Error installing bcl2fastq 2.20 in make step - Ubuntu 18.04

Question

[dfajar2]

After spending numerous hours trying to install bcl2fastq 2.20 in my server I decided to ask for help.

I am trying to install bcl2fastq 2.20 in Ubuntu 18.04. I have followed multiple recommendations for fixing inconveniences while installing bcl2fastq with newer boost versions (as in these posts here and here ).

I don't get any errors after running configure from the build directory. My error appears after typing make afterwards.

 $ make
Scanning dependencies of target BCL2FASTQ_OPT
[  0%] Built target BCL2FASTQ_OPT
Scanning dependencies of target bcl2fastq_common
[  1%] Building CXX object cxx/lib/common/CMakeFiles/bcl2fastq_common.dir/Logger.cpp.o
/media/software/bcl2fastq/bcl2fastq/src/cxx/lib/common/Logger.cpp: In constructor ‘bcl2fastq::common::detail::LogStream::LogStream()’:
/media/software/bcl2fastq/bcl2fastq/src/cxx/lib/common/Logger.cpp:122:13: error: ‘clog’ is not a member of ‘std’
 , ias_(std::clog)
             ^~~~
/media/software/bcl2fastq/bcl2fastq/src/cxx/lib/common/Logger.cpp:122:13: note: suggested alternative: ‘log’
 , ias_(std::clog)
             ^~~~
             log
/media/software/bcl2fastq/bcl2fastq/src/cxx/lib/common/Logger.cpp: In constructor ‘bcl2fastq::common::detail::LogStream::LogStream(bcl2fastq::common::LogLevel::value_type)’:
/media/software/bcl2fastq/bcl2fastq/src/cxx/lib/common/Logger.cpp:130:13: error: ‘clog’ is not a member of ‘std’
 , ias_(std::clog)
             ^~~~
/media/software/bcl2fastq/bcl2fastq/src/cxx/lib/common/Logger.cpp:130:13: note: suggested alternative: ‘log’
 , ias_(std::clog)
             ^~~~
             log
/media/software/bcl2fastq/bcl2fastq/src/cxx/lib/common/Logger.cpp: In copy constructor ‘bcl2fastq::common::detail::LogStream::LogStream(const bcl2fastq::common::detail::LogStream&)’:
/media/software/bcl2fastq/bcl2fastq/src/cxx/lib/common/Logger.cpp:146:13: error: ‘clog’ is not a member of ‘std’
 , ias_(std::clog)
             ^~~~
/media/software/bcl2fastq/bcl2fastq/src/cxx/lib/common/Logger.cpp:146:13: note: suggested alternative: ‘log’
 , ias_(std::clog)
             ^~~~
             log
cxx/lib/common/CMakeFiles/bcl2fastq_common.dir/build.make:57: recipe for target 'cxx/lib/common/CMakeFiles/bcl2fastq_common.dir/Logger.cpp.o' failed
make[2]: *** [cxx/lib/common/CMakeFiles/bcl2fastq_common.dir/Logger.cpp.o] Error 1
CMakeFiles/Makefile2:257: recipe for target 'cxx/lib/common/CMakeFiles/bcl2fastq_common.dir/all' failed
make[1]: *** [cxx/lib/common/CMakeFiles/bcl2fastq_common.dir/all] Error 2
Makefile:126: recipe for target 'all' failed
make: *** [all] Error 2

ANy ideas on how to fix this? Suggestions are highly appreciated.

[GenoMax]

Perhaps you should save yourself the trouble and use conda to install: https://anaconda.org/dranew/bcl2fastq ?

[finswimmer]

But the version in conda is still on 2.19.

What works for me, is to take the rpm file and simply unpack the files in it.

[GenoMax]

Unless OP needs to use this for a NovaSeq S4 flowcell, v. 2.19.0 should be ok for all other data.

[Arup Ghosh]

There is a patch available by Lior Galanti.

https://backwardincompatible.com/post/169360794395/compiling-illumina-bcl2fastq-220-on-ubuntu-with

[dfajar2]

Thanks everyone for their suggestions. I am looking to install version 2.20 rather to 2.19. I'll try the rpm approach and also the patch to see if that solves my problem. Thanks I appreciate your help :-)

[dfajar2]

I found a solution. Look below

Answer 1

[dfajar2]

I finally found a post on how to install bcl2fastq v2.20 from a tarball. I followed the instructions and installed it with no errors!!! https://sarahpenir.github.io/linux/Installing-bcl2fastq/

Answer 2

[swbarnes2]

FWIW, my IT guy couldn't install bcl2fastq like this either. He used the rpm.

[dfajar2]

Well, I'm glad I'm not the only one :-)

Answer 3

[Eric Lim]

Have you tried installing via freenome?

[~/Downloads]$ docker run -it --entrypoint /bin/bash ubuntu:18.04
root@2dc2434b4405:/# conda install -c freenome bcl2fastq
...
root@2dc2434b4405:/# bcl2fastq -v
BCL to FASTQ file converter
bcl2fastq v2.20.0.422
Copyright (c) 2007-2017 Illumina, Inc.

Answer 4

[irritable_phd_syndrome]

I had a similar error (CentOS 8.1) with

bcl2fastq/src/cxx/include/common/Logger.hh:38:14: error: ‘clog’ is not a member of ‘std’

Following motivation from stackoverflow, I added

#include <iostream> 

to line 24 of Logger.hh

This got past this error and then encountered the same issue experienced by backwards incompatible. Using his solution, in bcl2fastq/src/cxx/lib/io/Xml.cpp, I converted :

#ifndef WIN32
        boost::property_tree::write_xml(os, treeWithIndexAttributes, boost::property_tree::xml_writer_make_settings(' ', 2));
#else
        boost::property_tree::write_xml(os, treeWithIndexAttributes, boost::property_tree::xml_writer_make_settings<std::string>(' ', 2));
#endif
    }
    else
    {
#ifndef WIN32
        boost::property_tree::write_xml(os, tree, boost::property_tree::xml_writer_make_settings(' ', 2));
#else
        boost::property_tree::write_xml(os, tree, boost::property_tree::xml_writer_make_settings<std::string>(' ', 2));
#endif

to :

    boost::property_tree::write_xml(os, treeWithIndexAttributes, boost::property_tree:
}
else
{
    boost::property_tree::write_xml(os, tree, boost::property_tree::xml_writer_make_se
}

With this the compilation successfully completed.

[Alexander]

Both of these fixes were also necessary for me.

Answer 5

[GenoMax]

This is not an answer for the original question but since it is an important change I am adding this here:

You should consider installing bcl-convert (LINK) instead of bcl2fastq in 2021. bcl-convert is replacing bcl2fastq and will be supported in future. If you need to process NextSeq 2K data then bcl-convert is a requirement. bcl-convert can process data from all other sequencers Illumina makes and can fully replace bcl2fastq.