[ninad]

Heyy...

It was the problem of Memory.. the large file size was not been handled by my system.
I ran it on the higher config system and works fine.
Initially 4 GB ram didn't look like a problem though.

thanks all..

[ninad]

Heyy...

It was the problem of Memory.. the large file size was not been handled by my system.
I ran it on the higher config system and works fine.
Initially 4 GB ram didn't look like a problem though.

thanks all..

[GenoMax]

You will want to do:

samtools merge out.bam in1.bam in2.bam in3.bam

Check the manual page for samtools for more info: http://samtools.sourceforge.net/samtools.shtml

GenoMax,

Also, will simple cat *.bam work to combine bam files?

[ninad]

GenoMax,

This seems really great. Atleast heading towards the solution I feel.
I certainly will cautiously increase swap. Thanks a ton for this.

Also, will simple cat *.bam work to combine bam files?

[GenoMax]

Ninad,

You could try to increase your swap partition and see if that helps: https://help.ubuntu.com/community/SwapFaq

Amount of "free memory" would depend on what you have running on your system at any given time. I think you had said that you are new to linux so I would advise you to exercise caution. You can cause irreparable damage to your system messing with partition tables.

You could split the genome files into two and run the alignments. You can then combine the bam files later.

[ninad]

The memory and swap sizes can play a role in this I believe.

ninad@ninad-Studio-1555:~$ free -m
total used free shared buffers cached
Mem: 2862 1932 930 0 702 859
-/+ buffers/cache: 371 2491
Swap: 2395 0 2395

Also bwa needs 2.5 GB of memory. Suggest some changes if I need to make in my swap and memory.

[ninad]

GenoMax,

I believe the memory problem should not be there as memory requirement is 2.5GB whereas I have specified my config as above.

At the same time, I also need to ask, since this problem is persisting, Is it alright to split the
genome file into two and run bwtsw algorithm?

I am not sure that I will be able find a better hardware, so this option of splitting if
works fine, looks good.

Also please let me know if we can run bwa on windows machine and how?

and thank you everyone for patiently answering to all the threads..

[GenoMax]

Ninad,

You are most likely running into the problem of not having enough memory available. See indexing memory requirement info here: http://bio-bwa.sourceforge.net/bwa.shtml#8.

(check if you have the following files in your index directory, sizes listed for reference, actual sizes on your OS may be slightly different).

739M hg19.fa.pac
944 hg19.fa.ann
6.6K hg19.fa.amb
739M hg19.fa.rpac
1.1G hg19.fa.bwt
1.1G hg19.fa.rbwt
370M hg19.fa.sa
370M hg19.fa.rsa

You may need to find other hardware to do this.

Well I tried with cat remake in another directory, but the problem persists.
I am using Ubuntu 10.10 i686. 4GB RAM.

[ninad]

Well I tried with cat remake in another directory, but the problem persists.
I am using Ubuntu 10.10 i686. 4GB RAM.

[GenoMax]

Ninad: What linux variant are you using? Is this a 32-bit or 64-bit install? Can you also say something about the configuration of the hardware this is installed on?

[raonyguimaraes]

and please check the size of your hg19s.fa, also take a look at the beginning and the end of the file, just to make sure it's correct

[qtrinh]

ninad,
I think the issue started with your cat step. Try putting your hg19s.fa in another directory.

~/chromFa$ mkdir hg19
~/chromFa$ cat *.fa >hg19/hg19s.fa
~/chromFa$ bwa index -a bwtsw hg19/hg19s.fa

Q

[ninad]

@peter
I will try using the mentioned specifications by you Peter. my bwa is 0.5.7 (r1310)

@raonyguimaraes-
I have tried using chr1.fa file and it works perfectly fine.
My hg19.fa file is 3 GB big. So considering the bwa indexing limit of 4 GB, it should still work.

I have checked permissions for the file, they are perfectly fine.
I believe the problem is either in concatenation or size limit. I have used cat in both above mentioned ways and its now resolved.
I dont know what can be any other problem.

@sdvie -How to check whether enough memory is available or not?

[ninad]

I went through this even earlier, but I am not getting segmentatioon fault. I also have the latest version of bwa 0.5.7.

I am clueless too.

[ulz_peter]

I tried to reproduce the error but it worked perfectly with new downloaded chr*.fa files...

Is it possible that you have no read permissions on the file?
My bwa version is 0.5.9-r16

Besides that I can't think of anything else...