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10XGenomics / cellranger

10x Genomics Single Cell Analysis
https://www.10xgenomics.com/support/software/cell-ranger
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unknown error when running 'testrun' with CellRanger #105

Closed mengm5 closed 3 years ago

mengm5 commented 3 years ago

Hi @Cellranger_team, Firstly, thank you for your great job in CellRanger. Here is an error when using CellRanger and I don't know how to sovle it, the error is:

2020-12-03 07:36:55 [runtime] (failed) ID.S01-GEX.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER._CELLS_REPORTER.SUBSAMPLE_READS

[error] Pipestance failed. Error log at: S01-GEX/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_GEM_WELL_PROCESSOR/COUNT_GEM_WELL_PROCESSOR/_BASIC_SC_RNA_COUNTER/_CELLS_REPORTER/SUBSAMPLE_READS/fork0/chnk0-u82dec82511/_errors

Log message: Job failed in stage code

exit status 1

I use 'cellranger testrun --id=tiny' for checking system, but it also turns up error, please see pic.

kjjk

Information: CellRanger version: CellRanger 5.0.0 system information: centos7_7(x86_64), 32 CPU, 64G. command: cellranger count --include-introns --nosecondary --no-bam --localcores 30 --localmem 60 --id=S01-GEX --sample=S01-GEX --fastqs=fq_path --transcriptome=ref_path/refdata-gex-GRCh38-2020-A fastq: S01-GEX_S1_L001_R1_001.fastq.gz S01-GEX_S1_L001_R2_001.fastq.gz S01-GEX_S1_L002_R1_001.fastq.gz S01-GEX_S1_L002_R2_001.fastq.gz S01-GEX_S1_L003_R1_001.fastq.gz S01-GEX_S1_L003_R2_001.fastq.gz S01-GEX_S1_L004_R1_001.fastq.gz S01-GEX_S1_L004_R2_001.fastq.gz

Could you give me some suggestions? Thanks again! mengm

evolvedmicrobe commented 3 years ago

Hi, please contact support@10xgenomics.com for help with this issue, the upload would be very useful in helping to diagnose.