{
  "script": "05_realign_xbOstLuri2.Rmd",
  "date": "2026-09-27T16:56:27Z",
  "runtime_seconds": 385760,
  "parameters": {
    "genome_accession": "GCA_061535525.1",
    "genome_name": "xbOstLuri2 USDA-ARS PSRF primary",
    "genome_fasta": "data/genome/GCA_061535525.1_xbOstLuri2_USDA-ARS_PSRF_primary_genomic.fna",
    "sample_sheet": "output/01_align_and_visualize/metrics/sample_metadata.tsv",
    "aligner": "bwa mem",
    "read_group": "@RG ID/SM/LB=<sample_id> PL=ILLUMINA",
    "duplicates": "marked with samtools markdup, not removed",
    "threads_per_sample": 16,
    "memory_per_sample_gb": 40,
    "max_concurrent_tasks": 24,
    "slurm": {
      "account": "coenv",
      "partition": "cpu-g2"
    }
  },
  "software": {
    "container": "/mmfs1/gscratch/srlab/containers/srlab-R4.4-bioinformatics-container-c3d3116.sif",
    "bwa": "0.7.19-r1273",
    "samtools": "1.20",
    "R": "R version 4.4.3 (2025-02-28)"
  },
  "outputs": {
    "alignments": ["output/05_realign_xbOstLuri2/alignments/Blank_plate1.sorted.bam", "output/05_realign_xbOstLuri2/alignments/Blank_plate2.sorted.bam", "output/05_realign_xbOstLuri2/alignments/CS18_22_Wild_plate1_A7.sorted.bam", "output/05_realign_xbOstLuri2/alignments/CS18_22_Wild_plate1_C6.sorted.bam", "output/05_realign_xbOstLuri2/alignments/CS18_22_Wild_plate1_D6.sorted.bam", "output/05_realign_xbOstLuri2/alignments/CS18_22_Wild_plate1_E6.sorted.bam", "output/05_realign_xbOstLuri2/alignments/CS18_22_Wild_plate1_F6.sorted.bam", "output/05_realign_xbOstLuri2/alignments/CS18_22_Wild_plate1_G6.sorted.bam", "output/05_realign_xbOstLuri2/alignments/CS18_22_Wild_plate1_H6.sorted.bam", "output/05_realign_xbOstLuri2/alignments/Coos_Bay_10.sorted.bam", "output/05_realign_xbOstLuri2/alignments/Coos_Bay_4.sorted.bam", "output/05_realign_xbOstLuri2/alignments/Coos_Bay_5.sorted.bam", "output/05_realign_xbOstLuri2/alignments/Coos_Bay_6.sorted.bam", "output/05_realign_xbOstLuri2/alignments/Coos_Bay_7.sorted.bam", "output/05_realign_xbOstLuri2/alignments/Coos_Bay_8.sorted.bam", "output/05_realign_xbOstLuri2/alignments/Coos_Bay_9.sorted.bam", "output/05_realign_xbOstLuri2/alignments/Dogfish_Bay_10.sorted.bam", "output/05_realign_xbOstLuri2/alignments/Dogfish_Bay_11.sorted.bam", "output/05_realign_xbOstLuri2/alignments/Dogfish_Bay_12.sorted.bam", "output/05_realign_xbOstLuri2/alignments/Dogfish_Bay_13.sorted.bam", "output/05_realign_xbOstLuri2/alignments/Dogfish_Bay_14.sorted.bam", "output/05_realign_xbOstLuri2/alignments/Dogfish_Bay_7.sorted.bam", "output/05_realign_xbOstLuri2/alignments/Dogfish_Bay_8.sorted.bam", "output/05_realign_xbOstLuri2/alignments/Dogfish_Bay_9.sorted.bam", "output/05_realign_xbOstLuri2/alignments/FB18_Wild_10.sorted.bam", "output/05_realign_xbOstLuri2/alignments/FB18_Wild_11.sorted.bam", "output/05_realign_xbOstLuri2/alignments/FB18_Wild_12.sorted.bam", "output/05_realign_xbOstLuri2/alignments/FB18_Wild_8.sorted.bam", "output/05_realign_xbOstLuri2/alignments/FB18_Wild_9.sorted.bam", "output/05_realign_xbOstLuri2/alignments/Fidalgo_Bay_10.sorted.bam", "output/05_realign_xbOstLuri2/alignments/Fidalgo_Bay_11.sorted.bam", "output/05_realign_xbOstLuri2/alignments/Fidalgo_Bay_12.sorted.bam", "output/05_realign_xbOstLuri2/alignments/Fidalgo_Bay_8.sorted.bam", "output/05_realign_xbOstLuri2/alignments/Fidalgo_Bay_9.sorted.bam", "output/05_realign_xbOstLuri2/alignments/HC18_Triton_Wild_10.sorted.bam", "output/05_realign_xbOstLuri2/alignments/HC18_Triton_Wild_11.sorted.bam", "output/05_realign_xbOstLuri2/alignments/HC18_Triton_Wild_12.sorted.bam", "output/05_realign_xbOstLuri2/alignments/HC18_Triton_Wild_15.sorted.bam", "output/05_realign_xbOstLuri2/alignments/HC18_Triton_Wild_16.sorted.bam", "output/05_realign_xbOstLuri2/alignments/HC18_Triton_Wild_7.sorted.bam", "output/05_realign_xbOstLuri2/alignments/HC18_Triton_Wild_8.sorted.bam", "output/05_realign_xbOstLuri2/alignments/HC18_Triton_Wild_9.sorted.bam", "output/05_realign_xbOstLuri2/alignments/LS_10a.sorted.bam", "output/05_realign_xbOstLuri2/alignments/LS_11a.sorted.bam", "output/05_realign_xbOstLuri2/alignments/LS_12a.sorted.bam", "output/05_realign_xbOstLuri2/alignments/LS_13a.sorted.bam", "output/05_realign_xbOstLuri2/alignments/LS_14a.sorted.bam", "output/05_realign_xbOstLuri2/alignments/LS_8a.sorted.bam", "output/05_realign_xbOstLuri2/alignments/LS_9a.sorted.bam", "output/05_realign_xbOstLuri2/alignments/MB_11a.sorted.bam", "output/05_realign_xbOstLuri2/alignments/MB_12a.sorted.bam", "output/05_realign_xbOstLuri2/alignments/MB_13a.sorted.bam", "output/05_realign_xbOstLuri2/alignments/MB_14a.sorted.bam", "output/05_realign_xbOstLuri2/alignments/MB_1a.sorted.bam", "output/05_realign_xbOstLuri2/alignments/MB_2a.sorted.bam", "output/05_realign_xbOstLuri2/alignments/MB_3a.sorted.bam", "output/05_realign_xbOstLuri2/alignments/MB_4a.sorted.bam", "output/05_realign_xbOstLuri2/alignments/NS18_Disco_Wild_10.sorted.bam", "output/05_realign_xbOstLuri2/alignments/NS18_Disco_Wild_11.sorted.bam", "output/05_realign_xbOstLuri2/alignments/NS18_Disco_Wild_12.sorted.bam", "output/05_realign_xbOstLuri2/alignments/NS18_Disco_Wild_13.sorted.bam", "output/05_realign_xbOstLuri2/alignments/NS18_Disco_Wild_14.sorted.bam", "output/05_realign_xbOstLuri2/alignments/NS18_Disco_Wild_15.sorted.bam", "output/05_realign_xbOstLuri2/alignments/NS18_Disco_Wild_8.sorted.bam", "output/05_realign_xbOstLuri2/alignments/NS18_Disco_Wild_9.sorted.bam", "output/05_realign_xbOstLuri2/alignments/NS18_Sequim_Wild_4.sorted.bam", "output/05_realign_xbOstLuri2/alignments/NS18_Sequim_Wild_5.sorted.bam", "output/05_realign_xbOstLuri2/alignments/NS18_Sequim_Wild_55.sorted.bam", "output/05_realign_xbOstLuri2/alignments/NS18_Sequim_Wild_56.sorted.bam", "output/05_realign_xbOstLuri2/alignments/NS18_Sequim_Wild_57.sorted.bam", "output/05_realign_xbOstLuri2/alignments/NS18_Sequim_Wild_58.sorted.bam", "output/05_realign_xbOstLuri2/alignments/NS18_Sequim_Wild_6.sorted.bam", "output/05_realign_xbOstLuri2/alignments/NS18_Sequim_Wild_7.sorted.bam", "output/05_realign_xbOstLuri2/alignments/Ostrich_Bay_10.sorted.bam", "output/05_realign_xbOstLuri2/alignments/Ostrich_Bay_11.sorted.bam", "output/05_realign_xbOstLuri2/alignments/Ostrich_Bay_12.sorted.bam", "output/05_realign_xbOstLuri2/alignments/Ostrich_Bay_13.sorted.bam", "output/05_realign_xbOstLuri2/alignments/Ostrich_Bay_14.sorted.bam", "output/05_realign_xbOstLuri2/alignments/Ostrich_Bay_7.sorted.bam", "output/05_realign_xbOstLuri2/alignments/Ostrich_Bay_8.sorted.bam", "output/05_realign_xbOstLuri2/alignments/Ostrich_Bay_9.sorted.bam", "output/05_realign_xbOstLuri2/alignments/PGB18_Wild_10.sorted.bam", "output/05_realign_xbOstLuri2/alignments/PGB18_Wild_11.sorted.bam", "output/05_realign_xbOstLuri2/alignments/PGB18_Wild_12.sorted.bam", "output/05_realign_xbOstLuri2/alignments/PGB18_Wild_13.sorted.bam", "output/05_realign_xbOstLuri2/alignments/PGB18_Wild_14.sorted.bam", "output/05_realign_xbOstLuri2/alignments/PGB18_Wild_15.sorted.bam", "output/05_realign_xbOstLuri2/alignments/PGB18_Wild_8.sorted.bam", "output/05_realign_xbOstLuri2/alignments/PGB18_Wild_9.sorted.bam", "output/05_realign_xbOstLuri2/alignments/SS18_North_Bay_Wild_11.sorted.bam", "output/05_realign_xbOstLuri2/alignments/SS18_North_Bay_Wild_13.sorted.bam", "output/05_realign_xbOstLuri2/alignments/SS18_North_Bay_Wild_14.sorted.bam", "output/05_realign_xbOstLuri2/alignments/SS18_North_Bay_Wild_15.sorted.bam", "output/05_realign_xbOstLuri2/alignments/SS18_North_Bay_Wild_16.sorted.bam", "output/05_realign_xbOstLuri2/alignments/SS18_North_Bay_Wild_17.sorted.bam", "output/05_realign_xbOstLuri2/alignments/SS18_North_Bay_Wild_18.sorted.bam", "output/05_realign_xbOstLuri2/alignments/SS18_North_Bay_Wild_19.sorted.bam", "output/05_realign_xbOstLuri2/alignments/Squaxin_Island_10a.sorted.bam", "output/05_realign_xbOstLuri2/alignments/Squaxin_Island_11a.sorted.bam", "output/05_realign_xbOstLuri2/alignments/Squaxin_Island_12a.sorted.bam", "output/05_realign_xbOstLuri2/alignments/Squaxin_Island_6a.sorted.bam", "output/05_realign_xbOstLuri2/alignments/Squaxin_Island_7a.sorted.bam", "output/05_realign_xbOstLuri2/alignments/Squaxin_Island_8a.sorted.bam", "output/05_realign_xbOstLuri2/alignments/Squaxin_Island_9a.sorted.bam", "output/05_realign_xbOstLuri2/alignments/WB_11a.sorted.bam", "output/05_realign_xbOstLuri2/alignments/WB_12a.sorted.bam", "output/05_realign_xbOstLuri2/alignments/WB_13a.sorted.bam", "output/05_realign_xbOstLuri2/alignments/WB_14a.sorted.bam", "output/05_realign_xbOstLuri2/alignments/WB_15a.sorted.bam", "output/05_realign_xbOstLuri2/alignments/WB_16a.sorted.bam", "output/05_realign_xbOstLuri2/alignments/WB_17a.sorted.bam", "output/05_realign_xbOstLuri2/alignments/WB_18a.sorted.bam"],
    "reference": ["output/05_realign_xbOstLuri2/reference/GCA_061535525.1_xbOstLuri2_USDA-ARS_PSRF_primary_genomic.dict", "output/05_realign_xbOstLuri2/reference/GCA_061535525.1_xbOstLuri2_USDA-ARS_PSRF_primary_genomic.fna", "output/05_realign_xbOstLuri2/reference/GCA_061535525.1_xbOstLuri2_USDA-ARS_PSRF_primary_genomic.fna.amb", "output/05_realign_xbOstLuri2/reference/GCA_061535525.1_xbOstLuri2_USDA-ARS_PSRF_primary_genomic.fna.ann", "output/05_realign_xbOstLuri2/reference/GCA_061535525.1_xbOstLuri2_USDA-ARS_PSRF_primary_genomic.fna.bwt", "output/05_realign_xbOstLuri2/reference/GCA_061535525.1_xbOstLuri2_USDA-ARS_PSRF_primary_genomic.fna.fai", "output/05_realign_xbOstLuri2/reference/GCA_061535525.1_xbOstLuri2_USDA-ARS_PSRF_primary_genomic.fna.pac", "output/05_realign_xbOstLuri2/reference/GCA_061535525.1_xbOstLuri2_USDA-ARS_PSRF_primary_genomic.fna.sa"],
    "metrics": ["output/05_realign_xbOstLuri2/metrics/comparison_v081.tsv", "output/05_realign_xbOstLuri2/metrics/coverage_by_location.tsv", "output/05_realign_xbOstLuri2/metrics/coverage_summary.tsv"],
    "figures": "output/05_realign_xbOstLuri2/figures/depth_v081_vs_xbOstLuri2.png"
  }
}