Error: Segmentation Fault in BCL2FASTQ
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.
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
bcl2fastq
written by kilcdincer •
-
Error during demultiplexing by bcl2fastq
written by daffodil •
-
BCL2FASTQ: Segmentation Fault Error (segfault)
written by gillhuberfelix •
-
Bcl2fastq conversion
written by abiuma •
-
bcl2fastq dumps most of the reads as undetermined
written by rohitsatyam102
-
bcl2fastq error
written by 17318598206 •
-
bcl2fastq error? (bcl2fastq::common::InputDataError)
written by Clark_BioMorgan •
-
Demultiplex Novaseq run with mixed samples containing either UDI alone or UMI-UDI
written by diwasri •
-
Bcl2fastq conversion according to samples (demultiplexing)
written by 1234anjalianjali1234 •
-
bcl2fastq-V2 How to skip some line
written by BioRyder
That could very well be. Other thing to check is amount of RAM you have available for WSL2.
I think I do have enough. Are there any other options that I can try?
Do you get the segfault immediately or some time after the command starts running? Have you tried to capture/look at log files?
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.
If you try bcl2fastq -h or -v, does it return help or version ?
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.