Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260227_LH00519_0059_B23L5TMLT4__444aee1e--20260301-135529/alignments/recalibrated/1136_3QA-N1-BDNA-1_B23L5TMLT4_1/1136_3QA-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/be/8765b20725bd5545bcfca497d96284/.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/be/8765b20725bd5545bcfca497d96284/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260227_LH00519_0059_B23L5TMLT4__444aee1e--20260301-135529/alignments/recalibrated/1136_3QA-N1-BDNA-1_B23L5TMLT4_1/1136_3QA-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1136_3QA-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1136_3QA-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_3QA-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_3QA-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: 71074819 total, 59786 skipped (flags/unmapped)
Fragments: 35642639 total (35333444 tlen-paired, 3539 hash-paired, 508 singletons, 13119 discordant, 292029 orphans, 11146 too large [>5000 bp], 11958609 duplicates)
Reads: 75952443 total, 49026 skipped (flags/unmapped)
Fragments: 38093137 total (37778846 tlen-paired, 4235 hash-paired, 515 singletons, 8837 discordant, 300704 orphans, 9181 too large [>5000 bp], 12568374 duplicates)
Reads: 82854345 total, 54672 skipped (flags/unmapped)
Fragments: 41553952 total (41178025 tlen-paired, 6605 hash-paired, 459 singletons, 13667 discordant, 355196 orphans, 23712 too large [>5000 bp], 13979245 duplicates)
Reads: 83127981 total, 88079 skipped (flags/unmapped)
Fragments: 41808574 total (40906149 tlen-paired, 3322 hash-paired, 483 singletons, 172921 discordant, 725699 orphans, 74468 too large [>5000 bp], 14027124 duplicates)