Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260309_LH00166_0264_B23H3Y2LT3__5d7f62c6--20260311-041011/alignments/recalibrated/869_QL-N1-BDNA-1_B23H3Y2LT3_1/869_QL-N1-BDNA-1_B23H3Y2LT3_1.recalibrated.bam.bai
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260309_LH00166_0264_B23H3Y2LT3__5d7f62c6--20260311-041011/alignments/recalibrated/869_QL-N1-BDNA-1_B23H3Y2LT3_1/869_QL-N1-BDNA-1_B23H3Y2LT3_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/63/100fb227c37dd1902227a20ba4e61b/.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/63/100fb227c37dd1902227a20ba4e61b/.command.run
==> 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_QL-N1-BDNA-1_B23H3Y2LT3_1.recalibrated.bam.bai
The index file is older than the data file: 869_QL-N1-BDNA-1_B23H3Y2LT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 869_QL-N1-BDNA-1_B23H3Y2LT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 869_QL-N1-BDNA-1_B23H3Y2LT3_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: 93226086 total, 91972 skipped (flags/unmapped)
Fragments: 46843138 total (46250435 tlen-paired, 15017 hash-paired, 2762 singletons, 9708 discordant, 565216 orphans, 7908 too large [>5000 bp], 10716953 duplicates)
Reads: 93450097 total, 77044 skipped (flags/unmapped)
Fragments: 46973553 total (46341244 tlen-paired, 15004 hash-paired, 2734 singletons, 8766 discordant, 605805 orphans, 17243 too large [>5000 bp], 10663166 duplicates)
Reads: 102700389 total, 76491 skipped (flags/unmapped)
Fragments: 51622578 total (50959072 tlen-paired, 15442 hash-paired, 3044 singletons, 6804 discordant, 638216 orphans, 10001 too large [>5000 bp], 11720194 duplicates)
Reads: 105837554 total, 199114 skipped (flags/unmapped)
Fragments: 53480051 total (51400826 tlen-paired, 16309 hash-paired, 3277 singletons, 412776 discordant, 1646863 orphans, 164239 too large [>5000 bp], 12005797 duplicates)