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Old 08-14-2015, 06:42 AM   #1
cmccabe
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Default bowtie2 align out of memory

The bowtie2 align command below seems correct, except for the out of memory error.

I am running ubuntu 12.04 on an old machine with 3.8 GB RAM Intel® Core™2 CPU 6700 @ 2.66GHz × 2.

I provide the path to bowtie2 on the desktop and then the path to the indexes from a higher memory 64GB usb drive. The fastq and the sam output are redirected to another 128GB usb with the path in the comand and the cores are (2). Any ideas? Thank you .

Code:
dnascopev@ubuntu:~$ /home/dnascopev/Desktop/bowtie2-2.2.6/bowtie2 -p 2 -x /home/dnascopev/Desktop/bowtie2-2.2.6/indexes/my_hg19 /media/C2F8EFBFF8EFAFB9/IonXpress_009_150603_newheader.fq > /media/C2F8EFBFF8EFAFB9/IonXpress_009_150603_newheader.sam
Killed
(ERR): bowtie2-align exited with value 137
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Old 08-14-2015, 06:49 AM   #2
GenoMax
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Default

Is this a question or an observation?

Bowtie2 FM Index for human genome requires at least 3.2G of RAM before any other overhead is added. That does not leave much space for other important files like the OS (or the other way around) in your case.
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Old 08-14-2015, 06:53 AM   #3
cmccabe
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Looks like a new computer for me . Thank you .
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