# Nextflow workflow report

## `[condescending_almeida]`

#### Workflow execution completed unsuccessfully!

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`

Run times
  26-Jun-2026 01:08:31 - 26-Jun-2026 01:24:50 (duration: 16m 19s)

2 succeeded
0 cached
0 ignored
3 failed (0 retries)

Nextflow command

      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/

CPU-Hours
  `4.1 (2.1% failed)`
Launch directory
  `/media/luozize/Single_cell_processing`
Work directory
  `/media/luozize/Single_cell_processing/work`
Project directory
  `/media/luozize/Single_cell_processing`
Script name
  `main.nf`
Script ID
  `1b16dcbbe16331849f178d0754c0c49c`
Workflow session
  `41f7742c-0188-4c2f-a493-53ed89d33eca`
Workflow profile
  docker
Workflow container
  `scrna_pipeline_env:latest`
Container engine
  `docker`
Nextflow version
  version 25.04.2, build 5947 (13-05-2025 21:58 UTC)

## Resource Usage

These plots give an overview of the distribution of resource usage for each process.

#### CPU

#### Memory

#### Job Duration

#### I/O

## Tasks

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.

Values shown as:

(tasks table omitted because the dataset is too big)