I installed a following docker image,
REPOSITORY TAG IMAGE ID CREATED SIZE zymoresearch/bcl2fastq latest 037f216c2523 13 months ago 117MB
and run a following command;
docker run -d --name bcl2fastq -v /Volumes/Aura2/bcl_NU/170720_NB501488_0132_AH5V32BGX3:/mnt/run -v /Volumes/Aura2/output:/mnt/out zymoresearch/bcl2fastq:2.20 -R /mnt/run -o /mnt/out/Data/Intensities/BaseCalls/Alignment_1 --barcode-mismatches 0 --with-failed-reads --no-lane-splitting -p 24
This generates fastq files but they are all 0Ks. I looked at the log file but nothing stands out as a major error. Since I am really getting stuck trouble shooting this issue, I'd really appreciate any inputs and suggestions.