The exit status of the task that caused the workflow execution to fail was: 1.
The full error message was:
Error executing process > 'CELLRANGER_COUNT (MockB)' Caused by: Process `CELLRANGER_COUNT (MockB)` terminated with an error exit status (1) Command executed: cellranger count --id=MockB --transcriptome=Bos_taurus_ARS_UCD1_2_index --fastqs=$(pwd)/fastqs --sample=MockB --create-bam=false --localcores=8 --localmem=64 Command exit status: 1 Command output: 2026-06-25 17:24:30 [runtime] (ready) ID.MockB.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ 2026-06-25 17:24:30 [runtime] (ready) ID.MockB.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.RUST_BRIDGE 2026-06-25 17:24:30 [runtime] (ready) ID.MockB.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.MERGE_METRICS 2026-06-25 17:2SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SETUP_VDJ_DEMUX 2026-06-25 17:24:30 [runtime] (ready) ID.MockB.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SETUP_VDJ_DEMUX 2026-06-25 17:24:30 [runtime] (ready) ID.MockB.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SETUP_VDJ_DEMUX 2026-06-25 17:24:30 [runtime] (ready) ID.MockB.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.MULTI_SETUP_CHUNKS 2026-06-25 17:24:30 [runtime] (ready) ID.MockB.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.MULTI_SETUP_CHUNKS 2026-06-25 17:24:30 [runtime] (ready) ID.MockB.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.MAKE_SHARD 2026-06-25 17:24:30 [runtime] (ready) ID.MockB.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.MAKE_SHARD 2026-06-25 17:24:30 [runtime] (ready) ID.MockB.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.MAKE_SHARD 2026-06-25 17:24:30 [runtime] (ready) ID.MockB.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.BARCODE_CORRECTION 2026-06-25 17:24:30 [runtime] (ready) ID.MockB.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.BARCODE_CORRECTION 2026-06-25 17:24:30 [runtime] (ready) ID.MockB.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.RUST_BRIDGE 2026-06-25 17:24:30 [runtime] (ready) ID.MockB.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.BARCODE_CORRECTION 2026-06-25 17:24:30 [runtime] (ready) ID.MockB.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.RUST_BRIDGE 2026-06-25 17:24:30 [runtime] (ready) ID.MockB.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.MERGE_METRICS 2026-06-25 17:24:30 [runtime] (ready) ID.MockB.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ 2026-06-25 17:24:30 [runtime] (ready) ID.MockB.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.RUST_BRIDGE 2026-06-25 17:24:30 [runtime] (ready) ID.MockB.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.MERGE_METRICS 2026-06-25 17:24:30 [runtime] (ready) ID.MockB.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ 2026-06-25 17:24:30 [runtime] (ready) ID.MockB.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ 2026-06-25 17:24:30 [runtime] (ready) ID.MockB.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.MERGE_METRICS 2026-06-25 17:24:30 [runtime] (chunks_complete) ID.MockB.SC_RNA_COUNTER_CS.COPY_CHEMISTRY_SPEC 2026-06-25 17:24:30 [runtime] (chunks_complete) ID.MockB.SC_RNA_COUNTER_CS.SETUP_REFERENCE_INFO 2026-06-25 17:24:30 [runtime] (ready) ID.MockB.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR.DETECT_COUNT_CHEMISTRY 2026-06-25 17:24:30 [runtime] (run:local) ID.MockB.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR.DETECT_COUNT_CHEMISTRY.fork0.chnk0.main 2026-06-25 17:24:30 [runtime] (ready) ID.MockB.SC_RNA_COUNTER_CS.FULL_COUNT_INPUTS.WRITE_GENE_INDEX 2026-06-25 17:24:30 [runtime] (run:local) ID.MockB.SC_RNA_COUNTER_CS.FULL_COUNT_INPUTS.WRITE_GENE_INDEX.fork0.chnk0.main 2026-06-25 17:24:31 [runtime] (failed) ID.MockB.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR.DETECT_COUNT_CHEMISTRY [error] Pipestance failed. Error log at: MockB/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_CHEMISTRY_DETECTOR/DETECT_COUNT_CHEMISTRY/fork0/chnk0-u004d3d644e/_errors Log message: TXRNGR10001: There were not enough reads to auto detect the chemistry: Sample MockB in "/media/luozize/Single_cell_processing/nano_test_project/data/fastqs" Note that you can avoid auto detection by specifying the specific chemistry type and version. - Minimum number of required reads = 10000 - Number of reads available = 1000 For more information: https://10xgen.com/pipeline-error-codes Waiting 6 seconds for UI to do final refresh. Pipestance failed. Use --noexit option to keep UI running after failure. 2026-06-25 17:24:37 Shutting down. Saving pipestance info to "MockB/MockB.mri.tgz" For assistance, upload this file to 10x Genomics by running: cellranger upload"MockB/MockB.mri.tgz" Command error: 2026-06-25 17:24:30 [runtime] (ready) ID.MockB.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.RUST_BRIDGE 2026-06-25 17:24:30 [runtime] (ready) ID.MockB.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.BARCODE_CORRECTION 2026-06-25 17:24:30 [runtime] (ready) ID.MockB.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.RUST_BRIDGE 2026-06-25 17:24:30 [runtime] (ready) ID.MockB.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.MERGE_METRSC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SETUP_VDJ_DEMUX 2026-06-25 17:24:30 [runtime] (ready) ID.MockB.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SETUP_VDJ_DEMUX 2026-06-25 17:24:30 [runtime] (ready) ID.MockB.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SETUP_VDJ_DEMUX 2026-06-25 17:24:30 [runtime] (ready) ID.MockB.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.MULTI_SETUP_CHUNKS 2026-06-25 17:24:30 [runtime] (ready) ID.MockB.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.MULTI_SETUP_CHUNKS 2026-06-25 17:24:30 [runtime] (ready) ID.MockB.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.MAKE_SHARD 2026-06-25 17:24:30 [runtime] (ready) ID.MockB.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.MAKE_SHARD 2026-06-25 17:24:30 [runtime] (ready) ID.MockB.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.MAKE_SHARD 2026-06-25 17:24:30 [runtime] (ready) ID.MockB.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.BARCODE_CORRECTION 2026-06-25 17:24:30 [runtime] (ready) ID.MockB.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.BARCODE_CORRECTION 2026-06-25 17:24:30 [runtime] (ready) ID.MockB.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.RUST_BRIDGE 2026-06-25 17:24:30 [runtime] (ready) ID.MockB.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.BARCODE_CORRECTION 2026-06-25 17:24:30 [runtime] (ready) ID.MockB.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.RUST_BRIDGE 2026-06-25 17:24:30 [runtime] (ready) ID.MockB.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.MERGE_METRICS 2026-06-25 17:24:30 [runtime] (ready) ID.MockB.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ 2026-06-25 17:24:30 [runtime] (ready) ID.MockB.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.RUST_BRIDGE 2026-06-25 17:24:30 [runtime] (ready) ID.MockB.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.MERGE_METRICS 2026-06-25 17:24:30 [runtime] (ready) ID.MockB.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_B_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ 2026-06-25 17:24:30 [runtime] (ready) ID.MockB.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.ASSEMBLE_VDJ 2026-06-25 17:24:30 [runtime] (ready) ID.MockB.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_GEM_WELL_PROCESSOR.VDJ_T_GD_GEM_WELL_PROCESSOR.SC_VDJ_CONTIG_ASSEMBLER.MERGE_METRICS 2026-06-25 17:24:30 [runtime] (chunks_complete) ID.MockB.SC_RNA_COUNTER_CS.COPY_CHEMISTRY_SPEC 2026-06-25 17:24:30 [runtime] (chunks_complete) ID.MockB.SC_RNA_COUNTER_CS.SETUP_REFERENCE_INFO 2026-06-25 17:24:30 [runtime] (ready) ID.MockB.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR.DETECT_COUNT_CHEMISTRY 2026-06-25 17:24:30 [runtime] (run:local) ID.MockB.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR.DETECT_COUNT_CHEMISTRY.fork0.chnk0.main 2026-06-25 17:24:30 [runtime] (ready) ID.MockB.SC_RNA_COUNTER_CS.FULL_COUNT_INPUTS.WRITE_GENE_INDEX 2026-06-25 17:24:30 [runtime] (run:local) ID.MockB.SC_RNA_COUNTER_CS.FULL_COUNT_INPUTS.WRITE_GENE_INDEX.fork0.chnk0.main 2026-06-25 17:24:31 [runtime] (failed) ID.MockB.SC_RNA_COUNTER_CS.SC_MULTI_CORE.MULTI_CHEMISTRY_DETECTOR.DETECT_COUNT_CHEMISTRY [error] Pipestance failed. Error log at: MockB/SC_RNA_COUNTER_CS/SC_MULTI_CORE/MULTI_CHEMISTRY_DETECTOR/DETECT_COUNT_CHEMISTRY/fork0/chnk0-u004d3d644e/_errors Log message: TXRNGR10001: There were not enough reads to auto detect the chemistry: Sample MockB in "/media/luozize/Single_cell_processing/nano_test_project/data/fastqs" Note that you can avoid auto detection by specifying the specific chemistry type and version. - Minimum number of required reads = 10000 - Number of reads available = 1000 For more information: https://10xgen.com/pipeline-error-codes Waiting 6 seconds for UI to do final refresh. Pipestance failed. Use --noexit option to keep UI running after failure. 2026-06-25 17:24:37 Shutting down. Saving pipestance info to "MockB/MockB.mri.tgz" For assistance, upload this file to 10x Genomics by running: cellranger upload "MockB/MockB.mri.tgz" Work dir: /media/luozize/Single_cell_processing/work/99/8c48e0f813ade4e1f0af47888c8bd3 Container: scrna_pipeline_env:latest Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`
nextflow run main.nf -profile docker --samplesheet /media/luozize/Single_cell_processing/nano_test_project/samples.csv --ref_fa /media/luozize/Single_cell_processing/reference/GCF_002263795.3_ARS-UCD2.0_genomic.fna --ref_gtf /media/luozize/Single_cell_processing/reference/genomic.gtf --species_name Bos_taurus_ARS_UCD1_2 --mito_threshold 10 --pcs_use 30 --outdir ../Single_cell_processing/1b16dcbbe16331849f178d0754c0c49c41f7742c-0188-4c2f-a493-53ed89d33ecaThese plots give an overview of the distribution of resource usage for each process.
This table shows information about each task in the workflow. Use the search box on the right to filter rows for specific values. Clicking headers will sort the table by that value and scrolling side to side will reveal more columns.