#336 bad_alloc Bowtie 2.2.5

[Andres Aguilar]

I try to run bowtie2 but I get the following error :

./bowtie2 --local -x prueba/index/RIMD -f prueba/reads/VibrioparahaemolyticusO1K33str.CDC_K4557chromosomeI.fa -S prueba/results.sam
terminate called after throwing an instance of 'std::bad_alloc'
what(): std::bad_alloc
(ERR): bowtie2-align died with signal 6 (ABRT) (core dumped)

I'm using Bowtie 2.2.5

I used
./bowtie2-build -f prueba/reference/RIMDchromosome1.fasta prueba/index/RIMD
command to create the data base

[Val]

Not sure what to say about this. Bowtie2 local search works on the examples I have. Maybe If I can get somehow the data set you are using if possible. How big is your data?

Val

[Ben Langmead]

That error is often because memory is exhausted. Can you tell us more about how big your index is and how much RAM your computer has?

Ben