Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260227_LH00519_0059_B23L5TMLT4__444aee1e--20260301-135529/alignments/recalibrated/1029_BC1I-N1-BDNA-1_B23L5TMLT4_1/1029_BC1I-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6d/0f32db4c1d25c20033cd6937db5995/.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/6d/0f32db4c1d25c20033cd6937db5995/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260227_LH00519_0059_B23L5TMLT4__444aee1e--20260301-135529/alignments/recalibrated/1029_BC1I-N1-BDNA-1_B23L5TMLT4_1/1029_BC1I-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
==> 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: 1029_BC1I-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_BC1I-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 1029_BC1I-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
The index file is older than the data file: 1029_BC1I-N1-BDNA-1_B23L5TMLT4_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: 110788381 total, 88090 skipped (flags/unmapped)
Fragments: 55655435 total (54987026 tlen-paired, 5763 hash-paired, 583 singletons, 17385 discordant, 644678 orphans, 17341 too large [>5000 bp], 21754994 duplicates)
Reads: 117739973 total, 72517 skipped (flags/unmapped)
Fragments: 59156970 total (58466107 tlen-paired, 4355 hash-paired, 564 singletons, 12296 discordant, 673648 orphans, 13864 too large [>5000 bp], 22715969 duplicates)
Reads: 128309998 total, 77701 skipped (flags/unmapped)
Fragments: 64470182 total (63671335 tlen-paired, 4677 hash-paired, 581 singletons, 17945 discordant, 775644 orphans, 34079 too large [>5000 bp], 25261258 duplicates)
Reads: 130559463 total, 139699 skipped (flags/unmapped)
Fragments: 65922150 total (63687654 tlen-paired, 6076 hash-paired, 640 singletons, 440156 discordant, 1787624 orphans, 181864 too large [>5000 bp], 25632895 duplicates)