Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260227_LH00519_0059_B23L5TMLT4__444aee1e--20260301-135529/alignments/recalibrated/1047_D3-N1-BDNA-1_B23L5TMLT4_1/1047_D3-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260227_LH00519_0059_B23L5TMLT4__444aee1e--20260301-135529/alignments/recalibrated/1047_D3-N1-BDNA-1_B23L5TMLT4_1/1047_D3-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fe/5c1b8a1df7b8dae02ed8897ac6a2da/.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/fe/5c1b8a1df7b8dae02ed8897ac6a2da/.command.run
==> 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_D3-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1047_D3-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1047_D3-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1047_D3-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: 69456526 total, 54632 skipped (flags/unmapped)
Fragments: 34868293 total (34498150 tlen-paired, 3505 hash-paired, 395 singletons, 12458 discordant, 353785 orphans, 9744 too large [>5000 bp], 13023413 duplicates)
Reads: 73475157 total, 47896 skipped (flags/unmapped)
Fragments: 36887860 total (36509526 tlen-paired, 2615 hash-paired, 505 singletons, 8192 discordant, 367022 orphans, 9534 too large [>5000 bp], 13502378 duplicates)
Reads: 80283637 total, 50606 skipped (flags/unmapped)
Fragments: 40307512 total (39869822 tlen-paired, 3312 hash-paired, 419 singletons, 12595 discordant, 421364 orphans, 19895 too large [>5000 bp], 15047624 duplicates)
Reads: 81265501 total, 91201 skipped (flags/unmapped)
Fragments: 40961692 total (39787331 tlen-paired, 3505 hash-paired, 520 singletons, 229052 discordant, 941284 orphans, 96360 too large [>5000 bp], 15208860 duplicates)