Question: errors during cloud mapping of c elegans mutant genome
0
gravatar for madhushree.kamak
22 months ago by
madhushree.kamak0 wrote:

Dear all, I am trying to find variant in our whole genome sequencing data of various c elegans mutants as compared to the ref seq. I am using a previously published workflow from the Hobert lab. However this workflow was meant for single end reads , so I edited it for paired end reads - by adding an input for reverse end reads durong the mapping step. However once the workflow reaches the variant calling step it stops due to some error- which I have pasted below. 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: Unknown tribble type tabular: Field variant had provided type tabular but there's no such Tribble type. The compatible types are:
ERROR Name FeatureType Documentation
ERROR VCF VariantContext http://www.broadinstitute.org/gsa/gatkdocs/release/org_broadinstitute_sting_utils_codecs_vcf_VCFCodec.html
ERROR VCF3 VariantContext http://www.broadinstitute.org/gsa/gatkdocs/release/org_broadinstitute_sting_utils_codecs_vcf_VCF3Codec.html
ERROR ------------------------------------------------------------------------------------------

Please give me some ideas as to what this error means and how I could fix it !! Thanks mk

software error snp alignment • 488 views
ADD COMMENTlink modified 22 months ago by Jennifer Hillman Jackson23k • written 22 months ago by madhushree.kamak0
0
gravatar for Jennifer Hillman Jackson
22 months ago by
United States
Jennifer Hillman Jackson23k wrote:

Hello,

This is a standard GATK error message for when there is an input problem. It is unrelated to Galaxy and the help at the Broad website is the right place to understand expected input contents and the like. The underlying tools are the same whether used command-line or wrapped in a Galaxy server.

I suspect that the input data at this stage of the workflow are a mismatch for the parameters for the tool that threw the error. Start checking for empty inputs, error states of inputs, then proceed to format and content.

Thanks, Jen, Galaxy team

ADD COMMENTlink written 22 months ago by Jennifer Hillman Jackson23k
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