[AJenkins]

Was your human genome FASTA indexed previously using a different version?

[mastal]

Are you running it on a server or a PC, and do you have more than 3 Gb of memory available?

[FrankiB]

I'm running on a PC using VMware wokstation and I allowed 4 gb.

[FrankiB]

Was your human genome FASTA indexed previously using a different version?

No. I indexed it with the same version.

[GenoMax]

@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?

[FrankiB]

@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.

[GenoMax]

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

[FrankiB]

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...

[GenoMax]

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/)

[FrankiB]

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)...

[GenoMax]

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.

[FrankiB]

Sorry to have mistaken you, but I have generated the 5 files you are refering to.

[GenoMax]

Is it working now? You deleted a previous post that said that "aln" option was working but "mem" was not.

[FrankiB]

Yea. bwa aln is working well (it seems). Now I'm running bwa sampe to combine the *.sai files.

[MZB]

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