Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260410_LH00527_0075_A23NMNVLT4__0ce77ad5--20260414-073011/alignments/recalibrated/1136_7NC-N1-BDNA-1_A23NMNVLT4_1/1136_7NC-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/90/19f94e3425074c3af787a69934467d/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260410_LH00527_0075_A23NMNVLT4__0ce77ad5--20260414-073011/alignments/recalibrated/1136_7NC-N1-BDNA-1_A23NMNVLT4_1/1136_7NC-N1-BDNA-1_A23NMNVLT4_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/90/19f94e3425074c3af787a69934467d/.command.run
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1136_7NC-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_7NC-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1136_7NC-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1136_7NC-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: 79769898 total, 50945 skipped (flags/unmapped)
Fragments: 40078229 total (39616399 tlen-paired, 2370 hash-paired, 474 singletons, 7341 discordant, 451645 orphans, 7307 too large [>5000 bp], 11746493 duplicates)
Reads: 73668272 total, 58668 skipped (flags/unmapped)
Fragments: 37005137 total (36573618 tlen-paired, 3135 hash-paired, 360 singletons, 9828 discordant, 418196 orphans, 8943 too large [>5000 bp], 11060678 duplicates)
Reads: 87536647 total, 54094 skipped (flags/unmapped)
Fragments: 43981276 total (43463435 tlen-paired, 2997 hash-paired, 298 singletons, 10207 discordant, 504339 orphans, 12319 too large [>5000 bp], 13352445 duplicates)
Reads: 89163492 total, 93763 skipped (flags/unmapped)
Fragments: 45020296 total (43488684 tlen-paired, 3331 hash-paired, 586 singletons, 306782 discordant, 1220913 orphans, 125318 too large [>5000 bp], 13534470 duplicates)