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Old 01-28-2014, 08:49 AM   #21
FrankiB
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Quote:
Originally Posted by GenoMax View Post
@FrankiB: Just want to confirm that you are using 64-bit unix of some kind?

How much /tmp space have you allocated? Is adequate disk space allocated for the VM instance?
Yes I'm using a 64-bit ansd 250 gb allocated for VM.
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Old 01-28-2014, 08:55 AM   #22
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Can you increase the RAM allocated to VM (6 or 8 GB) if possible and try? Allocating 4 GB to the VM may mean that a single process may not be able to get ~3.2 GB, which is what you need for an alignment job: http://bio-bwa.sourceforge.net/bwa.shtml#8
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Old 01-28-2014, 08:59 AM   #23
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Quote:
Originally Posted by GenoMax View Post
Can you increase the RAM allocated to VM (6 or 8 GB) if possible and try? Allocating 4 GB to the VM may mean that a single process may not be able to get ~3.2 GB, which is what you need for an alignment job: http://bio-bwa.sourceforge.net/bwa.shtml#8
Yes I tried to allocated 7 gb and I got the same result...
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Old 01-28-2014, 09:17 AM   #24
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Can you try to capture the standard error output to see if there is any additional useful information? The exact procedure would differ based on the shell you are using (e.g. http://www.cyberciti.biz/faq/redirec...err-to-stdout/)
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Old 01-29-2014, 07:34 AM   #25
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Quote:
Originally Posted by GenoMax View Post
Can you try to capture the standard error output to see if there is any additional useful information? The exact procedure would differ based on the shell you are using (e.g. http://www.cyberciti.biz/faq/redirec...err-to-stdout/)
I got about the same information:
@SQ SN:1 LN:249250621
@SQ SN:2 LN:243199373
@SQ SN:3 LN:198022430
@SQ SN:4 LN:191154276
@SQ SN:5 LN:180915260
@SQ SN:6 LN:171115067
@SQ SN:7 LN:159138663
@SQ SN:8 LN:146364022
@SQ SN:9 LN:141213431
@SQ SN:10 LN:135534747
@SQ SN:11 LN:135006516
@SQ SN:12 LN:133851895
@SQ SN:13 LN:115169878
@SQ SN:14 LN:107349540
@SQ SN:15 LN:102531392
@SQ SN:16 LN:90354753
@SQ SN:17 LN:81195210
@SQ SN:18 LN:78077248
@SQ SN:19 LN:59128983
@SQ SN:20 LN:63025520
@SQ SN:21 LN:48129895
@SQ SN:22 LN:51304566
@SQ SN:X LN:155270560
@SQ SN:Y LN:59373566
@SQ SN:MT LN:16569
@SQ SN:GL000207.1 LN:4262
@SQ SN:GL000226.1 LN:15008
@SQ SN:GL000229.1 LN:19913
@SQ SN:GL000231.1 LN:27386
@SQ SN:GL000210.1 LN:27682
@SQ SN:GL000239.1 LN:33824
@SQ SN:GL000235.1 LN:34474
@SQ SN:GL000201.1 LN:36148
@SQ SN:GL000247.1 LN:36422
@SQ SN:GL000245.1 LN:36651
@SQ SN:GL000197.1 LN:37175
@SQ SN:GL000203.1 LN:37498
@SQ SN:GL000246.1 LN:38154
@SQ SN:GL000249.1 LN:38502
@SQ SN:GL000196.1 LN:38914
@SQ SN:GL000248.1 LN:39786
@SQ SN:GL000244.1 LN:39929
@SQ SN:GL000238.1 LN:39939
@SQ SN:GL000202.1 LN:40103
@SQ SN:GL000234.1 LN:40531
@SQ SN:GL000232.1 LN:40652
@SQ SN:GL000206.1 LN:41001
@SQ SN:GL000240.1 LN:41933
@SQ SN:GL000236.1 LN:41934
@SQ SN:GL000241.1 LN:42152
@SQ SN:GL000243.1 LN:43341
@SQ SN:GL000242.1 LN:43523
@SQ SN:GL000230.1 LN:43691
@SQ SN:GL000237.1 LN:45867
@SQ SN:GL000233.1 LN:45941
@SQ SN:GL000204.1 LN:81310
@SQ SN:GL000198.1 LN:90085
@SQ SN:GL000208.1 LN:92689
@SQ SN:GL000191.1 LN:106433
@SQ SN:GL000227.1 LN:128374
@SQ SN:GL000228.1 LN:129120
@SQ SN:GL000214.1 LN:137718
@SQ SN:GL000221.1 LN:155397
@SQ SN:GL000209.1 LN:159169
@SQ SN:GL000218.1 LN:161147
@SQ SN:GL000220.1 LN:161802
@SQ SN:GL000213.1 LN:164239
@SQ SN:GL000211.1 LN:166566
@SQ SN:GL000199.1 LN:169874
@SQ SN:GL000217.1 LN:172149
@SQ SN:GL000216.1 LN:172294
@SQ SN:GL000215.1 LN:172545
@SQ SN:GL000205.1 LN:174588
@SQ SN:GL000219.1 LN:179198
@SQ SN:GL000224.1 LN:179693
@SQ SN:GL000223.1 LN:180455
@SQ SN:GL000195.1 LN:182896
@SQ SN:GL000212.1 LN:186858
@SQ SN:GL000222.1 LN:186861
@SQ SN:GL000200.1 [M::main_mem] read 82646 sequences (10000166 bp)...
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Old 01-29-2014, 07:40 AM   #26
GenoMax
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Re-reading your previous posts I realized that in post #15 you said that index generated 2 files. That does not seem right. I have a feeling the indexing is the problem and did not work right the first time. Can you post a listing of index files for the genome? You may also want to try re-indexing.

There should be 5 index related files (*.amb, *.sa, *.bwt, *.ann, *.pac) besides the fasta file.

Last edited by GenoMax; 01-29-2014 at 07:45 AM.
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Old 01-29-2014, 08:06 AM   #27
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Sorry to have mistaken you, but I have generated the 5 files you are refering to.
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Old 01-29-2014, 08:23 AM   #28
GenoMax
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Is it working now? You deleted a previous post that said that "aln" option was working but "mem" was not.
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Old 01-29-2014, 08:31 AM   #29
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Yea. bwa aln is working well (it seems). Now I'm running bwa sampe to combine the *.sai files.
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Old 04-10-2015, 11:26 AM   #30
MZB
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Smile BWA.tar installation on windows

Hello Everyone!
I am looking a best software to align paired end reads from illumina MiSeq. Someone told me that I can use BWA-MEM or Subread to align paired end reads to the reference genome. I downloaded the BWA-MEM but I can't execute that because my computer has windows 32 bit version. the installation file has .tar.gz extension. Can anyone tell me how to open the execute the software on windows?
Many thanks!
MZB
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Old 04-10-2015, 02:50 PM   #31
GenoMax
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You won't be able to run bwa on windows directly unless you use cygwin or a virtual linux machine.

But before you get to that save yourself trouble and find new computer with 64-bit OS. 32-bit windows is going to pose a problem at some point soon where you are going to run into memory limit (that could be because of the size of your dataset or the size of the genome (e.g. human) you are working on).

If you are set on using your computer as is then look at BBMap suite (and BBDuk - trimming and BBMap - alignment) programs.http://seqanswers.com/forums/showthread.php?t=41057 They are native java programs and will run on windows directly. They will still be subject to above memory limits.
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Old 04-10-2015, 03:55 PM   #32
MZB
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Thank You GenoMax. I downloaded and installed ubuntu on my computer but I am not familiar with Ubuntu. When I am opening bwa.tar and find manu files inside but i do not know which kind of file should i use to execute the application. Its the same thing with the all software.tar That i am trying to install. There is no file with .exe for the installation but Just manu others files.
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