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Old 11-29-2010, 08:05 PM   #1
ketan_bnf
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Location: India

Join Date: Oct 2010
Posts: 59
Default Need help for installation of AMOS-2.0.8

Hi friends,

I am trying to install AMOS on my Ubuntu 9.10 system, it configure allright, but the problem is when applying "make" it gives following errors,


IDMap_AMOS.cc: In member function ‘void AMOS::IDMap_t::read(const std::string&)’:
IDMap_AMOS.cc:504: error: ‘fopen’ was not declared in this scope
IDMap_AMOS.cc:509: error: ‘fscanf’ was not declared in this scope
IDMap_AMOS.cc:515: error: ‘fscanf’ was not declared in this scope
IDMap_AMOS.cc:517: error: ‘getc’ was not declared in this scope
IDMap_AMOS.cc:529: error: ‘EOF’ was not declared in this scope
IDMap_AMOS.cc:540: error: ‘EOF’ was not declared in this scope
IDMap_AMOS.cc:557: error: ‘fclose’ was not declared in this scope
make[3]: *** [libAMOS_a-IDMap_AMOS.o] Error 1
make[3]: Leaving directory `/home/orf/amos-2.0.8/src/AMOS'
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory `/home/orf/amos-2.0.8/src'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/home/orf/amos-2.0.8'
make: *** [all] Error 2

Why?

And another thing i am trying to get BAM/SAM files using *_sorted.dat/.bin as said in the manual of MOSAIK, using MosaikText but i think it is not giving right output (output file size = 0 bytes).

When i open it in Gambit it shows nothing, it only shows name of the reference sequence, bases are not displayed.

Is there any other tool for conversion of Mosaik result to SAM/BAM format?
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Old 11-30-2010, 07:23 AM   #2
lcollado
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Location: Baltimore, MD

Join Date: Jun 2009
Posts: 65
Default

Check this thread on how to install AMOS:
http://seqanswers.com/forums/showthr...highlight=amos
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L. Collado Torres, Ph.D. student in Biostatistics.
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