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Old 04-05-2012, 07:15 AM   #1
Palgrave
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Default Bowtie out of memory

I am trying to run bowtie on paired end reads and I am getting the following error:

Out of memory allocating the ebwt[] array for the Bowtie index. Please try
again on a computer with more memory.

Whats wrong here and what can I do without changing computer?
I am aligning onto mm9, ebwt-files are downloaded from Bowtie-website.

I have an Acer Aspire, 3GB memory. Ubuntu.
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Old 04-05-2012, 07:26 AM   #2
kmcarr
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Quote:
Originally Posted by Palgrave View Post
I am trying to run bowtie on paired end reads and I am getting the following error:

Out of memory allocating the ebwt[] array for the Bowtie index. Please try
again on a computer with more memory.

Whats wrong here and what can I do without changing computer?
I am aligning onto mm9, ebwt-files are downloaded from Bowtie-website.

I have an Acer Aspire, 3GB memory. Ubuntu.
Palgrave,

What's wrong is clearly stated in the error message. Your computer does not have enough memory to load the mm9 indexes.

What can you do without changing computer? Add more RAM to the computer you have. There's really no (practical) way around this.
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Old 03-04-2013, 09:15 PM   #3
sridhar
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Default Bowtie 2 error

hi,


I got this error message when I wrong Bowtie/2.2.0 on Linux. Did you met this issue before?

Error: Encountered internal Bowtie 2 exception (#1)
Command: /opt/software/bowtie/2.2.0--GCC-4.4.5/bin/bowtie2-align --wrapper basic-0 -q -p 1 -S --phred64 < human genome index> <fastq> -S <sam>

Thanks in advance
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Old 03-04-2013, 10:02 PM   #4
AlexReynolds
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Perhaps index individual mm9 chromosomes and then run your alignment task on each chromosome, or add RAM to your system as kmcarr suggests.
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Old 03-04-2013, 10:12 PM   #5
sridhar
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thank you Mr .Alex,
i have one more doubt.
can we use fastg.gz file as input ?
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Old 03-04-2013, 10:15 PM   #6
AlexReynolds
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Quote:
Originally Posted by sridhar View Post
thank you Mr .Alex,
i have one more doubt.
can we use fastg.gz file as input ?
I was actually responding to the original poster (Palgrave). You might want to ask a separate question in order to get an answer to your question.
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Old 03-04-2014, 07:33 PM   #7
tokitky
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It is too late to answer this thread, but for the people who will face similar problems.

I've just had similar problems when I run the bowtie with ubuntu on Acer Aspireone netbook (4GB memory).

At that time , Ubuntu was run on VMware player and the size of virtual memory was set as 1GB (which was default value). If you use VMware Player , you can easily change the size up to theoretically 8GB(32 bit system) or 32GB (64 bit system). So I changed it to 4GB (I could not increase the size more than 4GB due to the capability of my machine).

At the same time, I did not have enough space on my hard drive since there were several fastq files on my netbook, and the system seemed not to be stable.I remove all of the fastq files other than the one which is using for bowtie.

Since then, I had never seen the error message(*).

(*) It is better to reboot the system when you finish one round of bowtie so as to release the memory. If you don't, you will sometimes face similar out of memory problems.

Last edited by tokitky; 03-06-2014 at 05:10 PM.
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