Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/86/4f162398a3a2e4a3e0ed253bae78b0/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260227_LH00519_0059_B23L5TMLT4__444aee1e--20260301-135529/alignments/recalibrated/659_cBd-N1-BDNA-1_B23L5TMLT4_1/659_cBd-N1-BDNA-1_B23L5TMLT4_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/86/4f162398a3a2e4a3e0ed253bae78b0/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260227_LH00519_0059_B23L5TMLT4__444aee1e--20260301-135529/alignments/recalibrated/659_cBd-N1-BDNA-1_B23L5TMLT4_1/659_cBd-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: 659_cBd-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_cBd-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_cBd-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_cBd-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: 74436083 total, 61718 skipped (flags/unmapped)
Fragments: 37336603 total (36999692 tlen-paired, 5901 hash-paired, 471 singletons, 14157 discordant, 316382 orphans, 9006 too large [>5000 bp], 13108373 duplicates)
Reads: 79033979 total, 50047 skipped (flags/unmapped)
Fragments: 39642325 total (39305388 tlen-paired, 4627 hash-paired, 433 singletons, 9672 discordant, 322205 orphans, 10960 too large [>5000 bp], 13753597 duplicates)
Reads: 86717241 total, 56232 skipped (flags/unmapped)
Fragments: 43499121 total (43103039 tlen-paired, 5184 hash-paired, 445 singletons, 14257 discordant, 376196 orphans, 19704 too large [>5000 bp], 15327195 duplicates)
Reads: 87507884 total, 95990 skipped (flags/unmapped)
Fragments: 44020758 total (43038437 tlen-paired, 3628 hash-paired, 472 singletons, 188645 discordant, 789576 orphans, 80213 too large [>5000 bp], 15468727 duplicates)