Re: [Samtools-help] samTools on solaris 10: samtools view [main_samview] fail to open file for reading

[Davide C. <dav...@if...>]

On Jun 15, 2010, at 3:14 PM, Duhaime Johanne wrote:

> Hello
>  
> I just installed samTools on Solaris 10 (SunOS 5.10 Generic_127128-11 i86pc i386 i86pc)  with samtools-0.1.7a.tar.bz2
>  
> Installation went OK (I could not installed in 64 bits but this is another problem).
>  

I could... we can share some hints.


> But I cannot make the program work as shown below. The SAM file input is from “bowtie –S”.
>  Here are the many tries I have done:
> -chmod 777 on my input file
> -run the program as ROOT
> -looking on the web, someone suggests to run the program from the directory where it is installed, which I did.
> -run MACS with –aligner SAM which was a success (so my file is recognized as a Sam file)

Don't be surprised about it... I've written SAM/BAM loader for MACS in a very loose format (and pure python...), so it doesn't make assumptions on file compliance...
Can you post some rows of your file (which are in text format)? My samtools+solaris (actually nexenta) combination works fine

$ uname -a
SunOS host001.instruments 5.11 NexentaOS_134e i86pc i386 i86pc Solaris

$ gcc --version
gcc (GCC) 4.2.3 (Ubuntu 4.2.3-2nexenta7)
Copyright (C) 2007 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

I may provide you the 64-bit binaries, as you have these libraries:


$ ldd `which samtools`
        libm.so.2 =>     /lib/64/libm.so.2
        libcurses.so.1 =>        /lib/64/libcurses.so.1
        libz.so.1 =>     /usr/lib/64/libz.so.1
        libsocket.so.1 =>        /lib/64/libsocket.so.1
        libc.so.1 =>     /lib/64/libc.so.1
        libgcc_s.so.1 =>         /lib/64/libgcc_s.so.1
        libnsl.so.1 =>   /lib/64/libnsl.so.1
        libmp.so.2 =>    /lib/64/libmp.so.2
        libmd.so.1 =>    /lib/64/libmd.so.1
        libscf.so.1 =>   /lib/64/libscf.so.1
        libuutil.so.1 =>         /lib/64/libuutil.so.1
        libgen.so.1 =>   /lib/64/libgen.so.1
        libsmbios.so.1 =>        /usr/lib/64/libsmbios.so.1

Otherwise I can build a static 32/64 bit executable.

d


/*
Davide Cittaro
Next Generation Sequencing and Microarray Data Analyst
Cogentech - Consortium for Genomic Technologies
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e-mail: dav...@if...
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