Production SNP Caller PluginV2 error (Good Barcodes Read and String index out of range)

Arthur Melo

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Jun 25, 2015, 1:04:04 PM6/25/15

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Hi Tassel team, I hope you are well...

In a couple of weeks I'm running Tassel 5.2.11 using a Unix server. In my guess all steps works normally. My SNPs are discovered and in have many variables estimated for its from SNP Quality Profiler. However, when I'm run the last step from GBS pipeline (Production SNP Caller Plugin) some error message are printed. There are two error messages related with Good Barcodes Read and String index out of range. Please, look:

Tassel Pipeline Arguments: -debug -fork1 -ProductionSNPCallerPluginV2 -db GBSV2.db -e PstI-MspI -i ./../HQ_data -k arguta_key.txt -o SNPs2.h5 -ko true -do true -mxTagL 64 -endPlugin -runfork1

[main] INFO net.maizegenetics.tassel.TasselLogging - Tassel Version: 5.2.11 Date: June 4, 2015

[main] INFO net.maizegenetics.tassel.TasselLogging - Max Available Memory Reported by JVM: 1365 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.pipeline.TasselPipeline - Tassel Pipeline Arguments: [-fork1, -ProductionSNPCallerPluginV2, -db, GBSV2.db, -e, PstI-MspI, -i, ./../HQ_data, -k, arguta_key.txt, -o, SNPs2.h5, -ko, true, -do, true, -mxTagL, 64, -endPlugin, -runfork1]

net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2

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

ProductionSNPCallerPluginV2 Parameters

i: ./../HQ_data

k: arguta_key.txt

e: PstI-MspI

db: GBSV2.db

o: SNPs2.h5

eR: 0.01

d: 0

ko: true

do: true

mxTagL: 64

minPosQS: 0.0

batchSize: 8

mnQS: 0

size of all tags in tag table=154792

size of all tags in mappingApproach table=2

size of all taxa in taxa table=54

ProductionSNPCallerPluginV2: Total batches to process: 1

size of all positions in snpPosition table=60228

[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 -

The target HDF5 file:

SNPs2.h5

does not exist. A new HDF5 file of that name will be created

to hold the genotypes from this run.

size of all positions in snpPosition table=60228

size of all alleles in allele table=123036

Start processing batch 1

Enzyme: PstI-MspI

[ForkJoinPool.commonPool-worker-25] INFO net.maizegenetics.analysis.gbs.v2.GBSUtils - /home/arthur/kiwi_GBS_project/Paper1_Bioinfo/TA/arg64_BWAmem/./../HQ_data/H0WE7ADXX_2_fastq.txt: Quality score base:33

[ForkJoinPool.commonPool-worker-18] INFO net.maizegenetics.analysis.gbs.v2.GBSUtils - /home/arthur/kiwi_GBS_project/Paper1_Bioinfo/TA/arg64_BWAmem/./../HQ_data/H8DUYADXX_2_fastq.txt: Quality score base:33

[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.GBSUtils - /home/arthur/kiwi_GBS_project/Paper1_Bioinfo/TA/arg64_BWAmem/./../HQ_data/H94NLADXX_1_fastq.txt: Quality score base:33

[ForkJoinPool.commonPool-worker-11] INFO net.maizegenetics.analysis.gbs.v2.GBSUtils - /home/arthur/kiwi_GBS_project/Paper1_Bioinfo/TA/arg64_BWAmem/./../HQ_data/H8DUYADXX_1_fastq.txt: Quality score base:33

[ForkJoinPool.commonPool-worker-25] ERROR net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Good Barcodes Read: 2

java.lang.StringIndexOutOfBoundsException: String index out of range: 69

at java.lang.String.substring(String.java:1951)

at net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2.processFastQ(ProductionSNPCallerPluginV2.java:289)

at net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2.processFastQFile(ProductionSNPCallerPluginV2.java:266)

at net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2.lambda$processData$88(ProductionSNPCallerPluginV2.java:207)

at net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2$$Lambda$8/1507544660.accept(Unknown Source)

at java.util.stream.ForEachOps$ForEachOp$OfRef.accept(ForEachOps.java:184)

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

at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:512)

at java.util.stream.ForEachOps$ForEachTask.compute(ForEachOps.java:291)

at java.util.concurrent.CountedCompleter.exec(CountedCompleter.java:731)

at java.util.concurrent.ForkJoinTask.doExec(ForkJoinTask.java:289)

at java.util.concurrent.ForkJoinPool$WorkQueue.runTask(ForkJoinPool.java:1056)

at java.util.concurrent.ForkJoinPool.runWorker(ForkJoinPool.java:1689)

at java.util.concurrent.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:157)

[pool-1-thread-1] ERROR net.maizegenetics.analysis.gbs.v2.ProductionSNPCallerPluginV2 - Good Barcodes Read: 0

java.lang.StringIndexOutOfBoundsException: String index out of range: 74