{
    "cmdline": "sc_ref_mapper -i /mnt/scratch4/dongze/read_lives_matter/index/mouse_spliceu_tx_index/index/piscem_idx -g chromium_v3 -1 /mnt/scratch4/dongze/read_lives_matter/data/chsz5k_mouse_cells_v3/SC3_v3_NextGem_DI_Neurons_5K_gex/SC3_v3_NextGem_DI_Neurons_5K_gex_S3_L001_R1_001.fastq.gz,/mnt/scratch4/dongze/read_lives_matter/data/chsz5k_mouse_cells_v3/SC3_v3_NextGem_DI_Neurons_5K_gex/SC3_v3_NextGem_DI_Neurons_5K_gex_S3_L002_R1_001.fastq.gz,/mnt/scratch4/dongze/read_lives_matter/data/chsz5k_mouse_cells_v3/SC3_v3_NextGem_DI_Neurons_5K_gex/SC3_v3_NextGem_DI_Neurons_5K_gex_S3_L003_R1_001.fastq.gz,/mnt/scratch4/dongze/read_lives_matter/data/chsz5k_mouse_cells_v3/SC3_v3_NextGem_DI_Neurons_5K_gex/SC3_v3_NextGem_DI_Neurons_5K_gex_S3_L004_R1_001.fastq.gz -2 /mnt/scratch4/dongze/read_lives_matter/data/chsz5k_mouse_cells_v3/SC3_v3_NextGem_DI_Neurons_5K_gex/SC3_v3_NextGem_DI_Neurons_5K_gex_S3_L001_R2_001.fastq.gz,/mnt/scratch4/dongze/read_lives_matter/data/chsz5k_mouse_cells_v3/SC3_v3_NextGem_DI_Neurons_5K_gex/SC3_v3_NextGem_DI_Neurons_5K_gex_S3_L002_R2_001.fastq.gz,/mnt/scratch4/dongze/read_lives_matter/data/chsz5k_mouse_cells_v3/SC3_v3_NextGem_DI_Neurons_5K_gex/SC3_v3_NextGem_DI_Neurons_5K_gex_S3_L003_R2_001.fastq.gz,/mnt/scratch4/dongze/read_lives_matter/data/chsz5k_mouse_cells_v3/SC3_v3_NextGem_DI_Neurons_5K_gex/SC3_v3_NextGem_DI_Neurons_5K_gex_S3_L004_R2_001.fastq.gz -t 16 -o /mnt/scratch4/dongze/read_lives_matter/quant/chsz5k_mouse_cells_quant/af_map",
    "num_mapped": 145720047,
    "num_reads": 157534418,
    "percent_mapped": 92.50045091733541,
    "runtime_seconds": 751.0
}
