Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4e/50b1f120af25cfff1c766d569fdb30/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00527_0067_B23KGCJLT4__d7a6b981--20260322-105015/alignments/recalibrated/1136_3MV-N1-BDNA-1_B23KGCJLT4_1/1136_3MV-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam
  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/4e/50b1f120af25cfff1c766d569fdb30/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00527_0067_B23KGCJLT4__d7a6b981--20260322-105015/alignments/recalibrated/1136_3MV-N1-BDNA-1_B23KGCJLT4_1/1136_3MV-N1-BDNA-1_B23KGCJLT4_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: 1136_3MV-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_3MV-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_3MV-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_3MV-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: 87550501 total, 48497 skipped (flags/unmapped)
Fragments: 43878426 total (43594279 tlen-paired, 2279 hash-paired, 445 singletons, 9272 discordant, 272151 orphans, 8874 too large [>5000 bp], 17042246 duplicates)
Reads: 82116716 total, 57431 skipped (flags/unmapped)
Fragments: 41152915 total (40867465 tlen-paired, 2917 hash-paired, 362 singletons, 13916 discordant, 268255 orphans, 11036 too large [>5000 bp], 16272223 duplicates)
Reads: 96836022 total, 53128 skipped (flags/unmapped)
Fragments: 48538162 total (48179704 tlen-paired, 6155 hash-paired, 329 singletons, 14767 discordant, 337207 orphans, 22053 too large [>5000 bp], 19295960 duplicates)
Reads: 97259159 total, 85464 skipped (flags/unmapped)
Fragments: 48837252 total (48053619 tlen-paired, 2373 hash-paired, 389 singletons, 150107 discordant, 630764 orphans, 65172 too large [>5000 bp], 19440386 duplicates)