Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260410_LH00527_0075_A23NMNVLT4__0ce77ad5--20260414-073011/alignments/recalibrated/1136_2QD-N1-BDNA-1_A23NMNVLT4_1/1136_2QD-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/01/7ae27dc5f907cc4c97505f47157284/.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/01/7ae27dc5f907cc4c97505f47157284/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260410_LH00527_0075_A23NMNVLT4__0ce77ad5--20260414-073011/alignments/recalibrated/1136_2QD-N1-BDNA-1_A23NMNVLT4_1/1136_2QD-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1136_2QD-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
Count mode: frac
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1136_2QD-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_2QD-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_2QD-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: 82653898 total, 59898 skipped (flags/unmapped)
Fragments: 41396039 total (41173345 tlen-paired, 2682 hash-paired, 346 singletons, 9942 discordant, 209724 orphans, 5996 too large [>5000 bp], 12043494 duplicates)
Reads: 89746559 total, 52851 skipped (flags/unmapped)
Fragments: 44947186 total (44718678 tlen-paired, 4111 hash-paired, 417 singletons, 6845 discordant, 217135 orphans, 8444 too large [>5000 bp], 12891102 duplicates)
Reads: 89368941 total, 54494 skipped (flags/unmapped)
Fragments: 44763894 total (44492051 tlen-paired, 2475 hash-paired, 287 singletons, 8661 discordant, 260420 orphans, 23683 too large [>5000 bp], 13183433 duplicates)
Reads: 98481898 total, 92114 skipped (flags/unmapped)
Fragments: 49394018 total (48761855 tlen-paired, 3425 hash-paired, 333 singletons, 123260 discordant, 505145 orphans, 53613 too large [>5000 bp], 14603743 duplicates)