Test-drive the GATK tools and Best Practices pipelines on Terra


Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.

java.lang.IllegalStateException: This method hasn't been implemented yet for (platform)

vaibhavvskvaibhavvsk Member
edited January 2013 in Ask the GATK team

I'm trying to run CountCovariates and getting the error as :

" java.lang.IllegalStateException: This method hasn't been implemented yet for GAIIx "

I have used following program arguments as given below :

Program Args: -T CountCovariates -R /home/adlab/ngs_data/databases/human_g1k_v37.fasta -I D5_b37_aligned_sorted_realn_DupRm.bam -knownSites:dbsnp,VCF /home/adlab/ngs_data/databases/dbsnp_132.b37.vcf -recalFile D5_b37_aligned_sorted_realn_DupRm_countcovariates.csv -cov ReadGroupCovariate -cov QualityScoreCovariate -cov CycleCovariate -cov DinucCovariate -standard

To trouble shoot it I found that I have added the read groups in bwa sampe by setting platform info as "GAIIx" as given below and it's root for the error.

"@RG\tID:Clone-D5\tPL:GAIIx\tLB:LIB-RDT\tSM:UNKNOWN\I:200"

What's the exact error in my argument list / read group syntax and What could be the cause of the error ? kindly help.

Post edited by Geraldine_VdAuwera on

Answers

Sign In or Register to comment.