Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260227_LH00519_0059_B23L5TMLT4__444aee1e--20260301-135529/alignments/recalibrated/659_drZ-N1-BDNA-1_B23L5TMLT4_1/659_drZ-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/fc/11f0d88fc4c3d95a2f762298277e1d/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fc/11f0d88fc4c3d95a2f762298277e1d/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260227_LH00519_0059_B23L5TMLT4__444aee1e--20260301-135529/alignments/recalibrated/659_drZ-N1-BDNA-1_B23L5TMLT4_1/659_drZ-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 659_drZ-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.baiThe index file is older than the data file: 659_drZ-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai

[W::hts_idx_load3] The index file is older than the data file: 659_drZ-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_drZ-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
Deduplicated 94 probes with identical coordinates
Loaded 472416 probes across 3366 contigs
Loaded 472416 probes across 3366 contigs
Deduplicated 94 probes with identical coordinates
Loaded 472416 probes across 3366 contigs
Reads: 79554233 total, 67408 skipped (flags/unmapped)
Fragments: 39885113 total (39561751 tlen-paired, 5984 hash-paired, 475 singletons, 14597 discordant, 302306 orphans, 9690 too large [>5000 bp], 14212765 duplicates)
Reads: 85088354 total, 58236 skipped (flags/unmapped)
Fragments: 42658038 total (42334896 tlen-paired, 5171 hash-paired, 441 singletons, 9979 discordant, 307551 orphans, 11017 too large [>5000 bp], 15013301 duplicates)
Reads: 93344733 total, 103075 skipped (flags/unmapped)
Fragments: 46910608 total (46005720 tlen-paired, 5568 hash-paired, 482 singletons, 171832 discordant, 727006 orphans, 73965 too large [>5000 bp], 16817635 duplicates)
Reads: 92420417 total, 61461 skipped (flags/unmapped)
Fragments: 46339185 total (45954410 tlen-paired, 5789 hash-paired, 456 singletons, 14958 discordant, 363572 orphans, 22307 too large [>5000 bp], 16649821 duplicates)