Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260227_LH00519_0059_B23L5TMLT4__444aee1e--20260301-135529/alignments/recalibrated/1173_IT6-N1-BDNA-01_B23L5TMLT4_1/1173_IT6-N1-BDNA-01_B23L5TMLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e5/aef271fca1730548d56e60f8d06d5a/.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/e5/aef271fca1730548d56e60f8d06d5a/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260227_LH00519_0059_B23L5TMLT4__444aee1e--20260301-135529/alignments/recalibrated/1173_IT6-N1-BDNA-01_B23L5TMLT4_1/1173_IT6-N1-BDNA-01_B23L5TMLT4_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: 1173_IT6-N1-BDNA-01_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 1173_IT6-N1-BDNA-01_B23L5TMLT4_1.recalibrated.bam.baiThe index file is older than the data file: 1173_IT6-N1-BDNA-01_B23L5TMLT4_1.recalibrated.bam.bai

[W::hts_idx_load3] The index file is older than the data file: 1173_IT6-N1-BDNA-01_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
Deduplicated 94 probes with identical coordinates
Loaded 472416 probes across 3366 contigs
Loaded 472416 probes across 3366 contigs
Reads: 65254364 total, 50606 skipped (flags/unmapped)
Fragments: 32715539 total (32457633 tlen-paired, 4399 hash-paired, 326 singletons, 10545 discordant, 242636 orphans, 7821 too large [>5000 bp], 10707390 duplicates)
Reads: 68791801 total, 40471 skipped (flags/unmapped)
Fragments: 34490987 total (34234109 tlen-paired, 3404 hash-paired, 463 singletons, 7326 discordant, 245685 orphans, 7752 too large [>5000 bp], 11074994 duplicates)
Reads: 75798268 total, 75863 skipped (flags/unmapped)
Fragments: 38100128 total (37355982 tlen-paired, 4209 hash-paired, 419 singletons, 141674 discordant, 597844 orphans, 60206 too large [>5000 bp], 12477402 duplicates)
Reads: 74935625 total, 44923 skipped (flags/unmapped)
Fragments: 37575510 total (37267580 tlen-paired, 4172 hash-paired, 416 singletons, 10536 discordant, 292806 orphans, 16452 too large [>5000 bp], 12330006 duplicates)