Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260508_LH00519_0089_A23TNVNLT4__8afaba2b--20260511-081020/alignments/recalibrated/1241_731-N1-BDNA-1_A23TNVNLT4_1/1241_731-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d3/2e14244dc6bf4ff6d8a430c81d39a0/.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/d3/2e14244dc6bf4ff6d8a430c81d39a0/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260508_LH00519_0089_A23TNVNLT4__8afaba2b--20260511-081020/alignments/recalibrated/1241_731-N1-BDNA-1_A23TNVNLT4_1/1241_731-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
==> 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_731-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai[W::hts_idx_load3] 
The index file is older than the data file: 1241_731-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_731-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_731-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: 99901914 total, 64916 skipped (flags/unmapped)
Fragments: 50085473 total (49707094 tlen-paired, 4057 hash-paired, 488 singletons, 17874 discordant, 355960 orphans, 11250 too large [>5000 bp], 19937931 duplicates)
Reads: 107676992 total, 56086 skipped (flags/unmapped)
Fragments: 53989615 total (53594170 tlen-paired, 3065 hash-paired, 606 singletons, 13080 discordant, 378694 orphans, 10488 too large [>5000 bp], 21075059 duplicates)
Reads: 107045336 total, 57381 skipped (flags/unmapped)
Fragments: 53670924 total (53259529 tlen-paired, 3873 hash-paired, 416 singletons, 15435 discordant, 391671 orphans, 19097 too large [>5000 bp], 21448784 duplicates)
Reads: 118429892 total, 104678 skipped (flags/unmapped)
Fragments: 59507970 total (58433802 tlen-paired, 4119 hash-paired, 530 singletons, 211775 discordant, 857744 orphans, 83774 too large [>5000 bp], 23763159 duplicates)