Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00527_0067_B23KGCJLT4__d7a6b981--20260322-105015/alignments/recalibrated/1136_1EQ-N1-BDNA-1_B23KGCJLT4_1/1136_1EQ-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/90/7da27bd27d0a983440aebdf44c3701/.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/90/7da27bd27d0a983440aebdf44c3701/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00527_0067_B23KGCJLT4__d7a6b981--20260322-105015/alignments/recalibrated/1136_1EQ-N1-BDNA-1_B23KGCJLT4_1/1136_1EQ-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam
==> 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_1EQ-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_1EQ-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_1EQ-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_1EQ-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
Deduplicated 94 probes with identical coordinates
Deduplicated 94 probes with identical coordinates
Loaded 472416 probes across 3366 contigs
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: 67318366 total, 46604 skipped (flags/unmapped)
Fragments: 33722753 total (33512234 tlen-paired, 2709 hash-paired, 246 singletons, 12694 discordant, 194870 orphans, 10686 too large [>5000 bp], 11407546 duplicates)
Reads: 71851507 total, 38524 skipped (flags/unmapped)
Fragments: 35996260 total (35788538 tlen-paired, 2190 hash-paired, 336 singletons, 8975 discordant, 196221 orphans, 8510 too large [>5000 bp], 11941157 duplicates)
Reads: 79076142 total, 64193 skipped (flags/unmapped)
Fragments: 39674142 total (39158633 tlen-paired, 1948 hash-paired, 288 singletons, 95528 discordant, 417745 orphans, 40849 too large [>5000 bp], 13508786 duplicates)
Reads: 79171187 total, 43043 skipped (flags/unmapped)
Fragments: 39669637 total (39403079 tlen-paired, 5730 hash-paired, 256 singletons, 13366 discordant, 247206 orphans, 18166 too large [>5000 bp], 13442238 duplicates)