Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/77/1f8bc4617c2e7c023177e501999cd4/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00527_0067_B23KGCJLT4__d7a6b981--20260322-105015/alignments/recalibrated/1047_FA-N1-BDNA-1_B23KGCJLT4_1/1047_FA-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
  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/77/1f8bc4617c2e7c023177e501999cd4/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00527_0067_B23KGCJLT4__d7a6b981--20260322-105015/alignments/recalibrated/1047_FA-N1-BDNA-1_B23KGCJLT4_1/1047_FA-N1-BDNA-1_B23KGCJLT4_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: 1047_FA-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1047_FA-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1047_FA-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1047_FA-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: 69097766 total, 48192 skipped (flags/unmapped)
Fragments: 34622283 total (34385227 tlen-paired, 3732 hash-paired, 240 singletons, 10524 discordant, 222560 orphans, 13904 too large [>5000 bp], 12962766 duplicates)
Reads: 64081326 total, 50630 skipped (flags/unmapped)
Fragments: 32103033 total (31894718 tlen-paired, 2921 hash-paired, 304 singletons, 12058 discordant, 193032 orphans, 8983 too large [>5000 bp], 11961426 duplicates)
Reads: 69923740 total, 43256 skipped (flags/unmapped)
Fragments: 35028273 total (34821335 tlen-paired, 2524 hash-paired, 339 singletons, 8506 discordant, 195569 orphans, 9923 too large [>5000 bp], 12713551 duplicates)
Reads: 75972219 total, 71681 skipped (flags/unmapped)
Fragments: 38116979 total (37602188 tlen-paired, 2005 hash-paired, 324 singletons, 97018 discordant, 415444 orphans, 41174 too large [>5000 bp], 14329680 duplicates)