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Here's what I'm running:

INFO  12:18:33,096 HelpFormatter - Program Args: -T BaseRecalibrator -I /home/sheenams/gatk_test/gatk2.2/H103.GATKinitialrmdup.srt.bam -
R /home/genetics/Genomes/gatk-bundle/human_g1k_v37.fasta -knownSites /home/genetics/Genomes/gatk-bundle/dbsnp_135.b37.vcf -cov ReadGroup
Covariate -cov QualityScoreCovariate -cov CycleCovariate -cov ContextCovariate -o /home/sheenams/gatk_test/gatk2.2/H103.recal_data.csv -
log /home/sheenams/gatk_test/gatk2.2/H103.gatk_log 

Here's the error I'm getting

INFO  12:18:33,309 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] 
INFO  12:18:33,310 ProgressMeter -        Location processed.reads  runtime per.1M.reads completed total.runtime remaining 
INFO  12:18:33,353 BaseRecalibrator - The covariates being used here:  
INFO  12:18:33,353 BaseRecalibrator -   ReadGroupCovariate 
INFO  12:18:33,354 BaseRecalibrator -   QualityScoreCovariate 
INFO  12:18:33,354 BaseRecalibrator -   ContextCovariate 
INFO  12:18:33,354 ContextCovariate -           Context sizes: base substitution model 2, indel substitution model 3 
INFO  12:18:33,354 BaseRecalibrator -   CycleCovariate 
INFO  12:18:33,355 NestedIntegerArray - Creating NestedIntegerArray with dimensions [1, 3] 
INFO  12:18:33,355 NestedIntegerArray - Pre-allocating first 2 dimensions 
INFO  12:18:33,355 NestedIntegerArray - Done pre-allocating first 2 dimensions 
INFO  12:18:33,356 NestedIntegerArray - Creating NestedIntegerArray with dimensions [1, 94, 3] 
INFO  12:18:33,356 NestedIntegerArray - Pre-allocating first 2 dimensions 
INFO  12:18:33,356 NestedIntegerArray - Done pre-allocating first 2 dimensions 
INFO  12:18:33,356 NestedIntegerArray - Creating NestedIntegerArray with dimensions [1, 94, 1012, 3] 
INFO  12:18:33,356 NestedIntegerArray - Pre-allocating first 2 dimensions 
INFO  12:18:33,356 NestedIntegerArray - Done pre-allocating first 2 dimensions 
INFO  12:18:33,356 NestedIntegerArray - Creating NestedIntegerArray with dimensions [1, 94, 2002, 3] 
INFO  12:18:33,356 NestedIntegerArray - Pre-allocating first 2 dimensions 
INFO  12:18:33,356 NestedIntegerArray - Done pre-allocating first 2 dimensions 
INFO  12:18:36,198 GATKRunReport - Uploaded run statistics report to AWS S3 
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR stack trace 
org.broadinstitute.sting.utils.exceptions.ReviewedStingException: Array length mismatch detected. Malformed read?
        at org.broadinstitute.sting.gatk.walkers.bqsr.BaseRecalibrator.calculateFractionalErrorArray(BaseRecalibrator.java:371)
        at org.broadinstitute.sting.gatk.walkers.bqsr.BaseRecalibrator.map(BaseRecalibrator.java:246)
        at org.broadinstitute.sting.gatk.walkers.bqsr.BaseRecalibrator.map(BaseRecalibrator.java:112)
        at org.broadinstitute.sting.gatk.traversals.TraverseReadsNano$TraverseReadsMap.apply(TraverseReadsNano.java:203)
        at org.broadinstitute.sting.gatk.traversals.TraverseReadsNano$TraverseReadsMap.apply(TraverseReadsNano.java:191)
        at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler.executeSingleThreaded(NanoScheduler.java:287)
        at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler.execute(NanoScheduler.java:252)
        at org.broadinstitute.sting.gatk.traversals.TraverseReadsNano.traverse(TraverseReadsNano.java:91)
        at org.broadinstitute.sting.gatk.traversals.TraverseReadsNano.traverse(TraverseReadsNano.java:55)
        at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:83)
        at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:281)
        at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:113)
        at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:236)
        at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:146)
        at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:93)
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A GATK RUNTIME ERROR has occurred (version 2.2-3-gde33222):
##### ERROR
##### ERROR Please visit the wiki to see if this is a known problem
##### ERROR If not, please post the error, with stack trace, to the GATK forum
##### ERROR Visit our website and forum for extensive documentation and answers to 
##### ERROR commonly asked questions http://www.broadinstitute.org/gatk
##### ERROR
##### ERROR MESSAGE: Array length mismatch detected. Malformed read?
##### ERROR ------------------------------------------------------------------------------------------

I used Picards' ValidateSam script on my bam file, but it says its fine. How do I fix this error?

Thanks