Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0b/3e2fd23f3e4f93ba879fb331f0325e/.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/0b/3e2fd23f3e4f93ba879fb331f0325e/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00527_0067_B23KGCJLT4__d7a6b981--20260322-105015/alignments/recalibrated/1136_5OE-N1-BDNA-1_B23KGCJLT4_1/1136_5OE-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_5OE-N1-BDNA-1_B23KGCJLT4_1/1136_5OE-N1-BDNA-1_B23KGCJLT4_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: 1136_5OE-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
The index file is older than the data file: 1136_5OE-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5OE-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5OE-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: 75923660 total, 58035 skipped (flags/unmapped)
Fragments: 38057270 total (37768122 tlen-paired, 3835 hash-paired, 353 singletons, 13502 discordant, 271458 orphans, 11448 too large [>5000 bp], 15160324 duplicates)
Reads: 81416255 total, 51065 skipped (flags/unmapped)
Fragments: 40819013 total (40476471 tlen-paired, 2741 hash-paired, 278 singletons, 12523 discordant, 327000 orphans, 27221 too large [>5000 bp], 16369608 duplicates)
Reads: 81482267 total, 47014 skipped (flags/unmapped)
Fragments: 40846961 total (40555146 tlen-paired, 2811 hash-paired, 433 singletons, 9671 discordant, 278900 orphans, 10332 too large [>5000 bp], 15972933 duplicates)
Reads: 90137275 total, 80733 skipped (flags/unmapped)
Fragments: 45281557 total (44483013 tlen-paired, 3027 hash-paired, 315 singletons, 156965 discordant, 638237 orphans, 65990 too large [>5000 bp], 18167145 duplicates)