cellranger count DETECT_COUNT_CHEMISTRY (failed)

Question

[mskr_]

I am learning scRNA-seq and the tutorial I follow uses dataset (1k pbmcs from healthy donor) from 10X genomics website. I downloaded fastq and reference transcriptome files and ran following command.

cellranger-6.1.1/cellranger count --id pbmc_1k_v2_example --transcriptome /home/murat/Share/single_cell/refdata-gex-GRCh38-2020-A --fastqs /home/murat/Share/single_cell/pbmc_1k_v2_fastqs

I get following message.

Martian Runtime - v4.0.6 Serving UI at http://murat:40949?auth=IEvhcoK_bfU67jhAts2hQ4pc88rKpmq4NYutUibXuak

Running preflight checks (please wait)... Checking sample info... Checking FASTQ folder... Checking reference... Checking reference_path (/home/murat/Share/single_cell/refdata-gex-GRCh38-2020-A) on murat... Checking optional arguments... mrc: v4.0.6

mrp: v4.0.6

Anaconda: Python 3.8.2

numpy: 1.19.2

scipy: 1.6.2

pysam: 0.16.0.1

h5py: 3.2.1

pandas: 1.2.4

STAR: 2.7.2a

samtools: samtools 1.10 Using htslib 1.10.2 Copyright (C) 2019 Genome Research Ltd.

2021-09-19 16:03:06 [runtime] (ready)
ID.pbmc_1k_v2_example.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR._GEM_WELL_CHEMISTRY_DETECTOR.DETECT_COUNT_CHEMISTRY 2021-09-19 16:03:06 [runtime] (run:local)
ID.pbmc_1k_v2_example.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR._GEM_WELL_CHEMISTRY_DETECTOR.DETECT_COUNT_CHEMISTRY.fork0.chnk0.main 2021-09-19 16:03:06 [runtime] (ready)
ID.pbmc_1k_v2_example.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MAKE_FULL_CONFIG._MAKE_VDJ_CONFIG 2021-09-19 16:03:06 [runtime] (run:local)
ID.pbmc_1k_v2_example.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MAKE_FULL_CONFIG._MAKE_VDJ_CONFIG.fork0.chnk0.main 2021-09-19 16:03:06 [runtime] (ready)
ID.pbmc_1k_v2_example.SC_RNA_COUNTER_CS.WRITE_GENE_INDEX 2021-09-19 16:03:06 [runtime] (run:local)
ID.pbmc_1k_v2_example.SC_RNA_COUNTER_CS.WRITE_GENE_INDEX.fork0.chnk0.main 2021-09-19 16:03:06 [runtime] (ready)
ID.pbmc_1k_v2_example.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.DISABLE_BAMS 2021-09-19 16:03:06 [runtime] (run:local)
ID.pbmc_1k_v2_example.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR._BASIC_SC_RNA_COUNTER.DISABLE_BAMS.fork0.chnk0.main 2021-09-19 16:03:06 [runtime] (ready)
ID.pbmc_1k_v2_example.SC_RNA_COUNTER_CS.SC_MULTI_CORE.SANITIZE_MAP_CALLS 2021-09-19 16:03:06 [runtime] (ready)
ID.pbmc_1k_v2_example.SC_RNA_COUNTER_CS.FULL_COUNT_INPUTS.WRITE_GENE_INDEX 2021-09-19 16:03:06 [runtime] (run:local)
ID.pbmc_1k_v2_example.SC_RNA_COUNTER_CS.FULL_COUNT_INPUTS.WRITE_GENE_INDEX.fork0.chnk0.main 2021-09-19 16:03:58 [runtime] (chunks_complete) ID.pbmc_1k_v2_example.SC_RNA_COUNTER_CS.FULL_COUNT_INPUTS.WRITE_GENE_INDEX 2021-09-19 16:03:58 [runtime] (ready)
ID.pbmc_1k_v2_example.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR.PARSE_TARGET_FEATURES 2021-09-19 16:03:58 [runtime] (run:local)
ID.pbmc_1k_v2_example.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.COUNT_GEM_WELL_PROCESSOR.PARSE_TARGET_FEATURES.fork0.chnk0.main 2021-09-19 16:04:08 [runtime]
ID.pbmc_1k_v2_example.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR._GEM_WELL_CHEMISTRY_DETECTOR.DETECT_COUNT_CHEMISTRY (failed)

[error] Pipestance failed. Error log at: pbmc_1k_v2_example/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_CHEMISTRY_DETECTOR/_GEM_WELL_CHEMISTRY_DETECTOR/DETECT_COUNT_CHEMISTRY/fork0/chnk0-u063e47431a/_errors

Log message: Job failed in stage code

exit status 108

Waiting 6 seconds for UI to do final refresh. Pipestance failed. Use --noexit option to keep UI running after failure.

2021-09-19 16:04:14 Shutting down.

I didnt find anything about this exit status and error log it points to says the same thing.

Any insight is appreciated!

Answer 1

[Andy]

I have had the same problem as you. Now I find that my server doesn't meet the minimum requirements, "Running Cell Ranger requires at least 8 CPUs, preferably 16, and at least 64GB of RAM, preferably 128. ", https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_in.

[Andy]

I guess this may be the reason of this error's happening.

[jiawei]

I also get the same error, but my computer configuration meets the requirements. I can't figure out what wrong with that