Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5e/79057b92dc6af0982f9514b540cee5/.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/5e/79057b92dc6af0982f9514b540cee5/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260323_LH00519_0074_B23KFG5LT4__d7a6b981--20260325-091021/alignments/recalibrated/1136_4QQ-N1-BDNA-1_B23KFG5LT4_1/1136_4QQ-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260323_LH00519_0074_B23KFG5LT4__d7a6b981--20260325-091021/alignments/recalibrated/1136_4QQ-N1-BDNA-1_B23KFG5LT4_1/1136_4QQ-N1-BDNA-1_B23KFG5LT4_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_4QQ-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
The index file is older than the data file: 1136_4QQ-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_4QQ-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_4QQ-N1-BDNA-1_B23KFG5LT4_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: 68557163 total, 49454 skipped (flags/unmapped)
Fragments: 34364856 total (34102241 tlen-paired, 2778 hash-paired, 359 singletons, 15244 discordant, 244234 orphans, 11295 too large [>5000 bp], 12917522 duplicates)
Reads: 73838539 total, 41942 skipped (flags/unmapped)
Fragments: 37013691 total (36752416 tlen-paired, 2180 hash-paired, 330 singletons, 10586 discordant, 248179 orphans, 8862 too large [>5000 bp], 13588588 duplicates)
Reads: 81750921 total, 71862 skipped (flags/unmapped)
Fragments: 41059146 total (40388385 tlen-paired, 2938 hash-paired, 309 singletons, 125248 discordant, 542266 orphans, 51671 too large [>5000 bp], 15561593 duplicates)
Reads: 80863595 total, 45903 skipped (flags/unmapped)
Fragments: 40537897 total (40219071 tlen-paired, 4135 hash-paired, 282 singletons, 16285 discordant, 298124 orphans, 20152 too large [>5000 bp], 15328953 duplicates)