need help to solve bowtie2-inspect error

[Shishir]

Dear all bowtie users,

I am new in NG-sequencing. I used following command to build index of repeat masked genome by repeatmasker.

bowtie2-build genome_scaffolds.masked.fa my_genome_index

during the execution of command I also faced the multiple warnings
'Warning: Encountered reference sequence with only gaps'

Furthermore, during using Tophat I got warning: could not find fasta file and error Error: bowtie-inspect returned an error log: bowtie2-inspect: bt2_inspect.cpp:218:

So, after reading some blogs I thought to build fasta from index and used

bowtie2-inspect my_genome_index

assert_eq: expected (24026, 0x5dda) got (23330, 0x5b22)
bt2_inspect.cpp:218
bowtie2-inspect: bt2_inspect.cpp:218: void print_ref_sequences(std:stream&, bool, const EList<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, 128>&, const uint32_t*, const std::string&): Assertion `0' failed.
Aborted

The command again failed with the above message. Could someone please help me to solve this problem

below is the footer first bowtie execution
len: 192701494
bwtLen: 192701495
sz: 48175374
bwtSz: 48175374
lineRate: 6
offRate: 4
offMask: 0xfffffff0
ftabChars: 10
eftabLen: 20
eftabSz: 80
ftabLen: 1048577
ftabSz: 4194308
offsLen: 12043844
offsSz: 48175376
lineSz: 64
sideSz: 64
sideBwtSz: 48
sideBwtLen: 192
numSides: 1003654
numLines: 1003654
ebwtTotLen: 64233856
ebwtTotSz: 64233856
color: 0
reverse: 1


Thank you for your HELP!

[11xinqi]

Did you fingure out what is the problem?