Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260209_LH00166_0241_B2377KTLT3__8aacaa71--20260305-220745/alignments/recalibrated/869_FHY-N1-BDNA-1_B2377KTLT3_2/869_FHY-N1-BDNA-1_B2377KTLT3_2.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/40/c677c727132205665acb2dc6feab7f/.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/40/c677c727132205665acb2dc6feab7f/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260209_LH00166_0241_B2377KTLT3__8aacaa71--20260305-220745/alignments/recalibrated/869_FHY-N1-BDNA-1_B2377KTLT3_2/869_FHY-N1-BDNA-1_B2377KTLT3_2.recalibrated.bam
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 869_FHY-N1-BDNA-1_B2377KTLT3_2.recalibrated.bam.baiThe index file is older than the data file: 869_FHY-N1-BDNA-1_B2377KTLT3_2.recalibrated.bam.bai

[W::hts_idx_load3] The index file is older than the data file: 869_FHY-N1-BDNA-1_B2377KTLT3_2.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 869_FHY-N1-BDNA-1_B2377KTLT3_2.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: 64972017 total, 62992 skipped (flags/unmapped)
Fragments: 32591474 total (32272517 tlen-paired, 23852 hash-paired, 5370 singletons, 6456 discordant, 283279 orphans, 7363 too large [>5000 bp], 5728823 duplicates)
Reads: 71207502 total, 57469 skipped (flags/unmapped)
Fragments: 35730417 total (35373024 tlen-paired, 24996 hash-paired, 5671 singletons, 4650 discordant, 322076 orphans, 8473 too large [>5000 bp], 6317879 duplicates)
Reads: 71889645 total, 56857 skipped (flags/unmapped)
Fragments: 36072021 total (35701485 tlen-paired, 25746 hash-paired, 5753 singletons, 6532 discordant, 332505 orphans, 13502 too large [>5000 bp], 6320969 duplicates)
Reads: 72943629 total, 101739 skipped (flags/unmapped)
Fragments: 36755968 total (35699882 tlen-paired, 26870 hash-paired, 5983 singletons, 198680 discordant, 824553 orphans, 80245 too large [>5000 bp], 6381561 duplicates)