I Have A Problem Using The Gem Mapper To Calculate Mappability. It Dies After All The Mapping Is Done.

Question

[KCC]

I used the following list of commands:

gem-do-index -i mygenome.fa -o mygenome_gem_index

gem-mappability -I mygenome.fa_gem_index -l 51 -o mappability_51.gem

The second command fails at the end of the mapping with the following errors:

Wed Feb 13 22:28:34 2013 -- ...done.
Wed Feb 13 22:28:34 2013 -- Loading locations... done.
Wed Feb 13 22:28:34 2013 -- Writing frequencies to disk...
Assertion failed: (bitmap==((uint8_t*)bitmap_buf->memory)+text_len-separators), function main, file gem-mappability.c, line 556.
Abort trap: 6

Can someone help me fix this? I am using a Mac Book Pro, Core i7, OS X 10.7.5

I used the OSX version of GEM found here: http://sourceforge.net/projects/gemlibrary/files/gem-library/Binary%20pre-release%201/GEM-binaries-MacOSX-i386-20100419-003425.tbz2/download

[toni]

Have you tried to ask the developers themselves via their "report a bug" interface ?

http://algorithms.cnag.cat/mantis/login_page.php?return=%2Fmantis%2Fmy_view_page.php

[KCC]

I guess I had no idea whether I had done anything wrong or not. So, I wanted to sort that out.

[toni]

OK. I don't have any clue myself. I have used it once or twice on a CentOS 5 platform and it worked fine. My guess would be that "OS X" is 'involved' but that doesn't help much !

[orr.shomroni]

Tony, can you perhaps post the exact code you used for GEM? I ran the code on RedHat6.3, but I got the same error:

gem-do-index -i /path/to/reference/ce10.fa -o /path/to/reference/gem/ce10.gem
gem-mappability -I /path/to/reference/gem/ce10.gem -l 36 -o /path/to/reference/gem/mappability/ce10.gem
gem-mappability: gem-mappability.c:556: main: Assertion 'bitmap==((uint8_t*)bitmap_buf->memory)+text_len-separators' failed.
Aborted (core dumped)

I tried to run the "gem-do-index" using "-o /path/to/reference/gem/ce10", but I got "Could not open file 'gem/ce10.gem.bwt.toc': No such file or directory"

[Istvan Albert]

perhaps send them an email via the request help link above.

[alaguraj.veluchamy]

Have you been able to find a solution. Please post here. i tried on Linux_x64. But it gives the same error. I mailed developers, but no reply.

[KCC]

No reply so far.

[alaguraj.veluchamy]

Hi, Use Tallymer for the k-mer based calculation.

[MathieuG]

Idem on my side. I'd be glad to get your feedback if you could ever find a solution.