Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260522_LH00527_0093_A23TY7KLT4__8afaba2b--20260524-103028/alignments/recalibrated/1241_BU9U-N1-BDNA-1_A23TY7KLT4_1/1241_BU9U-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/37/e7a74ebc41f78662f36bf10b70c1e7/.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/37/e7a74ebc41f78662f36bf10b70c1e7/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260522_LH00527_0093_A23TY7KLT4__8afaba2b--20260524-103028/alignments/recalibrated/1241_BU9U-N1-BDNA-1_A23TY7KLT4_1/1241_BU9U-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_BU9U-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_BU9U-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_BU9U-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_BU9U-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: 97799572 total, 65130 skipped (flags/unmapped)
Fragments: 48993247 total (48702734 tlen-paired, 3484 hash-paired, 497 singletons, 15511 discordant, 271021 orphans, 9733 too large [>5000 bp], 17124341 duplicates)
Reads: 104634255 total, 59321 skipped (flags/unmapped)
Fragments: 52423632 total (52096819 tlen-paired, 4863 hash-paired, 337 singletons, 13664 discordant, 307949 orphans, 17978 too large [>5000 bp], 18447036 duplicates)
Reads: 106058669 total, 57431 skipped (flags/unmapped)
Fragments: 53127900 total (52835037 tlen-paired, 3889 hash-paired, 442 singletons, 10746 discordant, 277786 orphans, 11833 too large [>5000 bp], 18256533 duplicates)
Reads: 115222298 total, 102440 skipped (flags/unmapped)
Fragments: 57803468 total (57042448 tlen-paired, 3863 hash-paired, 442 singletons, 146169 discordant, 610546 orphans, 61955 too large [>5000 bp], 20359161 duplicates)