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Old 10-15-2013, 06:50 AM   #1
sphil
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Location: Stuttgart, Germany

Join Date: Apr 2010
Posts: 192
Default Bowtie2 freezes with 7.5GB RAM

Hey guys,

I try to map approx. 30 mio reads onto a inhouse reference. The indexing worked without any error messages. Now I want to do the mapping. The reads are sequenced as paired end but i want to map them as single end with bowtie2 (64bit). Now starting the mapping bowtie crawls up to 7.5 GB allocated RAM and than kind of freezes. Checking the System Monitor (using CentOS 6.4) I get the futex_wat_queue_me for the waiting channel column. The index fastA file is 3.3GB large (so comparable to the human genome which bowtie2 should be capable of). The reads are 100bp illumina ones. my command line is as follows:

bowtie2 -p 7 --very-fast -x ./Bac_Vir_DB_NCBI_7102013 ./2236/unmapped_leftPool.fq

I tried the simplest i could think of but even with those settings it has the above described behaviour. Any suggestions what might go wrong?

Thanks,

Phil

Last edited by sphil; 10-15-2013 at 06:55 AM.
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