#314 bowtie2-inspect crash

[Andrew]

bowtie2-inspect crashes for bowtie2 indices downloadable from ccb.jhu.edu:

$ wget ftp://ftp.ccb.jhu.edu/pub/data/bowtie2_indexes/hg19.zip
$ unzip hg19.zip
$ wget 'http://sourceforge.net/projects/bowtie-bio/files/bowtie2/2.2.2/bowtie2-2.2.2-linux-x86_64.zip
$ unzip bowtie2-2.2.2-linux-x86_64.zip

$ ./bowtie2-2.2.2/bowtie2-inspect hg19 > hg19.fa
bowtie-inspect: reference.cpp:471: int BitPairReference::getStretch(uint32_t*, size_t, size_t, size_t, SStringExpandable<unsigned int,="" 1024,="" 2="">&) const: Assertion `0' failed.
Aborted (core dumped)

[Val]

This issue has been fixed but not released yet. Until we will release it you can download the latest source code from github (https://github.com/BenLangmead/bowtie2/) and build bowtie2 locally.

We apologize for any inconvenience.

Val

[Matt MacManes]

This issue is still present in the github code downloaded yesterday, 5/27/2014.

bowtie2-inspect ref-index
...
...
assert_gt: expected (0) > (60000)
reference.cpp:471
bowtie-inspect: reference.cpp:471: int BitPairReference::getStretch(uint32_t*, size_t, size_t, size_t, SStringExpandable<unsigned int>&) const: Assertion `0' failed.
Aborted (core dumped)

The reference is 2.5G - well under the 4GB limit for 'small' indexing. The index itself is fine - but the issue is that Tophat relies un bowtie2-inspect, and thus this bug causes failure.

If you can tell me which older version if bowtie2-inspect works, I'll gladly grab that one!

[Ben Langmead]

Thanks for these helpful reports! Val and I just fixed this in the bugs/313 branch, which will be merged imminently. Let me know if it crops up again.

Ben