h5 file read error

[ananta]

Hi, 

I downloaded the h5 file from panzea site (AllZeaGBSv2.7_publicSamples_rawGenos.hmp.h5)

trying to play with the data and get this error while reading the h5 data. any reason ? Thanks

Ananta

Error reading: <................>/AllZeaGBSv2.7_publicSamples_rawGenos.hmp.h5

HDF5-DIAG: Error detected in HDF5 (1.8.8) thread 0:

  #000: H5G.c line 452 in H5Gopen2(): unable to open group

    major: Symbol table

    minor: Can't open object

  #001: H5G.c line 1003 in H5G_open_name(): group not found

    major: Symbol table

    minor: Object not found

  #002: H5Gloc.c line 430 in H5G_loc_find(): can't find object

    major: Symbol table

    minor: Object not found

  #003: H5Gtraverse.c line 861 in H5G_traverse(): internal path traversal failed

    major: Symbol table

    minor: Object not found

  #004: H5Gtraverse.c line 641 in H5G_traverse_real(): traversal operator failed

    major: Symbol table

    minor: Callback failed

  #005: H5Gloc.c line 385 in H5G_loc_find_cb(): object 'Taxa' doesn't exist

    major: Symbol table

    minor: Object not found

ncsa.hdf.hdf5lib.exceptions.HDF5SymbolTableException: Symbol table:Object not found ["H5Gloc.c line 385 in H5G_loc_find_cb(): object 'Taxa' doesn't exist"]

at ch.systemsx.cisd.hdf5.hdf5lib.H5.H5Gopen(Native Method)

at ch.systemsx.cisd.hdf5.hdf5lib.H5GLO.H5Gopen(H5GLO.java:80)

at ch.systemsx.cisd.hdf5.HDF5.openGroup(HDF5.java:312)

at ch.systemsx.cisd.hdf5.HDF5$11.call(HDF5.java:435)

at ch.systemsx.cisd.hdf5.HDF5$11.call(HDF5.java:1)

at ch.systemsx.cisd.hdf5.cleanup.CleanUpCallable.call(CleanUpCallable.java:40)

at ch.systemsx.cisd.hdf5.HDF5.getGroupMemberLinkInfo(HDF5.java:462)

at ch.systemsx.cisd.hdf5.HDF5Reader.getAllGroupMemberInformation(HDF5Reader.java:465)

at net.maizegenetics.util.HDF5Utils.getAllTaxaNames(HDF5Utils.java:135)

at net.maizegenetics.taxa.TaxaListBuilder.buildFromHDF5Genotypes(TaxaListBuilder.java:114)

at net.maizegenetics.dna.snp.GenotypeTableBuilder.getInstance(GenotypeTableBuilder.java:424)

at net.maizegenetics.dna.snp.ImportUtils.readGuessFormat(ImportUtils.java:45)

at net.maizegenetics.analysis.imputation.FILLINFindHaplotypesPlugin.processData(FILLINFindHaplotypesPlugin.java:148)

at net.maizegenetics.plugindef.AbstractPlugin.performFunction(AbstractPlugin.java:83)

at net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:1164)

at net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)

[Jeff Glaubitz]

Hi Ananta,

This file is in the Tassel4 HDF5 format.  Please open it with the Tassel5 GUI (Data|Load). An “Error” message box will pop up that says:

“This file is in TASSEL4 HDF5 format. It will be converted to TASSEL5 HDF5 format with the t5.h5 suffix added. This may take a few minutes.”

Click OK on this message box and the file will be converted.  You can then delete the old copy (if you wish) and use the new copy:

AllZeaGBSv2.7_publicSamples_rawGenos.hmp.t5.h5

in the Tassel5 command line.

I’ll post the converted, TASSEL5 version on Panzea soon.

Sorry for the inconvenience,

Jeff

--
Jeff Glaubitz
Project Manager
Biology of Rare Alleles in Maize and its Wild Relatives
National Science Foundation award IOS-1238014
http://www.panzea.org
Institute for Genomic Diversity
Cornell University
175 Biotechnology Bldg
Ithaca, NY 14853
Phone: 607-255-1386
jcg...@cornell.edu

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[ananta]

Thanks Jeff, It worked. 

[manas...@gmail.com]

Hai, am also facing same problem, but the Sorghum data set, Yet today Tassel4 worked me fine, i don't understand why this is happening, and tried to upload .hdf5 filr to tassel5 it's saying formate error, plz help

Thanks in advance

Manasa

On Thursday, December 18, 2014 at 4:51:13 AM UTC+5:30, Jeff Glaubitz wrote:

Hi Ananta,

This file is in the Tassel4 HDF5 format.  Please open it with the Tassel5 GUI (Data|Load). An “Error” message box will pop up that says:

“This file is in TASSEL4 HDF5 format. It will be converted to TASSEL5 HDF5 format with the t5.h5 suffix added. This may take a few minutes.”

Click OK on this message box and the file will be converted.  You can then delete the old copy (if you wish) and use the new copy:

AllZeaGBSv2.7_publicSamples_rawGenos.hmp.t5.h5

in the Tassel5 command line.

I’ll post the converted, TASSEL5 version on Panzea soon.

Sorry for the inconvenience,

Jeff

--
Jeff Glaubitz
Project Manager
Biology of Rare Alleles in Maize and its Wild Relatives
National Science Foundation award IOS-1238014
http://www.panzea.org
Institute for Genomic Diversity
Cornell University
175 Biotechnology Bldg
Ithaca, NY 14853
Phone: 607-255-1386
jcg...@cornell.edu

To unsubscribe from this group and stop receiving emails from it, send an email to tas...@googlegroups.com.