Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20251222_LH00527_0042_A2375WFLT3__5d8e7d70--20260228-200339/alignments/recalibrated/1029_BBCQ-N1-BDNA-1_2375WFLT3_s21/1029_BBCQ-N1-BDNA-1_2375WFLT3_s21.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/12/f3fe7977e57a8f7756cfe547792883/.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/12/f3fe7977e57a8f7756cfe547792883/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20251222_LH00527_0042_A2375WFLT3__5d8e7d70--20260228-200339/alignments/recalibrated/1029_BBCQ-N1-BDNA-1_2375WFLT3_s21/1029_BBCQ-N1-BDNA-1_2375WFLT3_s21.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: 1029_BBCQ-N1-BDNA-1_2375WFLT3_s21.recalibrated.bam.baiThe index file is older than the data file: 1029_BBCQ-N1-BDNA-1_2375WFLT3_s21.recalibrated.bam.bai

[W::hts_idx_load3] The index file is older than the data file: 1029_BBCQ-N1-BDNA-1_2375WFLT3_s21.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BBCQ-N1-BDNA-1_2375WFLT3_s21.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: 73678463 total, 58119 skipped (flags/unmapped)
Fragments: 37019834 total (36558316 tlen-paired, 6140 hash-paired, 1148 singletons, 10964 discordant, 443266 orphans, 12545 too large [>5000 bp], 10664791 duplicates)
Reads: 66736320 total, 60296 skipped (flags/unmapped)
Fragments: 33530515 total (33119378 tlen-paired, 4263 hash-paired, 1046 singletons, 11628 discordant, 394200 orphans, 5120 too large [>5000 bp], 9765360 duplicates)
Reads: 72058597 total, 52247 skipped (flags/unmapped)
Fragments: 36208713 total (35770112 tlen-paired, 3420 hash-paired, 1100 singletons, 8097 discordant, 425984 orphans, 8004 too large [>5000 bp], 10400676 duplicates)
Reads: 75128412 total, 97272 skipped (flags/unmapped)
Fragments: 37955182 total (36602671 tlen-paired, 2981 hash-paired, 1217 singletons, 260782 discordant, 1087531 orphans, 104762 too large [>5000 bp], 10873484 duplicates)