Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260522_LH00527_0093_A23TY7KLT4__8afaba2b--20260524-103028/alignments/recalibrated/1241_QQR-N1-BDNA-1_A23TY7KLT4_1/1241_QQR-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260522_LH00527_0093_A23TY7KLT4__8afaba2b--20260524-103028/alignments/recalibrated/1241_QQR-N1-BDNA-1_A23TY7KLT4_1/1241_QQR-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/45/ac1ebd3a1a5741ce8abd139e995c14/.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/45/ac1ebd3a1a5741ce8abd139e995c14/.command.run
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1241_QQR-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_QQR-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_QQR-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1241_QQR-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: 72863945 total, 51719 skipped (flags/unmapped)
Fragments: 36487981 total (36293642 tlen-paired, 3231 hash-paired, 308 singletons, 10338 discordant, 180462 orphans, 8517 too large [>5000 bp], 11963167 duplicates)
Reads: 77942739 total, 41616 skipped (flags/unmapped)
Fragments: 39036119 total (38840662 tlen-paired, 2563 hash-paired, 339 singletons, 7487 discordant, 185068 orphans, 7146 too large [>5000 bp], 12535044 duplicates)
Reads: 77197596 total, 44455 skipped (flags/unmapped)
Fragments: 38666875 total (38456443 tlen-paired, 2490 hash-paired, 271 singletons, 8793 discordant, 198878 orphans, 9270 too large [>5000 bp], 12712958 duplicates)
Reads: 84756573 total, 72360 skipped (flags/unmapped)
Fragments: 42503670 total (41999103 tlen-paired, 3124 hash-paired, 315 singletons, 96412 discordant, 404716 orphans, 40952 too large [>5000 bp], 14025971 duplicates)