Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260522_LH00527_0093_A23TY7KLT4__8afaba2b--20260524-103028/alignments/recalibrated/1241_3VI-N1-BDNA-1_A23TY7KLT4_1/1241_3VI-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/42/5e8dd20f35d0e6562c8cb331c806ac/.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/42/5e8dd20f35d0e6562c8cb331c806ac/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260522_LH00527_0093_A23TY7KLT4__8afaba2b--20260524-103028/alignments/recalibrated/1241_3VI-N1-BDNA-1_A23TY7KLT4_1/1241_3VI-N1-BDNA-1_A23TY7KLT4_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: 1241_3VI-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_3VI-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_3VI-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_3VI-N1-BDNA-1_A23TY7KLT4_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: 91197618 total, 64046 skipped (flags/unmapped)
Fragments: 45669588 total (45422354 tlen-paired, 5446 hash-paired, 428 singletons, 12822 discordant, 228538 orphans, 11681 too large [>5000 bp], 16261685 duplicates)
Reads: 97386754 total, 51913 skipped (flags/unmapped)
Fragments: 48774812 total (48525957 tlen-paired, 4968 hash-paired, 449 singletons, 8884 discordant, 234554 orphans, 10110 too large [>5000 bp], 17130478 duplicates)
Reads: 96709286 total, 54833 skipped (flags/unmapped)
Fragments: 48438980 total (48145623 tlen-paired, 7575 hash-paired, 321 singletons, 10661 discordant, 274800 orphans, 25807 too large [>5000 bp], 17422886 duplicates)
Reads: 106282321 total, 90551 skipped (flags/unmapped)
Fragments: 53304798 total (52653374 tlen-paired, 3923 hash-paired, 420 singletons, 124817 discordant, 522264 orphans, 52429 too large [>5000 bp], 19220323 duplicates)