Error: Segmentation Fault in BCL2FASTQ

Question

[Luna]

I need to convert my data from bcl to fastq, but I kept on getting Segmentation fault error. I use the command

bcl2fastq \
  --input-dir /230810_MN01224_0003_A000H3C2HM/Data/Intensities/BaseCalls \
  --output-dir /230810_MN01224_0003_A000H3C2HM/fastq_files \
  --sample-sheet /230810_MN01224_0003_A000H3C2HM/SampleSheet.csv \
  --no-lane-splitting

I tried a solution from BCL2FASTQ: Segmentation Fault Error (segfault) but I still get the same error.

I'm running bcl2fastq on Ubuntu 22.04.3 LTS using WSL. Not sure if this might be one of the reason why I get this error.

Any insights or suggestions you can provide to help with this issue would be greatly appreciated.

[GenoMax]

I'm running bcl2fastq on Ubuntu 22.04.3 LTS using WSL. Not sure if this might be one of the reason why I get this error.

That could very well be. Other thing to check is amount of RAM you have available for WSL2.

[Luna]

I think I do have enough. Are there any other options that I can try?

[GenoMax]

Do you get the segfault immediately or some time after the command starts running? Have you tried to capture/look at log files?

[Luna]

I get the error immediately. I am now using virtualbox to run redhat 9.3 to see if I will still get the error. Still in the process of downloading all my data.

I just hope that I have allotted enough memory and storage to run everything.

[Florent]

If you try bcl2fastq -h or -v, does it return help or version ?

[Luna]

Yes. The problem could be due to the use of WSL. I was finally able to convert all my files into fastq when I used rhel in virtualbox.