Question: Error installing bcl2fastq 2.20 in make step - Ubuntu 18.04
0
gravatar for dfajar2
12 weeks ago by
dfajar260
dfajar260 wrote:

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.

ADD COMMENTlink modified 5 weeks ago • written 12 weeks ago by dfajar260
1

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

ADD REPLYlink written 12 weeks ago by genomax71k
1

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.

ADD REPLYlink modified 12 weeks ago • written 12 weeks ago by finswimmer12k

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

ADD REPLYlink written 12 weeks ago by genomax71k
1

There is a patch available by Lior Galanti.

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

ADD REPLYlink written 12 weeks ago by arup1.7k

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 :-)

ADD REPLYlink written 9 weeks ago by dfajar260

I found a solution. Look below

ADD REPLYlink modified 5 weeks ago • written 5 weeks ago by dfajar260
2
gravatar for dfajar2
5 weeks ago by
dfajar260
dfajar260 wrote:

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/

ADD COMMENTlink written 5 weeks ago by dfajar260
1
gravatar for swbarnes2
9 weeks ago by
swbarnes26.5k
United States
swbarnes26.5k wrote:

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

ADD COMMENTlink written 9 weeks ago by swbarnes26.5k

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

ADD REPLYlink written 5 weeks ago by dfajar260
1
gravatar for Eric Lim
9 weeks ago by
Eric Lim1.4k
Stoke Therapeutics, Inc
Eric Lim1.4k wrote:

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.
ADD COMMENTlink written 9 weeks ago by Eric Lim1.4k
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