sff file problems

[clostridium40]

I'm trying to separate and trim the MIDs off my reads from my .sff files using the sfffile that is provided by Roche. However, every time that I attempt to execute the program it gives me the following error:

bash: /usr/local/genome/bin/sfffile: cannot execute binary file

I have checked and confirmed that I am the owner and have permission to execute the file. I really need to get this file working so that I can remove the MIDs in order to run the reads through MIRA, so any help that you could provide would very much appreciated.

[kmcarr]

A few questions:

What platform (computer/OS) are you using?
How did you install the software?
What was the command you used to try to run the program?

[AAWT]

Hi every one,
i want to ask that how could I download to convert my sff. files to fasta from 454 seq data, I tried with link but I couldn't do that, it need to install python,,,,,,,

http://bioinf.comav.upv.es/sff_extract/download.html

Could you please help me in this regard

Thanks

[clostridium40]

kmcarr,

I'm running Ubuntu 11.04 32-bit OS, the files were given to me on a jump drive and I copied them and moved the executable file into my $PATH variable. I used the command sfffile, however I'm not completely clear on the commands and variables for sfffile. If you could help that would be very much appreciated.

thank you

[kmcarr]

kmcarr,

I'm running Ubuntu 11.04 32-bit OS, the files were given to me on a jump drive and I copied them and moved the executable file into my $PATH variable. I used the command sfffile, however I'm not completely clear on the commands and variables for sfffile. If you could help that would be very much appreciated.

thank you

Since you didn't use the proper install procedure you might not have the correct binary installed for your system (i.e. 32 bit). Run this command to see what architecture the program was built for:

file /usr/local/genome/bin/sfffile

For example, when I run it on my machine the output tells me that it is a 64bit linux executable

file /opt/454/bin/sfffile
/opt/454/bin/sfffile: ELF 64-bit LSB executable, AMD x86-64, version 1 (SYSV), for GNU/Linux 2.4.3, statically linked, for GNU/Linux 2.4.3, stripped

[clostridium40]

Since you didn't use the proper install procedure you might not have the correct binary installed for your system (i.e. 32 bit). Run this command to see what architecture the program was built for:

file /usr/local/genome/bin/sfffile

For example, when I run it on my machine the output tells me that it is a 64bit linux executable

file /opt/454/bin/sfffile
/opt/454/bin/sfffile: ELF 64-bit LSB executable, AMD x86-64, version 1 (SYSV), for GNU/Linux 2.4.3, statically linked, for GNU/Linux 2.4.3, stripped

I ran the command, and you're correct that it was not installed properly for my system and that is the problem, I got:

/usr/local/genome/bin/sfffile: ELF 64-bit LSB executable, x86-64, version 1 (SYSV), statically linked, for GNU/Linux 2.4.3, not stripped

I'm not an expert but I'm guessing a program 64-bit LSB executable running on a 32-bit system will not execute properly. The problem is I don't have anything except this file that I was given by another person. How do I go about getting the proper programs to install the correct sfffile on my computer? Is there a place that I could download the software or what should I ask the other person for when it comes to getting the correct files? I really need this software so that I can separate my .sff files by the MIDs so that I can assembly with our Illumina reads.

kmcarr, thank you so much for your help, I've been really panicking about the situation. I need to get moving with this assembly however until I get a functioning sfffile to parse the reads by the MIDs I can't move forward. Thanks again

[kmcarr]

I ran the command, and you're correct that it was not installed properly for my system and that is the problem, I got:

/usr/local/genome/bin/sfffile: ELF 64-bit LSB executable, x86-64, version 1 (SYSV), statically linked, for GNU/Linux 2.4.3, not stripped

I'm not an expert but I'm guessing a program 64-bit LSB executable running on a 32-bit system will not execute properly. The problem is I don't have anything except this file that I was given by another person. How do I go about getting the proper programs to install the correct sfffile on my computer? Is there a place that I could download the software or what should I ask the other person for when it comes to getting the correct files? I really need this software so that I can separate my .sff files by the MIDs so that I can assembly with our Illumina reads.

kmcarr, thank you so much for your help, I've been really panicking about the situation. I need to get moving with this assembly however until I get a functioning sfffile to parse the reads by the MIDs I can't move forward. Thanks again

You are correct, that executable file will not run on your hardware. Roche/454 will provide their analysis software free of charge, just go to this website and fill out the form.

They officially only support RedHat Linux, I run it on CentOS which is clone of RedHat. There may be some issues installing it on Ubuntu; search these forums for any discussions about installing the software on Ubuntu. You should also consider using a 64bit installation if you will be doing assembly.

[clostridium40]

You are correct, that executable file will not run on your hardware. Roche/454 will provide their analysis software free of charge, just go to this website and fill out the form.

They officially only support RedHat Linux, I run it on CentOS which is clone of RedHat. There may be some issues installing it on Ubuntu; search these forums for any discussions about installing the software on Ubuntu. You should also consider using a 64bit installation if you will be doing assembly.

kmcarr - you are a life saver, I can't thank you enough for all your help. Thank you, very very much appreciated.

[TheLight]

I used SFF Workbench to extract MIDs. Note that the MID module is delivered as beta at this moment.

They officially only support RedHat Linux, I run it on CentOS which is clone of RedHat. There may be some issues installing it on Ubuntu; search these forums for any discussions about installing the software on Ubuntu. You should also consider using a 64bit installation if you will be doing assembly.

Unfortunately, it is not for Linux. Only for Windows.