Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20251222_LH00527_0042_A2375WFLT3__5d8e7d70--20260228-200339/alignments/recalibrated/1029_BS78-N1-BDNA-1_2375WFLT3_s51/1029_BS78-N1-BDNA-1_2375WFLT3_s51.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/11/43bbc94d5be3682c856190a37f19cf/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20251222_LH00527_0042_A2375WFLT3__5d8e7d70--20260228-200339/alignments/recalibrated/1029_BS78-N1-BDNA-1_2375WFLT3_s51/1029_BS78-N1-BDNA-1_2375WFLT3_s51.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/11/43bbc94d5be3682c856190a37f19cf/.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: 1029_BS78-N1-BDNA-1_2375WFLT3_s51.recalibrated.bam.bai
[W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 1029_BS78-N1-BDNA-1_2375WFLT3_s51.recalibrated.bam.baiThe index file is older than the data file: 1029_BS78-N1-BDNA-1_2375WFLT3_s51.recalibrated.bam.bai

[W::hts_idx_load3] The index file is older than the data file: 1029_BS78-N1-BDNA-1_2375WFLT3_s51.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: 81114873 total, 72282 skipped (flags/unmapped)
Fragments: 40756259 total (40254254 tlen-paired, 4769 hash-paired, 1415 singletons, 15087 discordant, 480734 orphans, 6111 too large [>5000 bp], 12443917 duplicates)
Reads: 88620563 total, 63985 skipped (flags/unmapped)
Fragments: 44531049 total (43988340 tlen-paired, 4981 hash-paired, 1315 singletons, 10268 discordant, 526145 orphans, 10970 too large [>5000 bp], 13457431 duplicates)
Reads: 91748560 total, 118797 skipped (flags/unmapped)
Fragments: 46349797 total (44704976 tlen-paired, 3514 hash-paired, 1448 singletons, 318108 discordant, 1321751 orphans, 126684 too large [>5000 bp], 13944749 duplicates)
Reads: 89828864 total, 69842 skipped (flags/unmapped)
Fragments: 45136861 total (44570389 tlen-paired, 3649 hash-paired, 1366 singletons, 14607 discordant, 546850 orphans, 16758 too large [>5000 bp], 13668785 duplicates)