KeyError: "unable to open object (Symbol table: Can't open object)"

The error mesage:

KeyError: "unable to open object (Symbol table: Can't open object)"

can indicate:

• a problem with specifying bas.h5/bax.h5 SMRT Pipe inputs
• a potentially corrupted HDF5 file.

Starting with SMRT Analysis 2.0, a new file format was introduced, bax.h5. The details of this change are in the bas.h5 Reference Guide at http://files.pacb.com/software/instrument/2.0.0/bas.h5%20Reference%20Guide.pdf

Users running custom scripts in conjunction with SMRT Pipe must take into account these changes. See Specifying SMRT Pipe Inputs at: https://github.com/PacificBiosciences/SMRT-Analysis/wiki/SMRT-Pipe-Reference-Guide-v2.0#wiki-PipeInputs

To diagnose a corrupted HDF5 file:

$ source $SEYMOUR_HOME/etc/setup.sh
$ h5debug /path/to/bas.h5

Output should be similar to:

Reading signature at address 0 (rel)
File Super Block...
File name:                                         ./m130405_225601_42171_c100502282550000001823069308081393_s1_p0.bas.h5
File access flags                                  0x00000000
File open reference count:                         1
Address of super block:                            0 (abs)
Size of userblock:                                 0 bytes
Superblock version number:                         0
Free list version number:                          0
Root group symbol table entry version number:      0
Shared header version number:                      0
Size of file offsets (haddr_t type):               8 bytes
Size of file lengths (hsize_t type):               8 bytes
Symbol table leaf node 1/2 rank:                   4
Symbol table internal node 1/2 rank:               16
File status flags:                                 0x00
Superblock extension address:                      UNDEF (rel)
Shared object header message table address:        UNDEF (rel)
Shared object header message version number:       0
Number of shared object header message indexes:    0
Address of driver information block:               UNDEF (rel)
Root group symbol table entry:
   Name offset into private heap:                  0
   Object header address:                          96
   Dirty:                                          No
   Cache info type:                                Symbol Table
   Cached entry information:
      B-tree address:                              136
      Heap address:                                680

An error message means the file is corrupt.