Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00527_0067_B23KGCJLT4__d7a6b981--20260322-105015/alignments/recalibrated/1136_6K2-N1-BDNA-1_B23KGCJLT4_1/1136_6K2-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ea/5e6ea40bf2b68c2296af722da2c965/.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/ea/5e6ea40bf2b68c2296af722da2c965/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00527_0067_B23KGCJLT4__d7a6b981--20260322-105015/alignments/recalibrated/1136_6K2-N1-BDNA-1_B23KGCJLT4_1/1136_6K2-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: 1136_6K2-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_6K2-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_6K2-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_6K2-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
Deduplicated 94 probes with identical coordinates
Loaded 472416 probes across 3366 contigs
Loaded 472416 probes across 3366 contigs
Deduplicated 94 probes with identical coordinates
Loaded 472416 probes across 3366 contigs
Reads: 66863738 total, 49496 skipped (flags/unmapped)
Fragments: 33497931 total (33280750 tlen-paired, 2763 hash-paired, 334 singletons, 13042 discordant, 201042 orphans, 9878 too large [>5000 bp], 12842336 duplicates)
Reads: 71389833 total, 38453 skipped (flags/unmapped)
Fragments: 35768144 total (35556086 tlen-paired, 2023 hash-paired, 395 singletons, 8517 discordant, 201123 orphans, 8305 too large [>5000 bp], 13428839 duplicates)
Reads: 78903264 total, 44606 skipped (flags/unmapped)
Fragments: 39535881 total (39264060 tlen-paired, 4018 hash-paired, 295 singletons, 13531 discordant, 253977 orphans, 20584 too large [>5000 bp], 15208443 duplicates)
Reads: 79266259 total, 69899 skipped (flags/unmapped)
Fragments: 39769446 total (39241420 tlen-paired, 1446 hash-paired, 279 singletons, 98464 discordant, 427837 orphans, 42792 too large [>5000 bp], 15334779 duplicates)