Countcovariates Error

Question

[ananth.ccamp]

Dear All

        I am getting following error while runing GATK for quality recalibration.

Any help would be appreciated.

Command used:

java -Xmx1g -jar GenomeAnalysisTK.jar -R resources/exampleFASTA.fasta -I resources/exampleBAM.bam -T CountCovariates -cov ReadGroupCovariate -cov QualityScoreCovariate -cov CycleCovariate -cov DinucCovariate ‐recalFile table.recal_data.csv

error

##### ERROR

<h5>ERROR A USER ERROR has occurred (version 1.5-31-gadad76b):</h5> <h5>ERROR The invalid arguments or inputs must be corrected before the</h5>

GATK can proceed

<h5>ERROR Please do not post this error to the GATK forum</h5> <h5>ERROR</h5> <h5>ERROR See the documentation (rerun with -h) for this tool to view</h5>

allowable command-line arguments.

<h5>ERROR Visit our wiki for extensive documentation</h5>

http://www.broadinstitute.org/gsa/wiki

<h5>ERROR Visit our forum to view answers to commonly asked questions</h5>

http://getsatisfaction.com/gsa

<h5>ERROR</h5> <h5>ERROR MESSAGE: Invalid argument value '‐recalFile' at position 14.</h5>

##### ERROR Invalid argument value 'table.recal_data.csv' at position 15.

Answer 1

[Zev.Kronenberg]

I would start by regenerating your recal files.

Answer 2

[Johan]

I think that the problem is that the input is malformated, and should be "--recal_file", rather than "‐recalFile".

Have a look here: http://www.broadinstitute.org/gsa/gatkdocs/release/org_broadinstitute_sting_gatk_walkers_recalibration_CountCovariatesWalker.html for the exact command line arguments.