Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260508_LH00519_0089_A23TNVNLT4__8afaba2b--20260511-081020/alignments/recalibrated/1241_F1Y-N1-BDNA-1_A23TNVNLT4_1/1241_F1Y-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260508_LH00519_0089_A23TNVNLT4__8afaba2b--20260511-081020/alignments/recalibrated/1241_F1Y-N1-BDNA-1_A23TNVNLT4_1/1241_F1Y-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/99/b89093e41e354af7e6fd84245b119d/.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/99/b89093e41e354af7e6fd84245b119d/.command.run
==> 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_F1Y-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai[W::hts_idx_load3] The index file is older than the data file: 1241_F1Y-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai

[W::hts_idx_load3] The index file is older than the data file: 1241_F1Y-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_F1Y-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: 82017123 total, 56799 skipped (flags/unmapped)
Fragments: 41123097 total (40798522 tlen-paired, 3294 hash-paired, 377 singletons, 13783 discordant, 307121 orphans, 10814 too large [>5000 bp], 15359559 duplicates)
Reads: 88739434 total, 49643 skipped (flags/unmapped)
Fragments: 44498906 total (44158974 tlen-paired, 2993 hash-paired, 523 singletons, 10090 discordant, 326326 orphans, 9414 too large [>5000 bp], 16352989 duplicates)
Reads: 88239952 total, 50551 skipped (flags/unmapped)
Fragments: 44251589 total (43888567 tlen-paired, 3656 hash-paired, 384 singletons, 12467 discordant, 346515 orphans, 16561 too large [>5000 bp], 16619671 duplicates)
Reads: 98132120 total, 93764 skipped (flags/unmapped)
Fragments: 49325208 total (48367282 tlen-paired, 2789 hash-paired, 480 singletons, 191617 discordant, 763040 orphans, 75730 too large [>5000 bp], 18483298 duplicates)