Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260508_LH00519_0089_A23TNVNLT4__8afaba2b--20260511-081020/alignments/recalibrated/1241_296-N1-BDNA-1_A23TNVNLT4_1/1241_296-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5f/4a6c1c95e3407f3140c83ba9aacc47/.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/5f/4a6c1c95e3407f3140c83ba9aacc47/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260508_LH00519_0089_A23TNVNLT4__8afaba2b--20260511-081020/alignments/recalibrated/1241_296-N1-BDNA-1_A23TNVNLT4_1/1241_296-N1-BDNA-1_A23TNVNLT4_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_296-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
The index file is older than the data file: 1241_296-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_296-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_296-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: 94704584 total, 67283 skipped (flags/unmapped)
Fragments: 47483500 total (47111332 tlen-paired, 3068 hash-paired, 392 singletons, 17319 discordant, 351389 orphans, 11041 too large [>5000 bp], 16698617 duplicates)
Reads: 101309830 total, 57809 skipped (flags/unmapped)
Fragments: 50801397 total (50416948 tlen-paired, 3632 hash-paired, 451 singletons, 11988 discordant, 368378 orphans, 9028 too large [>5000 bp], 17602127 duplicates)
Reads: 111789230 total, 63912 skipped (flags/unmapped)
Fragments: 56050517 total (55604417 tlen-paired, 4778 hash-paired, 416 singletons, 18100 discordant, 422806 orphans, 23753 too large [>5000 bp], 19949887 duplicates)
Reads: 113060700 total, 112916 skipped (flags/unmapped)
Fragments: 56826625 total (55738702 tlen-paired, 3970 hash-paired, 471 singletons, 210575 discordant, 872907 orphans, 83956 too large [>5000 bp], 20227162 duplicates)