Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260410_LH00527_0075_A23NMNVLT4__0ce77ad5--20260414-073011/alignments/recalibrated/1136_88T-N1-BDNA-1_A23NMNVLT4_1/1136_88T-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/50/ae8d3feb1dc5afa19125db17a2a6e2/.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/50/ae8d3feb1dc5afa19125db17a2a6e2/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260410_LH00527_0075_A23NMNVLT4__0ce77ad5--20260414-073011/alignments/recalibrated/1136_88T-N1-BDNA-1_A23NMNVLT4_1/1136_88T-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
==> 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: 1136_88T-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_88T-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_88T-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_88T-N1-BDNA-1_A23NMNVLT4_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: 87602188 total, 65053 skipped (flags/unmapped)
Fragments: 43895611 total (43609346 tlen-paired, 2833 hash-paired, 375 singletons, 13287 discordant, 269770 orphans, 8029 too large [>5000 bp], 13988537 duplicates)
Reads: 93711236 total, 55542 skipped (flags/unmapped)
Fragments: 46956547 total (46669170 tlen-paired, 3469 hash-paired, 479 singletons, 8860 discordant, 274569 orphans, 8824 too large [>5000 bp], 14812422 duplicates)
Reads: 104381056 total, 95581 skipped (flags/unmapped)
Fragments: 52407179 total (51589311 tlen-paired, 2688 hash-paired, 420 singletons, 156261 discordant, 658499 orphans, 65018 too large [>5000 bp], 16937070 duplicates)
Reads: 103789115 total, 60272 skipped (flags/unmapped)
Fragments: 52013625 total (51664766 tlen-paired, 3283 hash-paired, 336 singletons, 13299 discordant, 331941 orphans, 16935 too large [>5000 bp], 16788768 duplicates)