Conversion Issue with bcl2fastq2

Question

[Christopher]

Hello, everyone. I'm currently facing an issue that seems easy to fix, but I'm unsure about the solution. I've been trying to resolve it for the past few days.

Let me explain. I'm trying to convert some CBCL files to FASTQ using the bcl2fastq2 software by Illumina. I have four lanes, and only one is converting successfully, while the other three are encountering issues.

Upon reviewing the warning log, the following text is present:

(base) [root@localhost Logs]# cat warning_00000.log
....
2024-01-25, 10:57:18, Thread 18, Tile 4_151076, Cycle 1, 0, Could not locate upper left fiducial with initial sub-region size. Using default location.
2024-01-25, 11:04:23, Thread 13, Tile 2_131026, Cycle 2, Registration failure
2024-01-25, 11:04:23, Thread 13, Tile 2_131026, Cycle 2, Number of sampled clusters for phasing correction was 0 (target sample count is 10000).
2024-01-25, 11:04:23, Thread 13, Tile 2_131026, Cycle 2, Number of sampled clusters for FitGaussians was 0 (target sample count is 7000).
 ....

Is there an issue with my run, or is the bcl2fastq2 software not processing the other lanes? If it's not running, are there alternative options to process each lane separately?

Thank you in advance

[GenoMax]

Did you do this run or did someone else (and the data folder was handed to you)? Were you given to understand that there were no problems during this run, if you did not do the run? There appears to be a problem with the registration of the flowcell position markers and may require assistance of Illumina tech support. Have never seen fiducial errors during post-processing of data.

You could try using bclconvert instead of bcl2fastq. Providing lane specific samplesheets will allow you to process just one lane at a time with either software, if you want to try that.