Count Covariates GATK error

Question: Count Covariates GATK error

2.6 years ago by

up652214 • 0 wrote:

Hi, I am trying to run a pipe-line for calling variants and have encountered this error while trying to use the tool Count Covariates:

Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/galaxy-repl/main/scratch

ERROR ------------------------------------------------------------------------------------------

ERROR A USER ERROR has occurred (version exported):

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: Invalid command line: The requested covariate type () isn't a valid covariate option. Use --list to see possible covariates.

ERROR ------------------------------------------------------------------------------------------

I have run this pipe-line before recently and did not receive the same error. I would be very grateful for any advice.

Thanks,

Louisa

snp gatk • 803 views

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modified 2.6 years ago • written 2.6 years ago by up652214 • 0

2.6 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

If you are using GATK at Galaxy Main (http://usegalaxy.org), the tools have been deprecated. Meaning that they are no longer supported and there will be no further changes. The usage is "as-is" - and some may fail as time passes and server configuration changes.

If using in a local/cloud Galaxy of your own, an upgraded version of the tools is likely in use. Double check usage, then if there is a problem with one of the options it would be best to submit the problem to the tool authors for review. Do this through the Tool Shed (http://usegalaxy.org/toolshed). Log in, navigate to the tool/version in use, and the option to contact authors is in the top right menu "Repository Actions".

If using at some other public server, contacting the administrators is probably the best place to start. They can investigate more to see if there is a configuration problem, a usage problem, or a true issue with the tool wrapper.

Thanks, Jen, Galaxy team

ADD COMMENT • link written 2.6 years ago by Jennifer Hillman Jackson ♦ 25k

Sorry I meant to comment this here: Thanks

I am using GATK at Galaxy Main. I was wondering if you knew of any alternative tools I could use for Base Recalibration instead of Count Covariates/Table Recalibration?

Many thanks,

Louisa

ADD REPLY • link written 2.6 years ago by up652214 • 0

2.6 years ago by

up652214 • 0

up652214 • 0 wrote:

Hi,

I am using GATK at Galaxy Main. I was wondering if you knew of any alternative tools I could use for Base Recalibration instead of Count Covariates/Table Recalibration?

Many thanks,

Louisa

ADD COMMENT • link written 2.6 years ago by up652214 • 0

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ERROR ------------------------------------------------------------------------------------------

ERROR A USER ERROR has occurred (version exported):

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: Invalid command line: The requested covariate type () isn't a valid covariate option. Use --list to see possible covariates.

ERROR ------------------------------------------------------------------------------------------

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