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cryptic invocationTargetException error

ncamardancamarda DFCIMember, Broadie
edited November 2016 in MuTect v1


I am posting the full debug output here so that this hopefully can be solved quickly. I cannot figure out where the issue is here. I am running mutect-1.1.7, using this java version

version "1.7.0_25"
Java(TM) SE Runtime Environment (build 1.7.0_25-b15)
Java HotSpot(TM) 64-Bit Server VM (build 23.25-b01, mixed mode)

All of the input files appear to be read correctly, but it looks like it can't find a Sun plugin for the java version I'm using? I highly doubt that's the reason why this is all failing. Does MuTect1 require a certain version of R? S3 looks like an R object I've seen in the past...

Please advise. Thank you so much.

INFO 14:37:29,064 HelpFormatter - --------------------------------------------------------------------------------
INFO 14:37:29,066 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.1-0-g72492bb, Compiled 2015/01/21 17:10:56
INFO 14:37:29,066 HelpFormatter - Copyright (c) 2010 The Broad Institute
INFO 14:37:29,066 HelpFormatter - For support and documentation go to
DEBUG 14:37:29,067 HelpFormatter - Current directory: /PHShome/nc678
INFO 14:37:29,071 HelpFormatter - Program Args: -T MuTect -l DEBUG --intervals /PHShome/nc678/whole_exome_illumina_coding_v1_plus_10bp_padding_minus_mito.Homo_sapiens_assembly19.targets.interval_list -I:tumor wolpin/PancAdenoCA_B3_STS0004c/1808_T-CEPH_1341FM12/1808_T.dedup.cleaned.bam -I:normal wolpin/PancAdenoCA_B3_STS0004c/1808_N-CEPH_1341FM12/1808_N.dedup.cleaned.bam --reference_sequence /PHShome/nc678/Homo_sapiens_assembly19.fasta --dbsnp /PHShome/nc678/dbsnp_134_b37.leftAligned.vcf --cosmic /PHShome/nc678/hg19_cosmic_v54_120711.vcf --normal_panel /PHShome/nc678/refseq_exome_10bp_hg19_300_1kg_normal_panel.vcf --out /PHShome/nc678/mutect/out/1808/1808.call_stats.tsv --coverage_file /PHShome/nc678/mutect/out/1808/1808.coverage.wig.txt --power_file /PHShome/nc678/mutect/out/1808/1808.power.wig.txt --downsample_to_coverage 100000 --enable_extended_output --fraction_contamination 0.001
INFO 14:37:29,086 HelpFormatter - Executing as [email protected] on Linux 2.6.32-431.29.2.el6.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_25-b15.
INFO 14:37:29,087 HelpFormatter - Date/Time: 2016/11/09 14:37:29
INFO 14:37:29,087 HelpFormatter - --------------------------------------------------------------------------------
INFO 14:37:29,087 HelpFormatter - --------------------------------------------------------------------------------
DEBUG 14:37:29,117 ArgumentTypeDescriptor - Dynamically determined type of /PHShome/nc678/dbsnp_134_b37.leftAligned.vcf to be VCF
DEBUG 14:37:29,123 ArgumentTypeDescriptor - Dynamically determined type of /PHShome/nc678/hg19_cosmic_v54_120711.vcf to be VCF
DEBUG 14:37:29,128 ArgumentTypeDescriptor - Dynamically determined type of /PHShome/nc678/refseq_exome_10bp_hg19_300_1kg_normal_panel.vcf to be VCF
INFO 14:37:29,845 GenomeAnalysisEngine - Strictness is SILENT
DEBUG 14:37:29,903 GenomeLocParser - Prepared reference sequence contig dictionary
INFO 14:37:29,962 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 100000
INFO 14:37:29,970 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
DEBUG 14:37:29,991 SAMDataSource$SAMReaders - Processing file (1 of 2) wolpin/PancAdenoCA_B3_STS0004c/1808_T-CEPH_1341FM12/1808_T.dedup.cleaned.bam...
DEBUG 14:37:29,997 SAMDataSource$SAMReaders - Processing file (2 of 2) wolpin/PancAdenoCA_B3_STS0004c/1808_N-CEPH_1341FM12/1808_N.dedup.cleaned.bam...
INFO 14:37:29,998 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.03
DEBUG 14:37:30,025 RMDTrackBuilder - Loading Tribble index from disk for file /PHShome/nc678/dbsnp_134_b37.leftAligned.vcf
DEBUG 14:37:30,132 RMDTrackBuilder - Loading Tribble index from disk for file /PHShome/nc678/hg19_cosmic_v54_120711.vcf
DEBUG 14:37:30,184 RMDTrackBuilder - Loading Tribble index from disk for file /PHShome/nc678/refseq_exome_10bp_hg19_300_1kg_normal_panel.vcf
DEBUG 14:37:30,221 GATKRunReport - Aggregating data for run report
DEBUG 14:37:30,284 GATKRunReport - Posting report of type AWS
DEBUG 14:37:30,285 GATKRunReport - Generating GATK report to AWS S3 with key
DEBUG 14:37:30,416 DefaultHttpParams - Set parameter http.useragent = Jakarta Commons-HttpClient/3.1
DEBUG 14:37:30,417 DefaultHttpParams - Set parameter http.protocol.version = HTTP/1.1
DEBUG 14:37:30,418 DefaultHttpParams - Set parameter http.connection-manager.class = class org.apache.commons.httpclient.SimpleHttpConnectionManager
DEBUG 14:37:30,418 DefaultHttpParams - Set parameter http.protocol.cookie-policy = default
DEBUG 14:37:30,418 DefaultHttpParams - Set parameter http.protocol.element-charset = US-ASCII
DEBUG 14:37:30,419 DefaultHttpParams - Set parameter http.protocol.content-charset = ISO-8859-1
DEBUG 14:37:30,420 DefaultHttpParams - Set parameter http.method.retry-handler = [email protected]2d8
DEBUG 14:37:30,420 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 14:37:30,420 Jets3tProperties - s3service.https-only=true
DEBUG 14:37:30,421 Jets3tProperties - storage-service.internal-error-retry-max=5
DEBUG 14:37:30,424 Jets3tProperties - httpclient.connection-timeout-ms=60000
DEBUG 14:37:30,424 DefaultHttpParams - Set parameter http.connection.timeout = 60000
DEBUG 14:37:30,424 Jets3tProperties - httpclient.socket-timeout-ms=60000
DEBUG 14:37:30,425 DefaultHttpParams - Set parameter http.socket.timeout = 60000
DEBUG 14:37:30,425 Jets3tProperties - httpclient.stale-checking-enabled=true
DEBUG 14:37:30,425 DefaultHttpParams - Set parameter http.connection.stalecheck = true
DEBUG 14:37:30,425 Jets3tProperties - httpclient.max-connections=20
DEBUG 14:37:30,426 Jets3tProperties - httpclient.max-connections-per-host=0
DEBUG 14:37:30,426 DefaultHttpParams - Set parameter http.connection-manager.max-per-host = {HostConfiguration[]=20}
DEBUG 14:37:30,426 DefaultHttpParams - Set parameter http.connection-manager.max-total = 20
DEBUG 14:37:30,427 DefaultHttpParams - Set parameter http.tcp.nodelay = true
DEBUG 14:37:30,432 Jets3tProperties - httpclient.useragent=null
DEBUG 14:37:30,435 RestUtils - Setting user agent string: JetS3t/0.8.1 (Linux/2.6.32-431.29.2.el6.x86_64; amd64; en; JVM 1.7.0_25)
DEBUG 14:37:30,435 DefaultHttpParams - Set parameter http.useragent = JetS3t/0.8.1 (Linux/2.6.32-431.29.2.el6.x86_64; amd64; en; JVM 1.7.0_25)
DEBUG 14:37:30,436 DefaultHttpParams - Set parameter http.protocol.version = HTTP/1.1
DEBUG 14:37:30,436 DefaultHttpParams - Set parameter http.protocol.expect-continue = true
DEBUG 14:37:30,436 Jets3tProperties - httpclient.retry-max=5
DEBUG 14:37:30,437 DefaultHttpParams - Set parameter http.method.retry-handler = [email protected]
DEBUG 14:37:30,437 Jets3tProperties - httpclient.connection-manager-timeout=0
DEBUG 14:37:30,437 DefaultHttpParams - Set parameter http.connection-manager.timeout = 0
DEBUG 14:37:30,439 HttpClient - Java version: 1.7.0_25
DEBUG 14:37:30,439 HttpClient - Java vendor: Oracle Corporation
DEBUG 14:37:30,439 HttpClient - Java class path: /PHShome/nc678/mutect-1.1.7.jar
DEBUG 14:37:30,439 HttpClient - Operating system name: Linux
DEBUG 14:37:30,440 HttpClient - Operating system architecture: amd64
DEBUG 14:37:30,440 HttpClient - Operating system version: 2.6.32-431.29.2.el6.x86_64
DEBUG 14:37:30,442 HttpClient - SUN 1.7: 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 14:37:30,442 HttpClient - SunRsaSign 1.7: Sun RSA signature provider
DEBUG 14:37:30,442 HttpClient - SunEC 1.7: Sun Elliptic Curve provider (EC, ECDSA, ECDH)
DEBUG 14:37:30,443 HttpClient - SunJSSE 1.7: Sun JSSE provider(PKCS12, SunX509 key/trust factories, SSLv3, TLSv1)
DEBUG 14:37:30,443 HttpClient - SunJCE 1.7: SunJCE Provider (implements RSA, DES, Triple DES, AES, Blowfish, ARCFOUR, RC2, PBE, Diffie-Hellman, HMAC)
DEBUG 14:37:30,443 HttpClient - SunJGSS 1.7: Sun (Kerberos v5, SPNEGO)
DEBUG 14:37:30,444 HttpClient - SunSASL 1.7: Sun SASL provider(implements client mechanisms for: DIGEST-MD5, GSSAPI, EXTERNAL, PLAIN, CRAM-MD5, NTLM; server mechanisms for: DIGEST-MD5, GSSAPI, CRAM-MD5, NTLM)
DEBUG 14:37:30,444 HttpClient - XMLDSig 1.0: XMLDSig (DOM XMLSignatureFactory; DOM KeyInfoFactory)
DEBUG 14:37:30,444 HttpClient - SunPCSC 1.7: Sun PC/SC provider
DEBUG 14:37:30,446 Jets3tProperties - s3service.s3-endpoint=null
DEBUG 14:37:30,446 Jets3tProperties - s3service.default-storage-class=null
DEBUG 14:37:30,447 Jets3tProperties - httpclient.proxy-autodetect=true
DEBUG 14:37:30,447 Jets3tProperties -
DEBUG 14:37:30,451 PluginProxyUtil - About to attempt auto proxy detection under Java version:1.7.0_25-b15
DEBUG 14:37:30,451 PluginProxyUtil - Sun Plugin reported java version not 1.3.X, 1.4.X, 1.5.X or 1.6.X - trying failover detection...
DEBUG 14:37:30,451 PluginProxyUtil - Using failover proxy detection...
DEBUG 14:37:30,452 PluginProxyUtil - Plugin Proxy Config List Property:null
DEBUG 14:37:30,452 PluginProxyUtil - No configured plugin proxy list
DEBUG 14:37:30,452 Jets3tProperties - devpay.user-token=null
DEBUG 14:37:30,452 Jets3tProperties - devpay.product-token=null
DEBUG 14:37:30,453 Jets3tProperties - httpclient.requester-pays-buckets-enabled=false
DEBUG 14:37:30,457 RestStorageService - Creating Object with key in bucket
DEBUG 14:37:30,458 RestStorageService - Uploading object data with Content-Length: 1332
DEBUG 14:37:30,459 Jets3tProperties -
DEBUG 14:37:30,459 Jets3tProperties - s3service.s3-endpoint=null
DEBUG 14:37:30,459 Jets3tProperties - s3service.enable-storage-classes=true
DEBUG 14:37:30,460 RestStorageService - Creating object,, storageClass=null. Content-Type=application/octet-stream Including data? true Metadata: {Content-Length=1332, Content-MD5=QSINTLFYYYRKZ4UquC4Qpg==, md5-hash=41220d4cb15861844a67852ab82e10a6, Content-Type=application/octet-stream} ACL: null
DEBUG 14:37:30,461 Jets3tProperties - s3service.disable-dns-buckets=false
DEBUG 14:37:30,461 Jets3tProperties -
DEBUG 14:37:30,462 Jets3tProperties - s3service.s3-endpoint-virtual-path=
DEBUG 14:37:30,462 Jets3tProperties - s3service.s3-endpoint-https-port=443
DEBUG 14:37:30,463 RestStorageService - S3 URL:
DEBUG 14:37:30,481 RestStorageService - Performing PUT request for '', expecting response codes: [200,204]
DEBUG 14:37:30,482 RestStorageService - Adding authorization for Access Key 'AKIAI22FBBJ37D5X62OQ'.
DEBUG 14:37:30,482 Jets3tProperties -
DEBUG 14:37:30,482 RestStorageService - Canonical string ('|' is a newline): PUT|QSINTLFYYYRKZ4UquC4Qpg==|application/octet-stream|Wed, 09 Nov 2016 19:37:30 GMT|x-amz-meta-md5-hash:41220d4cb15861844a67852ab82e10a6|/
DEBUG 14:37:30,489 MultiThreadedHttpConnectionManager - HttpConnectionManager.getConnection: config = HostConfiguration[host=], timeout = 0
DEBUG 14:37:30,490 MultiThreadedHttpConnectionManager$ConnectionPool - Allocating new connection, hostConfig=HostConfiguration[host=]
DEBUG 14:37:30,493 HttpConnection - Open connection to
DEBUG 14:37:30,630 Wire - >> "PUT / HTTP/1.1[\r][\n]"
DEBUG 14:37:30,631 HttpMethodBase - Adding Host request header
DEBUG 14:37:30,639 HttpConnection - Releasing connection back to connection manager.
DEBUG 14:37:30,639 MultiThreadedHttpConnectionManager$ConnectionPool - Freeing connection, hostConfig=HostConfiguration[host=]
DEBUG 14:37:30,639 IdleConnectionHandler - Adding connection at: 1478720250639
DEBUG 14:37:30,639 MultiThreadedHttpConnectionManager$ConnectionPool - Notifying no-one, there are no waiting threads
DEBUG 14:37:30,640 RestStorageService - Releasing HttpClient connection after error: org.apache.commons.httpclient.cookie.IgnoreCookiesSpec
DEBUG 14:37:30,641 GATKRunReport - A problem occurred during GATK run reporting [*** everything is fine, but no report could be generated; please do not post this to the support forum ***]. Message is: S3 exception occurred. Error message is: Request Error: java.lang.NoClassDefFoundError: org.apache.commons.httpclient.cookie.IgnoreCookiesSpec

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

java.lang.RuntimeException: java.lang.reflect.InvocationTargetException
at org.broad.tribble.index.IndexFactory.loadIndex(
at org.broadinstitute.sting.gatk.refdata.tracks.RMDTrackBuilder.loadFromDisk(
at org.broadinstitute.sting.gatk.refdata.tracks.RMDTrackBuilder.attemptToLockAndLoadIndexFromDisk(
at org.broadinstitute.sting.gatk.refdata.tracks.RMDTrackBuilder.loadIndex(
at org.broadinstitute.sting.gatk.refdata.tracks.RMDTrackBuilder.getFeatureSource(
at org.broadinstitute.sting.gatk.refdata.tracks.RMDTrackBuilder.createInstanceOfTrack(
at org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedQueryDataPool.(
at org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource.(
at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.getReferenceOrderedDataSources(
at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.initializeDataSources(
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.commandline.CommandLineProgram.start(
at org.broadinstitute.sting.gatk.CommandLineGATK.main(
Caused by: java.lang.reflect.InvocationTargetException
at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
at sun.reflect.NativeConstructorAccessorImpl.newInstance(
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(
at java.lang.reflect.Constructor.newInstance(
at org.broad.tribble.index.IndexFactory.loadIndex(
... 14 more
Caused by:
at org.broad.tribble.util.LittleEndianInputStream.readFully(
at org.broad.tribble.util.LittleEndianInputStream.readLong(
at org.broad.tribble.index.linear.LinearIndex$
at org.broad.tribble.index.linear.LinearIndex.(
... 19 more

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 3.1-0-g72492bb):
ERROR This might be a bug. Please check the documentation guide to see if this is a known problem.
ERROR If not, please post the error message, with stack trace, to the GATK forum.
ERROR Visit our website and forum for extensive documentation and answers to
ERROR commonly asked questions
ERROR MESSAGE: java.lang.reflect.InvocationTargetException
ERROR ------------------------------------------------------------------------------------------

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