Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260427_LH00519_0087_A23TY32LT4__manual_run_31e2bab--20260430-043425/alignments/recalibrated/1241_B9L-N1-BDNA-1_A23TY32LT4_1/1241_B9L-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260427_LH00519_0087_A23TY32LT4__manual_run_31e2bab--20260430-043425/alignments/recalibrated/1241_B9L-N1-BDNA-1_A23TY32LT4_1/1241_B9L-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fc/36a5bef28f554db851b1a83e99ad12/.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/fc/36a5bef28f554db851b1a83e99ad12/.command.run
==> 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_B9L-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.baiThe index file is older than the data file: 1241_B9L-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai

[W::hts_idx_load3] The index file is older than the data file: 1241_B9L-N1-BDNA-1_A23TY32LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_B9L-N1-BDNA-1_A23TY32LT4_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: 93830225 total, 69823 skipped (flags/unmapped)
Fragments: 47045555 total (46665038 tlen-paired, 5267 hash-paired, 480 singletons, 16156 discordant, 358614 orphans, 14193 too large [>5000 bp], 18536736 duplicates)
Reads: 101028381 total, 62301 skipped (flags/unmapped)
Fragments: 50657884 total (50266107 tlen-paired, 4668 hash-paired, 433 singletons, 10453 discordant, 376223 orphans, 13484 too large [>5000 bp], 19711956 duplicates)
Reads: 110797803 total, 62729 skipped (flags/unmapped)
Fragments: 55556357 total (55106499 tlen-paired, 3677 hash-paired, 380 singletons, 16217 discordant, 429584 orphans, 26162 too large [>5000 bp], 22060814 duplicates)
Reads: 112124326 total, 112245 skipped (flags/unmapped)
Fragments: 56372903 total (55238903 tlen-paired, 3489 hash-paired, 490 singletons, 220644 discordant, 909377 orphans, 88071 too large [>5000 bp], 22323072 duplicates)