Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00527_0067_B23KGCJLT4__d7a6b981--20260322-105015/alignments/recalibrated/1136_7JV-N1-BDNA-1_B23KGCJLT4_1/1136_7JV-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00527_0067_B23KGCJLT4__d7a6b981--20260322-105015/alignments/recalibrated/1136_7JV-N1-BDNA-1_B23KGCJLT4_1/1136_7JV-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/98/ae24ad2424085059e52b323f5cd4ad/.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/98/ae24ad2424085059e52b323f5cd4ad/.command.run
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] [W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 1136_7JV-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.baiThe index file is older than the data file: 1136_7JV-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
The index file is older than the data file: 1136_7JV-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai

[W::hts_idx_load3] The index file is older than the data file: 1136_7JV-N1-BDNA-1_B23KGCJLT4_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: 63261066 total, 43063 skipped (flags/unmapped)
Fragments: 31698332 total (31491025 tlen-paired, 2601 hash-paired, 363 singletons, 11793 discordant, 192550 orphans, 7126 too large [>5000 bp], 10941885 duplicates)
Reads: 68686916 total, 37707 skipped (flags/unmapped)
Fragments: 34414131 total (34206493 tlen-paired, 2590 hash-paired, 332 singletons, 8281 discordant, 196435 orphans, 8857 too large [>5000 bp], 11607584 duplicates)
Reads: 68380700 total, 40229 skipped (flags/unmapped)
Fragments: 34266020 total (34026044 tlen-paired, 2598 hash-paired, 250 singletons, 10295 discordant, 226833 orphans, 17757 too large [>5000 bp], 11879070 duplicates)
Reads: 75321949 total, 61529 skipped (flags/unmapped)
Fragments: 37798667 total (37276376 tlen-paired, 2238 hash-paired, 311 singletons, 99853 discordant, 419889 orphans, 41643 too large [>5000 bp], 13137569 duplicates)