Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/cgp_dna_exp0024/20260212_LH00166_0244_A237CFYLT3__aa3fd045--20260224-223853/alignments/recalibrated/1136_2F2-N1-BDNA-1_A237CFYLT3_1/1136_2F2-N1-BDNA-1_A237CFYLT3_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7d/d71d0da983640e4ab38322bcabbf08/.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/7d/d71d0da983640e4ab38322bcabbf08/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/cgp_dna_exp0024/20260212_LH00166_0244_A237CFYLT3__aa3fd045--20260224-223853/alignments/recalibrated/1136_2F2-N1-BDNA-1_A237CFYLT3_1/1136_2F2-N1-BDNA-1_A237CFYLT3_1.recalibrated.bam.bai
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1136_2F2-N1-BDNA-1_A237CFYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_2F2-N1-BDNA-1_A237CFYLT3_1.recalibrated.bam.bai
Count mode: frac
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1136_2F2-N1-BDNA-1_A237CFYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_2F2-N1-BDNA-1_A237CFYLT3_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: 78722376 total, 83871 skipped (flags/unmapped)
Fragments: 39603306 total (39005104 tlen-paired, 6758 hash-paired, 12291 singletons, 11509 discordant, 567644 orphans, 5914 too large [>5000 bp], 7910549 duplicates)
Reads: 85508232 total, 78982 skipped (flags/unmapped)
Fragments: 43022320 total (42373025 tlen-paired, 6694 hash-paired, 12921 singletons, 8043 discordant, 621637 orphans, 9584 too large [>5000 bp], 8542669 duplicates)
Reads: 86562629 total, 80680 skipped (flags/unmapped)
Fragments: 43549447 total (42877042 tlen-paired, 8481 hash-paired, 12952 singletons, 11375 discordant, 639597 orphans, 17802 too large [>5000 bp], 8652115 duplicates)
Reads: 89642634 total, 185175 skipped (flags/unmapped)
Fragments: 45396692 total (43327719 tlen-paired, 7971 hash-paired, 13692 singletons, 401481 discordant, 1645829 orphans, 161798 too large [>5000 bp], 8909076 duplicates)