Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260522_LH00527_0093_A23TY7KLT4__8afaba2b--20260524-103028/alignments/recalibrated/1241_BVH5-N1-BDNA-1_A23TY7KLT4_1/1241_BVH5-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2f/bd5f8ac23b82c75f0f1ccf24ef7f85/.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/2f/bd5f8ac23b82c75f0f1ccf24ef7f85/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260522_LH00527_0093_A23TY7KLT4__8afaba2b--20260524-103028/alignments/recalibrated/1241_BVH5-N1-BDNA-1_A23TY7KLT4_1/1241_BVH5-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] [W::hts_idx_load3] The index file is older than the data file: 1241_BVH5-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.baiThe index file is older than the data file: 1241_BVH5-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai

[W::hts_idx_load3] The index file is older than the data file: 1241_BVH5-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_BVH5-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: 59272379 total, 53665 skipped (flags/unmapped)
Fragments: 29700533 total (29489407 tlen-paired, 2653 hash-paired, 231 singletons, 12675 discordant, 195567 orphans, 6723 too large [>5000 bp], 9720852 duplicates)
Reads: 62119964 total, 44896 skipped (flags/unmapped)
Fragments: 31129517 total (30919913 tlen-paired, 1720 hash-paired, 232 singletons, 9270 discordant, 198382 orphans, 7324 too large [>5000 bp], 9949851 duplicates)
Reads: 62769471 total, 49559 skipped (flags/unmapped)
Fragments: 31456907 total (31223135 tlen-paired, 3995 hash-paired, 191 singletons, 10879 discordant, 218707 orphans, 12498 too large [>5000 bp], 10345129 duplicates)
Reads: 68769444 total, 72278 skipped (flags/unmapped)
Fragments: 34516571 total (33998453 tlen-paired, 1993 hash-paired, 256 singletons, 97667 discordant, 418202 orphans, 41241 too large [>5000 bp], 11375799 duplicates)