Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/26/176c9718aa700058b78609183df0e5/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-resources/beds/altera_subpanels/hg38/foresight/xgen-exome-hyb-panel-v2_AND_altera_v3_probes_short_hg38_AND_cdx_spike_custom30off4x_hg38_AND_foresight_clarity.bed
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/26/176c9718aa700058b78609183df0e5/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260227_LH00519_0059_B23L5TMLT4__444aee1e--20260301-135529/alignments/recalibrated/1047_II-N1-BDNA-1_B23L5TMLT4_1/1047_II-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260227_LH00519_0059_B23L5TMLT4__444aee1e--20260301-135529/alignments/recalibrated/1047_II-N1-BDNA-1_B23L5TMLT4_1/1047_II-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1047_II-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1047_II-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1047_II-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1047_II-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
Deduplicated 94 probes with identical coordinates
Loaded 472416 probes across 3366 contigs
Deduplicated 94 probes with identical coordinates
Loaded 472416 probes across 3366 contigs
Deduplicated 94 probes with identical coordinates
Loaded 472416 probes across 3366 contigs
Deduplicated 94 probes with identical coordinates
Loaded 472416 probes across 3366 contigs
Reads: 32622554 total, 38401 skipped (flags/unmapped)
Fragments: 16676394 total (15889968 tlen-paired, 2785 hash-paired, 238 singletons, 3460 discordant, 779943 orphans, 5773 too large [>5000 bp], 7185119 duplicates)
Reads: 34402088 total, 36095 skipped (flags/unmapped)
Fragments: 17614021 total (16736623 tlen-paired, 2074 hash-paired, 318 singletons, 2473 discordant, 872533 orphans, 5401 too large [>5000 bp], 7376477 duplicates)
Reads: 34572511 total, 35100 skipped (flags/unmapped)
Fragments: 17684979 total (16829571 tlen-paired, 2412 hash-paired, 203 singletons, 3477 discordant, 849316 orphans, 8486 too large [>5000 bp], 7678532 duplicates)
Reads: 41021807 total, 78613 skipped (flags/unmapped)
Fragments: 21442976 total (18350025 tlen-paired, 2112 hash-paired, 366 singletons, 640121 discordant, 2450352 orphans, 253980 too large [>5000 bp], 8764753 duplicates)