Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260316_LH00166_0268_B23H2GYLT3__d7a6b981--20260318-065009/alignments/recalibrated/1029_V13-N1-BDNA-1_B23H2GYLT3_1/1029_V13-N1-BDNA-1_B23H2GYLT3_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0d/f40e871691e048abca84407569b225/.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/0d/f40e871691e048abca84407569b225/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260316_LH00166_0268_B23H2GYLT3__d7a6b981--20260318-065009/alignments/recalibrated/1029_V13-N1-BDNA-1_B23H2GYLT3_1/1029_V13-N1-BDNA-1_B23H2GYLT3_1.recalibrated.bam
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1029_V13-N1-BDNA-1_B23H2GYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_V13-N1-BDNA-1_B23H2GYLT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_V13-N1-BDNA-1_B23H2GYLT3_1.recalibrated.bam.bai
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1029_V13-N1-BDNA-1_B23H2GYLT3_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: 83334624 total, 71693 skipped (flags/unmapped)
Fragments: 41812881 total (41402887 tlen-paired, 16129 hash-paired, 6466 singletons, 8400 discordant, 378999 orphans, 11317 too large [>5000 bp], 9094445 duplicates)
Reads: 83870841 total, 63036 skipped (flags/unmapped)
Fragments: 42097200 total (41664081 tlen-paired, 15079 hash-paired, 6310 singletons, 7181 discordant, 404549 orphans, 12132 too large [>5000 bp], 9112190 duplicates)
Reads: 91900203 total, 61022 skipped (flags/unmapped)
Fragments: 46131033 total (45666592 tlen-paired, 15791 hash-paired, 6718 singletons, 5993 discordant, 435939 orphans, 9886 too large [>5000 bp], 10006940 duplicates)
Reads: 94030420 total, 106361 skipped (flags/unmapped)
Fragments: 47403043 total (46020484 tlen-paired, 16059 hash-paired, 7077 singletons, 273703 discordant, 1085720 orphans, 105385 too large [>5000 bp], 10169882 duplicates)