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  • #16
    and do you think that expanding RAM is not the solution because VM is also a problem to run alignment?

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    • #17
      simobioinfo: I do not want to discourage you but if you are able to use institutional resources to do the actual computing you would find the experience much more enjoyable. You can certainly try and get started on the Mac and depending on your experience you may want to move to another resource using your Mac as the terminal to connect to that resource.

      Note: Since you have a Mac you strictly do not need to use a VM. OS X is unix compatible and there are binary versions of tuxedo suite programs available that will natively run on OS X.

      You can download pre-formatted indexes/annotations for human genome from the iGenomes site: http://support.illumina.com/sequenci...e/igenome.html This is a big download but hopefully you are using institutional network and would not have bandwidth issues.
      Last edited by GenoMax; 08-20-2014, 10:32 AM.

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      • #18
        I would like to use institutional resources but I have been wait for a new PC for 2 years (in Italy research is very difficult) and now I have to start my work. So I think that using my Mac could be a faster and more reliable solution. Are you agree?

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        • #19
          I think your indexing is taking so long because with only 1.5GB allocated to the VM, bowtie2-build doesn't have near enough RAM so it is having to use a swapfile which will lead to thrashing and will make the process take a really, really long time. I just indexed the mouse genome mm10 for Bowtie2 using default settings and it used 5GB of RAM while building the index and took 4 hours on a large server, but even on a reasonably fast desktop computer as long as you have enough RAM it should be able to build overnight. I've indexed the mouse genome mm9 on an i7-2720QM in 6-8 hours. But anyways, as has already been mentioned you can download pre-built indexes. So you'll either have to download them or upgrade your RAM.

          Also why are you using a VM? Bowtie2 is available for Linux, Windows, and Mac so you should be able to run it natively. With only 4GB of RAM you still won't have enough to build the index but when it comes to aligning then 4GB may be enough as long as you don't run many other processes at the same time.
          Last edited by biocomputer; 08-20-2014, 11:05 AM.

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          • #20
            Starting with your Mac is certainly under your control.

            Are you running a new(er) version of OS X (10.7.x or later)? Working natively in OS X would allow you to avoid the VM issue entirely.

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            • #21
              Biocomputer: I'm using VM because a Windows PC is available and I don't know how to use bowtie in windows because I use it from command line. I have a question 1.5Gb is enough to run alignments?
              Genomax: I use version 10.9.4 of OS X. Is it a problem?

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              • #22
                Originally posted by simobioinfo View Post
                Genomax: I use version 10.9.4 of OS X. Is it a problem?
                That is good. I was checking to see that you were not using an older version where you may run into problems.

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                • #23
                  Originally posted by GenoMax View Post
                  That is good. I was checking to see that you were not using an older version where you may run into problems.
                  Thank you Genomax! Now you encouraged me!

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                  • #24
                    That is actually one of the nice things about Macs, they are bioinformatics software friendly. You can use Linux on a PC since Windows doesn't run a lot of the software, but with Mac OS can you can use the Bash shell, many scripts programs etc.

                    Skip the virtual machine. Use a computing core/cluster if you can, or your Mac, or a PC with Linux. Dual boot with Windows if need be rather than virtual machine. Just my 2c, I have seen a dramatic improvement running some of the same Java programs on 64-bit Ubuntu compared to 32-bit Windows 7, some just won't run and give errors.

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                    • #25
                      Originally posted by simobioinfo View Post
                      Biocomputer: I'm using VM because a Windows PC is available and I don't know how to use bowtie in windows because I use it from command line. I have a question 1.5Gb is enough to run alignments?
                      Genomax: I use version 10.9.4 of OS X. Is it a problem?
                      Bowtie under windows is also run from the command line, cmd.exe. Or you can install Cygwin in Windows which will let you run the Windows version of Bowtie2 in Windows but using Linux style commands.

                      1.5GB is not enough for alignments, the Bowtie2 manuals says the human genome index needs 3.2GB so you'll probably need a computer with at least 4GB.

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                      • #26
                        Hi again... first of all I would like to thank you everybody.
                        Yesterday I tried to index human genome on my Mac with this command:
                        bowtie2-build * genome.fa>genome
                        Shell has been showing me this line:"building SMALL index" for 4 hours.
                        Did I make some error launching indexing? or is it normal?
                        I don't know what to do now
                        Simona

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                        • #27
                          You just want "bowtie2-build genome.fa genome", without the asterisk and redirect ('>').

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                          • #28
                            I will try...

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                            • #29
                              Don't be surprised if it take a couple hours. For reference, on my (likely faster) machines it takes ~1.5 hours to index the human or mouse genome. You can follow the progress by looking at the sizes of the 6 files produced. I recall that the .3.bt2 and .4.bt2 files are produced first and the first half of the process is done once the .2.bt2 file is about the same size as the .4.bt2 file. The .rev.1.bt2 and .rev.2.bt2 files will be the same size as their forward counterparts, so you can gauge how far along they are once that half of the indexing commences.

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                              • #30
                                Originally posted by dpryan View Post
                                Don't be surprised if it take a couple hours. For reference, on my (likely faster) machines it takes ~1.5 hours to index the human or mouse genome. You can follow the progress by looking at the sizes of the 6 files produced. I recall that the .3.bt2 and .4.bt2 files are produced first and the first half of the process is done once the .2.bt2 file is about the same size as the .4.bt2 file. The .rev.1.bt2 and .rev.2.bt2 files will be the same size as their forward counterparts, so you can gauge how far along they are once that half of the indexing commences.
                                Thank you. Indexing is started now. I have 4 files:
                                3.bt2 of 4kb
                                4.bt2 of 716.2 Mb
                                1.bt2 and 2.bt2 are 0 byte at the moment.
                                Is that ok?

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