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Old 05-07-2011, 09:52 AM   #1
Location: Wellington

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Default Approximate botwie runtime

this maybe a general question, from reading the article at, I kind of feel that the instance of bowtie that I am running right now is behaving differently than mentioned in the article in terms of the time print... I maybe doing something wrong or something

I have SRA paired-end data downloaded from I am mapping against the human reference genome that is provided by bowtie... the file is roughly about 19 million reads and is about 6 GB in size. The article says it should be possible to use a normal desktop computer to be able to carry out the task in a very short time, they mentioned a matter of minutes without the indexing step (building BWT). But later on they mentioned that a server computer can take upto 21 hours building the index. My laptop is Ubuntu 32 bits, 2 GB ram, 4 GB swap, dual core and I have been running a multi-threaded bowtie instance for the past 3 days, does this sound normal ? How long did it estimably for you my colleagues when you ran bowtie ??

Here is how my query looks like :

$ bowtie hg19 -q /PATH/SRR065070.fastq -S --offrate 20 -p 2

the 'hg19' argument passed to the bowtie is just a placeholder for the reference since I am invoking bowtie from within the directory where the was extracted.. It generates an alignment file but it is getting populated on a very slow rate that over the past 3 days and 10 hours only 205 MB were written to it
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Old 05-07-2011, 11:49 AM   #2
Nils Homer
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You say you only have 2GB of RAM. How much is specified as a minimum requirement in the manual and/or paper? Consider that hg19 is 3.2 billion bases.
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Old 05-07-2011, 05:11 PM   #3
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According to the paper (

'A Bowtie index for the human genome fits in 2.2 GB on disk and has a memory footprint of as little as 1.3 GB at alignment time, allowing it to be queried on a workstation with under 2 GB of RAM.'

However, the current pre-built hg indices on their site are larger than 2.2 GB. Also, the memory footprint might be bigger for p>1; have you tried running this single threaded? Use something like the System Monitor or 'top' to figure out if your job fits in the machine's RAM - if your system is forced to use swap just to hold the index I expect the run will be desperately slow.
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Old 05-08-2011, 12:01 AM   #4
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Speaking of parallel performance; the paper says that the memory image of the index is shared by threads which could increase performance on multiple cores and that there will not be a 'substantial' increase in memory consumption upon using multiple threads. So these threads they synchronize their activities (fetching reads, outputting results, switching between indices and marking jobs).

On your cue, RDW, I checked whether or not SWAP was involved, so I see that both processors are running full blast and the bowtie job occupies 1.5 GB of RAM, however, I see the swap with 1.3 GB consumption but it is not clear to me whether this is coming from bowtie, I haven't tried running a single threaded job, my decision to run a dual thread was the notion that parallelism was gonna cut short the time...

Nilshomer, in the paper they ran bowtie on a server and on a PC and benchmarked the performance, the PC had 2 GB of RAM and this is why I was optimistic...
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Old 05-09-2011, 04:51 AM   #5

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the human genome takes about 3.3GB of memory, so the swapping is caused by bowtie. this is your major bottleneck.
multithreading does not increase memory requirement.
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Old 05-09-2011, 05:46 AM   #6
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When I run Bowtie on a Core 2 Duo 2.0 Ghz using both cores (-p 2) with 3.3 GB available RAM under Ubuntu 32 bit it would take a few hours to align 19 million reads to hg19, depending on what options I'm using. I often run it overnight so I don't know exactly how long, but definitely less than 8 hours.

You should probably add more RAM (put in 4GB to get the max ~3.3 available on a 32 bit system).
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Old 05-09-2011, 05:49 AM   #7
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use -t to know the run time
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bowtie, time

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