Seeking Help with Cell Ranger Multi Error in fixed-RNA-profiling

Question

[lam]

Hello everyone,

I am encountering an issue while attempting to execute Cell Ranger Multi on fixed RNA profiling sequencing data in the context of Multiplex FRP with 1 Probe Barcode per sample. I work on sequenced four samples within a single library.

Here is the command I executed:

 ./cellranger multi --id=SourisKI_manip_10X_run_16012024 \
              --csv=path/to/SourisKI_manip_10X_run_16012024.csv \
              --localcores=80 \
              --localmem=128 \
              --output-dir=path/to/outputs

However, I am facing the following error:

[error] Pipestance failed. Error log at: resultats_localcore/SC_MULTI_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/FILTER_BARCODES/fork0/chnk0-uae9ef2e0ee/_errors

Log message:

Job failed in stage code
signal: segmentation fault (core dumped)

Has anyone encountered this error before and managed to resolve it?

Thank you in advance for your help.

[GenoMax]

seg faults may point to not enough memory being available for the job. Using 80 cores seems like an overkill. Please try reducing that number to something smaller (say 12 or 16) and see if that makes the job "go".

[naveau]

EDIT : upgrading cellranger to v8.0.0 solve the problem. According to the 10x support, some other users experience the same issue with version 7 of the pipeline.

---

Thanks for pointing this out. We tried to run the same job using different CPU/MEM config but every time with the same error (16 localcores and 64 localmem also crashed with a SegFault at the FILTER_BARCODES step).

I verified the _sitecheck and increased the maximum number of open file which was probably too low but that doesn't solve the problem.

We would appreciate any hints on where to look for to debug the error.