Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260410_LH00527_0075_A23NMNVLT4__0ce77ad5--20260414-073011/alignments/recalibrated/1136_10O-N1-BDNA-1_A23NMNVLT4_1/1136_10O-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260410_LH00527_0075_A23NMNVLT4__0ce77ad5--20260414-073011/alignments/recalibrated/1136_10O-N1-BDNA-1_A23NMNVLT4_1/1136_10O-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f8/4843e1a05d1efe8a18862ecc1d5c3a/.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/f8/4843e1a05d1efe8a18862ecc1d5c3a/.command.run
==> 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_10O-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai[W::hts_idx_load3] 
The index file is older than the data file: 1136_10O-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_10O-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_10O-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: 73391884 total, 45965 skipped (flags/unmapped)
Fragments: 36780677 total (36539478 tlen-paired, 2369 hash-paired, 333 singletons, 9235 discordant, 229262 orphans, 7080 too large [>5000 bp], 9740532 duplicates)
Reads: 78943836 total, 42761 skipped (flags/unmapped)
Fragments: 39566431 total (39289225 tlen-paired, 3196 hash-paired, 264 singletons, 8257 discordant, 265489 orphans, 16983 too large [>5000 bp], 10622416 duplicates)
Reads: 79466942 total, 41610 skipped (flags/unmapped)
Fragments: 39825846 total (39575086 tlen-paired, 2838 hash-paired, 420 singletons, 6548 discordant, 240954 orphans, 7507 too large [>5000 bp], 10303930 duplicates)
Reads: 86993074 total, 76360 skipped (flags/unmapped)
Fragments: 43687287 total (42957808 tlen-paired, 4119 hash-paired, 349 singletons, 144850 discordant, 580161 orphans, 61325 too large [>5000 bp], 11723669 duplicates)