Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8b/e38303340fc22b0741f58c6b571af9/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00527_0067_B23KGCJLT4__d7a6b981--20260322-105015/alignments/recalibrated/1029_N5D-N1-BDNA-1_B23KGCJLT4_1/1029_N5D-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
  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/8b/e38303340fc22b0741f58c6b571af9/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00527_0067_B23KGCJLT4__d7a6b981--20260322-105015/alignments/recalibrated/1029_N5D-N1-BDNA-1_B23KGCJLT4_1/1029_N5D-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam
==> 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: 1029_N5D-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_N5D-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_N5D-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_N5D-N1-BDNA-1_B23KGCJLT4_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: 68503407 total, 49324 skipped (flags/unmapped)
Fragments: 34307335 total (34112542 tlen-paired, 3147 hash-paired, 302 singletons, 11505 discordant, 179839 orphans, 9777 too large [>5000 bp], 12563728 duplicates)
Reads: 73595259 total, 43108 skipped (flags/unmapped)
Fragments: 36862862 total (36652254 tlen-paired, 2495 hash-paired, 361 singletons, 9526 discordant, 198226 orphans, 12507 too large [>5000 bp], 13534578 duplicates)
Reads: 73893338 total, 41078 skipped (flags/unmapped)
Fragments: 37008798 total (36814461 tlen-paired, 2503 hash-paired, 389 singletons, 8222 discordant, 183223 orphans, 9138 too large [>5000 bp], 13174423 duplicates)
Reads: 80626301 total, 68263 skipped (flags/unmapped)
Fragments: 40432345 total (39954088 tlen-paired, 2785 hash-paired, 351 singletons, 90030 discordant, 385091 orphans, 39395 too large [>5000 bp], 14923318 duplicates)