Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d7/f3ee7bb1132a5895db5b01311033c6/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260427_LH00519_0087_A23TY32LT4__manual_run_31e2bab--20260430-043425/alignments/recalibrated/1047_MH-N1-BDNA-1_A23TY32LT4_1/1047_MH-N1-BDNA-1_A23TY32LT4_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/d7/f3ee7bb1132a5895db5b01311033c6/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260427_LH00519_0087_A23TY32LT4__manual_run_31e2bab--20260430-043425/alignments/recalibrated/1047_MH-N1-BDNA-1_A23TY32LT4_1/1047_MH-N1-BDNA-1_A23TY32LT4_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: 1047_MH-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1047_MH-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1047_MH-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1047_MH-N1-BDNA-1_A23TY32LT4_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: 73576700 total, 54040 skipped (flags/unmapped)
Fragments: 36927687 total (36565808 tlen-paired, 2719 hash-paired, 334 singletons, 8856 discordant, 349970 orphans, 8795 too large [>5000 bp], 15090466 duplicates)
Reads: 79493092 total, 48605 skipped (flags/unmapped)
Fragments: 39905372 total (39510940 tlen-paired, 3000 hash-paired, 448 singletons, 6429 discordant, 384555 orphans, 9373 too large [>5000 bp], 15990214 duplicates)
Reads: 87111671 total, 49100 skipped (flags/unmapped)
Fragments: 43734922 total (43288642 tlen-paired, 2435 hash-paired, 277 singletons, 9086 discordant, 434482 orphans, 13743 too large [>5000 bp], 17940607 duplicates)
Reads: 88609801 total, 91101 skipped (flags/unmapped)
Fragments: 44665169 total (43391570 tlen-paired, 3185 hash-paired, 364 singletons, 255162 discordant, 1014888 orphans, 101807 too large [>5000 bp], 18216002 duplicates)