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Old 12-13-2010, 02:26 AM   #1
papori
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Default twoBitToFa: command not found

Hey, when i try to convert 2bit file to fasta file by using twoBitToFa prog,
and i get "command not found" message..
why?
thanks in advance..
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Old 12-13-2010, 04:36 AM   #2
dawe
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Quote:
Originally Posted by papori View Post
why?
Either because it is not in your path or because you didn't install itů

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Old 12-13-2010, 04:42 AM   #3
papori
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what do you mean : it is not in your path..
where do i have to change?
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Old 12-13-2010, 04:49 AM   #4
papori
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now the error is :
bash: ./twoBitToFa: cannot execute binary file
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Old 12-13-2010, 04:52 AM   #5
dawe
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Quote:
Originally Posted by papori View Post
what do you mean : it is not in your path..
where do i have to change?
the "path" is the set of directories that are "scanned" by default when you need to run an executable. This set is included in the $PATH environmental variable, i.e.

Code:
$ echo $PATH
/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/opt/X11/bin:/usr/X11/bin:/opt/local/bin:/Users/dawe/Library/Bioinfo/bin:/usr/local/cuda/bin/:/usr/local/mysql/bin:/usr/local/root/bin
All you have to do is one of these:
  • place twoBitToFa into a directory included in $PATH
  • add the directory containing twoBitToFa to the $PATH
  • run twoBitToFa specifying the full qualified path (i.e. /directory/where/you/have/twoBitToFa)

Also, take a look at this

HTH
d
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Old 12-13-2010, 04:56 AM   #6
dawe
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Quote:
Originally Posted by papori View Post
now the error is :
bash: ./twoBitToFa: cannot execute binary file
Mmm... you probably downloaded the binary for a wrong arch/os. check the output of these commands:

Code:
$ uname -ps
$ file twoBitToFa
They somehow have to match (i.e. Linux x86_64 will match ELF 64-bit for GNU/Linux, Darwin will match Mach-O file type)

d
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Old 12-13-2010, 05:03 AM   #7
papori
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sorry, when i am doing:
echo$PATH
i get:
bash: echo/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games: No such file or directory

i was wrong before..
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Old 12-13-2010, 05:20 AM   #8
dawe
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Code:
$ echo <SPACE> $PATH
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Old 12-13-2010, 05:28 AM   #9
papori
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Ok, my fault...
so my output is:
/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games

So, i copy the twoBitToFa to /usr/sbin.
now, when i am doing twoBitToFa hg18.2bit hg18.fa
i have this error:
bash: /usr/sbin/twoBitToFa: cannot execute binary file

Thanks for your patience...
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Old 12-13-2010, 05:31 AM   #10
papori
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when i am doing: uname -ps
i get: Linux unknown

or , when doing: file twoBitToFa
i get: twoBitToFa: ERROR: cannot open `twoBitToFa' (No such file or directory)
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Old 12-13-2010, 06:14 AM   #11
dawe
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Quote:
Originally Posted by papori View Post
Ok, my fault...
so my output is:
/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games

So, i copy the twoBitToFa to /usr/sbin.
now, when i am doing twoBitToFa hg18.2bit hg18.fa
i have this error:
bash: /usr/sbin/twoBitToFa: cannot execute binary file

Thanks for your patience...
I believe you need to study a little bit more about bash and command line interfaces. Take a look at the Bash Beginner Guide and, please, practice a little bit.
Also, I understand you couldn't know, but /usr/sbin is preferred for system commands available to the super user. You'd better place your custom commands into /usr/local/bin.
About the "file" command... again, you need to specify the fully qualified path.
Lastly, about the impossibility to execute, you may look at this http://tinyurl.com/2uka6tq :-)

d
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Old 07-06-2011, 05:36 AM   #12
salturki
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I got same issue but thanks for dawe's answers I solved it and thought the solution may benefit someone later.

All you need is just download the right version and change the file permissions

first download the right version for your machine from this link (Mac i386 or PPC or Linux 32 or 64)

http://hgdownload.cse.ucsc.edu/admin/exe/


then go to the directory where you downloaded the file in the terminal and write:

chmod 755 twoBitToFa

this will make twoBitToFa file executable.
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