Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/30/c5dcf78059b2bc306608959bc116f0/.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/30/c5dcf78059b2bc306608959bc116f0/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260323_LH00519_0074_B23KFG5LT4__d7a6b981--20260325-091021/alignments/recalibrated/1029_IEQ-N1-BDNA-1_B23KFG5LT4_1/1029_IEQ-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/1029_IEQ-N1-BDNA-1_B23KFG5LT4_1/1029_IEQ-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] The index file is older than the data file: 1029_IEQ-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 1029_IEQ-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
The index file is older than the data file: 1029_IEQ-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_IEQ-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: 60518656 total, 48887 skipped (flags/unmapped)
Fragments: 30376242 total (30061030 tlen-paired, 2629 hash-paired, 334 singletons, 10952 discordant, 301297 orphans, 9458 too large [>5000 bp], 12423381 duplicates)
Reads: 64392880 total, 41065 skipped (flags/unmapped)
Fragments: 32328081 total (31994685 tlen-paired, 2778 hash-paired, 350 singletons, 7653 discordant, 322615 orphans, 9309 too large [>5000 bp], 12863174 duplicates)
Reads: 71505083 total, 45579 skipped (flags/unmapped)
Fragments: 35894962 total (35511023 tlen-paired, 3009 hash-paired, 286 singletons, 11518 discordant, 369126 orphans, 19496 too large [>5000 bp], 14662706 duplicates)
Reads: 72363478 total, 76811 skipped (flags/unmapped)
Fragments: 36467366 total (35457639 tlen-paired, 2302 hash-paired, 346 singletons, 198632 discordant, 808447 orphans, 80364 too large [>5000 bp], 14795019 duplicates)