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

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

Reading the file:

> /apps/programs/samtools faidx mm9.fa
> ls -l mm9.fa.fai
-rw-r--r--   1 duhaimj  si            21 Jun 21 10:50 mm9.fa.fai
> ls -l s_3.sam
-rwxrwxrwx   1 duhaimj  si       5053665320 Jun 14 16:26 s_3.sam
> /apps/programs/samtools view -bt mm9.fa.fai s_3.sam > s_3.bam
[main_samview] fail to open file for reading.


Running the provided 64 bits binary:
# crle -64

Default configuration file (/var/ld/64/ld.config) not found
  Default Library Path (ELF):   /lib/64:/usr/lib/64  (system default)
  Trusted Directories (ELF):    /lib/secure/64:/usr/lib/secure/64  (system default)

 ./samtools
ld.so.1: samtools: fatal: libz.so.1: version `ZLIB_1.2.2' not found (required by file samtools)
ld.so.1: samtools: fatal: libz.so.1: open failed: No such file or directory
Killed

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
        libz.so.1 (ZLIB_1.2.2) =>        (version not found)
        libsocket.so.1 =>        /lib/64/libsocket.so.1
        libc.so.1 =>     /lib/64/libc.so.1
        libgcc_s.so.1 =>         (file not found)
        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
        libdoor.so.1 =>  /lib/64/libdoor.so.1
        libuutil.so.1 =>         /lib/64/libuutil.so.1
        libgen.so.1 =>   /lib/64/libgen.so.1


file /usr/lib/64/libz.so.1
/usr/lib/64/libz.so.1:  ELF 64-bit LSB dynamic lib AMD64 Version 1, dynamically linked, not stripped, no debugging information available.

I guest I first need to upgrade the library. Will version ZLIB 1.2.5 (current) work?


De : Davide Cittaro [mailto:dav...@if...]
Envoyé : 21 juin 2010 10:24
À : Duhaime Johanne
Cc : sam...@li...
Objet : Re: [Samtools-help] samTools on solaris 10: samtools view [main_samview] fail to open file for reading

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

/*
Davide Cittaro

Cogentech - Consortium for Genomic Technologies
via adamello, 16
20139 Milano
Italy

tel.: +39(02)574303007
e-mail: dav...@if...<mailto:dav...@if...>
*/