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

[Duhaime J. <Joh...@ir...>]

Hello

I just installed samTools on Solaris 10 (SunOS 5.10 Generic_127128-11 i86pc i386 i86pc)  with samtools-0.1.7a.tar.bz2<http://sourceforge.net/projects/samtools/files/samtools/0.1.7/samtools-0.1.7a.tar.bz2/download>

Installation went OK (I could not installed in 64 bits but this is another problem).

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)
-as said I went through the web to look for that problem, but most of the time the solution was not there.

I would appreciate very much if you could help me. Thank you in advance.

# ./samtools view

Usage:   samtools view [options] <in.bam>|<in.sam> [region1 [...]]

Options: -b       output BAM
         -h       print header for the SAM output
         -H       print header only (no alignments)
         -S       input is SAM
         -u       uncompressed BAM output (force -b)
         -x       output FLAG in HEX (samtools-C specific)
         -X       output FLAG in string (samtools-C specific)
         -t FILE  list of reference names and lengths (force -S) [null]
         -T FILE  reference sequence file (force -S) [null]
         -o FILE  output file name [stdout]
         -f INT   required flag, 0 for unset [0]
         -F INT   filtering flag, 0 for unset [0]
         -q INT   minimum mapping quality [0]
         -l STR   only output reads in library STR [null]
         -r STR   only output reads in read group STR [null]
         -?       longer help

# ./samtools view -S s_3.sam
[main_samview] fail to open file for reading.

Johanne Duhaime
IRCM
du...@ir...