Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260227_LH00519_0059_B23L5TMLT4__444aee1e--20260301-135529/alignments/recalibrated/1029_IRX-N1-BDNA-1_B23L5TMLT4_1/1029_IRX-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c3/a4a13ba0b3fb5760e7163999b33c13/.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/c3/a4a13ba0b3fb5760e7163999b33c13/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260227_LH00519_0059_B23L5TMLT4__444aee1e--20260301-135529/alignments/recalibrated/1029_IRX-N1-BDNA-1_B23L5TMLT4_1/1029_IRX-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
==> 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: 1029_IRX-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_IRX-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_IRX-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_IRX-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: 69248360 total, 61818 skipped (flags/unmapped)
Fragments: 34738552 total (34404347 tlen-paired, 4317 hash-paired, 368 singletons, 16800 discordant, 312720 orphans, 11263 too large [>5000 bp], 12123436 duplicates)
Reads: 74879288 total, 49194 skipped (flags/unmapped)
Fragments: 37564140 total (37229827 tlen-paired, 4198 hash-paired, 409 singletons, 12037 discordant, 317669 orphans, 9946 too large [>5000 bp], 12907899 duplicates)
Reads: 73537985 total, 51778 skipped (flags/unmapped)
Fragments: 36895166 total (36529599 tlen-paired, 6570 hash-paired, 390 singletons, 14712 discordant, 343895 orphans, 20080 too large [>5000 bp], 12946391 duplicates)
Reads: 80964879 total, 89893 skipped (flags/unmapped)
Fragments: 40722683 total (39834573 tlen-paired, 5340 hash-paired, 383 singletons, 169482 discordant, 712905 orphans, 71454 too large [>5000 bp], 14303921 duplicates)