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An Error Has Occurred During The Traversal

This error could be due to excessive network traffic, low system resources, or one of the Servers in the domain shutting down unexpectedly. Examples include waiting for a string to appear on the screen, the cursor to enter a specific location, or the host to update a particular region of the screen. Koob,Clifford G. This can result from a request with invalid position parameters or from an internal error. http://svbuckeye.com/an-error/an-error-has-occurred-an-exception-has-occurred-sony-vegas.php

Generated Fri, 30 Sep 2016 10:29:36 GMT by s_bd40 (squid/3.5.20) I have attached 200bp region from my BAM, reference and vcf file, so you can reproduce this issue. I'm following the pipeline propose... Best, SK

0 0 12/12/12--07:40: Changes in the logfile and a long wait between reading the BAMs and starting to Genotype Contact us about this article I've noticed a change http://gatkforums.broadinstitute.org/gatk/discussion/1809/runtime-error-version-1-5-16-g58245bf-message-an-error-occurred-during-the-traversal

If the problem persists, contact Attachmate Technical Support. [2866] Socket Error - No more socket descriptors available.The system cannot create any more connections. poisson20007-08-2011, 10:45 PMHi, Sorry, it was a while ago but I think I solved this by checking out latest version of GATK from cvs (rather than download the one from their Example: http:///Xtraction Not what you were looking for?

INFO 20:34:49,281 HelpFormatter - --------------------------------------------------------------------------- INFO 20:34:49,283 HelpFormatter - The Genome Analysis Toolkit (GATK) v1.0.5974, Compiled 2011/06/10 13:26:59 INFO 20:34:49,283 HelpFormatter - Copyright (c) 2010 The Broad Institute INFO 20:34:49,283 HelpFormatter This error means that the defined period of time elapsed without finding any of the desired entities. [2632] The file specified is not a valid Host Integrator settings file.The file has Another administrator is in configure mode. Start the Server and try again. [3123] Could not get authorization package.Deprecated in version 7.0.

Considering the sequencing coverage for each individual is low or median, will there be any difference between genotyping them on individual level and on a cohort of population level? 2) I Check the variable's spelling and case. [2920] Entity [name] is not a valid startup entity for model [name] in session pool [name].Check the entity's spelling and case. [2922] Model variable [name] Preview this book » What people are saying-Write a reviewWe haven't found any reviews in the usual places.Selected pagesTitle PageIndexReferencesContentsSelfChecking and SelfExercising Design for Hierarchic LongLife FaultTolerant Systems3 DESIGN OF SELFCHECKING https://www.biostars.org/p/42602/ Error When Running Gatk I am Calling snps and indels using the pipeline referred in this post: http://www.biostars.org/po...

If this continues to occur, please contact the application administrator." When Logging into Xtraction Document ID:TEC1126449 Last Modified Date:3/14/2016 ShowHide Technical Document Details Products CA Service Desk Manager Releases CA Service Contact Attachmate Technical Support. [2518] Application window creation failed.An internal error occurred during product initialization. Error with MuTect: SAM/BAM file SAMFileReader is malformed I tried to run MuTect with following command line; /usr/lib/jvm/java-1.6.0/bin/java -Xmx2g -jar ... Contact your system administrator. [2894] User [name] at [location] was refused a connection to model [name], session pool [name].

If the timeout elapses, the host session will terminate or return to the pool. [3153] Local session failed sending release to MS.An internal communication error occurred. When I looked at a sample to compare variant sites using VariantEval, it showed that Filter JexlExpression Novelty nTi nTv tiTvRatio called Intersection known 14624 4563 3.2 called Intersection novel 856 Even though I set "genotypeFullActiveRegion" or "fullHaplotype", haplotypeCaller doesn't seem to emit genotype at all sites. Koob, Clifford G.

it looks like it should be a probability in the range (0, 1) for the haplotype score to make sense. navigate here If the problem persists, contact Attachmate Technical Support. [3158] The server failed to launch a secondary process. Contact Attachmate Technical Support. [2692] Unable to initialize the ATKeybds keyboard DLL.An essential DLL could not be loaded. Contact us about this article Hello the team, For some genotypes, it seems are wrong, I know it's model based, and base q, map q, etc are considered in the model.

On the Connection menu, click Session Setup to correct the terminal type and model ID. [2682] The keyboard key name entered [(name)] is not a PC key or scan code key.An If the problem persists, contact Attachmate Technical Support. [3162] A required password was not supplied from the client.Server security is enabled, but the client did not provide a password for authorization. The token provided by the webstation or management server was not valid. Check This Out I looked in previous logs and saw that there aren't such line in the log, but the clock jumps a similar amount of time.

Contact us about this article Hello, I have been successfully using the GATK pipeline and Unified Genotyper to call snps. Why muTect Error? Check your network settings.

This error could be due to excessive network traffic or low system resources.

But when I use UnifiedGenotyper with --genotype_likelihoods_model INDEL --output_mode EMIT_ALL_CONFIDENT_SITES I only get non-reference calls, everything else (i.e. A . 11642 . Check your client and server versions. 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

LauNo preview available - 1994Common terms and phrasesadder algorithm algorithm-based application architecture array backup channels Berger check Berger code buffer flush checkpoint checksum code checker compiler computational block concurrent error detection This error means that Host Integrator tried to move the cursor into the location specified, but the global move cursor timeout expired during a tab routine. On these hosts, you must override the cursor movement by specifying a different command, such as a tab key. this contact form Can it be ignored ?

For more information please contact Attachmate Technical Support. [2838] Socket callback not valid or not registered.Contact Attachmate Technical Support. [2840] Could not allocate new resources.Your system is running low on memory. Search Again> Product Information Support by Product> Product Documentation> Communities Join a Community> Education Find training by product> Please help us improve! How To Provide Reference Sequence Dictionary To Reordersam? If the problem persists, contact Attachmate Technical Support. [2854] Socket Error - Socket has shutdown.Contact Attachmate Technical Support. [2856] Socket Error - Socket would block.Cannot transmit data to the remote object.

We now strip the AD field out whenever the alleles change in the combined file." I was wondering whether you could confirm if cases like the one above would benefit from Will this information enable you to resolve your issue? Do you know what is wrong ?

0 0 11/09/12--12:25: UnifiedGenotyper --genotype_likelihoods_model INDEL --output_mode EMIT_ALL_CONFIDENT_SITES Contact us about this article Hi, When I use UnifiedGenotyper with --genotype_likelihoods_model SNP --output_mode EMIT_ALL_CONFIDENT_SITES Claim or contact us about this channel Embed this content in your HTML Search confirm cancel Report adult content: click to rate: Account: (login) More Channels Showcase RSS Channel Showcase 8285869

Check your hosts file for accuracy.Check your hosts file or DNS configuration for accuracy. I would run samtools view your.bam > /dev/null and/or gunzip -t your.bam to see if there's something wrong.