Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/cgp_dna_exp0024/20260212_LH00166_0244_A237CFYLT3__aa3fd045--20260224-223853/alignments/recalibrated/869_FH7-N1-BDNA-1_A237CFYLT3_1/869_FH7-N1-BDNA-1_A237CFYLT3_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0f/8799ea34eaf617ad3afa62fa31df95/.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/0f/8799ea34eaf617ad3afa62fa31df95/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/cgp_dna_exp0024/20260212_LH00166_0244_A237CFYLT3__aa3fd045--20260224-223853/alignments/recalibrated/869_FH7-N1-BDNA-1_A237CFYLT3_1/869_FH7-N1-BDNA-1_A237CFYLT3_1.recalibrated.bam.bai
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] [W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 869_FH7-N1-BDNA-1_A237CFYLT3_1.recalibrated.bam.baiThe index file is older than the data file: 869_FH7-N1-BDNA-1_A237CFYLT3_1.recalibrated.bam.baiThe index file is older than the data file: 869_FH7-N1-BDNA-1_A237CFYLT3_1.recalibrated.bam.bai


[W::hts_idx_load3] The index file is older than the data file: 869_FH7-N1-BDNA-1_A237CFYLT3_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: 87320760 total, 85769 skipped (flags/unmapped)
Fragments: 43889389 total (43301627 tlen-paired, 11306 hash-paired, 14101 singletons, 7887 discordant, 554468 orphans, 12391 too large [>5000 bp], 9179462 duplicates)
Reads: 79823893 total, 92183 skipped (flags/unmapped)
Fragments: 40119843 total (39579190 tlen-paired, 10499 hash-paired, 13171 singletons, 11222 discordant, 505761 orphans, 5478 too large [>5000 bp], 8397590 duplicates)
Reads: 88111363 total, 89328 skipped (flags/unmapped)
Fragments: 44286858 total (43678960 tlen-paired, 13578 hash-paired, 14272 singletons, 11187 discordant, 568861 orphans, 15726 too large [>5000 bp], 9229077 duplicates)
Reads: 90670870 total, 192131 skipped (flags/unmapped)
Fragments: 45832023 total (44004953 tlen-paired, 10824 hash-paired, 14749 singletons, 350427 discordant, 1451070 orphans, 140256 too large [>5000 bp], 9477843 duplicates)