[Staden] gap4 running problem load_alignment_matrix error
(by alison.gardner from adelaide.edu.au)
Sun Feb 1 18:20:54 EST 2009
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
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
> 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
> 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.
> On Thu, Jan 29, 2009 at 06:27:19PM -0800, alig wrote:
>> I am trying to install Staden Gap4 on a 64 bit machine with Ubuntu
>> It appears that trev & pregap will start. But when I type gap4& I get
>> message -
>> invalid command name "load_alignment_matrix"
>> while executing
>> "load_alignment_matrix [keylget gap_defs ALIGNMENT.MATRIX_FILE]"
>> line 683)
>> I have followed a number of suggestions from this site & others &
>> some missing libraries, but still get this message.
>> Have done strace -o output.txt gap4 and not sure of any more errors in
>> I will try to attach the file
>> http://www.nabble.com/file/p21740409/output.txt output.txt
>> Can anyone help please
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