Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260318_LH00166_0269_A23H3W5LT3__d7a6b981--20260320-054016/alignments/recalibrated/1136_5CN-N1-BDNA-1_A23H3W5LT3_1/1136_5CN-N1-BDNA-1_A23H3W5LT3_1.recalibrated.bam.bai
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260318_LH00166_0269_A23H3W5LT3__d7a6b981--20260320-054016/alignments/recalibrated/1136_5CN-N1-BDNA-1_A23H3W5LT3_1/1136_5CN-N1-BDNA-1_A23H3W5LT3_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/64/7baf6ce9c50da64ce918a54fd64d50/.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/64/7baf6ce9c50da64ce918a54fd64d50/.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: 1136_5CN-N1-BDNA-1_A23H3W5LT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5CN-N1-BDNA-1_A23H3W5LT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5CN-N1-BDNA-1_A23H3W5LT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_5CN-N1-BDNA-1_A23H3W5LT3_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: 87332609 total, 72804 skipped (flags/unmapped)
Fragments: 43812034 total (43406992 tlen-paired, 13954 hash-paired, 5211 singletons, 9617 discordant, 376260 orphans, 8604 too large [>5000 bp], 10300375 duplicates)
Reads: 88184508 total, 64385 skipped (flags/unmapped)
Fragments: 44248065 total (43825083 tlen-paired, 13607 hash-paired, 5158 singletons, 8324 discordant, 395893 orphans, 12522 too large [>5000 bp], 10353757 duplicates)
Reads: 96199534 total, 64345 skipped (flags/unmapped)
Fragments: 48272176 total (47823415 tlen-paired, 14400 hash-paired, 5576 singletons, 7328 discordant, 421457 orphans, 8935 too large [>5000 bp], 11275276 duplicates)
Reads: 98676082 total, 110463 skipped (flags/unmapped)
Fragments: 49703198 total (48379547 tlen-paired, 14522 hash-paired, 5880 singletons, 260256 discordant, 1042993 orphans, 104048 too large [>5000 bp], 11557719 duplicates)