Unified Genotyper error

Question: Unified Genotyper error

13 months ago by

Hello, everyone: I am building workflow for SNV on whole genome sequences. I was following best-practice for GATK. However, I am new to the field and have problem with it. I have error when I used input file created by GALAXY after steps such as map to reference, duplicate call and indel realign. The file is BAM and sequences were sorted by coordinates. Reading error description left me clueless because it is too much information in the debugger window. Could anyone to guide me through the troubleshooting and fixing the issue? Thank you in advance. PS. I am reading materials listed in the debugger and have no clarity what to do.

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: Lexicographically sorted human genome sequence detected in reads.

ERROR For safety's sake the GATK requires human contigs in karyotypic order: 1, 2, ..., 10, 11, ..., 20, 21, 22, X, Y with M either leading or trailing these contigs.

ERROR This is because all distributed GATK resources are sorted in karyotypic order, and your processing will fail when you need to use these files.

ERROR You can use the ReorderSam utility to fix this problem:

annotation sort genome gatk custom • 426 views

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modified 13 months ago by Jennifer Hillman Jackson ♦ 25k • written 13 months ago by viktoria.evdokimova • 30

13 months ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

As described in the error and at the GATK website resources, chromosome order is important. This is true whether working in Galaxy or line-command. My guess is that the order of some of your inputs follow the ordering guidelines but other inputs do not. All must be sorted - this includes the reference genome used in alignment and other steps, reference annotation data, aligned data (BAMs).

FAQs:

Small warning: the Galaxy wrapped GATK tools are at least one version old (in the Tool Shed) and even older in the deprecated set hosted at https://usegalaxy.org. These are not recommended. Changes in licensing may mean that a decision in the future to update the tools is a possible, but nothing is certain. For now, see the alternative variant analysis tools in the tutorials.

Galaxy tutorials:

https://galaxyproject.org/learn/

Thanks! Jen, Galaxy team

ADD COMMENT • link modified 13 months ago • written 13 months ago by Jennifer Hillman Jackson ♦ 25k

13 months ago by

viktoria.evdokimova • 30

viktoria.evdokimova • 30 wrote:

Thank you for prompt reply. I see what you are talking about. Please, correct if I am wrong. I should sort in chromosome order not only files I am analyzing but all files used in the tool, including reference sequences in FASTA and BED formats. Did I get it right?

ADD COMMENT • link written 13 months ago by viktoria.evdokimova • 30

Yes, all should be the same. Consistent sort order in all inputs is required. You may need to recreate your custom genome, then start over from mapping.

This situation is somewhat common when going through these tools the first time. The prepped data from GATK is already formatted this way but doesn't cover all genomes.

ADD REPLY • link written 13 months ago by Jennifer Hillman Jackson ♦ 25k

Great, thank you very much!

ADD REPLY • link written 13 months ago by viktoria.evdokimova • 30

13 months ago by

viktoria.evdokimova • 30

viktoria.evdokimova • 30 wrote:

In addition, thank you for the tip on alternative tools. I am going to try them.

ADD COMMENT • link written 13 months ago by viktoria.evdokimova • 30

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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: Lexicographically sorted human genome sequence detected in reads.

ERROR For safety's sake the GATK requires human contigs in karyotypic order: 1, 2, ..., 10, 11, ..., 20, 21, 22, X, Y with M either leading or trailing these contigs.

ERROR This is because all distributed GATK resources are sorted in karyotypic order, and your processing will fail when you need to use these files.

ERROR You can use the ReorderSam utility to fix this problem:

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