Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1a/63fde29cc1966b35be3b5d257f143b/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260318_LH00166_0269_A23H3W5LT3__d7a6b981--20260320-054016/alignments/recalibrated/1136_47X-N1-BDNA-1_A23H3W5LT3_1/1136_47X-N1-BDNA-1_A23H3W5LT3_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1a/63fde29cc1966b35be3b5d257f143b/.command.run
  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-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260318_LH00166_0269_A23H3W5LT3__d7a6b981--20260320-054016/alignments/recalibrated/1136_47X-N1-BDNA-1_A23H3W5LT3_1/1136_47X-N1-BDNA-1_A23H3W5LT3_1.recalibrated.bam.bai
==> 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: 1136_47X-N1-BDNA-1_A23H3W5LT3_1.recalibrated.bam.bai
The index file is older than the data file: 1136_47X-N1-BDNA-1_A23H3W5LT3_1.recalibrated.bam.bai
[W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 1136_47X-N1-BDNA-1_A23H3W5LT3_1.recalibrated.bam.bai
The index file is older than the data file: 1136_47X-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: 69264946 total, 52016 skipped (flags/unmapped)
Fragments: 34782635 total (34391547 tlen-paired, 8840 hash-paired, 4633 singletons, 6422 discordant, 371193 orphans, 11743 too large [>5000 bp], 6809576 duplicates)
Reads: 69038998 total, 61276 skipped (flags/unmapped)
Fragments: 34655527 total (34286434 tlen-paired, 7582 hash-paired, 4819 singletons, 6915 discordant, 349777 orphans, 10632 too large [>5000 bp], 6804456 duplicates)
Reads: 76029067 total, 50764 skipped (flags/unmapped)
Fragments: 38182703 total (37768338 tlen-paired, 7608 hash-paired, 5134 singletons, 5390 discordant, 396233 orphans, 7132 too large [>5000 bp], 7476535 duplicates)
Reads: 77514132 total, 91265 skipped (flags/unmapped)
Fragments: 39117029 total (37851267 tlen-paired, 7992 hash-paired, 5424 singletons, 250385 discordant, 1001961 orphans, 98097 too large [>5000 bp], 7589616 duplicates)