Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00519_0072_A23KFG7LT4__d7a6b981--20260322-104015/alignments/recalibrated/1029_E5O-N1-BDNA-1_A23KFG7LT4_1/1029_E5O-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9b/7bf061804ee6d34d210678f3fb2207/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00519_0072_A23KFG7LT4__d7a6b981--20260322-104015/alignments/recalibrated/1029_E5O-N1-BDNA-1_A23KFG7LT4_1/1029_E5O-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam
  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/9b/7bf061804ee6d34d210678f3fb2207/.command.run
==> 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: 1029_E5O-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
The index file is older than the data file: 1029_E5O-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_E5O-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_E5O-N1-BDNA-1_A23KFG7LT4_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: 57132903 total, 42510 skipped (flags/unmapped)
Fragments: 28703111 total (28358356 tlen-paired, 2617 hash-paired, 339 singletons, 10817 discordant, 330982 orphans, 7746 too large [>5000 bp], 9797605 duplicates)
Reads: 60560300 total, 36473 skipped (flags/unmapped)
Fragments: 30426766 total (30072115 tlen-paired, 2373 hash-paired, 344 singletons, 7279 discordant, 344655 orphans, 7647 too large [>5000 bp], 10095030 duplicates)
Reads: 66511054 total, 38747 skipped (flags/unmapped)
Fragments: 33421987 total (33010631 tlen-paired, 3414 hash-paired, 295 singletons, 11375 discordant, 396272 orphans, 12450 too large [>5000 bp], 11427481 duplicates)
Reads: 67728129 total, 64465 skipped (flags/unmapped)
Fragments: 34188792 total (33071226 tlen-paired, 2324 hash-paired, 350 singletons, 219618 discordant, 895274 orphans, 90852 too large [>5000 bp], 11632908 duplicates)