Bowtie / Bugs / #342 bowtie2-build

Val - 2015-11-04

I will take a quick shot out in the dark. If you downloaded the source code try to build bowtie2 again on your local machine.

cd /gwork/cmoore/installers/bowtie2-2.2.6/
make clean
make -j

Then try to run your build command again using the local binaries.

./bowtie2-build example/reference/lambda_virus.fa lambda_virus

Let me know how it goes.

Val

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- Clayton Moore - 2015-11-04
  
  Still getting an error:
  
  [cmoore@saw-login1 ~]$ cd /work/cmoore/installers/
  
  [cmoore@saw-login1 installers]$ ls
  
  bowtie2-2.2.6/ cutadapt-1.8.3/ FastQC-0.10.1/ samtools-1.2/
  tophat-2.0.13/
  
  [cmoore@saw-login1 installers]$ cd bowtie2-2.2.6/
  
  [cmoore@saw-login1 bowtie2-2.2.6]$ make clean
  
  make: *** No rule to make target `clean'. Stop.
  
  [cmoore@saw-login1 bowtie2-2.2.6]$ make -j
  
  make: *** No targets specified and no makefile found. Stop.
  
  [cmoore@saw-login1 bowtie2-2.2.6]$
  
  On Wed, Nov 4, 2015 at 12:56 PM, Val valduboisvert@users.sf.net wrote:
  
  I will take a quick shot out in the dark. If you downloaded the source
  code try to build bowtie2 again on your local machine.
  
  cd /gwork/cmoore/installers/bowtie2-2.2.6/
  make clean
  make -j
  
  Then try to run your build command again using the local binaries.
  
  ./bowtie2-build example/reference/lambda_virus.fa lambda_virus
  
  Let me know how it goes.
  
  Val
  
  [bugs:#342] http://sourceforge.net/p/bowtie-bio/bugs/342/
  bowtie2-build*
  
  Status: open
  Group: v0.9.0
  Created: Wed Nov 04, 2015 05:12 PM UTC by Clayton Moore
  Last Updated: Wed Nov 04, 2015 05:12 PM UTC
  Owner: nobody
  
  I'm trying to figure this whole bowtie2 thing out, so I tried running
  through the tutorials, but I can't seem to get the bowtie2-build command to
  work.
  
  I make a temp directory in /gwork/cmoore/ and then tried to run the
  following command:
  
  bowtie2-build
  /gwork/cmoore/installers/bowtie2-2.2.6/example/reference/lambda_virus.fa
  lambda_virus
  
  Every time, I get the following error:
  
  Traceback (most recent call last):
  File "/gwork/cmoore/installers/bowtie2-2.2.6/bowtie2-build", line 95, in
  <module>
  main()
  File "/gwork/cmoore/installers/bowtie2-2.2.6/bowtie2-build", line 92, in
  main
  os.execv(build_bin_spec, argv)
  OSError: [Errno 8] Exec format error
  
  Any ideas?
  
  Sent from sourceforge.net because you indicated interest in
  https://sourceforge.net/p/bowtie-bio/bugs/342/
  
  To unsubscribe from further messages, please visit
  https://sourceforge.net/auth/subscriptions/
  
  --
  Regards,
  Clayton Moore
  BSc. Molecular Biology and Genetics (Honours)
  University of Guelph
  
  Related
  
  Bugs: ~~#342~~
  
  If you would like to refer to this comment somewhere else in this project, copy and paste the following link:

Clayton Moore - 2015-11-04

Still getting an error:

[cmoore@saw-login1 ~]$ cd /work/cmoore/installers/

[cmoore@saw-login1 installers]$ ls

bowtie2-2.2.6/ cutadapt-1.8.3/ FastQC-0.10.1/ samtools-1.2/ tophat-2.0.13/

[cmoore@saw-login1 installers]$ cd bowtie2-2.2.6/

[cmoore@saw-login1 bowtie2-2.2.6]$ make clean

make: *** No rule to make target `clean'. Stop.

[cmoore@saw-login1 bowtie2-2.2.6]$ make -j

make: *** No targets specified and no makefile found. Stop.

[cmoore@saw-login1 bowtie2-2.2.6]$

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Val - 2015-11-04

Ok, you do not have the source code. Could you please let me know the output of the command uname -a please?

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Clayton Moore - 2015-11-04

[cmoore@saw-login1 bowtie2-2.2.6]$ uname -a
Linux saw-login1 2.6.32-358.14.1.el6.x86_64 #1 SMP Tue Jul 16 23:51:20 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux

Last edit: Clayton Moore 2015-11-04

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Val - 2015-11-04

Not sure if you got my message. I sent you a few commands to run. Do not forget the dot in front of ./bowtie-build command.
thanks,
Val

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I believe you're talking about these commands:

[cmoore@saw-login1 bowtie2-2.2.6]$ cd /gwork/cmoore/installers/bowtie2-2.2.6/
[cmoore@saw-login1 bowtie2-2.2.6]$ ./bowtie2-build example/reference/lambda_virus.fa lambda_virus
Traceback (most recent call last):
  File "./bowtie2-build", line 95, in <module>
    main()
  File "./bowtie2-build", line 92, in main
    os.execv(build_bin_spec, argv)
OSError: [Errno 8] Exec format error
[cmoore@saw-login1 bowtie2-2.2.6]$ ldd bowtie2-build-s
    not a dynamic executable
[cmoore@saw-login1 bowtie2-2.2.6]$ ././bowtie2-build-s example/reference/lambda_virus.fa lambda_virus
-bash: ././bowtie2-build-s: cannot execute binary file
[cmoore@saw-login1 bowtie2-2.2.6]$

Still not having any luck... sorry if I've missed any commands you sent.

Val - 2015-11-04

Sorry, it was a typo in my original message. Here is the command again:
./bowtie2-build-s example/reference/lambda_virus.fa lambda_virus

That double ./ should not be there.

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Even with the single ./ I'm having no luck. Still getting the binary error.

[cmoore@saw-login1 bowtie2-2.2.6]$ cd /gwork/cmoore/installers/bowtie2-2.2.6/
[cmoore@saw-login1 bowtie2-2.2.6]$ ./bowtie2-build example/reference/lambda_virus.fa lambda_virus
Traceback (most recent call last):
  File "./bowtie2-build", line 95, in <module>
    main()
  File "./bowtie2-build", line 92, in main
    os.execv(build_bin_spec, argv)
OSError: [Errno 8] Exec format error
[cmoore@saw-login1 bowtie2-2.2.6]$ ldd bowtie2-build-s
    not a dynamic executable
[cmoore@saw-login1 bowtie2-2.2.6]$ ./bowtie2-build-s example/reference/lambda_virus.fa lambda_virus
-bash: ./bowtie2-build-s: cannot execute binary file
[cmoore@saw-login1 bowtie2-2.2.6]$

Val - 2015-11-04

Do you have the proper right to execute from that directory? Did you install bowtie2 into that location? A quick way to check if this is related with the system is to download bowtie into your home dir and try it from there. Something like this:

cd
wget http://sourceforge.net/projects/bowtie-bio/files/bowtie2/2.2.6/bowtie2-2.2.6-linux-x86_64.zip/download
unzip bowtie2-2.2.6-linux-x86_64.zip
cd bowtie2-2.2.6
./bowtie2-build-s example/reference/lambda_virus.fa lambda_virus

I have a similar system and I just retested the bowtie2 build we have on sourceforge over there. It works fine on my end. We need to figure out what is happening on your system now.

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Clayton Moore - 2015-11-04

I've never had any problems running any other programs from that directory. I just uninstalled the bowtie2 I had, and reinstalled it and it seems to have worked... Still no clue what the problem was... but I it seems to work now.

As another quick question, what's the difference between bowtie2-build and bowtie2-build-s?

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Val - 2015-11-04

Glad that worked. bowtie2-build is just a wrapper that calls the proper binaries. In the case of bowtie2 the wrapper is taking care of much more. In the case of bowtie2-build it is just calling the "large" or "small" binaries. That is the binaries that can build a very large index or those that can build a small one.

Val

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Clayton Moore - 2015-11-04

Awesome. Thanks so much for your help!!!

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Val - 2015-11-04

I will close this for now.

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Val - 2015-11-04

status: open --> closed

assigned_to: Val
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Val

Any ideas?

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