Question: Installation of Bcl2Fastq Fails
0
gravatar for dec986
2.0 years ago by
dec986100
United States
dec986100 wrote:

I am trying to install Illumina's bcl2fastq but I am getting errors I can't find solutions to:

-- Found Doxygen: /usr/bin/doxygen 
-- Doxygen: /usr/bin/doxygen. Dot: DOXYGEN_DOT_EXECUTABLE-NOTFOUND.
-- Creating Doxygen config file: /home/con/Downloads/bcl2fastq_v1.8.4/src/c++/Doxyfile
-- Configuring incomplete, errors occurred! Couldn't configure the project

Google doesn't have anything on this... and Illumina technical support is very very slow... does anyone know how to solve this?

thanks :)

ADD COMMENTlink modified 2.0 years ago • written 2.0 years ago by dec986100

If your system accepts RPMs, then that'll be easier than getting this compiled.

ADD REPLYlink written 2.0 years ago by Devon Ryan80k

What sequencer are you hoping to process the data from? If that is NextSeq 500 or HiSeq 3K/4K then you should get the new version of bcl2fastq (v. 2.17.x). As @Devon said use the RPM if you can.

ADD REPLYlink modified 2.0 years ago • written 2.0 years ago by genomax49k

As Devon suggested, I downloaded the RPM, and am trying to convert to deb but this fails:

con@e:~/Downloads/bcl2fastq_v1.8.4$ fakeroot alien bcl2fastq-1.8.4-Linux-x86_64.rpm Unpacking of 'bcl2fastq-1.8.4-Linux-x86_64.rpm' failed at /usr/share/perl5/Alien/Package/Rpm.pm line 168.

I looked at the line 168:

$this->do("rpm2cpio '".$this->filename."' | (cd $workdir; $decomp cpio --extract --make-directories --no-absolute-filenames --preserve-modification-time) 2>&1")
    or die "Unpacking of '".$this->filename."' failed";

I have no idea how to fix this :(

ADD REPLYlink written 2.0 years ago by dec986100

Which perl are you using? As I recollect, Bcl2fastq v.1.x requires perl v.5.12.

ADD REPLYlink written 2.0 years ago by genomax49k

hi genomax2,

I'm using 5.22.1, I tried this, as you said,

use 5.12.0;

but it outputs Name "Alien::Version" used only once: possible typo at alien.pl line 375.

and no output file. I comment this line out, and nothing happens.

-still stuck

ADD REPLYlink modified 2.0 years ago • written 2.0 years ago by dec986100

I suggest that you get bcl2fastq v.2.17.x. It is backwards compatible with all sequencer types and should install easier than v.1.x.

That said see if these two threads help: http://seqanswers.com/forums/showthread.php?t=45649
http://seqanswers.com/forums/showthread.php?t=45649

ADD REPLYlink written 2.0 years ago by genomax49k

Do you just have to demultiplex stuff this one time or is this going to be a regular thing? If this is just a one-off instance, then it might be simplest to setup a Centos-based docker container and directly install bcl2fastq in it. You could then demultiplex stuff inside the container. Yes, this seems convoluted, but it might prove quicker.

ADD REPLYlink written 2.0 years ago by Devon Ryan80k
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