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.