SEQanswers

Go Back   SEQanswers > Sequencing Technologies/Companies > Illumina/Solexa



Similar Threads
Thread Thread Starter Forum Replies Last Post
cufflinks source install error peromhc Bioinformatics 11 04-21-2013 07:26 PM
Error found while mapping Illumina data using BWA nirav99 Bioinformatics 15 01-14-2013 07:30 PM
fastq-dump error: table not found lionelguy Bioinformatics 1 11-20-2012 08:47 PM
ABySS install error Wallysb01 Bioinformatics 1 06-03-2011 06:11 PM
illumina2srf error: .params file not found Pepe Bioinformatics 6 04-10-2009 04:07 AM

Reply
 
Thread Tools
Old 07-25-2011, 12:34 AM   #1
soofree
Junior Member
 
Location: NWSUAF

Join Date: Apr 2011
Posts: 3
Unhappy HELP! CASAVA_v1.7.0 Install error:pthread library not found

Hi everyone,

I've been trying to install CASAVA 1.7 and run into following errors when configuration.

$../CASAVA_v1.7.0/src/configure

cmake version "cmake version 2.8.0" is already installed at /usr/local/bio-soft/CASAVA_v1.7.0-build/bootstrap/bin/cmake
nothing to be done
Using installed /usr/local/bio-soft/CASAVA_v1.7.0-build/bootstrap/bin/cmake
-- The C compiler identification is GNU
-- The CXX compiler identification is GNU
-- Check for working C compiler: /usr/bin/gcc
-- Check for working C compiler: /usr/bin/gcc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- install prefix: /usr/local
-- install exec prefix: .
-- install bin dir: ./bin
-- install lib dir: ./lib/CASAVA-1.7.0
-- install libexec dir: ./libexec/CASAVA-1.7.0
-- install include dir: include/CASAVA-1.7.0
-- install data dir: share/CASAVA-1.7.0
-- install doc dir: doc/CASAVA-1.7.0
-- install man dir: man
-- Verifying target directories access
-- Creating external tools in subdirectory opt
-- Could NOT find Boost
-- Boost 1.41.0 not found. Boost will be built from the distribution...
Decompressing /usr/local/bio-soft/CASAVA_v1.7.0/src/../redist/boost_1_41_0.tar.gz
Building Boost.Jam with toolset gcc... tools/jam/src/bin.linuxx86_64/bjam
Unicode/ICU support for Boost.Regex?... not found.
Backing up existing Boost.Build configuration in project-config.jam.1
Generating Boost.Build configuration in project-config.jam...

Bootstrapping is done. To build, run:

./bjam

To adjust configuration, edit 'project-config.jam'.
Further information:

- Command line help:
./bjam --help

- Getting started guide:
http://www.boost.org/more/getting_st...-variants.html

- Boost.Build documentation:
http://www.boost.org/boost-build2/doc/html/index.html

warning: Building Boost.Regex with the optional Unicode/ICU support disabled.
note: Please refer to the Boost.Regex documentation for more information
note: this is a strictly optional feature.
...patience...
...patience...
...found 16182 targets...
boost-1_41_0 installed successfully
-- Successfuly built boost 1.41.0 from the distribution package...
-- Installing Post-Run Command Framework
-- Check if the system is big endian
-- Searching 16 bit integer
-- Looking for sys/types.h
-- Looking for sys/types.h - found
-- Looking for stdint.h
-- Looking for stdint.h - found
-- Looking for stddef.h
-- Looking for stddef.h - found
-- Check size of unsigned short
-- Check size of unsigned short - done
-- Using unsigned short
-- Check if the system is big endian - little endian
-- Looking for floorf
-- Looking for floorf - found
-- Looking for round
-- Looking for round - found
-- Looking for roundf
-- Looking for roundf - found
-- Looking for powf
-- Looking for powf - found
-- Looking for erf
-- Looking for erf - found
-- Looking for erf
-- Looking for erf - found
-- Looking for erfc
-- Looking for erfc - found
-- Looking for erfc
-- Looking for erfc - found
-- Found ZLIB header: /usr/include/zlib.h
-- Found ZLIB library: /usr/lib/libz.so
-- gzip compression supported
-- Found BZIP2 header: /usr/include/bzlib.h
-- Found BZIP2 library: /usr/lib/libbz2.so
-- bzip2 compression supported
-- pthread headers: /usr/include
-- pthread library: PTHREAD_LIBRARY-NOTFOUND
CMake Error at cmake/macros.cmake:87 (message):
pthread library is required to build the CASAVA
Call Stack (most recent call first):
cmake/cxxConfigure.cmake:84 (casava_find_boost)
c++/CMakeLists.txt:30 (include)


-- Configuring incomplete, errors occurred!
Couldn't configure the project:

/usr/local/bio-soft/CASAVA_v1.7.0-build/bootstrap/bin/cmake -H"/usr/local/bio-soft/CASAVA_v1.7.0/src" -B"/usr/local/bio-soft/CASAVA_v1.7.0-build" -G"Unix Makefiles" -DCASAVA_PREFIX:PATH= -DCASAVA_EXEC_PREFIX:PATH= -DCMAKE_INSTALL_PREFIX:PATH= -DCASAVA_BINDIR:PATH= -DCASAVA_LIBDIR:PATH= -DCASAVA_LIBEXECDIR:PATH= -DCASAVA_INCLUDEDIR:PATH= -DCASAVA_DATADIR:PATH= -DCASAVA_DOCDIR:PATH= -DCASAVA_MANDIR:PATH= -DCMAKE_BUILD_TYPE:STRING=RelWithDebInfo

Moving CMakeCache.txt to CMakeCache.txt.removed
soofree is offline   Reply With Quote
Old 07-25-2011, 07:08 AM   #2
GenoMax
Senior Member
 
Location: East Coast USA

Join Date: Feb 2008
Posts: 7,127
Default

Not directly answering your question but is there a specific reason that you are trying to install pipeline v.1.7? Pipeline v.1.8 is out.
GenoMax is offline   Reply With Quote
Old 07-25-2011, 05:36 PM   #3
soofree
Junior Member
 
Location: NWSUAF

Join Date: Apr 2011
Posts: 3
Default

Quote:
Originally Posted by GenoMax View Post
Not directly answering your question but is there a specific reason that you are trying to install pipeline v.1.7? Pipeline v.1.8 is out.
I have installed V1.8 , but some related scripts prefer v.1.7. Thank you for your replies.

Regards,
soofree is offline   Reply With Quote
Old 07-26-2011, 07:03 PM   #4
soofree
Junior Member
 
Location: NWSUAF

Join Date: Apr 2011
Posts: 3
Default

Quote:
Originally Posted by GenoMax View Post
Not directly answering your question but is there a specific reason that you are trying to install pipeline v.1.7? Pipeline v.1.8 is out.
The CASAVA 1.7 output is Illumina 1.3+ FASTQ format, Our script only support that format. However, CASAVA 1.8 gives out Sanger FASTQ files. I want to know if the CASAVA 1.8 FASTQ format supported by SOAP denovo and BWA directly?
soofree is offline   Reply With Quote
Old 09-13-2011, 12:31 PM   #5
dweebis
Junior Member
 
Location: California

Join Date: May 2009
Posts: 8
Default

Hi Soofree -

I'm having the same issue - any resolution?

Dweeb
dweebis is offline   Reply With Quote
Old 12-08-2011, 08:36 AM   #6
tgenahmet
Member
 
Location: Phoenix

Join Date: Apr 2009
Posts: 11
Default --static

I ran into the same problem when I used --static while running configure. Removed --static and now it is past that step.
tgenahmet is offline   Reply With Quote
Old 12-08-2011, 11:08 AM   #7
Richard Finney
Senior Member
 
Location: bethesda

Join Date: Feb 2009
Posts: 700
Default

Lots of information but the critical lines here are

-- pthread library: PTHREAD_LIBRARY-NOTFOUND
CMake Error at cmake/macros.cmake:87 (message):
pthread library is required to build the CASAVA

You need the pthread library.
Richard Finney is offline   Reply With Quote
Old 12-23-2011, 02:10 PM   #8
weasteam
Member
 
Location: FL

Join Date: Dec 2008
Posts: 26
Default

Ho yeah, I am back with solutions:

In linux, try following two lines in termnal:

sudo ln -s /usr/lib/x86_64_linux_gun/lib2.so /usr/lib
sudo ln -s /usr/lib/x86_64_linux_gun/libpth* /usr/lib
weasteam is offline   Reply With Quote
Old 04-02-2013, 12:10 PM   #9
sheenams
Member
 
Location: Seattle, Washington

Join Date: Oct 2011
Posts: 15
Default

The two link commands worked for me. Just make sure you don't copy and paste as they both say 'gun' instead of 'gnu'
sheenams is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 06:53 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO