Re: [Seqan-dev] bug report readSequence()

[Eik Dahms <eik.dahms@gmail.com>]

Hello,

my sequence alphabet uses strictly "ACTG". This seems not to be causing this allocation error. Also it shouldn't work on any system then.

Cordially
Eik Dahms

Christophe VROLAND <christophe.vroland@ed.univ-lille1.fr> schrieb am Fr., 30. Okt. 2015 um 13:49 Uhr:

On 30/10/2015 13:21, Eik Dahms wrote:

Dear all,

i recently upgraded sequan from 1.4.0 to 2.0.0. I did not change my code. 

When i now try to run the program  i get the following allocation error when i try to read a sequence via readSequence() from a FaiIndex:

/seqan/basic/basic_exception.h:368 FAILED!  (Uncaught exception of type std::bad_alloc: std::bad_alloc)

This error occurs only on my laptop with 4GB RAM. When i run the program on a Server with 500GB RAM - it works.

It seems that the memory that is allocated, for the string that the sequence is read in, is to high.

I appended the stacktrace from gnu debugger.  

Thanks in advance !

Eik

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Hello,
I have ever got this problem when my sequence alphabet used in the code doesn't include all the alphabet of the sequence I try to read.
You use a Dna5 alphabet, maybe, there's an other letter than "ACGTN" in your sequence (a "X" ?).

Cordially

-- 
Christophe VROLAND