Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260508_LH00519_0089_A23TNVNLT4__8afaba2b--20260511-081020/alignments/recalibrated/659_n7-N1-BDNA-1_A23TNVNLT4_1/659_n7-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/54/c6c6f871964c4ec0c7a25dcf677aef/.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/54/c6c6f871964c4ec0c7a25dcf677aef/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260508_LH00519_0089_A23TNVNLT4__8afaba2b--20260511-081020/alignments/recalibrated/659_n7-N1-BDNA-1_A23TNVNLT4_1/659_n7-N1-BDNA-1_A23TNVNLT4_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: 659_n7-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_n7-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_n7-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_n7-N1-BDNA-1_A23TNVNLT4_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: 75594233 total, 51342 skipped (flags/unmapped)
Fragments: 37868124 total (37635903 tlen-paired, 4140 hash-paired, 328 singletons, 10648 discordant, 217105 orphans, 12038 too large [>5000 bp], 12524619 duplicates)
Reads: 81700808 total, 42480 skipped (flags/unmapped)
Fragments: 40935382 total (40696953 tlen-paired, 3770 hash-paired, 375 singletons, 7309 discordant, 226975 orphans, 7457 too large [>5000 bp], 13262103 duplicates)
Reads: 89030500 total, 79740 skipped (flags/unmapped)
Fragments: 44691334 total (44022700 tlen-paired, 3999 hash-paired, 373 singletons, 128209 discordant, 536053 orphans, 52259 too large [>5000 bp], 14882175 duplicates)
Reads: 87992041 total, 44185 skipped (flags/unmapped)
Fragments: 44089964 total (43812506 tlen-paired, 3833 hash-paired, 321 singletons, 10589 discordant, 262715 orphans, 15482 too large [>5000 bp], 14647738 duplicates)