Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260227_LH00519_0059_B23L5TMLT4__444aee1e--20260301-135529/alignments/recalibrated/1136_5R4-N1-BDNA-1_B23L5TMLT4_1/1136_5R4-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/76/f5bd9434fb225f8f436cc3c4b5ffc7/.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/76/f5bd9434fb225f8f436cc3c4b5ffc7/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260227_LH00519_0059_B23L5TMLT4__444aee1e--20260301-135529/alignments/recalibrated/1136_5R4-N1-BDNA-1_B23L5TMLT4_1/1136_5R4-N1-BDNA-1_B23L5TMLT4_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_5R4-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5R4-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5R4-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5R4-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: 82973310 total, 72920 skipped (flags/unmapped)
Fragments: 41636470 total (41219794 tlen-paired, 4757 hash-paired, 573 singletons, 15431 discordant, 395915 orphans, 11969 too large [>5000 bp], 15798882 duplicates)
Reads: 88482232 total, 56933 skipped (flags/unmapped)
Fragments: 44406309 total (43979337 tlen-paired, 3176 hash-paired, 605 singletons, 10211 discordant, 412980 orphans, 13133 too large [>5000 bp], 16675210 duplicates)
Reads: 96802998 total, 63601 skipped (flags/unmapped)
Fragments: 48583520 total (48080430 tlen-paired, 7091 hash-paired, 512 singletons, 15158 discordant, 480329 orphans, 26599 too large [>5000 bp], 18486464 duplicates)
Reads: 98004150 total, 109202 skipped (flags/unmapped)
Fragments: 49363345 total (48071374 tlen-paired, 3414 hash-paired, 538 singletons, 253079 discordant, 1034940 orphans, 101868 too large [>5000 bp], 18695461 duplicates)