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Old 10-26-2013, 02:45 AM   #1
min1204
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Default install bcl2fastq-1.8.4

Hi everyone,

I'm trying to install illumina's software bcl2fastq-1.8.4, but there are some problems that I can't resolve. Hope someone can help me.

First, I installed it using "bcl2fastq-1.8.4.tar.bz2". It went smoothly when I did configure. But the problem came when I type make, like this:

[[email protected] CASAVA-build]# make
[ 0%] Unpacking merge.xslt
[ 2%] Built target CASAVA_MERGE_XSLT
[ 2%] Built target CASAVA_OPT
[ 48%] Built target casava_common
[ 53%] Built target casava_io
[ 61%] Built target casava_alignment
[ 64%] Built target casava_basecalling
[ 74%] Built target casava_kagu
[ 76%] Building CXX object c++/lib/demultiplex/CMakeFiles/casava_demultiplex.dir/BclDemultiplexer.cpp.o
/home/liumin/software/bcl2fastq/src/c++/lib/demultiplex/BclDemultiplexer.cpp: In member function ‘const casava::demultiplex::BclDemultiplexer::ClusterCorrectedBarcodeIndex casava::demultiplex::BclDemultiplexer::mapClusterBarcodes(unsigned int) const’:
/home/liumin/software/bcl2fastq/src/c++/lib/demultiplex/BclDemultiplexer.cpp:65: error: no matching function for call to ‘bind(<unresolved overloaded function type>, boost::arg<1>&)’
make[2]: *** [c++/lib/demultiplex/CMakeFiles/casava_demultiplex.dir/BclDemultiplexer.cpp.o] Error 1
make[1]: *** [c++/lib/demultiplex/CMakeFiles/casava_demultiplex.dir/all] Error 2
make: *** [all] Error 2

Could someone tell me why this happen?

And I also tried rpm method to install it. It gave me a message:

[[email protected] software]# rpm -i bcl2fastq-1.8.4-Linux-x86_64.rpm
error: Failed dependencies:
perl(XML::Simple) is needed by bcl2fastq-1.8.4-1.x86_64

But I already have this perl module (XML::Simple) in my server. Following list contain all perl modules:

B::Flags -- 0.10
Bio -- ???
Carp -- 1.32
Class:ata::Inheritable -- 0.08
DBD::Multiplex -- 2.11
DBD::mysql -- 4.024
DBI -- 1.628
DBI::Shell -- 11.95
Data -- ???
Devel::StackTrace -- 1.30
Digest::SHA1 -- 2.13
Exception::Class -- 1.37
ExtUtils::MakeMaker -- 6.80
IO::String -- 1.08
IO::Tee -- 0.64
IPC::Run -- 0.92
List::Util -- 1.27
Math:erivative -- undef
Math::Spline -- 0.02
Net:aemon -- 0.48
OLE::Storage_Lite -- 0.19
Opcodes -- 0.12
Parse::RecDescent -- 1.967009
Perl -- 5.10.1
SVG -- 2.59
Spreadsheet::WriteExcel -- 2.39
Statistics:escriptive -- 3.0605
Storable -- 2.45
Sub::Uplevel -- 0.24
Test:eep -- 0.110
Test::Exception -- 0.32
Test::Harness -- 3.29
Test::NoWarnings -- 1.04
Test::Simple -- 0.98
Test::Tester -- 0.109
Text::Reform -- 1.20
Thread::Cancel -- 1.13
Thread::Queue -- 3.02
Thread::Semaphore -- 2.12
Thread::Suspend -- 1.22
XML-DOM -- ???
XML:OM::XPath -- 0.14
XML::LibXML -- 2.0106
XML::NamespaceSupport -- 1.11
XML::RegExp -- 0.04
XML::SAX -- 0.99
XML::SAX::Base -- 1.08
XML::SAX::Expat -- 0.50
XML::Simple -- 2.20
XML::Twig -- 3.44
XML::Writer -- 0.623
XML::XPathEngine -- 0.14
YAML -- 0.84
threads -- 1.86
threads::shared -- 1.43

Could someone help me?
Thank you very much!

Min
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Old 10-26-2013, 02:53 AM   #2
min1204
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The system is CentOS 6.4
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Old 10-26-2013, 03:45 AM   #3
maubp
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The compilation fails due to missing a function which looks like it is part of BOOST - do the install instructions mention that you should install BOOST first?
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Old 10-26-2013, 04:34 AM   #4
min1204
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Quote:
Originally Posted by maubp View Post
The compilation fails due to missing a function which looks like it is part of BOOST - do the install instructions mention that you should install BOOST first?
Hi Peter, thank you for your answer.
But BOOST has been installed. You see,

[[email protected] ~]# yum install boost
Loaded plugins: fastestmirror, refresh-packagekit
Loading mirror speeds from cached hostfile
base | 3.7 kB 00:00
extras | 3.4 kB 00:00
updates | 3.4 kB 00:00
Setting up Install Process
Package boost-1.41.0-17.el6_4.x86_64 already installed and latest version
Nothing to do

So there might be some other problems.
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Old 10-26-2013, 04:51 AM   #5
maubp
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Have you installed the BOOST compiler header files etc using:
Code:
yum install boost-devel
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Old 10-26-2013, 05:04 AM   #6
min1204
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Quote:
Originally Posted by maubp View Post
Have you installed the BOOST compiler header files etc using:
Code:
yum install boost-devel
Yes, I have installed boost-devel.

[[email protected] ~]# yum install boost-devel
Loaded plugins: fastestmirror, refresh-packagekit
Loading mirror speeds from cached hostfile
Setting up Install Process
Package boost-devel-1.41.0-17.el6_4.x86_64 already installed and latest version
Nothing to do
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Old 10-26-2013, 05:11 AM   #7
maubp
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Hmm. The PDF instructions don't mention BOOST as a requirement when installing from source, so perhaps my guess from the error was wrong. They list:

Quote:
The following software is required to run bcl2fastq; check whether it has been installed:
  • GNU make (3.81 recommended)
  • Perl (>= 5.8)
  • libxslt
  • libxslt-devel
  • libxml2
  • libxml2-devel
  • gcc (4.0.0 or newer, except 4.0.2), with c++
  • ImageMagick
  • bzip2
  • bzip2-devel-zlib
  • zlib-devel
However, they do provide a precompiled RPM file which would perhaps work on CentOS:
http://support.illumina.com/download...tware_184.ilmn

Last edited by maubp; 10-26-2013 at 05:15 AM. Reason: correction (see page 27 of PDF)
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Old 10-26-2013, 05:18 AM   #8
maubp
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See also this thread for bcl2fastq 1.8.3 which it is suggested (part of) boost is bundled with it:
http://seqanswers.com/forums/showthread.php?t=26963
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Old 10-26-2013, 05:38 AM   #9
min1204
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Thank you very much.

I have installed all the softwares listed in the PDF document . I also tried RPM file.

[[email protected] software]# rpm -i bcl2fastq-1.8.4-Linux-x86_64.rpm
error: Failed dependencies:
perl(XML::Simple) is needed by bcl2fastq-1.8.4-1.x86_64

But I have installed this perl module. It is so weird. I just began to use Linux about two months ago. This makes me feel very confused.
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Old 10-26-2013, 06:28 AM   #10
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Hi maubp, I re-configured the bcl2fastq. Although it said configuration was successful.

-- Found X11 header: /usr/include/X11/X.h
-- Found X11 library: /usr/lib64/libX11.so
-- Found LibXml2: /usr/lib64/libxml2.so
-- using compiler: gcc version 4.4.7
-- Adding the c++ library subdirectory: common
-- Adding the c++ library subdirectory: io
-- Adding the c++ library subdirectory: alignment
-- Adding the c++ library subdirectory: basecalling
-- Adding the c++ library subdirectory: kagu
-- Adding the c++ library subdirectory: demultiplex
-- Adding the c++ program subdirectory: bin
-- Adding the c++ program subdirectory: BaseCalls
-- Adding the c++ program subdirectory: Demultiplex
-- Found Doxygen: /usr/bin/doxygen
-- Doxygen: /usr/bin/doxygen. Dot: DOXYGEN_DOT_EXECUTABLE-NOTFOUND.
-- Creating Doxygen config file: /home/liumin/software/bcl2fastq/BUILD/c++/Doxyfile
-- Adding the verifyBoost dynamic link binary checker: verifyBoost
-- Found PTHREAD header: /usr/include/pthread.h
-- Found PTHREAD library: /usr/lib64/libpthread.so
-- pthread supported
-- Configuring done
-- Generating done
-- Build files have been written to: /home/liumin/software/bcl2fastq/BUILD
The build directory /home/liumin/software/bcl2fastq/BUILD was configured successfully

Type make at the top level of the root directory to build the BCL2FASTQ converter


during the process of configuration, there were many failure tests. I didn't noticed these before, because it ran very fast. I used printscreen to get a picture.

Could you please see it and maybe you can find the problem. Thanks!
Attached Images
File Type: png configure.png (83.7 KB, 18 views)
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Old 10-26-2013, 03:32 PM   #11
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I'd recommend using the boost distribution provided with bcl2fastq. Newer versions of boost may give problems. If you have installed boost on your system, then configure will use that installation. Compile the boost 1.44 from Illumina and make it known to configure.

It is always fun installing illumina (linux) software :-)
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Old 12-11-2013, 10:31 AM   #12
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I had the same issue, and it was because of the boost library version.

go to the redist folder in the bcl2fastq distribution, and build boost 1.44 that comes in there. Then make sure that LD_LIBRARY_PATH and other system elements point to where boost is.

I finally compiled the thing

Now to see if I can make it work with my data...

Daniel
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Old 12-11-2013, 11:26 AM   #13
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Unfortunately it doesn't work...
e.g. locs file are now clocs file, Assumes certain filenames that are different, etc... I don't think it was done for use with MiSeq.

Anyone has any experience with this??

Thanks,
Daniel
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Old 12-11-2013, 11:45 AM   #14
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Did you check the manual that goes with it? Look at the options for the conversion/demultiplexing that should allow you to make the necessary adjustments (e.g. --positions-format clocs vs locs).

AFAIK it should work with MiSeq data (you would need the entire data folder). We use CASAVA regularly with MiSeq data and this is just a fraction of that package.
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Old 12-11-2013, 12:13 PM   #15
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Yes, I'm reading the documentation from here:
http://supportres.illumina.com/docum...38058brpmi.pdf

It actually complains that the SampleSheet does not have the correct format:

configureBclToFastq.pl --input-dir Data/Intensities/BaseCalls --output-dir Unaligned --positions-format .locs --no-eamss
"ERROR: Wrong number of fields in sample sheet (expected: 10, got 2: IEMFileVersion,4)"

Good to know someone is using the software for MiSeq... there's still hope then.

Thanks,
Daniel
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Old 12-11-2013, 12:19 PM   #16
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Quote:
Originally Posted by dsobral View Post
Yes, I'm reading the documentation from here:
http://supportres.illumina.com/docum...38058brpmi.pdf

It actually complains that the SampleSheet does not have the correct format:

configureBclToFastq.pl --input-dir Data/Intensities/BaseCalls --output-dir Unaligned --positions-format .locs --no-eamss
"ERROR: Wrong number of fields in sample sheet (expected: 10, got 2: IEMFileVersion,4)"

Good to know someone is using the software for MiSeq... there's still hope then.

Thanks,
Daniel
I am going to let you go through what I posted in the new thread you started. Let us work through that thread since your problem is no longer about installation. We can fix the samplesheet easily.

Once you respond to the questions in the other thread we can continue.
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Old 12-11-2013, 12:31 PM   #17
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Thanks. I'm continuing this in the other thread:
http://seqanswers.com/forums/showthread.php?t=39153

Daniel
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Old 07-23-2014, 05:37 AM   #18
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I had the confusing trouble at the installing for Hiseq v4 but I solved it. (^^)
In my case it was because of the Boost library version and the incompatibility with gcc in my default environment on Linux.

The following version set is NG.
Boost C++ library v 1.55.0 or v 1.44.0
gcc 4.8.1, with c++

The following version set is OK !!
Boost C++ library v 1.44.0
gcc 4.6.2, with c++

We need to set the following environment variables to use specified Boost and gcc for configuring the build.
CC
CXX

BOOST_ROOT #location of the boost library
BOOST_INCLUDEDIR #location of the include directory of boost
BOOST_LIBRARYDIR #location of the lib directory of boost

*For details, refer to "configure help".
$ bcl2fastq-1.8.4/src/configure --help

Last edited by roko-t; 07-23-2014 at 05:36 PM.
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