bcl2fastq can't find config.xml

Question

[filges.stefan]

Hi,

I am trying to demultiplex an Illumina run folder using bcl2fastq. I have previously done this on a different system, which has since been changed. I am repeating it on a new CentOS 7 cluster (on which I have sudo rights), but I am getting the following error:

[filges_stefan@centos data]$ /usr/local/bin/configureBclToFastq.pl --use-bases-mask=Y26,I8,Y98   --fastq-cluster-count=20000000 --no-eamss   --ignore-missing-control --ignore-missing-stats --ignore-missing-bcl --mismatches=1   --sample-sheet $SAMPLES   --input-dir=$FLOWCELL_ID/Data/Intensities/BaseCalls  --output-dir=$OUTPUT_DIR

Use of qw(...) as parentheses is deprecated at /usr/local/lib/bcl2fastq-1.8.4/perl/Casava/Alignment/Config.pm line 747.

Use of qw(...) as parentheses is deprecated at /usr/local/lib/bcl2fastq-1.8.4/perl/Casava/Alignment/Config.pm line 751.

2019-10-23 07:17:20] [configureBclToFastq.pl] INFO: Creating directory '/home/filges_stefan/data/fastq'

ERROR: /home/filges_stefan/data/190328_NB501037_0388_AH5W7MBGXB/Data/Intensities/BaseCalls/config.xml: file does not exist at /usr/local/lib/bcl2fastq-1.8.4/perl/Casava/Demultiplex.pm line 116.

The file really does not exist. I also checked other run folders that our core facility uploaded for us and that have all been fine to use previously, even though they too don't have a config.xml file in the BaseCalls directory...

A quick google search didn't give any results for this either. Any suggestions on what might be the problem and how to fix it?

edit: I tried setting --flowcell-id=$FLOWCELL_ID as well, but it yields the same error.

[Devon Ryan]

Why not use bcl2fastq2? bcl2fastq 1.8.4 has been deprecated for years.

Answer 1

[Arup Ghosh]

Looks like bcl2fastq-1.8.4 is not compatible with the default Perl version of Centos 7. Use the latest version of Bcl2Fastq, download and install the RPM file.

[filges.stefan]

Thank you! Indeed, that was the problem, bcl2fastq2 works fine!

[GenoMax]

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