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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
INFO 17:17:23,655 HelpFormatter - For support, please view our support site at
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/' -- 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:, 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

at java.nio.Buffer.nextGetIndex(
at java.nio.HeapByteBuffer.getInt(
at org.broadinstitute.sting.gatk.datasources.reads.GATKBAMIndex.readInteger(
at org.broadinstitute.sting.gatk.datasources.reads.GATKBAMIndex.readReferenceSequence(
at org.broadinstitute.sting.gatk.datasources.reads.BAMSchedule.(
at org.broadinstitute.sting.gatk.datasources.reads.BAMScheduler.getNextOverlappingBAMScheduleEntry(
at org.broadinstitute.sting.gatk.datasources.reads.BAMScheduler.advance(
at net.sf.picard.util.PeekableIterator.advance(
at org.broadinstitute.sting.gatk.executive.HierarchicalMicroScheduler.execute(
at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(
at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(
at org.broadinstitute.sting.commandline.CommandLineProgram.start(
at org.broadinstitute.sting.gatk.CommandLineGATK.main(

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 1.0-6121-g8a78414):
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
ERROR Visit our forum to view answers to commonly asked questions
ERROR MESSAGE: Code exception (see stack trace for error itself)
ERROR ------------------------------------------------------------------------------------------



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