Re: [TASSEL-Group] HDF5 to Hapmap

[Terry Casstevens]

This should work for you.

/opt/TASSEL5/run_pipeline.pl -Xmx50G -h5 ./GBSgenofile.H5 -export ./GBSgenofile.hmp.txt -exportType Hapmap

/opt/TASSEL5/run_pipeline.pl -Xmx50G -h5 ./GBSgenofile.H5 -GenotypeSummaryPlugin -endPlugin -export summary

On Wed, Jun 17, 2015 at 1:01 PM, Abby L. <ladejo...@gmail.com> wrote:

Hi,

I have been trying to convert HDF5 file to hapmap in Tassel5 unsuccessfully. I am also trying to get genotype summary in the latest build of Tassel5 also not working. I don't know what I'm getting wrong. I am pasting the commands below

/opt/TASSEL5/run_pipeline.pl -Xmx50G -fork1 -h5 ./GBSgenofile.H5 -fork2 -export ./GBSgenofile.hmp.txt -exportType Hapmap -runfork1 -runfork2

Memory Settings: -Xms512m -Xmx50G

Tassel Pipeline Arguments: -fork1 -h5 ./GBSgenofile.H5 -fork2 -export ./GBSgenofile.hmp.txt -exportType Hapmap -runfork1 -runfork2

[main] INFO net.maizegenetics.tassel.TasselLogging - Tassel Version: 5.2.11  Date: June 4, 2015

[main] INFO net.maizegenetics.tassel.TasselLogging - Max Available Memory Reported by JVM: 45511 MB

[main] INFO net.maizegenetics.tassel.TasselLogging - Java Version: 1.8.0_40

[main] INFO net.maizegenetics.tassel.TasselLogging - OS: Linux

[main] INFO net.maizegenetics.pipeline.TasselPipeline - Tassel Pipeline Arguments: [-fork1, -h5, ./GBSgenofile.H5, -fork2, -export, ./GBSgenofile.hmp.txt, -exportType, Hapmap, -runfork1, -runfork2]

[main] INFO net.maizegenetics.pipeline.TasselPipeline - loadFile: ./GBSgenofile.H5

net.maizegenetics.analysis.data.FileLoadPlugin

net.maizegenetics.analysis.data.ExportMultiplePlugin

[pool-1-thread-1] INFO net.maizegenetics.pipeline.TasselPipeline - net.maizegenetics.analysis.data.FileLoadPlugin: progress: 100%

[pool-1-thread-1] INFO net.maizegenetics.plugindef.AbstractPlugin - net.maizegenetics.analysis.data.FileLoadPlugin  Citation: Bradbury PJ, Zhang Z, Kroon DE, Casstevens TM, Ramdoss Y, Buckler ES. (2007) TASSEL: Software for association mapping of complex traits in diverse samples. Bioinformatics 23:2633-2635.

/opt/TASSEL5/run_pipeline.pl -Xmx50G -fork1 -h5 ./GBSgenofile.H5 -fork2 -genotypeSummary overall,site,taxa -runfork1 -runfork2

Memory Settings: -Xms512m -Xmx50G

Tassel Pipeline Arguments: -fork1 -h5 ./GBSgenofile.H5 -fork2 -genotypeSummary overall,site,taxa -runfork1 -runfork2

[main] INFO net.maizegenetics.tassel.TasselLogging - Tassel Version: 5.2.11  Date: June 4, 2015

[main] INFO net.maizegenetics.tassel.TasselLogging - Max Available Memory Reported by JVM: 45511 MB

[main] INFO net.maizegenetics.tassel.TasselLogging - Java Version: 1.8.0_40

[main] INFO net.maizegenetics.tassel.TasselLogging - OS: Linux

[main] INFO net.maizegenetics.pipeline.TasselPipeline - Tassel Pipeline Arguments: [-fork1, -h5, ./GBSgenofile.H5, -fork2, -genotypeSummary, overall,site,taxa, -runfork1, -runfork2]

[main] INFO net.maizegenetics.pipeline.TasselPipeline - loadFile: ./GBSgenofile.H5

net.maizegenetics.analysis.data.FileLoadPlugin

net.maizegenetics.analysis.data.GenotypeSummaryPlugin

[pool-1-thread-2] ERROR net.maizegenetics.plugindef.AbstractPlugin - GenotypeSummaryPlugin: Invalid selection.  Please select one genotype table.

[pool-1-thread-2] INFO net.maizegenetics.plugindef.AbstractPlugin -

Usage:

GenotypeSummaryPlugin <options>

-overview <true | false> : Get Overview Report (Default: true)

-siteSummary <true | false> : Get Site Summary (Default: true)

-taxaSummary <true | false> : Get Taxa Summary (Default: true)

Thanks for your help.

[Daniel]

Hi Terry,

I have the same problem to export H5 file to hmp file. It seems your command lines run successfully but no output produced. Is the following command still working? Thanks.

Best Regards,
Daniel

在 2015年6月17日星期三 UTC-4下午1:30:47，Terry写道：

[Terry Casstevens]

Yes, it still works.

https://bitbucket.org/tasseladmin/tassel-5-source/wiki/docs/ReportingTassel5Issues.pdf

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[donz]

Dear Terry,

Does TASSEL5 provide function converting hapmap to H5? I tried both -hmp and -hapmap to specify input. But neither one works.

Thanks.

--Donz

[Terry Casstevens]

./run_pipeline.pl -h filename.hmp.txt -export filename.h5 -exportType HDF5

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[Dong Zhang]

Hi Terry,

The command was terminated without errors. But there is no HDF5 result generated.

I tried to run the command in Tassel3 and to convert hapmap generated by UNEAK. Does this function work for hapmap created by UNEAK?

Thanks.

--Donz

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[Guriqbal Singh Dhillon]

None is working for me. It says

FileLoadPlugin Parameters

format: HDF5

sortPositions: false

[pool-1-thread-1] INFO net.maizegenetics.analysis.data.FileLoadPlugin - Start Loading File: New.HDF5 time: Dec 26, 2016 8:52:5

[pool-1-thread-1] INFO net.maizegenetics.analysis.data.FileLoadPlugin - Nothing Loaded for File: New.HDF5 time: Dec 26, 2016 8:52:6

[pool-1-thread-1] INFO net.maizegenetics.plugindef.AbstractPlugin - Finished net.maizegenetics.analysis.data.FileLoadPlugin: time: Dec 26, 2016 8:52:6

[pool-1-thread-1] INFO net.maizegenetics.plugindef.AbstractPlugin - net.maizegenetics.analysis.data.ExportMultiplePlugin  Citation: Bradbury PJ, Zhang Z, Kroon DE, Casstevens TM, Ramdoss Y, Buckler ES. (2007) TASSEL: Software for association mapping of complex traits in diverse samples. Bioinformatics 23:2633-2635.

[pool-1-thread-1] INFO net.maizegenetics.pipeline.TasselPipeline - net.maizegenetics.analysis.data.FileLoadPlugin: time: Dec 26, 2016 8:52:6: progress: 100%

But no output file is formed

[Mao Huang]

Hi Terry,

I have a h5 file, and I have TASSEL 5 on mac. I go to "file" "save as" choosing "hap map" format with the taxa annotations included.

But the output file is not really accurate, it shows the "chrome" column is the taking part of the marker names from "rs" column, rather than giving me the accurate chromosome names.

I can email you the example h5 file if you need it.

Could you help with this issue?

Thanks,

Mao

On Wednesday, June 17, 2015 at 1:30:47 PM UTC-4, Terry wrote:

[Terry Casstevens]

Yes please send me the file.

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[Mao Huang]

Hi Terry, thanks.

I just sent it to your gmail tcass...@gmail.com, as it may be too big to be attached here.

Mao

[Terry Casstevens]

This data was store as scaffolds instead of chromosomes. The
chromosome names may be what was intended. The SNP names don't seem
great because they are duplicated. But that doesn't cause a problem
because the chromosome / positions are different.

Can you ask the person who created the .h5?

Best,


Terry

> https://groups.google.com/d/msgid/tassel/5c6f3413-3268-4145-8478-ad36fc5835e6%40googlegroups.com.

[Mao Huang]

Hi Terry,

Yes, I’ll ask and confirm. Thank you for your help.

Mao