Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00527_0067_B23KGCJLT4__d7a6b981--20260322-105015/alignments/recalibrated/1136_2LG-N1-BDNA-1_B23KGCJLT4_1/1136_2LG-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00527_0067_B23KGCJLT4__d7a6b981--20260322-105015/alignments/recalibrated/1136_2LG-N1-BDNA-1_B23KGCJLT4_1/1136_2LG-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ff/0f2699e1a2c3f4fa2a30da3d6e9361/.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/ff/0f2699e1a2c3f4fa2a30da3d6e9361/.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_2LG-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_2LG-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_2LG-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_2LG-N1-BDNA-1_B23KGCJLT4_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: 83971962 total, 57381 skipped (flags/unmapped)
Fragments: 42110953 total (41763562 tlen-paired, 2808 hash-paired, 411 singletons, 13434 discordant, 330738 orphans, 11912 too large [>5000 bp], 16267674 duplicates)
Reads: 77855172 total, 64655 skipped (flags/unmapped)
Fragments: 39043787 total (38700177 tlen-paired, 4175 hash-paired, 420 singletons, 19076 discordant, 319939 orphans, 11651 too large [>5000 bp], 15328066 duplicates)
Reads: 91975769 total, 90950 skipped (flags/unmapped)
Fragments: 46238718 total (45337420 tlen-paired, 2845 hash-paired, 384 singletons, 169758 discordant, 728311 orphans, 68039 too large [>5000 bp], 18252174 duplicates)
Reads: 91602500 total, 59147 skipped (flags/unmapped)
Fragments: 45941920 total (45520257 tlen-paired, 3317 hash-paired, 394 singletons, 20159 discordant, 397793 orphans, 28850 too large [>5000 bp], 18147129 duplicates)