Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9e/c94b0b6a8f345925fd1a868f01797c/.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/9e/c94b0b6a8f345925fd1a868f01797c/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260508_LH00519_0089_A23TNVNLT4__8afaba2b--20260511-081020/alignments/recalibrated/659_egZ-N1-BDNA-1_A23TNVNLT4_1/659_egZ-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260508_LH00519_0089_A23TNVNLT4__8afaba2b--20260511-081020/alignments/recalibrated/659_egZ-N1-BDNA-1_A23TNVNLT4_1/659_egZ-N1-BDNA-1_A23TNVNLT4_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: 659_egZ-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_egZ-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 659_egZ-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
The index file is older than the data file: 659_egZ-N1-BDNA-1_A23TNVNLT4_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: 54892043 total, 50541 skipped (flags/unmapped)
Fragments: 27491927 total (27325364 tlen-paired, 2349 hash-paired, 257 singletons, 8516 discordant, 155441 orphans, 6673 too large [>5000 bp], 8070298 duplicates)
Reads: 59234239 total, 44239 skipped (flags/unmapped)
Fragments: 29672649 total (29485440 tlen-paired, 2945 hash-paired, 189 singletons, 7072 discordant, 177003 orphans, 10947 too large [>5000 bp], 8820877 duplicates)
Reads: 60235327 total, 43417 skipped (flags/unmapped)
Fragments: 30172594 total (29996841 tlen-paired, 2849 hash-paired, 286 singletons, 6046 discordant, 166572 orphans, 6790 too large [>5000 bp], 8710718 duplicates)
Reads: 65386619 total, 70110 skipped (flags/unmapped)
Fragments: 32807654 total (32344414 tlen-paired, 3175 hash-paired, 302 singletons, 90136 discordant, 369627 orphans, 35565 too large [>5000 bp], 9780960 duplicates)