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

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

Dear Johanne

On Jun 21, 2010, at 3:14 PM, Duhaime Johanne wrote:

> Thank you for your help
>  
> 1-      about reading  sam file
> Here are the  first lines from my SAM file
> 



> > /apps/programs/bin/samtools view -S s_3.sam -b s_3_bam
> [main_samview] fail to open file for reading.

Mmm... here's working. I may be asking a dummy question, but are you sure the file exists in your cwd? I mean, that error comes when samtools can't find the file... BTW, to make an exact conversion I've did  like this:

samtools view -bt path/to/mm9/genome/fasta/file/indexed/for/samtools/fai s_3.sam > s_3.bam

>  
>  
> 2-      about compiling in 64 bits
> I do have the libraries except libncurses.so.5 (which I think is necessary only for tview) in /lib/64 and /usr/lib/64. It would be nice to have your 64 binaries if possible. I will continue to try to compile samtools but meanwhile users could use it.

can you check the output of 

$ crle  -64          

?

Also, can you try this binary:

http://dl.dropbox.com/u/275606/samtools.sol64

and check it works on your solaris box?

d

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