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java error when using UnifiedGenotyper

npd75npd75 AustraliaMember

Hi ,

I am using the UnifiedGenotyper command but got the following error. Can some one put a light what it could mean!!


INFO 17:17:23,650 HelpFormatter - -----------------------------------------------------------------------------------
INFO 17:17:23,653 HelpFormatter - The Genome Analysis Toolkit (GATK) v1.0-6121-g8a78414, Compiled 2011/07/11 16:05:10
INFO 17:17:23,654 HelpFormatter - Copyright (c) 2010 The Broad Institute
INFO 17:17:23,654 HelpFormatter - Please view our documentation at http://www.broadinstitute.org/gsa/wiki
INFO 17:17:23,655 HelpFormatter - For support, please view our support site at http://getsatisfaction.com/gsa
INFO 17:17:23,655 HelpFormatter - Program Args: -T UnifiedGenotyper -R /projects/u71/nandan/Sven_Uthicke_populationGenomics/analysis/SNP_SFG/seaurchin_topHit_Ids.fasta -I merged_realigned_woUnsafe_1.bam -stand_call_conf 20.0 -stand_emit_conf 20.0 -o raw_snps_indels_Q20_all.vcf -nt 12
INFO 17:17:23,655 HelpFormatter - Date/Time: 2016/01/07 17:17:23
INFO 17:17:23,656 HelpFormatter - -----------------------------------------------------------------------------------
INFO 17:17:23,656 HelpFormatter - -----------------------------------------------------------------------------------
INFO 17:17:23,699 GenomeAnalysisEngine - Strictness is SILENT
INFO 17:17:26,575 MicroScheduler - Running the GATK in parallel mode with 12 concurrent threads
WARN 17:17:29,044 RestStorageService - Error Response: PUT '/GATK_Run_Reports/Ar4GP2YBVmBmWH6kz3hZjIAP6ikSNlHP.report.xml.gz' -- ResponseCode: 403, ResponseStatus: Forbidden, Request Headers: [Content-Length: 1993, Content-MD5: ykLRiVk7ELWpIyvrZz9dyg==, Content-Type: application/octet-stream, x-amz-meta-md5-hash: ca42d189593b10b5a9232beb673f5dca, Date: Thu, 07 Jan 2016 06:17:27 GMT, Authorization: AWS AKIAJXU7VIHBPDW4TDSQ:Ul22+ARecieW4VAUerP/AzNX3qQ=, User-Agent: JetS3t/0.8.0 (Linux/3.0.76-0.11-default; amd64; en; JVM 1.6.0_30), Host: s3.amazonaws.com, Expect: 100-continue], Response Headers: [x-amz-request-id: 6FAAE2E0B5A437DF, x-amz-id-2: oJ9rYHwvwv7LZ2xpsni+V3YQF+6emAiSko8wGj5d09v7CX9nG7E+Duz0KEXFKj2u7jJNNFPOJ4Y=, Content-Type: application/xml, Transfer-Encoding: chunked, Date: Thu, 07 Jan 2016 06:17:28 GMT, Connection: close, Server: AmazonS3]

ERROR ------------------------------------------------------------------------------------------
ERROR stack trace

java.nio.BufferUnderflowException
at java.nio.Buffer.nextGetIndex(Buffer.java:478)
at java.nio.HeapByteBuffer.getInt(HeapByteBuffer.java:336)
at org.broadinstitute.sting.gatk.datasources.reads.GATKBAMIndex.readInteger(GATKBAMIndex.java:299)
at org.broadinstitute.sting.gatk.datasources.reads.GATKBAMIndex.readReferenceSequence(GATKBAMIndex.java:125)
at org.broadinstitute.sting.gatk.datasources.reads.BAMSchedule.(BAMSchedule.java:107)
at org.broadinstitute.sting.gatk.datasources.reads.BAMScheduler.getNextOverlappingBAMScheduleEntry(BAMScheduler.java:205)
at org.broadinstitute.sting.gatk.datasources.reads.BAMScheduler.advance(BAMScheduler.java:108)
at org.broadinstitute.sting.gatk.datasources.reads.BAMScheduler.next(BAMScheduler.java:79)
at org.broadinstitute.sting.gatk.datasources.reads.BAMScheduler.next(BAMScheduler.java:47)
at net.sf.picard.util.PeekableIterator.advance(PeekableIterator.java:71)
at net.sf.picard.util.PeekableIterator.next(PeekableIterator.java:57)
at org.broadinstitute.sting.gatk.datasources.reads.LowMemoryIntervalSharder.next(LowMemoryIntervalSharder.java:61)
at org.broadinstitute.sting.gatk.datasources.reads.LowMemoryIntervalSharder.next(LowMemoryIntervalSharder.java:36)
at org.broadinstitute.sting.gatk.datasources.reads.LocusShardStrategy.next(LocusShardStrategy.java:142)
at org.broadinstitute.sting.gatk.datasources.reads.LocusShardStrategy.next(LocusShardStrategy.java:42)
at org.broadinstitute.sting.gatk.executive.HierarchicalMicroScheduler.execute(HierarchicalMicroScheduler.java:104)
at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:234)
at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:113)
at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:221)
at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:87)

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 1.0-6121-g8a78414):
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 wiki for extensive documentation http://www.broadinstitute.org/gsa/wiki
ERROR Visit our forum to view answers to commonly asked questions http://getsatisfaction.com/gsa
ERROR
ERROR MESSAGE: Code exception (see stack trace for error itself)
ERROR ------------------------------------------------------------------------------------------

Regards,

Nandan

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