Re: [TASSEL-Group] Errors to use ABH Genotype plugin

[Terry Casstevens]

Files parentA and parentB shouldn't be a hapmap file. see this link

https://bitbucket.org/tasseladmin/tassel-5-source/wiki/UserManual/GenosToABH/GenosToABHPlugin

On Fri, Jun 17, 2022 at 7:01 AM 081A許博程 <ken92...@gmail.com> wrote:
>
> Hi everyone,
> I want to ask about the errors output from the ABH plugin in Tassel 5. Below are the error messages from my terminal window. I have also include parent in my genotype table, but it still output same messages.
>
> Commands:
>
> run_pipeline.pl -h ./F2parent_variant.hmp.txt -GenosToABHPlugin -o ./F2_ABH.csv -parentA ./V9.mapped.bam.hmp.txt -parentB ./BTx623.mapped.bam.hmp.txt -outputFormat c -endPlugin
>
>
> Error messages:
>
> [pool-1-thread-1] ERROR net.maizegenetics.analysis.data.GenosToABHPlugin - Parent rs# alleles chrom pos strandassembly# center protLSID assayLSID panelLSID QCcode V9.mapped.bam missing from the genotype file
>
> [pool-1-thread-1] ERROR net.maizegenetics.analysis.data.GenosToABHPlugin - Parent rs# alleles chrom pos strandassembly# center protLSID assayLSID panelLSID QCcode BTx623.mapped.bam missing from the genotype file
>
> [pool-1-thread-1] INFO net.maizegenetics.plugindef.AbstractPlugin - Finished net.maizegenetics.analysis.data.GenosToABHPlugin: time: Jun 17, 2022 10:35:19
>
> [pool-1-thread-1] INFO net.maizegenetics.pipeline.TasselPipeline - net.maizegenetics.analysis.data.GenosToABHPlugin: time: Jun 17, 2022 10:35:19: progress: 100%
>
> [pool-1-thread-1] INFO net.maizegenetics.plugindef.AbstractPlugin - net.maizegenetics.analysis.data.GenosToABHPlugin Citation: Stefan Reuscher, Jeff Glaubitz, Lynn Johnson (2015) First Annual TASSEL Hackathon
>
> [pool-1-thread-1] INFO net.maizegenetics.pipeline.TasselPipeline - net.maizegenetics.analysis.data.FileLoadPlugin: time: Jun 17, 2022 10:35:19: progress: 100%
>
>
>
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