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Re: [Samtools-help] samTools on solaris 10: samtools view [main_samview] fail to open file for reading
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From: Duhaime J. <Joh...@ir...> - 2010-06-21 13:28:34
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thank for the precision. But I still have the problem. > /apps/programs/samtools view -bS s_3.sam > s_3_bam [main_samview] fail to open file for reading. -----Message d'origine----- De : Tom Blackwell [mailto:tb...@um...] Envoyé : 21 juin 2010 09:26 À : Duhaime Johanne Cc : Davide Cittaro; sam...@li... Objet : Re: [Samtools-help] samTools on solaris 10: samtools view [main_samview] fail to open file for reading Johanne - In the samtools command line, all flags come before the input file name, and the output -- even in .bam format -- is written to stdout. I would have used instead: /apps/programs/bin/samtools view -bS s_3.sam > s_3_bam - tom blackwell - On Mon, 21 Jun 2010, Duhaime Johanne wrote: > Thank you for your help > > 1- about reading sam file > > /apps/programs/bin/samtools view -S s_3.sam -b s_3_bam > > [main_samview] fail to open file for reading. > > 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. > > Thank you very much > Johanne > > De : Davide Cittaro [mailto:dav...@if...] > Envoyé : 19 juin 2010 09:23 > À : Duhaime Johanne > Cc : sam...@li... > Objet : Re: [Samtools-help] samTools on solaris 10: samtools view [main_samview] fail to open file for reading > > > 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<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). > > > 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 > via adamello, 16 > 20139 Milano > Italy > > tel.: +39(02)574303007 > e-mail: dav...@if...<mailto:dav...@if...> > */ > > > > > > |
