Hi, I have been having problems with the installation of Lofreq. I'm quite in this but I have previously install samtools and when I follow your steps to install lofreq it seems that it work but when I run lofreq_snpcaller.py -f ref.fa -b mapping.bam -o raw-snv-output-file this message appear:
Segmentation fault:11
As I have a mac with Xcode I decided to do ./configure CFLAGS="-arch x86_64" LDFLAGS="-arch x86_64", as you recommend to see if it fix the problem but then I get after make install this error:
make [1] *** [lofreq_samtools] Error 1.
I don't know what else to try.
Thanks
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
A segmentation fault is usually a sign, that something is very wrong.
Which version of LoFreq are you using?
What is the OS X version you are working on?
Would you mind to give the precompiled beta version a try? See http://sourceforge.net/projects/lofreq/files/lofreq_star-2.0.0-beta-3-macosx.tgz/download
The only problem there is that the documentation is very much
incomplete for now. Have a look at the contained README. Basically,
all LoFreq functions should be accessible through the main binary in
src/lofreq/lofreq.
Hi, I have been having problems with the installation of Lofreq. I'm quite
in this but I have previously install samtools and when I follow your steps
to install lofreq it seems that it work but when I run lofreq_snpcaller.py
-f ref.fa -b mapping.bam -o raw-snv-output-file this message appear:
Segmentation fault:11
As I have a mac with Xcode I decided to do ./configure CFLAGS="-arch x86_64"
LDFLAGS="-arch x86_64", as you recommend to see if it fix the problem but
then I get after make install this error:
make [1] *** [lofreq_samtools] Error 1.
I download lofreq-0.6.1. I have mac os x 10.9 maverick. I have python 2.7.5, I install the c compiler and also zlib through homebrew as well as samtools, this last one works perfectly. I don't know if lofreq is not working cos I missing some of the headers file. I'm quite new with programs and I'm learning in the go.
I download the beta version but when I try to do ./configure it saids no such file or directory. It could be cos the beta version does not have any src folder as the 0.6.1 version?
Sorry for such basics questions but I really appreciate any help.
Thanks
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
the beta is already compiled. You don't need to run configure or make.
The binary should be there already. That's why it should be easier to
use this version (even though it still lacks documentation).
As for lofreq-0.6.1: it sounds like this should work given your setup.
Could you please send me the file named config.log and the console
output you get if you run make clean and then make? If you don't want
to post it on the mailing list, feel free to email me directly:
andreas.wilm@gmail.com
I download lofreq-0.6.1. I have mac os x 10.9 maverick. I have python 2.7.5,
I install the c compiler and also zlib through homebrew as well as samtools,
this last one works perfectly. I don't know if lofreq is not working cos I
missing some of the headers file. I'm quite new with programs and I'm
learning in the go.
I download the beta version but when I try to do ./configure it saids no
such file or directory. It could be cos the beta version does not have any
src folder as the 0.6.1 version?
Sorry for such basics questions but I really appreciate any help.
Thanks
Hi, I have been having problems with the installation of Lofreq. I'm quite in this but I have previously install samtools and when I follow your steps to install lofreq it seems that it work but when I run lofreq_snpcaller.py -f ref.fa -b mapping.bam -o raw-snv-output-file this message appear:
Segmentation fault:11
As I have a mac with Xcode I decided to do ./configure CFLAGS="-arch x86_64" LDFLAGS="-arch x86_64", as you recommend to see if it fix the problem but then I get after make install this error:
make [1] *** [lofreq_samtools] Error 1.
I don't know what else to try.
Thanks
Hi Elena,
A segmentation fault is usually a sign, that something is very wrong.
Which version of LoFreq are you using?
What is the OS X version you are working on?
Would you mind to give the precompiled beta version a try? See
http://sourceforge.net/projects/lofreq/files/lofreq_star-2.0.0-beta-3-macosx.tgz/download
The only problem there is that the documentation is very much
incomplete for now. Have a look at the contained README. Basically,
all LoFreq functions should be accessible through the main binary in
src/lofreq/lofreq.
Andreas
On 16 February 2014 07:47, Elena marulin@users.sf.net wrote:
--
Andreas Wilm
andreas.wilm@gmail.com | mail@andreas-wilm.com | 0x7C68FBCC
Hi Andreas,
I download lofreq-0.6.1. I have mac os x 10.9 maverick. I have python 2.7.5, I install the c compiler and also zlib through homebrew as well as samtools, this last one works perfectly. I don't know if lofreq is not working cos I missing some of the headers file. I'm quite new with programs and I'm learning in the go.
I download the beta version but when I try to do ./configure it saids no such file or directory. It could be cos the beta version does not have any src folder as the 0.6.1 version?
Sorry for such basics questions but I really appreciate any help.
Thanks
Hi Elena,
the beta is already compiled. You don't need to run configure or make.
The binary should be there already. That's why it should be easier to
use this version (even though it still lacks documentation).
As for lofreq-0.6.1: it sounds like this should work given your setup.
Could you please send me the file named config.log and the console
output you get if you run make clean and then make? If you don't want
to post it on the mailing list, feel free to email me directly:
andreas.wilm@gmail.com
Thanks,
Andreas
On 17 February 2014 15:27, Elena marulin@users.sf.net wrote:
--
Andreas Wilm
andreas.wilm@gmail.com | mail@andreas-wilm.com | 0x7C68FBCC