Error GATK CountCovariates - v.1.2.65

[m_elena_bioinfo]

hi NGS users, I'm using the last version of GATK to recalibrate the score of my alignment.
In the first step, the CountCovariates command returns me an error.

When I run:
java -jar /GenomeAnalysisTK-1.2-65-ge4a583a/GenomeAnalysisTK.jar -I sample.bam -R hg19.fasta -T CountCovariates -cov ReadGroupCovariate -cov QualityScoreCovariate -cov CycleCovariate -cov DinucCovariate -recalFile table_sample.csv -knownSites:dbsnp,VCF dbsnp132.hg19.vcf

the program returns me this error:
##### ERROR MESSAGE: This method hasn't been implemented yet for ILL

Anyone has any idea?

[Aicen]

hi

This error i got also, a few weeks ago. It seems, that in your Readgroup file the PL: flag is not as it has to be for GATK, it has to be written this way: "illumina" no uppercase, i think. Another solution: u can force the PL flag to either illumina or other PL's .
I hope it helped

best regards Alex

[neha]

Error in running CountCovariates

Hello Everyone,

I am using GenomeAnalysisTK-1.3-21-gcb284ee version. I want to recalibrate the score for calling SNP. whenever I am using CountCovariate tool I am getting following error

Argument --DBSNP is not defined. I also tried running it using -KnownSites but still get the same error.

Any help would be really appreciated.

Thanks in advance

Neha

[m_elena_bioinfo]

Dear Neha, I run GATK to recalibrate score as: (i'm using version 1.3-25-g32cdef9) (this way it's ok)

> java -jar GenomeAnalysisTK.jar -R hg19.fasta -I sample.bam.sorted.bam --knownSites:dbsnp,VCF dbsnp_132.hg19.vcf -T CountCovariates -cov ReadGroupCovariate -cov QualityScoreCovariate -cov CycleCovariate -cov DinucCovariate -recalFile table.csv

>java -jar GenomeAnalysisTK.jar -R hg19.fasta -I sample.bam.sorted.bam -T TableRecalibration -recalFile tablecsv --baq RECALCULATE --out sample_recal_baq.bam

> samtools sort sample_recal_baq.bam sample_recal_baq.bam.sorted

[neha]

Dear Neha, I run GATK to recalibrate score as: (i'm using version 1.3-25-g32cdef9) (this way it's ok)

> java -jar GenomeAnalysisTK.jar -R hg19.fasta -I sample.bam.sorted.bam --knownSites:dbsnp,VCF dbsnp_132.hg19.vcf -T CountCovariates -cov ReadGroupCovariate -cov QualityScoreCovariate -cov CycleCovariate -cov DinucCovariate -recalFile table.csv

>java -jar GenomeAnalysisTK.jar -R hg19.fasta -I sample.bam.sorted.bam -T TableRecalibration -recalFile tablecsv --baq RECALCULATE --out sample_recal_baq.bam

> samtools sort sample_recal_baq.bam sample_recal_baq.bam.sorted

Hi,

I used the same parameters as you suggested but still getting the same error that KnownSites is not defined.

I dont know what is the issue now as I am unable to run the GATK.

Neha

[m_elena_bioinfo]

Maybe the format of your dbsnp.vcf is the problem. Can you post your error message?

[neha]

Maybe the format of your dbsnp.vcf is the problem. Can you post your error message?

I am getting this error for CountCovariate
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A USER ERROR has occurred (version 1.4-30-gf2ef8d1):
##### ERROR The invalid arguments or inputs must be corrected before the GATK can proceed
##### ERROR Please do not post this error to the GATK forum
##### ERROR
##### ERROR See the documentation (rerun with -h) for this tool to view allowable command-line arguments.
##### ERROR Visit our wiki for extensive documentation http://www.broadinstitute.org/gsa/wiki
##### ERROR Visit our forum to view answers to commonly asked questions http://getsatisfaction.com/gsa
##### ERROR
##### ERROR MESSAGE: Argument with name 'KnowbSites' isn't defined.


I also tried to run the Unifiedgenotyper. First time it ran well without any error but found SNP only for chrX chrY and ChrM. Then I gace the interval file as I am working with exome data, then it gave me following error
ERROR stack trace
java.lang.NullPointerException
at org.broadinstitute.sting.gatk.datasources.reads.BAMScheduler.getNextOverlappingBAMScheduleEntry(BAMScheduler.java:248)
at org.broadinstitute.sting.gatk.datasources.reads.BAMScheduler.advance(BAMScheduler.java:170)
at org.broadinstitute.sting.gatk.datasources.reads.BAMScheduler.populateFilteredIntervalList(BAMScheduler.java:99)
at org.broadinstitute.sting.gatk.datasources.reads.BAMScheduler.createOverIntervals(BAMScheduler.java:74)
at org.broadinstitute.sting.gatk.datasources.reads.IntervalSharder.shardOverIntervals(IntervalSharder.java:58)
at org.broadinstitute.sting.gatk.datasources.reads.SAMDataSource.createShardIteratorOverIntervals(SAMDataSource.java:1148)
at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.getShardStrategy(GenomeAnalysisEngine.java:452)
at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:230)
at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:122)
at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:236)
at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:146)
at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:90)
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A GATK RUNTIME ERROR has occurred (version 1.4-30-gf2ef8d1):
##### 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 wiki for extensive documentation http://www.broadinstitute.org/gsa/wiki
##### ERROR Visit our forum to view answers to commonly asked questions http://getsatisfaction.com/gsa
##### ERROR
##### ERROR MESSAGE: Code exception (see stack trace for error itself)

[m_elena_bioinfo]

The program return:ERROR MESSAGE: Argument with name 'KnowbSites' isn't defined.

But it is not "knowbsites", but knownSites, with the same uppercase letters!

[neha]

The program return:ERROR MESSAGE: Argument with name 'KnowbSites' isn't defined.

But it is not "knowbsites", but knownSites, with the same uppercase letters!

Hey sorry for that error message. By mistake I ran the wrong command but even after correcting it to --KnownSites I am getting the same error.

##### ERROR
##### ERROR MESSAGE: Argument with name 'KnownSites' isn't defined.

And it would be nice if you could also tell me why it give me run time error when i trie to run UnifiedGenotyper module for calling SNP without recalibrating the score.

##### ERROR A GATK RUNTIME ERROR has occurred (version 1.4-30-gf2ef8d1):
##### 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 wiki for extensive documentation http://www.broadinstitute.org/gsa/wiki
##### ERROR Visit our forum to view answers to commonly asked questions http://getsatisfaction.com/gsa
##### ERROR
##### ERROR MESSAGE: Code exception (see stack trace for error itself)

Sorry to bother you again and agian but its been almost a week I am trying to run this software and I am not able to.

Thanks,
Neha

[m_elena_bioinfo]

Please, post me how you run the program!

[P-Richmond]

http://getsatisfaction.com/gsa

You are in the wrong place for this. Post your error to the above address. However, they will insist that you first download the newest version of GATK since they won't support you otherwise.

However, your error has probably already been solved at that website.

Cheers,
Phil

[m_elena_bioinfo]

try --knownSites and not --KnownSites

[neha]

try --knownSites and not --KnownSites

Thank you so much. I dont know why I was doing the blunder of typing KnownSites instead of "knownSites". Now it is running perfectly fine.

My UnifiedGenotyper module is also running perfectly fine now.

Thanks alot!!!

[Anjali]

Error in CountCovariates

I use the latest version of GATK, During the Quality score recalibration I found the following error.
The code was as follows: java -Xmx4g -jar GenomeAnalysisTK.jar -l INFO -R ~/SCZ_data/ref_hg19/hg19sum_upper.fa --DBSNP dbsnp132.txt -I ../output.marked.realigned.fixed.bam -T CountCovariates -cov ReadGroupCovariate -cov QualityScoreCovariate -cov CycleCovariate -cov DinucCovariate -recalFile input.recal_data.csv


##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A USER ERROR has occurred (version 2.0-23-ge9a19be):
##### ERROR The invalid arguments or inputs must be corrected before the GATK can proceed
##### ERROR Please do not post this error to the GATK forum
##### ERROR
##### ERROR See the documentation (rerun with -h) for this tool to view allowable command-line arguments.
##### ERROR Visit our website and forum for extensive documentation and answers to
##### ERROR commonly asked questions http://www.broadinstitute.org/gatk
##### ERROR
##### ERROR MESSAGE: Could not find walker with name: CountCovariates

Can anyone please suggest me what is getting wrong during the process??

Thanks

[yeppomonkey]

use http://www.broadinstitute.org/gatk/g...alibrator.html CountCovariates not in the updated version