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Old 12-26-2011, 09:02 AM   #1
tgenahmet
Member
 
Location: Phoenix

Join Date: Apr 2009
Posts: 11
Default bowtie index problem (bowtie-build and then bowtie-inspect)

I used bowtie-build to build an index:
Code:
~/bin/bowtie/bowtie-build human_g1k_v37.fa human_g1k_v37
It seemed to complete just fine:
Quote:
ebwtTotLen: 818510080
ebwtTotSz: 818510080
reverse: 0
Total time for backward call to driver() for mirror index: 05:24:17
Created these files:
Quote:
-rw-r--r-- 1 akurdogl asiniard 684M Dec 25 09:33 human_g1k_v37.4.ebwt
-rw-r--r-- 1 akurdogl asiniard 3.7K Dec 25 09:33 human_g1k_v37.3.ebwt
-rw-r--r-- 1 akurdogl asiniard 829M Dec 25 16:58 human_g1k_v37.1.ebwt
-rw-r--r-- 1 akurdogl asiniard 361M Dec 25 16:58 human_g1k_v37.2.ebwt
-rw-r--r-- 1 akurdogl asiniard 785M Dec 25 22:23 human_g1k_v37.rev.1.ebwt
-rw-r--r-- 1 akurdogl asiniard 342M Dec 25 22:23 human_g1k_v37.rev.2.ebwt
But when I run bowtie-inspect:
Code:
bowtie-inspect human_g1k_v37
It immediately crashes with this error:
Quote:
assert_eq: expected (1, 0x1) got (84, 0x54)
bowtie_inspect.cpp:242
bowtie-inspect: bowtie_inspect.cpp:242: void print_ref_sequences(std:stream&, bool, const std::vector<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::basic_string<char, std::char_traits<char>, std::allocator<char> > > >&, const uint32_t*, const std::string&): Assertion `0' failed.
Aborted
Or if I run:
Code:
bowtie-inspect -s human_g1k_v37
I get this:
Quote:
Colorspace 0
SA-Sample 1 in 32
FTab-Chars 10
Sequence-1 ?M???F=?w?Q???!~? /m?_}u?????w??}?????_o?C_Q??stߕ[5?{d??]?q??w?t?}g?>0 249250621
Sequence-2 x??x?????????????????????????????...
Any help is appreciated.
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