Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260227_LH00519_0059_B23L5TMLT4__444aee1e--20260301-135529/alignments/recalibrated/1029_BHXH-N1-BDNA-1_B23L5TMLT4_1/1029_BHXH-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c5/0f6c4846c014bc12de0d569ff680aa/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260227_LH00519_0059_B23L5TMLT4__444aee1e--20260301-135529/alignments/recalibrated/1029_BHXH-N1-BDNA-1_B23L5TMLT4_1/1029_BHXH-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam
  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/c5/0f6c4846c014bc12de0d569ff680aa/.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: 1029_BHXH-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BHXH-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BHXH-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BHXH-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: 95858931 total, 74499 skipped (flags/unmapped)
Fragments: 48099307 total (47641246 tlen-paired, 5002 hash-paired, 577 singletons, 18383 discordant, 434099 orphans, 10247 too large [>5000 bp], 18796539 duplicates)
Reads: 102718648 total, 62317 skipped (flags/unmapped)
Fragments: 51541440 total (51073099 tlen-paired, 4827 hash-paired, 551 singletons, 13039 discordant, 449924 orphans, 11963 too large [>5000 bp], 19822948 duplicates)
Reads: 111868990 total, 68741 skipped (flags/unmapped)
Fragments: 56135473 total (55597383 tlen-paired, 5165 hash-paired, 542 singletons, 18570 discordant, 513813 orphans, 21829 too large [>5000 bp], 21988858 duplicates)
Reads: 113184901 total, 115778 skipped (flags/unmapped)
Fragments: 56976110 total (55603677 tlen-paired, 5037 hash-paired, 595 singletons, 264379 discordant, 1102422 orphans, 109960 too large [>5000 bp], 22247448 duplicates)