Are .h5 files empty?

[LeoVincenzi]

Dear developers, I am trying to use TE_density on a plant genome assembly, but I'm facing some problems getting the results. I run process_genome.py correctly, without any message error. Once the script ends, I get my output folder with the .h5 files, the filtered_input_data folder and the tmp one. I tried to open any of the h5 files with h5dump, but the structure is the one that follows:

HDF5 "Cosetinii_HiC_scaffold_1233.h5" { GROUP "/" { DATASET "CHROMOSOME_ID" { DATATYPE H5T_STRING { STRSIZE H5T_VARIABLE; STRPAD H5T_STR_NULLTERM; CSET H5T_CSET_UTF8; CTYPE H5T_C_S1; } DATASPACE SIMPLE { ( 1 ) / ( 1 ) } DATA { (0): "HiC_scaffold_1233" } } DATASET "GENE_NAMES" { DATATYPE H5T_STRING { STRSIZE H5T_VARIABLE; STRPAD H5T_STR_NULLTERM; CSET H5T_CSET_UTF8; CTYPE H5T_C_S1; } DATASPACE SIMPLE { ( 2 ) / ( 2 ) } DATA { (0): "g1636", "g1637" } } DATASET "ORDER_NAMES" { DATATYPE H5T_STRING { STRSIZE H5T_VARIABLE; STRPAD H5T_STR_NULLTERM; CSET H5T_CSET_UTF8; CTYPE H5T_C_S1; } DATASPACE SIMPLE { ( 5 ) / ( 5 ) } DATA { (0): "LTR", "S_Revision", "Simple_repeat", "Total_TE_Density", (4): "Unknown" } } DATASET "RHO_ORDERS_INTRA" { DATATYPE H5T_IEEE_F32LE DATASPACE SIMPLE { ( 5, 1, 2 ) / ( 5, 1, 2 ) } DATA {h5dump error: unable to print data

  }

} DATASET "RHO_ORDERS_LEFT" { DATATYPE H5T_IEEE_F32LE DATASPACE SIMPLE { ( 5, 20, 2 ) / ( 5, 20, 2 ) } DATA {h5dump error: unable to print data

  }

} DATASET "RHO_ORDERS_RIGHT" { DATATYPE H5T_IEEE_F32LE DATASPACE SIMPLE { ( 5, 20, 2 ) / ( 5, 20, 2 ) } DATA {h5dump error: unable to print data

  }

} DATASET "RHO_SUPERFAMILIES_INTRA" { DATATYPE H5T_IEEE_F32LE DATASPACE SIMPLE { ( 5, 1, 2 ) / ( 5, 1, 2 ) } DATA {h5dump error: unable to print data

  }

} DATASET "RHO_SUPERFAMILIES_LEFT" { DATATYPE H5T_IEEE_F32LE DATASPACE SIMPLE { ( 5, 20, 2 ) / ( 5, 20, 2 ) } DATA {h5dump error: unable to print data

  }

} DATASET "RHO_SUPERFAMILIES_RIGHT" { DATATYPE H5T_IEEE_F32LE DATASPACE SIMPLE { ( 5, 20, 2 ) / ( 5, 20, 2 ) } DATA {h5dump error: unable to print data

  }

} DATASET "SUPERFAMILY_NAMES" { DATATYPE H5T_STRING { STRSIZE H5T_VARIABLE; STRPAD H5T_STR_NULLTERM; CSET H5T_CSET_UTF8; CTYPE H5T_C_S1; } DATASPACE SIMPLE { ( 5 ) / ( 5 ) } DATA { (0): "Copia", "Gypsy", "O_Revision", "Total_TE_Density", "Unknown" } } DATASET "WINDOWS" { DATATYPE H5T_STRING { STRSIZE H5T_VARIABLE; STRPAD H5T_STR_NULLTERM; CSET H5T_CSET_UTF8; CTYPE H5T_C_S1; } DATASPACE SIMPLE { ( 20 ) / ( 20 ) } DATA { (0): "5000", "10000", "15000", "20000", "25000", "30000", "35000", (7): "40000", "45000", "50000", "55000", "60000", "65000", "70000", (14): "75000", "80000", "85000", "90000", "95000", "100000" } } } }

The fact that each dataset presents the message h5dump error: unable to print data makes me think the output is empty, I also tried HDFview and it shows all empty. What can be the problem in this case?