Mismatch of alleles.
At Chromosome 1, Position 208787.
Allele ID larger than number of alleles
at net.maizegenetics.dna.snp.io.ProcessVCFBlock.call(BuilderFromVCF.java:635)
at net.maizegenetics.dna.snp.io.ProcessVCFBlock.call(BuilderFromVCF.java:428)
... 4 more
[pool-2-thread-1] DEBUG net.maizegenetics.analysis.data.FileLoadPlugin - java.lang.IllegalStateException:
Error Processing VCF block: Mismatch of alleles.
At Chromosome 1, Position 208787.
Allele ID larger than number of alleles
java.lang.IllegalStateException: java.lang.IllegalStateException:
Error Processing VCF block: Mismatch of alleles.
At Chromosome 1, Position 208787.
Allele ID larger than number of alleles
at net.maizegenetics.dna.snp.io.BuilderFromVCF.buildEngine(BuilderFromVCF.java:216)
at net.maizegenetics.dna.snp.io.BuilderFromVCF.buildAndSortInMemory(BuilderFromVCF.java:111)
at net.maizegenetics.dna.snp.ImportUtils.readFromVCF(ImportUtils.java:132)
at net.maizegenetics.analysis.data.FileLoadPlugin.processDatum(FileLoadPlugin.java:542)
at net.maizegenetics.analysis.data.FileLoadPlugin.processData(FileLoadPlugin.java:347)
at net.maizegenetics.plugindef.AbstractPlugin.performFunction(AbstractPlugin.java:112)
at net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:2018)
at net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:30)
at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:572)
at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:317)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1144)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:642)
at java.base/java.lang.Thread.run(Thread.java:1583)
[pool-2-thread-1] DEBUG net.maizegenetics.plugindef.AbstractPlugin - Problem loading file: Supplemental_SV_dataset_1of7_reformatted.vcf.
Error: java.lang.IllegalStateException:
Error Processing VCF block: Mismatch of alleles.
At Chromosome 1, Position 208787.
Allele ID larger than number of alleles
java.lang.IllegalStateException: Problem loading file: Supplemental_SV_dataset_1of7_reformatted.vcf.
Error: java.lang.IllegalStateException:
Error Processing VCF block: Mismatch of alleles.
At Chromosome 1, Position 208787.
Allele ID larger than number of alleles
at net.maizegenetics.analysis.data.FileLoadPlugin.processDatum(FileLoadPlugin.java:604)
at net.maizegenetics.analysis.data.FileLoadPlugin.processData(FileLoadPlugin.java:347)
at net.maizegenetics.plugindef.AbstractPlugin.performFunction(AbstractPlugin.java:112)
at net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:2018)
at net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:30)
at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:572)
at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:317)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1144)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:642)
at java.base/java.lang.Thread.run(Thread.java:1583)
[pool-2-thread-1] INFO net.maizegenetics.plugindef.AbstractPlugin -
Usage:
FileLoadPlugin <options>
-format <Format> : Import file format [SqrMatrix, Sequence, Unknown, Fasta, Hapmap, HapmapLIX, Plink, Phenotype, ProjectionAlignment, ProjectPCsandRunModelSelection, Phylip_Seq, Phylip_Inter, Table, Serial, HapmapDiploid, Newick, VCF, HDF5, TOPM, HDF5Schema, Filter, NumericGenotype, TaxaList, PositionList, SqrMatrixRaw, SqrMatrixBin, GOBII, Depth, ReferenceProbability, Report, PlinkPhenotype, SqrMatrixDARwinDIS, Avro, Flapjack] (Default: Make Best Guess)
-sortPositions <true | false> : Whether to sort genotype positions if that's possible. (Default: false)
-keepDepth <true | false> : Whether to keep depth if that's possible. (Default: false)
[pool-2-thread-1] ERROR net.maizegenetics.plugindef.AbstractPlugin - Problem loading file: Supplemental_SV_dataset_1of7_reformatted.vcf.
Error: java.lang.IllegalStateException:
Error Processing VCF block: Mismatch of alleles.
At Chromosome 1, Position 208787.
Allele ID larger than number of alleles
java.lang.IllegalStateException:
Error Processing VCF block: Mismatch of alleles.
At Chromosome 1, Position 28678198.
Allele ID larger than number of alleles
at net.maizegenetics.dna.snp.io.ProcessVCFBlock.call(BuilderFromVCF.java:635)
at net.maizegenetics.dna.snp.io.ProcessVCFBlock.call(BuilderFromVCF.java:428)
at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:317)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1144)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:642)
at java.base/java.lang.Thread.run(Thread.java:1583)
/Applications/TASSEL\ 5/run_pipeline.pl -debug -vcf Supplemental_SV_dataset_1of7_reformatted.vcf -sortPositions -export Supplemental_SV_dataset_1of7_reformatted.hmp.txt -exportType HapmapDiploid
/Applications/TASSEL 5/lib/sTASSEL.jar:/Applications/TASSEL 5/lib/biojava-genome-6.0.4.jar:/Applications/TASSEL 5/lib/htsjdk-2.24.1.jar:/Applications/TASSEL 5/lib/protobuf-kotlin-3.23.0.jar:/Applications/TASSEL 5/lib/jhdf5-14.12.5.jar:/Applications/TASSEL 5/lib/kotlin-stdlib-jdk7-1.6.10.jar:/Applications/TASSEL 5/lib/snappy-java-1.1.8.4.jar:/Applications/TASSEL 5/lib/ini4j-0.5.4.jar:/Applications/TASSEL 5/lib/scala-library-2.10.1.jar:/Applications/TASSEL 5/lib/javax.json-1.0.4.jar:/Applications/TASSEL 5/lib/biojava-alignment-6.0.4.jar:/Applications/TASSEL 5/lib/junit-4.10.jar:/Applications/TASSEL 5/lib/gs-ui-1.3.jar:/Applications/TASSEL 5/lib/commons-io-2.11.0.jar:/Applications/TASSEL 5/lib/guava-22.0.jar:/Applications/TASSEL 5/lib/sshj-0.32.0.jar:/Applications/TASSEL 5/lib/kotlin-stdlib-jdk8-1.6.10.jar:/Applications/TASSEL 5/lib/ahocorasick-0.2.4.jar:/Applications/TASSEL 5/lib/kotlin-stdlib-1.6.10.jar:/Applications/TASSEL 5/lib/jfreechart-1.0.19.jar:/Applications/TASSEL 5/lib/forester-1.039.jar:/Applications/TASSEL 5/lib/postgresql-42.6.0.jar:/Applications/TASSEL 5/lib/jackson-core-2.13.2.jar:/Applications/TASSEL 5/lib/kotlin-reflect-1.6.10.jar:/Applications/TASSEL 5/lib/colt-1.2.0.jar:/Applications/TASSEL 5/lib/jackson-databind-2.13.2.2.jar:/Applications/TASSEL 5/lib/biojava-core-6.0.4.jar:/Applications/TASSEL 5/lib/jackson-module-kotlin-2.13.2.jar:/Applications/TASSEL 5/lib/json-simple-1.1.1.jar:/Applications/TASSEL 5/lib/commons-math3-3.4.1.jar:/Applications/TASSEL 5/lib/ejml-core-0.41.jar:/Applications/TASSEL 5/lib/mail-1.4.jar:/Applications/TASSEL 5/lib/kotlinx-coroutines-core-jvm-1.6.0.jar:/Applications/TASSEL 5/lib/commons-codec-1.10.jar:/Applications/TASSEL 5/lib/log4j-api-2.21.1.jar:/Applications/TASSEL 5/lib/protobuf-java-3.23.0.jar:/Applications/TASSEL 5/lib/jackson-annotations-2.13.2.jar:/Applications/TASSEL 5/lib/jfreesvg-3.2.jar:/Applications/TASSEL 5/lib/itextpdf-5.1.0.jar:/Applications/TASSEL 5/lib/ejml-ddense-0.41.jar:/Applications/TASSEL 5/lib/slf4j-simple-1.7.10.jar:/Applications/TASSEL 5/lib/protobuf-java-util-3.23.0.jar:/Applications/TASSEL 5/lib/gs-core-1.3.jar:/Applications/TASSEL 5/lib/jcommon-1.0.23.jar:/Applications/TASSEL 5/lib/log4j-core-2.21.1.jar:/Applications/TASSEL 5/lib/sqlite-jdbc-3.39.2.1.jar:/Applications/TASSEL 5/lib/biojava-phylo-4.2.12.jar:/Applications/TASSEL 5/lib/error_prone_annotations-2.19.1.jar:/Applications/TASSEL 5/lib/fastutil-8.2.2.jar:/Applications/TASSEL 5/lib/slf4j-api-1.7.10.jar:/Applications/TASSEL 5/lib/phg.jar:/Applications/TASSEL 5/lib/trove-3.0.3.jar:/Applications/TASSEL 5/sTASSEL.jar
Memory Settings: -Xms512m -Xmx1536m
Tassel Pipeline Arguments: -debug -vcf Supplemental_SV_dataset_1of7_reformatted.vcf -sortPositions -export Supplemental_SV_dataset_1of7_reformatted.hmp.txt -exportType HapmapDiploid
[main] INFO net.maizegenetics.tassel.TasselLogging - Tassel Version: 5.2.93 Date: December 21, 2023
[main] INFO net.maizegenetics.tassel.TasselLogging - Max Available Memory Reported by JVM: 1536 MB
[main] INFO net.maizegenetics.tassel.TasselLogging - Java Version: 21.0.2
[main] INFO net.maizegenetics.tassel.TasselLogging - OS: Mac OS X
[main] INFO net.maizegenetics.tassel.TasselLogging - Number of Processors: 8
[main] INFO net.maizegenetics.tassel.TasselLogging - Tassel 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.
[main] INFO net.maizegenetics.tassel.TasselLogging -
[main] INFO net.maizegenetics.tassel.TasselLogging - Tassel Using Library: Practical Haplotype Graph (PHG): Version: 1.9 Date: December 21, 2023
[main] INFO net.maizegenetics.tassel.TasselLogging - PHG Citation: Bradbury PJ, Casstevens T, Jensen SE, Johnson LC, Miller ZR, Monier B, Romay MC, Song B, Buckler ES. The Practical Haplotype Graph, a platform for storing and using pangenomes for imputation. Bioinformatics. 2022 Aug 2;38(15):3698-3702. doi: 10.1093/bioinformatics/btac410. PMID: 35748708; PMCID: PMC9344836.
[main] INFO net.maizegenetics.pipeline.TasselPipeline - Tassel Pipeline Arguments: [-fork1, -vcf, Supplemental_SV_dataset_1of7_reformatted.vcf, -sortPositions, -export, Supplemental_SV_dataset_1of7_reformatted.hmp.txt, -exportType, HapmapDiploid, -runfork1]
net.maizegenetics.analysis.data.FileLoadPlugin
net.maizegenetics.analysis.data.ExportMultiplePlugin
[pool-2-thread-1] INFO net.maizegenetics.plugindef.AbstractPlugin - Starting net.maizegenetics.analysis.data.FileLoadPlugin: time: Mar 15, 2024 11:09:24
[pool-2-thread-1] INFO net.maizegenetics.plugindef.AbstractPlugin -
FileLoadPlugin Parameters
format: VCF
sortPositions: true
keepDepth: false
[pool-2-thread-1] INFO net.maizegenetics.analysis.data.FileLoadPlugin - Start Loading File: Supplemental_SV_dataset_1of7_reformatted.vcf time: Mar 15, 2024 11:09:24
java.lang.IllegalStateException:
Error Processing VCF block: Mismatch of alleles.
At Chromosome 1, Position 208787.
Allele ID larger than number of alleles
at net.maizegenetics.dna.snp.io.ProcessVCFBlock.call(BuilderFromVCF.java:635)
at net.maizegenetics.dna.snp.io.ProcessVCFBlock.call(BuilderFromVCF.java:428)
at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:317)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1144)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:642)
at java.base/java.lang.Thread.run(Thread.java:1583)
java.lang.IllegalStateException:
Error Processing VCF block: Mismatch of alleles.
At Chromosome 1, Position 3912448.
Allele ID larger than number of alleles
at net.maizegenetics.dna.snp.io.ProcessVCFBlock.call(BuilderFromVCF.java:635)
at net.maizegenetics.dna.snp.io.ProcessVCFBlock.call(BuilderFromVCF.java:428)
at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:317)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1144)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:642)
at java.base/java.lang.Thread.run(Thread.java:1583)
java.lang.IllegalStateException:
Error Processing VCF block: Mismatch of alleles.
At Chromosome 1, Position 7781289.
Allele ID larger than number of alleles
at net.maizegenetics.dna.snp.io.ProcessVCFBlock.call(BuilderFromVCF.java:635)
at net.maizegenetics.dna.snp.io.ProcessVCFBlock.call(BuilderFromVCF.java:428)
at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:317)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1144)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:642)
at java.base/java.lang.Thread.run(Thread.java:1583)
[pool-2-thread-1] DEBUG net.maizegenetics.dna.snp.io.BuilderFromVCF - java.lang.IllegalStateException:
Error Processing VCF block: Mismatch of alleles.
At Chromosome 1, Position 208787.
Allele ID larger than number of alleles
java.util.concurrent.ExecutionException: java.lang.IllegalStateException:
Error Processing VCF block: Mismatch of alleles.
At Chromosome 1, Position 208787.
Allele ID larger than number of alleles
at java.base/java.util.concurrent.FutureTask.report(FutureTask.java:122)
at java.base/java.util.concurrent.FutureTask.get(FutureTask.java:191)
at net.maizegenetics.dna.snp.io.BuilderFromVCF.buildEngine(BuilderFromVCF.java:212)
at net.maizegenetics.dna.snp.io.BuilderFromVCF.buildAndSortInMemory(BuilderFromVCF.java:111)
at net.maizegenetics.dna.snp.ImportUtils.readFromVCF(ImportUtils.java:132)
at net.maizegenetics.analysis.data.FileLoadPlugin.processDatum(FileLoadPlugin.java:542)
at net.maizegenetics.analysis.data.FileLoadPlugin.processData(FileLoadPlugin.java:347)
at net.maizegenetics.plugindef.AbstractPlugin.performFunction(AbstractPlugin.java:112)
at net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:2018)
at net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:30)
at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:572)
at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:317)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1144)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:642)
at java.base/java.lang.Thread.run(Thread.java:1583)
Caused by: java.lang.IllegalStateException:
Error Processing VCF block: Mismatch of alleles.
At Chromosome 1, Position 208787.
Allele ID larger than number of alleles
at net.maizegenetics.dna.snp.io.ProcessVCFBlock.call(BuilderFromVCF.java:635)
at net.maizegenetics.dna.snp.io.ProcessVCFBlock.call(BuilderFromVCF.java:428)
... 4 more
[pool-2-thread-1] DEBUG net.maizegenetics.analysis.data.FileLoadPlugin - java.lang.IllegalStateException:
Error Processing VCF block: Mismatch of alleles.
At Chromosome 1, Position 208787.
Allele ID larger than number of alleles
java.lang.IllegalStateException: java.lang.IllegalStateException:
Error Processing VCF block: Mismatch of alleles.
At Chromosome 1, Position 208787.
Allele ID larger than number of alleles
at net.maizegenetics.dna.snp.io.BuilderFromVCF.buildEngine(BuilderFromVCF.java:216)
at net.maizegenetics.dna.snp.io.BuilderFromVCF.buildAndSortInMemory(BuilderFromVCF.java:111)
at net.maizegenetics.dna.snp.ImportUtils.readFromVCF(ImportUtils.java:132)
at net.maizegenetics.analysis.data.FileLoadPlugin.processDatum(FileLoadPlugin.java:542)
at net.maizegenetics.analysis.data.FileLoadPlugin.processData(FileLoadPlugin.java:347)
at net.maizegenetics.plugindef.AbstractPlugin.performFunction(AbstractPlugin.java:112)
at net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:2018)
at net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:30)
at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:572)
at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:317)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1144)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:642)
at java.base/java.lang.Thread.run(Thread.java:1583)
[pool-2-thread-1] DEBUG net.maizegenetics.plugindef.AbstractPlugin - Problem loading file: Supplemental_SV_dataset_1of7_reformatted.vcf.
Error: java.lang.IllegalStateException:
Error Processing VCF block: Mismatch of alleles.
At Chromosome 1, Position 208787.
Allele ID larger than number of alleles
java.lang.IllegalStateException: Problem loading file: Supplemental_SV_dataset_1of7_reformatted.vcf.
Error: java.lang.IllegalStateException:
Error Processing VCF block: Mismatch of alleles.
At Chromosome 1, Position 208787.
Allele ID larger than number of alleles
at net.maizegenetics.analysis.data.FileLoadPlugin.processDatum(FileLoadPlugin.java:604)
at net.maizegenetics.analysis.data.FileLoadPlugin.processData(FileLoadPlugin.java:347)
at net.maizegenetics.plugindef.AbstractPlugin.performFunction(AbstractPlugin.java:112)
at net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:2018)
at net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:30)
at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:572)
at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:317)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1144)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:642)
at java.base/java.lang.Thread.run(Thread.java:1583)
[pool-2-thread-1] INFO net.maizegenetics.plugindef.AbstractPlugin -
Usage:
FileLoadPlugin <options>
-format <Format> : Import file format [SqrMatrix, Sequence, Unknown, Fasta, Hapmap, HapmapLIX, Plink, Phenotype, ProjectionAlignment, ProjectPCsandRunModelSelection, Phylip_Seq, Phylip_Inter, Table, Serial, HapmapDiploid, Newick, VCF, HDF5, TOPM, HDF5Schema, Filter, NumericGenotype, TaxaList, PositionList, SqrMatrixRaw, SqrMatrixBin, GOBII, Depth, ReferenceProbability, Report, PlinkPhenotype, SqrMatrixDARwinDIS, Avro, Flapjack] (Default: Make Best Guess)
-sortPositions <true | false> : Whether to sort genotype positions if that's possible. (Default: false)
-keepDepth <true | false> : Whether to keep depth if that's possible. (Default: false)
[pool-2-thread-1] ERROR net.maizegenetics.plugindef.AbstractPlugin - Problem loading file: Supplemental_SV_dataset_1of7_reformatted.vcf.
Error: java.lang.IllegalStateException:
Error Processing VCF block: Mismatch of alleles.
At Chromosome 1, Position 208787.
Allele ID larger than number of alleles
java.lang.IllegalStateException:
Error Processing VCF block: Mismatch of alleles.
At Chromosome 1, Position 28678198.
Allele ID larger than number of alleles
at net.maizegenetics.dna.snp.io.ProcessVCFBlock.call(BuilderFromVCF.java:635)
at net.maizegenetics.dna.snp.io.ProcessVCFBlock.call(BuilderFromVCF.java:428)
at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:317)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1144)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:642)
at java.base/java.lang.Thread.run(Thread.java:1583)
Terry Casstevens
Mar 15, 2024, 1:41:48 PMMar 15
to tas...@googlegroups.com
Sounds like your genotype is referencing an allele that isn't listed
in the alleles field. For example 2/2, wouldn't have an allele if only
one alt allele is specified
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in the alleles field. For example 2/2, wouldn't have an allele if only
one alt allele is specified
> You received this message because you are subscribed to the Google Groups "TASSEL - Trait Analysis by Association, Evolution and Linkage" group.
> To unsubscribe from this group and stop receiving emails from it, send an email to tassel+un...@googlegroups.com.
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Ryan Disney
Mar 15, 2024, 1:47:48 PMMar 15
to tas...@googlegroups.com
Thanks! That seems to have been at least part of the problem. I changed my script to modify the ALT based on the maximum "allele" in the samples and that got rid of most of my errors.
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