An Error Has Occurred During The Traversal
Ask the GATK team GATK Documentation Guide Tutorials FAQs Presentations Common Problems Methods and Algorithms Dictionary Pipelining with Queue Developer Zone Archive Tools related to GATK MuTect v1 MuTect v1 Documentation ReCapSeg ReCapSeg Documentation Oncotator Oncotator documentation GenomeSTRiP GenomeSTRiP Documentation XHMM Firepony Base Recalibrator search subcategories search archived Tags What to search discussions questions comments answers groups Date within 1 day 3 days 1 week 2 weeks 1 month 2 months 6 months 1 year of Examples: Monday, today, last week, Mar 26, 3/26/04 Search Howdy, Stranger! It looks like you're new here. If you want to get involved, click one of these buttons! Sign In Register Categories Recent Discussions Activity Best Of... Unanswered Groups Categories 6.3K All Categories184 Announcements 5.5K Ask the GATK team 205 GATK Documentation Guide 30 Tutorials 44 FAQs 12 Presentations 11 Common Problems 32 Methods and Algorithms 18 Dictionary 1 Pipelining with Queue 29 Developer Zone 28 Archive 449 Tools related to GATK 128 MuTect v1 11 ReCapSeg 36 Oncotator 245 GenomeSTRiP 26 XHMM 3 Firepony Base Recalibrator Powered by Vanilla. Made with Bootstrap. RUNTIME ERROR(version 1.5-16-g58245bf) - MESSAGE:An error occurred during the traversal. jmartin Posts: 1Member ✭ November 2012 in Ask the GATK team I'm running the UnifiedGenotyper on a large number of metagenomic samples (~110) that have been mapped by BWA against a database of 671 reference genomes. I know that the UG is meant only for diploid use, but I was hoping to use the vcf output to get at base frequencies at specific loci (as opposed to the probability of whatever diploid genotype is predicted). I'm running the UG with a 63Gb memory allocation, using 12 threads. Here is the error message I received: ERROR ------------------------------------------------------------------------------------------ ERROR stack trace org.broadinstitute.sting.utils.exceptions.ReviewedStingException: An error occurred during the traversal. at org.broadinstitute.sting.gatk.executive.HierarchicalMicroScheduler.getTraversalError(HierarchicalMicroScheduler.java:356) at org.broadinstitute.sting.gatk.executive.HierarchicalMicroScheduler.execute(HierarchicalMicroScheduler.java:105) at org.broadinstitute.sting.gatk.GenomeA
faq • rss Community Log In Sign Up Add New Post Question: Gatk Error 0 4.5 years ago by Leandro Batista • 100 Paris Leandro Batista • 100 http://gatkforums.broadinstitute.org/gatk/discussion/1809/runtime-error-version-1-5-16-g58245bf-message-an-error-occurred-during-the-traversal wrote: Hello, I've been using GATK tools for Bam processing and SNP calling in whole exome and whole genome sequencing data. It has been doing just fine on several samples. Today, unexpectedly, when https://www.biostars.org/p/42602/ running CountCovariates, some gave an error it had never given before. I've searched on the internet, but apparently it is not a common error in GATK and I couldn't find an explanation. INFO 18:29:04,407 TraversalEngine - 11:70058337 6.44e+07 62.8 m 58.5 s 14.6% 7.2 h 6.1 h INFO 18:29:34,450 TraversalEngine - 11:70419912 6.48e+07 63.3 m 58.6 s 14.6% 7.2 h 6.2 h
ERROR ------------------------------------------------------------------------------------------
ERROR stack trace
java.lang.RuntimeException: java.util.zip.DataFormatException: invalid stored block lengths at net.sf.samtools.util.BlockGunzipper.unzipBlock(BlockGunzipper.java:112) at net.sf.samtools.util.BlockCompressedInputStream.inflateBlock(BlockCompressedInputStream.java:379) at net.sf.samtools.util.BlockCompressedInputStream.readBlock(BlockCompressedInputStream.java:361) at net.sf.samtools.util.BlockCompressedInputStream.available(BlockCompressedInputStream.java:109) at net.sf.samtools.util.BlockCompressedInputStream.read(BlockCompressedInputStream.java:234) at java.io.DataInputStream.read(DataInputStream.java:132) at net.sf.samtools.util.BinaryCodec.readBytesOrFewer(BinaryCodec.java:394) at net.sf.samtools.util.BinaryCodec.readBytes(BinaryCodec.java:371) at net.sf.samtools.util.BinaryCodec.readByteBuffer(BinaryCodec.java:480) at net.sf.samtools.util.BinaryCodec.readInt(BinaryCodec.java:491) at net.sf.samtools.BAMRecordCodec.decode(BAMRecordCodec.java:176) at net.sf.samtools.BAMFileSupport. [ 146] Severe exception at [msg]Contact Attachmate Technical Support. [ 189] The max concurrent session limit has been set above the value set by the installation. Current Limit: http://docs2.attachmate.com/verastream/vhi/7.7/en/topic/com.attachmate.vhi.help/html/reference/h_rte.html [n] Installation Limit: [n][Under Construction] [2503] The server could not create the models folder.Check for file system hardware errors or file access settings problems.The application may have to be reinstalled. [2504] Out of memory.There was not enough system memory to execute the application. [2506] Application was not properly installed, please run setup to repair the installation.The installation file has either been corrupted or could not an error be found. [2508] Event handler name is invalid : [reason]Event handler names chosen by the user must conform to the rules of the respective programming language. [2512] Invalid command line syntax.The arguments supplied to the application on the command line were invalid. [2516] Application object creation failed.An internal error occurred during product initialization. Contact Attachmate Technical Support. [2518] Application window creation failed.An internal error occurred during an error has product initialization. Contact Attachmate Technical Support. [2520] Application initialization failed.An internal error occurred during product initialization. Contact Attachmate Technical Support. [2522] [filename] - Invalid command line file.A file specified on the command line is either missing or invalid. [2524] National character set library not found.An internal error occurred during product initialization. Contact Attachmate Technical Support. [2530] ROM start failed.An internal error occurred during product initialization. Contact Attachmate Technical Support. [2532] The local IP address could not be established. Check your hosts file for accuracy.Check your hosts file or DNS configuration for accuracy. The IP address may be incorrectly specified in your hosts file. [2534] Application time limit expired.The application is a time-limited version that has expired. Contact Attachmate Technical Support. [2536] Unrecognized option.An unrecognized option was specified on the application command line. [2542] Management server registration failed.An internal error occurred during product initialization. Deprecated. [2544] Application kernel initialization failed.An internal error occurred during product initialization. Contact Attachmate Technical Support. [2546] The server is already running.Only one instance of the Host Integrator Server may be run on a given machine at one time. [2548] [name] is not a valid installation file.The installation file has