gap4 running problem load_alignment_matrix error

[alig]

Hi,

I am trying to install Staden Gap4 on a 64 bit machine with Ubuntu installed.

It appears that trev & pregap will start.  But when I type gap4&  I get this message -

invalid command name "load_alignment_matrix"
    while executing
"load_alignment_matrix       [keylget gap_defs ALIGNMENT.MATRIX_FILE]"
    (file "/usr/local/staden-linux-x86_64-1-7-1b/linux-x86_64-bin/../lib/gap/gap.tcl" line 683)

I have followed a number of suggestions from this site & others & installed some missing libraries, but still get this message.
Have done strace -o output.txt gap4 and not sure of any more errors in that file.
I will try to attach the fileoutput.txt

Can anyone help please

[Paul Donohue-4]

I don't see anything in particular in your strace output after a quick look.

Try running 'export STADEN_DEBUG=1' before running staden, and see what that says.
You can ignore the 'libiwidgets.so' error, but any other errors need to be fixed.

Note that you can use the 'Search the contents of packages' form at http://packages.ubuntu.com/ to figure out the appropriate package to install for any missing libraries.

Hope that helps.
-Paul

On Thu, Jan 29, 2009 at 06:27:19PM -0800, alig wrote:

>
> Hi,
>
> I am trying to install Staden Gap4 on a 64 bit machine with Ubuntu
> installed.
>
> It appears that trev & pregap will start.  But when I type gap4&  I get this
> message -
>
> invalid command name "load_alignment_matrix"
>     while executing
> "load_alignment_matrix       [keylget gap_defs ALIGNMENT.MATRIX_FILE]"
>     (file
> "/usr/local/staden-linux-x86_64-1-7-1b/linux-x86_64-bin/../lib/gap/gap.tcl"
> line 683)
>
> I have followed a number of suggestions from this site & others & installed
> some missing libraries, but still get this message.
> Have done strace -o output.txt gap4 and not sure of any more errors in that
> file.
> I will try to attach the file
> http://www.nabble.com/file/p21740409/output.txt output.txt
>
> Can anyone help please
> --
> View this message in context: http://www.nabble.com/gap4-running-problem-load_alignment_matrix-error-tp21740409p21740409.html
> Sent from the Bio.net - Staden mailing list archive at Nabble.com.
>
> _______________________________________________
> Staden mailing list
> Staden@...
> http://www.bio.net/biomail/listinfo/staden
>

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[alig]

Thank you, that fixed it & now I can run Gap4 so I'm very happy.

This was the error I got after running 'export STADEN_DEBUG=1'

load libcopy_reads.so => couldn't load file "libcopy_reads.so": /usr/lib/libstdc++.so.5: version `CXXABI_1.2' not found (required by /usr/local/staden-linux-x86_64-1-7-1b/linux-x86_64-bin/../lib/linux-x86_64-binaries/libmutlib.so)

I had linked it to a newer version.  So I unlinked & reinstalled libstdc++5 & that seemed to fix my problem.

Thanks again   alig

Paul Donohue-4 wrote:

I don't see anything in particular in your strace output after a quick look.

Try running 'export STADEN_DEBUG=1' before running staden, and see what that says.
You can ignore the 'libiwidgets.so' error, but any other errors need to be fixed.

Note that you can use the 'Search the contents of packages' form at http://packages.ubuntu.com/ to figure out the appropriate package to install for any missing libraries.

Hope that helps.
-Paul

On Thu, Jan 29, 2009 at 06:27:19PM -0800, alig wrote:
>
> Hi,
>
> I am trying to install Staden Gap4 on a 64 bit machine with Ubuntu
> installed.
>
> It appears that trev & pregap will start.  But when I type gap4&  I get this
> message -
>
> invalid command name "load_alignment_matrix"
>     while executing
> "load_alignment_matrix       [keylget gap_defs ALIGNMENT.MATRIX_FILE]"
>     (file
> "/usr/local/staden-linux-x86_64-1-7-1b/linux-x86_64-bin/../lib/gap/gap.tcl"
> line 683)
>
> I have followed a number of suggestions from this site & others & installed
> some missing libraries, but still get this message.
> Have done strace -o output.txt gap4 and not sure of any more errors in that
> file.
> I will try to attach the file
> http://www.nabble.com/file/p21740409/output.txt output.txt
>
> Can anyone help please
> --
> View this message in context: http://www.nabble.com/gap4-running-problem-load_alignment_matrix-error-tp21740409p21740409.html
> Sent from the Bio.net - Staden mailing list archive at Nabble.com.
>
> _______________________________________________
> Staden mailing list
> [e-mail]
> http://www.bio.net/biomail/listinfo/staden
>

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Staden mailing list
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