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Old 08-20-2014, 11:09 AM   #21
simobioinfo
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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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Old 08-20-2014, 11:31 AM   #22
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Quote:
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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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Old 08-20-2014, 11:38 AM   #23
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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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Old 08-20-2014, 11:41 AM   #24
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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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Old 08-20-2014, 11:47 AM   #25
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Quote:
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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Old 08-22-2014, 12:34 AM   #26
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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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Old 08-22-2014, 01:03 AM   #27
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You just want "bowtie2-build genome.fa genome", without the asterisk and redirect ('>').
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Old 08-22-2014, 01:06 AM   #28
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I will try...
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Old 08-22-2014, 01:12 AM   #29
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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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Old 08-22-2014, 02:36 AM   #30
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Quote:
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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Old 08-22-2014, 02:40 AM   #31
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Yeah, they'll take a while to get generated.
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Old 08-23-2014, 01:11 AM   #32
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Hi... now 24 hours are passed and indexing is still running on my MAc (see previous post of this thread). What can I do now? My processor is dual core... I have to insert an option into the command line to take into account that processor has 2 core?
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Old 08-23-2014, 03:22 AM   #33
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24 hours seems excessive. Can you see it still using one of your cores? I don't think the indexing can be run multi-core. What species are you trying to index? Perhaps one of us can just create and post the indices so you can download them.
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Old 08-23-2014, 04:00 AM   #34
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simobioinfo is indexing GRCh37/human. If bandwidth is not a problem then you can download the preformatted bundle (sequence, indexes and annotations) from this link: http://support.illumina.com/sequenci...e/igenome.html

@simobioinfo: This is the sort of thing I was trying to warn you about in terms of user experience.

@Devon: If you have indexes for that known to work on a Mac you could post them for simobioinfo.
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Old 08-23-2014, 06:54 AM   #35
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I'll give it a whirl on my macbook pro, but it's rather old and low on RAM. Assuming that doesn't work, on Tuesday I'll be back in the office and just use one of our beefier Macs if this isn't resolved by then.
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Old 08-23-2014, 09:30 AM   #36
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Quote:
Originally Posted by simobioinfo View Post
Hi... now 24 hours are passed and indexing is still running on my MAc (see previous post of this thread). What can I do now? My processor is dual core... I have to insert an option into the command line to take into account that processor has 2 core?
How much RAM does this Mac have? If you look at my previous post you'll see where I said that if you don't have enough RAM it will take very, very long to build in the index. To build the human genome you probably need 5-6GB but you will have to monitor RAM usage as the index is building to know for sure. And it doesn't matter how many cores you have Bowtie2-build is a single process.
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Old 08-23-2014, 10:54 PM   #37
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Quote:
Originally Posted by biocomputer View Post
How much RAM does this Mac have? If you look at my previous post you'll see where I said that if you don't have enough RAM it will take very, very long to build in the index. To build the human genome you probably need 5-6GB but you will have to monitor RAM usage as the index is building to know for sure. And it doesn't matter how many cores you have Bowtie2-build is a single process.
My mac has 4Gb of RAM. I suppose that it could be enough to build index. I don't know how to check ram usage.
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Old 08-24-2014, 12:33 AM   #38
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I was able to build the index on another machine and use it on my macbook pro with 3 gigs of RAM. I really wouldn't recommend doing this on a machine with that little RAM as you end up swapping all the time. Since you have more RAM than my old laptop, hopefully you'll get better performance. I'll post the indices later today and send you a link.
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Old 08-24-2014, 10:41 AM   #39
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@simbioinfo: I just sent you a PM with some links to the bowtie2 indices that worked on my Mac. Let me know if they work for you.
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Old 09-17-2014, 05:25 AM   #40
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Thank you everybody. I was on vacation. I will try soon indexes you sent me
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