Was your human genome FASTA indexed previously using a different version?
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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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Originally posted by GenoMax View PostCan 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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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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Originally posted by GenoMax View PostCan 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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@SQ SN:GL000200.1 [M::main_mem] read 82646 sequences (10000166 bp)...
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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, 08:45 AM.
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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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