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Need help with the BaseRecalibrator -- Run time error ?

SJLSJL Posts: 4Member
edited February 2013 in Ask the GATK team

Hi, I am trying to run the base recalibrator. For some of my sequences, it work perfectly, but for others, it's always crashing and giving the following error message :

INFO 16:49:21,718 HelpFormatter - -------------------------------------------------------------------------------- INFO 16:49:21,720 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.3-6-gebbba25, Compiled 2013/01/08 19:29:18 INFO 16:49:21,720 HelpFormatter - Copyright (c) 2010 The Broad Institute INFO 16:49:21,720 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk INFO 16:49:21,724 HelpFormatter - Program Args: -T BaseRecalibrator -I alnSortedNoDupRGRealigned1.bam -l INFO -R 1.198.A.contig22.fa -knownSites alnSortedNoDupRGRealigned1_t0.01.vcf -o test.rcl -fixMisencodedQuals --filter_mismatching_base_and_quals INFO 16:49:21,725 HelpFormatter - Date/Time: 2013/02/11 16:49:21 INFO 16:49:21,725 HelpFormatter - -------------------------------------------------------------------------------- INFO 16:49:21,725 HelpFormatter - -------------------------------------------------------------------------------- INFO 16:49:21,737 ArgumentTypeDescriptor - Dynamically determined type of alnSortedNoDupRGRealigned1_t0.01.vcf to be VCF INFO 16:49:21,744 GenomeAnalysisEngine - Strictness is SILENT INFO 16:49:21,970 GenomeAnalysisEngine - Downsampling Settings: No downsampling INFO 16:49:21,977 SAMDataSource$SAMReaders - Initializing SAMRecords in serial INFO 16:49:21,992 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01 INFO 16:49:22,005 RMDTrackBuilder - Loading Tribble index from disk for file alnSortedNoDupRGRealigned1_t0.01.vcf INFO 16:49:22,040 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] INFO 16:49:22,040 ProgressMeter - Location processed.reads runtime per.1M.reads completed total.runtime remaining INFO 16:49:22,134 BaseRecalibrator - The covariates being used here:
INFO 16:49:22,134 BaseRecalibrator - ReadGroupCovariate INFO 16:49:22,134 BaseRecalibrator - QualityScoreCovariate INFO 16:49:22,134 BaseRecalibrator - ContextCovariate INFO 16:49:22,135 ContextCovariate - Context sizes: base substitution model 2, indel substitution model 3 INFO 16:49:22,135 BaseRecalibrator - CycleCovariate INFO 16:49:22,137 NestedIntegerArray - Creating NestedIntegerArray with dimensions [1, 3] INFO 16:49:22,138 NestedIntegerArray - Pre-allocating first 2 dimensions INFO 16:49:22,139 NestedIntegerArray - Done pre-allocating first 2 dimensions INFO 16:49:22,139 NestedIntegerArray - Creating NestedIntegerArray with dimensions [1, 94, 3] INFO 16:49:22,139 NestedIntegerArray - Pre-allocating first 2 dimensions INFO 16:49:22,140 NestedIntegerArray - Done pre-allocating first 2 dimensions INFO 16:49:22,140 NestedIntegerArray - Creating NestedIntegerArray with dimensions [1, 94, 1012, 3] INFO 16:49:22,140 NestedIntegerArray - Pre-allocating first 2 dimensions INFO 16:49:22,140 NestedIntegerArray - Done pre-allocating first 2 dimensions INFO 16:49:22,140 NestedIntegerArray - Creating NestedIntegerArray with dimensions [1, 94, 1002, 3] INFO 16:49:22,140 NestedIntegerArray - Pre-allocating first 2 dimensions INFO 16:49:22,141 NestedIntegerArray - Done pre-allocating first 2 dimensions INFO 16:49:22,145 ReadShardBalancer$1 - Loading BAM index data for next contig INFO 16:49:22,147 ReadShardBalancer$1 - Done loading BAM index data for next contig INFO 16:49:24,487 GATKRunReport - Uploaded run statistics report to AWS S3

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

java.lang.ArrayIndexOutOfBoundsException: -31 at org.broadinstitute.sting.utils.baq.BAQ.calcEpsilon(BAQ.java:158) at org.broadinstitute.sting.utils.baq.BAQ.hmm_glocal(BAQ.java:225) at org.broadinstitute.sting.utils.baq.BAQ.calcBAQFromHMM(BAQ.java:542) at org.broadinstitute.sting.utils.baq.BAQ.calcBAQFromHMM(BAQ.java:595) at org.broadinstitute.sting.utils.baq.BAQ.calcBAQFromHMM(BAQ.java:530) at org.broadinstitute.sting.utils.baq.BAQ.baqRead(BAQ.java:663) at org.broadinstitute.sting.gatk.walkers.bqsr.BaseRecalibrator.calculateBAQArray(BaseRecalibrator.java:428) at org.broadinstitute.sting.gatk.walkers.bqsr.BaseRecalibrator.map(BaseRecalibrator.java:243) 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:248) at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler.execute(NanoScheduler.java:219) 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:237) at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:147) at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:91)

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 2.3-6-gebbba25):
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: -31
ERROR ------------------------------------------------------------------------------------------

Here is the command line I am using: java -Xmx4g -jar /mit/sjlabrie/software/GenomeAnalysisTK-2.3-6-gebbba25/GenomeAnalysisTK.jar \ -T BaseRecalibrator \ -I alnSortedNoDupRGRealigned1.bam \ -l INFO \ -R 1.198.A.contig22.fa \ -knownSites alnSortedNoDupRGRealigned1_t0.01.vcf \ -o test.rcl \ -fixMisencodedQuals \ --filter_mismatching_base_and_quals \

Any Idea what's going on ?

Thank you,

Simon

Post edited by SJL on

Best Answer

Answers

  • SJLSJL Posts: 4Member

    I ran it also with the DEBUG flag : `INFO 18:09:43,801 HelpFormatter - -------------------------------------------------------------------------------- INFO 18:09:43,804 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.3-9-ge5ebf34, Compiled 2013/01/11 22:43:14 INFO 18:09:43,804 HelpFormatter - Copyright (c) 2010 The Broad Institute INFO 18:09:43,804 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk DEBUG 18:09:43,804 HelpFormatter - Current directory: /net/eaps-80-11/data/sjlabrie/vibrioPhage/1.198.A INFO 18:09:43,808 HelpFormatter - Program Args: -T BaseRecalibrator -I alnSortedNoDupRGRealigned1.bam -l DEBUG -R 1.198.A.contig22.fa -knownSites alnSortedNoDupRGRealigned1_t0.01.vcf -o test.rcl --filter_mismatching_base_and_quals INFO 18:09:43,809 HelpFormatter - Date/Time: 2013/02/11 18:09:43 INFO 18:09:43,809 HelpFormatter - -------------------------------------------------------------------------------- INFO 18:09:43,809 HelpFormatter - -------------------------------------------------------------------------------- INFO 18:09:43,829 ArgumentTypeDescriptor - Dynamically determined type of alnSortedNoDupRGRealigned1_t0.01.vcf to be VCF INFO 18:09:43,837 GenomeAnalysisEngine - Strictness is SILENT DEBUG 18:09:43,950 GenomeLocParser - Prepared reference sequence contig dictionary DEBUG 18:09:43,950 GenomeLocParser - 1.198.A (44361 bp) INFO 18:09:44,156 GenomeAnalysisEngine - Downsampling Settings: No downsampling INFO 18:09:44,164 SAMDataSource$SAMReaders - Initializing SAMRecords in serial DEBUG 18:09:44,180 SAMDataSource$SAMReaders - Processing file (1 of 1) alnSortedNoDupRGRealigned1.bam... INFO 18:09:44,182 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02 INFO 18:09:44,197 RMDTrackBuilder - Loading Tribble index from disk for file alnSortedNoDupRGRealigned1_t0.01.vcf DEBUG 18:09:44,233 GenomeLocParser - Prepared reference sequence contig dictionary DEBUG 18:09:44,234 GenomeLocParser - 1.198.A (44361 bp) INFO 18:09:44,235 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] INFO 18:09:44,236 ProgressMeter - Location processed.reads runtime per.1M.reads completed total.runtime remaining INFO 18:09:44,344 BaseRecalibrator - The covariates being used here:
    INFO 18:09:44,344 BaseRecalibrator - ReadGroupCovariate INFO 18:09:44,344 BaseRecalibrator - QualityScoreCovariate INFO 18:09:44,344 BaseRecalibrator - ContextCovariate INFO 18:09:44,344 ContextCovariate - Context sizes: base substitution model 2, indel substitution model 3 INFO 18:09:44,344 BaseRecalibrator - CycleCovariate INFO 18:09:44,349 NestedIntegerArray - Creating NestedIntegerArray with dimensions [1, 3] INFO 18:09:44,349 NestedIntegerArray - Pre-allocating first 2 dimensions INFO 18:09:44,350 NestedIntegerArray - Done pre-allocating first 2 dimensions INFO 18:09:44,350 NestedIntegerArray - Creating NestedIntegerArray with dimensions [1, 94, 3] INFO 18:09:44,350 NestedIntegerArray - Pre-allocating first 2 dimensions INFO 18:09:44,350 NestedIntegerArray - Done pre-allocating first 2 dimensions INFO 18:09:44,350 NestedIntegerArray - Creating NestedIntegerArray with dimensions [1, 94, 1012, 3] INFO 18:09:44,350 NestedIntegerArray - Pre-allocating first 2 dimensions INFO 18:09:44,350 NestedIntegerArray - Done pre-allocating first 2 dimensions INFO 18:09:44,351 NestedIntegerArray - Creating NestedIntegerArray with dimensions [1, 94, 1002, 3] INFO 18:09:44,351 NestedIntegerArray - Pre-allocating first 2 dimensions INFO 18:09:44,351 NestedIntegerArray - Done pre-allocating first 2 dimensions INFO 18:09:44,356 ReadShardBalancer$1 - Loading BAM index data for next contig DEBUG 18:09:44,369 ReadShardBalancer$1 - Encountered monolithic FilePointer: FilePointer:%n locations = {}%n regions = %n/net/eaps-80-11/data/sjlabrie/vibrioPhage/1.198.A/alnSortedNoDupRGRealigned1.bam= {0:1336-140737488355327:65535;} INFO 18:09:44,371 ReadShardBalancer$1 - Done loading BAM index data for next contig DEBUG 18:09:44,380 ReadShardBalancer$1 - Next contig FilePointer: FilePointer:%n locations = {}%n regions = %n/net/eaps-80-11/data/sjlabrie/vibrioPhage/1.198.A/alnSortedNoDupRGRealigned1.bam= {0:1336-140737488355327:65535;} DEBUG 18:09:45,476 TraverseReadsNano - TraverseReadsNano.traverse Covered dataset is /net/eaps-80-11/data/sjlabrie/vibrioPhage/1.198.A/alnSortedNoDupRGRealigned1.bam: 0:1336-140737488355327:65535;
    DEBUG 18:09:45,887 GATKRunReport - Aggregating data for run report DEBUG 18:09:46,100 GATKRunReport - Posting report of type STANDARD DEBUG 18:09:46,101 GATKRunReport - Generating GATK report to AWS S3 with key QeTQ5IlTVuSyIOWRCCOFIkqxjlq4W5Kz.report.xml.gz DEBUG 18:09:46,211 DefaultHttpParams - Set parameter http.useragent = Jakarta Commons-HttpClient/3.1 DEBUG 18:09:46,212 DefaultHttpParams - Set parameter http.protocol.version = HTTP/1.1 DEBUG 18:09:46,213 DefaultHttpParams - Set parameter http.connection-manager.class = class org.apache.commons.httpclient.SimpleHttpConnectionManager DEBUG 18:09:46,214 DefaultHttpParams - Set parameter http.protocol.cookie-policy = default DEBUG 18:09:46,214 DefaultHttpParams - Set parameter http.protocol.element-charset = US-ASCII DEBUG 18:09:46,214 DefaultHttpParams - Set parameter http.protocol.content-charset = ISO-8859-1 DEBUG 18:09:46,215 DefaultHttpParams - Set parameter http.method.retry-handler = org.apache.commons.httpclient.DefaultHttpMethodRetryHandler@66bccad2 DEBUG 18:09:46,215 DefaultHttpParams - Set parameter http.dateparser.patterns = [EEE, dd MMM yyyy HH:mm:ss zzz, EEEE, dd-MMM-yy HH:mm:ss zzz, EEE MMM d HH:mm:ss yyyy, EEE, dd-MMM-yyyy HH:mm:ss z, EEE, dd-MMM-yyyy HH-mm-ss z, EEE, dd MMM yy HH:mm:ss z, EEE dd-MMM-yyyy HH:mm:ss z, EEE dd MMM yyyy HH:mm:ss z, EEE dd-MMM-yyyy HH-mm-ss z, EEE dd-MMM-yy HH:mm:ss z, EEE dd MMM yy HH:mm:ss z, EEE,dd-MMM-yy HH:mm:ss z, EEE,dd-MMM-yyyy HH:mm:ss z, EEE, dd-MM-yyyy HH:mm:ss z] DEBUG 18:09:46,215 Jets3tProperties - s3service.https-only=true DEBUG 18:09:46,215 Jets3tProperties - storage-service.internal-error-retry-max=5 DEBUG 18:09:46,219 Jets3tProperties - httpclient.connection-timeout-ms=60000 DEBUG 18:09:46,219 DefaultHttpParams - Set parameter http.connection.timeout = 60000 DEBUG 18:09:46,219 Jets3tProperties - httpclient.socket-timeout-ms=60000 DEBUG 18:09:46,219 DefaultHttpParams - Set parameter http.socket.timeout = 60000 DEBUG 18:09:46,219 Jets3tProperties - httpclient.stale-checking-enabled=true DEBUG 18:09:46,219 DefaultHttpParams - Set parameter http.connection.stalecheck = true DEBUG 18:09:46,219 Jets3tProperties - httpclient.max-connections=20 DEBUG 18:09:46,219 Jets3tProperties - httpclient.max-connections-per-host=0 DEBUG 18:09:46,220 DefaultHttpParams - Set parameter http.connection-manager.max-per-host = {HostConfiguration[]=20} DEBUG 18:09:46,220 DefaultHttpParams - Set parameter http.connection-manager.max-total = 20 DEBUG 18:09:46,220 DefaultHttpParams - Set parameter http.tcp.nodelay = true DEBUG 18:09:46,226 Jets3tProperties - httpclient.useragent=null DEBUG 18:09:46,230 RestUtils - Setting user agent string: JetS3t/0.8.1 (Linux/2.6.43.8-1.fc15.x86_64; amd64; en; JVM 1.6.0_22) DEBUG 18:09:46,230 DefaultHttpParams - Set parameter http.useragent = JetS3t/0.8.1 (Linux/2.6.43.8-1.fc15.x86_64; amd64; en; JVM 1.6.0_22) DEBUG 18:09:46,230 DefaultHttpParams - Set parameter http.protocol.version = HTTP/1.1 DEBUG 18:09:46,231 DefaultHttpParams - Set parameter http.protocol.expect-continue = true DEBUG 18:09:46,231 Jets3tProperties - httpclient.retry-max=5 DEBUG 18:09:46,231 DefaultHttpParams - Set parameter http.method.retry-handler = org.jets3t.service.utils.RestUtils$1@64fe7a67 DEBUG 18:09:46,231 Jets3tProperties - httpclient.connection-manager-timeout=0 DEBUG 18:09:46,232 DefaultHttpParams - Set parameter http.connection-manager.timeout = 0 DEBUG 18:09:46,233 HttpClient - Java version: 1.6.0_22 DEBUG 18:09:46,233 HttpClient - Java vendor: Sun Microsystems Inc. DEBUG 18:09:46,233 HttpClient - Java class path: /mit/sjlabrie/software/GenomeAnalysisTK-2.3-9-ge5ebf34/GenomeAnalysisTK.jar DEBUG 18:09:46,233 HttpClient - Operating system name: Linux DEBUG 18:09:46,233 HttpClient - Operating system architecture: amd64 DEBUG 18:09:46,233 HttpClient - Operating system version: 2.6.43.8-1.fc15.x86_64 DEBUG 18:09:46,257 HttpClient - SUN 1.6: SUN (DSA key/parameter generation; DSA signing; SHA-1, MD5 digests; SecureRandom; X.509 certificates; JKS keystore; PKIX CertPathValidator; PKIX CertPathBuilder; LDAP, Collection CertStores, JavaPolicy Policy; JavaLoginConfig Configuration) DEBUG 18:09:46,258 HttpClient - SunRsaSign 1.7: Sun RSA signature provider DEBUG 18:09:46,258 HttpClient - SunJSSE 1.6: Sun JSSE provider(PKCS12, SunX509 key/trust factories, SSLv3, TLSv1) DEBUG 18:09:46,258 HttpClient - SunJCE 1.7: SunJCE Provider (implements RSA, DES, Triple DES, AES, Blowfish, ARCFOUR, RC2, PBE, Diffie-Hellman, HMAC) DEBUG 18:09:46,258 HttpClient - SunJGSS 1.0: Sun (Kerberos v5, SPNEGO) DEBUG 18:09:46,258 HttpClient - SunSASL 1.5: Sun SASL provider(implements client mechanisms for: DIGEST-MD5, GSSAPI, EXTERNAL, PLAIN, CRAM-MD5; server mechanisms for: DIGEST-MD5, GSSAPI, CRAM-MD5) DEBUG 18:09:46,258 HttpClient - XMLDSig 1.0: XMLDSig (DOM XMLSignatureFactory; DOM KeyInfoFactory) DEBUG 18:09:46,258 HttpClient - SunPCSC 1.6: Sun PC/SC provider DEBUG 18:09:46,260 Jets3tProperties - s3service.s3-endpoint=null DEBUG 18:09:46,260 Jets3tProperties - s3service.default-storage-class=null DEBUG 18:09:46,261 Jets3tProperties - httpclient.proxy-autodetect=true DEBUG 18:09:46,261 Jets3tProperties - s3service.s3-endpoint=s3.amazonaws.com DEBUG 18:09:46,264 PluginProxyUtil - About to attempt auto proxy detection under Java version:1.6.0_22-b22 DEBUG 18:09:46,265 PluginProxyUtil - Sun Plugin 1.4+ proxy detection class not found, will try failover detection DEBUG 18:09:46,265 PluginProxyUtil - Using failover proxy detection... DEBUG 18:09:46,265 PluginProxyUtil - Plugin Proxy Config List Property:null DEBUG 18:09:46,265 PluginProxyUtil - No configured plugin proxy list DEBUG 18:09:46,265 Jets3tProperties - devpay.user-token=null DEBUG 18:09:46,265 Jets3tProperties - devpay.product-token=null DEBUG 18:09:46,266 Jets3tProperties - httpclient.requester-pays-buckets-enabled=false DEBUG 18:09:46,272 RestStorageService - Creating Object with key QeTQ5IlTVuSyIOWRCCOFIkqxjlq4W5Kz.report.xml.gz in bucket GATK_Run_Reports DEBUG 18:09:46,272 RestStorageService - Uploading object data with Content-Length: 911 DEBUG 18:09:46,273 Jets3tProperties - httpclient.read-throttle=0 DEBUG 18:09:46,273 Jets3tProperties - s3service.s3-endpoint=null DEBUG 18:09:46,273 Jets3tProperties - s3service.enable-storage-classes=true DEBUG 18:09:46,274 RestStorageService - Creating object bucketName=GATK_Run_Reports, objectKey=QeTQ5IlTVuSyIOWRCCOFIkqxjlq4W5Kz.report.xml.gz, storageClass=null. Content-Type=application/octet-stream Including data? true Metadata: {Content-Length=911, Content-MD5=MEiOpW7bu0NAtuiaNB4rLA==, md5-hash=30488ea56edbbb4340b6e89a341e2b2c, Content-Type=application/octet-stream} ACL: null DEBUG 18:09:46,274 Jets3tProperties - s3service.disable-dns-buckets=false DEBUG 18:09:46,274 Jets3tProperties - s3service.s3-endpoint=s3.amazonaws.com DEBUG 18:09:46,275 Jets3tProperties - s3service.s3-endpoint-virtual-path= DEBUG 18:09:46,275 Jets3tProperties - s3service.s3-endpoint-https-port=443 DEBUG 18:09:46,275 RestStorageService - S3 URL: https://s3.amazonaws.com:443/GATK_Run_Reports/QeTQ5IlTVuSyIOWRCCOFIkqxjlq4W5Kz.report.xml.gz DEBUG 18:09:46,302 RestStorageService - Performing PUT request for 'https://s3.amazonaws.com/GATK_Run_Reports/QeTQ5IlTVuSyIOWRCCOFIkqxjlq4W5Kz.report.xml.gz', expecting response codes: [200,204] DEBUG 18:09:46,302 RestStorageService - Adding authorization for Access Key 'AKIAJXU7VIHBPDW4TDSQ'. DEBUG 18:09:46,302 Jets3tProperties - s3service.s3-endpoint=s3.amazonaws.com DEBUG 18:09:46,303 RestStorageService - Canonical string ('|' is a newline): PUT|MEiOpW7bu0NAtuiaNB4rLA==|application/octet-stream|Mon, 11 Feb 2013 23:09:46 GMT|x-amz-meta-md5-hash:30488ea56edbbb4340b6e89a341e2b2c|/GATK_Run_Reports/QeTQ5IlTVuSyIOWRCCOFIkqxjlq4W5Kz.report.xml.gz DEBUG 18:09:46,313 MultiThreadedHttpConnectionManager - HttpConnectionManager.getConnection: config = HostConfiguration[host=https://s3.amazonaws.com], timeout = 0 DEBUG 18:09:46,314 MultiThreadedHttpConnectionManager$ConnectionPool - Allocating new connection, hostConfig=HostConfiguration[host=https://s3.amazonaws.com] DEBUG 18:09:46,317 HttpConnection - Open connection to s3.amazonaws.com:443 DEBUG 18:09:46,694 Wire - >> "PUT /GATK_Run_Reports/QeTQ5IlTVuSyIOWRCCOFIkqxjlq4W5Kz.report.xml.gz HTTP/1.1[\r][\n]" DEBUG 18:09:46,694 HttpMethodBase - Adding Host request header DEBUG 18:09:46,711 Wire - >> "Content-Length: 911[\r][\n]" DEBUG 18:09:46,715 Wire - >> "Content-MD5: MEiOpW7bu0NAtuiaNB4rLA==[\r][\n]" DEBUG 18:09:46,716 Wire - >> "Content-Type: application/octet-stream[\r][\n]" DEBUG 18:09:46,716 Wire - >> "x-amz-meta-md5-hash: 30488ea56edbbb4340b6e89a341e2b2c[\r][\n]" DEBUG 18:09:46,716 Wire - >> "Date: Mon, 11 Feb 2013 23:09:46 GMT[\r][\n]" DEBUG 18:09:46,716 Wire - >> "Authorization: AWS AKIAJXU7VIHBPDW4TDSQ:bZPyWYvGer/EfmziZuLGDM0/G4w=[\r][\n]" DEBUG 18:09:46,716 Wire - >> "User-Agent: JetS3t/0.8.1 (Linux/2.6.43.8-1.fc15.x86_64; amd64; en; JVM 1.6.0_22)[\r][\n]" DEBUG 18:09:46,716 Wire - >> "Host: s3.amazonaws.com[\r][\n]" DEBUG 18:09:46,717 Wire - >> "Expect: 100-continue[\r][\n]" DEBUG 18:09:46,717 Wire - >> "[\r][\n]" DEBUG 18:09:46,988 Wire - << "HTTP/1.1 100 Continue[\r][\n]" DEBUG 18:09:46,988 Wire - << "HTTP/1.1 100 Continue[\r][\n]" DEBUG 18:09:46,989 Wire - << "[\r][\n]" DEBUG 18:09:46,989 HttpMethodBase - OK to continue received DEBUG 18:09:46,990 Wire - >> "[0x1f][0x8b][0x8][0x0][0x0][0x0][0x0][0x0][0x0][0x0][0xbd]W[0xdf]o[0xdb]8[0xc]~[0xdf][0x11][0xc]{[0xc8]=H[0x8e][0x13];M[0xe]>[0x3]i[0xd1][0xed][0x82][0xad][0xed][0xda][0x6][0xb7][0xc7][0x81][0xb1]YG[0x8d]-[0xa7][0x92][0xdc]%[0xf7][0xd7][0x1f]-[0xc7][0xf9][0x1d]H[0xda]{[0xb2]E~[0xe4]GR[0xb4]D[0x7][0x6][0xa3][0xaf]L[0x15][0x92])[0x9c][0xe5][0xca][0x84][0x1f][0x1a][0x8d]F [0xe2][0xf0][0x1e]G[0xf7][0xfe]0[0x1d][0xfd]S<.[0x86]w?[0x1e][0xae][0xae][0xee]>[0xf][0xa7]/[0xf3][0xe7][0xf4][0xc5][0xfb][0xe1][0xfd]7p[0x8]d[0xc1]8[0x8f]pfD.[0xed][0xb2][0x94]d[0xa8]5$[0x18][0xb2]v;p[0xea]E[0xad][0xd4][0x6][0xa2][0xa9]Q[0x10]a#JA[0xeb][0xbf]>>[0xc3]+[0xf0][0xc2][0x88][0x94][0xf][0x94][0x82][0xc5]7[0xa1][0xcd][0xc7][0x1a]^Y(![0x93]0W[0x9][0x1f][0xab][0x1c]b![0xb5][0x11][0xa6]0[0xc8][0xe9])[0x13]k[0xaa][0xf9][0x18]^[0xf8][0xe5][0xe0][0x9e]G[0x90]F[0xd7]3-[0xd2]\6[0xcb]u[0xe9][0xfd]O[0xd7][0xef][0xfd][0x11]8KG'[0xbb][0x9e]d[0xd9][0xcf]$[0xcd][0x89]a[0xed][0xb9][0xed]u[0xdf][0xc0]s[0x19]4=?[0xab]<[0xfb][0xfb][0xe6]f[0xed][0xdd][0xf7][0xda][0xef][0xe9][0xbd][0xef][0xbf][0xa7][0xf7]N[0xeb][\r][0xbc][0xd3][0xf3][0x1]!^[0xbb][0xed]v;'[0xb9]M[0xc0]L[0xf9]/H[0xa7][0xa8][0xc8][0xfb][0x8b]V[0xfc][0x12]4> [0x85]/[0xc6][\n]" DEBUG 18:09:46,990 Wire - >> "L[0xae]l&E[\n]" DEBUG 18:09:46,990 Wire - >> "[0x6][0x89][0xcc][0xb6]bs[0xf]bC[0xf0][0xda][0xa7]u[0xd3]o[0x84][0x90][0xc1][0xec][0x8]i[0xdb]{[0xb7][0xbc][0x8f][0x93][0xba][0xee]i[0xfd]gI[0xe9]#%R[0xa0][0xdd][0x1c]U[0xaf]Xn[0xa5][0xbe][0x5][0x99][0xda][0x92][0xdc][0xc0][0x8c][0xc3]l[0x96].[0x9a]{[0xc0]e[0xf2][0xad]3[0x92][0xc3]8[0xdc][0xbe]{FOK[0xf2][0xf3][0x18]M0.RT[0xfc]vk[0x85]s[0x8c][0x8][0xff]H[0xe8][0x14]G[0x13]E[0xbc][0x18]7[0xb7]1[0xcb]>80xe7[0xd7][0xf5][0xcc][0xb5][0x92][0x9][0xcd][\n]" DEBUG 18:09:46,990 Wire - >> "[0x8d][0x8a][0xad][0xa7][0xb7]'[0xfa]N[0x90][0xc6][0xba]=Em[0xb2][0x92]0;[0xb8][0x85]vnK[0x81]b[0xb4][0x97][0xe5]P[0xc6]8[0xbf]+[0xcc][0xdd][0xd3]e^[0xc8]X_[0xd7][0xf0][0xc0][0xd9][0xb5][0xb4]s[0xa3][0xb3][0xcd][0x10][0xd8][0xf2]1#2[0xc][0xdb]-[0xb7][0xe3][0xb4][0xda][0x8e][0xeb]6[0xdc][0x1e]o[0xf5][0xb9][0xd7][0xb1]I[0xd4][0xfa]j[0xee][0x94][0xf1]1[0xb4]O[0xce]k[0xad][0xc5][0x96][0x3]n[0x85][\r][0x9c][0xd5][0xbb][0xd5]T7#[0x93]@[0x82][0xdd];0p6[0xb5]U[0x90][0xaf][0x92][0x95][0xa7]E[0x19]u[0x9b]wX[0x9f]%[0xe8][0xe3][0xf8][0xa9][0xe3]Q[0x80][0x1b]:[0xb]6[0xb9][0x81][0x94]e[0x98][0xe5]j[0x11][0xd2][0xd5][0xe1][0xb9][0xad]~[0xdf][0xa7][0x10][0xb6][0x14][0x16][0x9a][0xc1][0xbc]^wz[0xee][0xc5]E[0xbf][0xdf][0xed][0xb5]hx^[0x8b]-[0xcc][0xee][0x8c][0x8d]F?[0xa7]0V[0x82]6l-[0xb3][0x90]I[0xae]M[0xb5]D[0x98]i[0xd6]k1[0xd7]GN[[0xaf][0x13]%bN}[0x16]8k[0x8c]5)72|,d[0xc3][0x1e]Ez[0xa1][\r]f[0xba]1[0x94][0x11]g.[0xef][0xf2][0xd6][0xcf]r[0x8e][0xb7][0xa0]e[0xac][0xd1][0x84]z.[0xa4][0xc6]+[0xe6][0xc][0xb2][0xb8][0xeb][0x95][0x91]V[0xc2][0xea][0xff][0xc1] [0x15][0x90][0xea][0xa0]CJbcU[0x95][0x5][0x92][0xf0]v@U[0x80][0xaa]E[0x3]Yd[0xcc][0xd8]+O[0x87]n[0xe0]l.[0xad]~[0x86]*BY[0xed]}[0xf9][0xaf]"[0xcb][0xe6].=[0x1c]T[0xec][0x9b][0xfc][0x2]a[0xe][0x9a][0xd4][0x8a]}[0x93]1[0x8d][0xf9][0xd3][0x83]6+[0xcd]Q[0x1e][0xf6][0x94]+&[0xf2][0xa3]t[0xb5][0xfe]C[0xe0][0xec][0xfe]}[0xfd][0x7][0xc8][0xd9];[0xa0][0x8f][\r][0x0][0x0]" DEBUG 18:09:46,991 EntityEnclosingMethod - Request body sent DEBUG 18:09:47,044 Wire - << "HTTP/1.1 200 OK[\r][\n]" DEBUG 18:09:47,044 Wire - << "HTTP/1.1 200 OK[\r][\n]" DEBUG 18:09:47,044 Wire - << "x-amz-id-2: vIaqebtBmdhyThJKI7yGaPeUpXNZ4vpVBfRUZbMH43B4Ms+7TRBeVlkPS6Ufu+jv[\r][\n]" DEBUG 18:09:47,044 Wire - << "x-amz-request-id: 91B2A0C90D387C61[\r][\n]" DEBUG 18:09:47,045 Wire - << "Date: Mon, 11 Feb 2013 23:09:45 GMT[\r][\n]" DEBUG 18:09:47,045 Wire - << "ETag: "30488ea56edbbb4340b6e89a341e2b2c"[\r][\n]" DEBUG 18:09:47,045 Wire - << "Content-Length: 0[\r][\n]" DEBUG 18:09:47,045 Wire - << "Server: AmazonS3[\r][\n]" DEBUG 18:09:47,045 Wire - << "[\r][\n]" DEBUG 18:09:47,046 RestStorageService - Response for '/GATK_Run_Reports/QeTQ5IlTVuSyIOWRCCOFIkqxjlq4W5Kz.report.xml.gz'. Content-Type: , Headers: [x-amz-id-2: vIaqebtBmdhyThJKI7yGaPeUpXNZ4vpVBfRUZbMH43B4Ms+7TRBeVlkPS6Ufu+jv , x-amz-request-id: 91B2A0C90D387C61 , Date: Mon, 11 Feb 2013 23:09:45 GMT , ETag: "30488ea56edbbb4340b6e89a341e2b2c" , Content-Length: 0 , Server: AmazonS3 ] DEBUG 18:09:47,046 RestStorageService - Releasing response without content DEBUG 18:09:47,047 HttpMethodBase - Buffering response body DEBUG 18:09:47,047 HttpMethodBase - Resorting to protocol version default close connection policy DEBUG 18:09:47,047 HttpMethodBase - Should NOT close connection, using HTTP/1.1 DEBUG 18:09:47,048 HttpConnection - Releasing connection back to connection manager. DEBUG 18:09:47,048 MultiThreadedHttpConnectionManager$ConnectionPool - Freeing connection, hostConfig=HostConfiguration[host=https://s3.amazonaws.com] DEBUG 18:09:47,048 IdleConnectionHandler - Adding connection at: 1360624187048 DEBUG 18:09:47,048 MultiThreadedHttpConnectionManager$ConnectionPool - Notifying no-one, there are no waiting threads DEBUG 18:09:47,049 ServiceUtils - Cleaning up REST metadata items DEBUG 18:09:47,049 ServiceUtils - Removed Amazon header prefix x-amz- from key: x-amz-request-id=>request-id DEBUG 18:09:47,049 ServiceUtils - Leaving header item unchanged: ETag="30488ea56edbbb4340b6e89a341e2b2c" DEBUG 18:09:47,049 ServiceUtils - Leaving header item unchanged: Date=Mon, 11 Feb 2013 23:09:45 GMT DEBUG 18:09:47,049 ServiceUtils - Parsing date string 'Mon, 11 Feb 2013 23:09:45 GMT' into Date object for key: Date DEBUG 18:09:47,050 ServiceUtils - Leaving HTTP header item unchanged: Content-Length=911 DEBUG 18:09:47,050 ServiceUtils - Removed Amazon header prefix x-amz- from key: x-amz-id-2=>id-2 DEBUG 18:09:47,050 ServiceUtils - Leaving HTTP header item unchanged: Content-MD5=MEiOpW7bu0NAtuiaNB4rLA== DEBUG 18:09:47,050 ServiceUtils - Ignoring metadata item: md5-hash=30488ea56edbbb4340b6e89a341e2b2c DEBUG 18:09:47,050 ServiceUtils - Leaving HTTP header item unchanged: Content-Type=application/octet-stream DEBUG 18:09:47,050 ServiceUtils - Ignoring metadata item: Server=AmazonS3 INFO 18:09:47,051 GATKRunReport - Uploaded run statistics report to AWS S3 DEBUG 18:09:47,051 GATKRunReport - Uploaded to AWS: S3Object [key=QeTQ5IlTVuSyIOWRCCOFIkqxjlq4W5Kz.report.xml.gz, bucket=, lastModified=Mon Feb 11 18:09:45 EST 2013, dataInputStream=null, Metadata={ETag="30488ea56edbbb4340b6e89a341e2b2c", Date=Mon Feb 11 18:09:45 EST 2013, Content-Length=911, id-2=vIaqebtBmdhyThJKI7yGaPeUpXNZ4vpVBfRUZbMH43B4Ms+7TRBeVlkPS6Ufu+jv, request-id=91B2A0C90D387C61, Content-MD5=MEiOpW7bu0NAtuiaNB4rLA==, Content-Type=application/octet-stream}]

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

    java.lang.ArrayIndexOutOfBoundsException: -22 at org.broadinstitute.sting.utils.baq.BAQ.calcEpsilon(BAQ.java:158) at org.broadinstitute.sting.utils.baq.BAQ.hmm_glocal(BAQ.java:246) at org.broadinstitute.sting.utils.baq.BAQ.calcBAQFromHMM(BAQ.java:542) at org.broadinstitute.sting.utils.baq.BAQ.calcBAQFromHMM(BAQ.java:595) at org.broadinstitute.sting.utils.baq.BAQ.calcBAQFromHMM(BAQ.java:530) at org.broadinstitute.sting.utils.baq.BAQ.baqRead(BAQ.java:663) at org.broadinstitute.sting.gatk.walkers.bqsr.BaseRecalibrator.calculateBAQArray(BaseRecalibrator.java:428) at org.broadinstitute.sting.gatk.walkers.bqsr.BaseRecalibrator.map(BaseRecalibrator.java:243) 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:248) at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler.execute(NanoScheduler.java:219) 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:237) at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:147) at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:91)

    ERROR ------------------------------------------------------------------------------------------
    ERROR A GATK RUNTIME ERROR has occurred (version 2.3-9-ge5ebf34):
    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: -22
    ERROR ------------------------------------------------------------------------------------------

    `

  • SJLSJL Posts: 4Member

    Thank you, I will keep an eye open for the latest release. Simon

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