Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260227_LH00519_0059_B23L5TMLT4__444aee1e--20260301-135529/alignments/recalibrated/659_dAn-N1-BDNA-1_B23L5TMLT4_1/659_dAn-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260227_LH00519_0059_B23L5TMLT4__444aee1e--20260301-135529/alignments/recalibrated/659_dAn-N1-BDNA-1_B23L5TMLT4_1/659_dAn-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/09/32fd6d6bd54bc256887aebe99794f7/.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/09/32fd6d6bd54bc256887aebe99794f7/.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: 659_dAn-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.baiThe index file is older than the data file: 659_dAn-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai

[W::hts_idx_load3] The index file is older than the data file: 659_dAn-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_dAn-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
Deduplicated 94 probes with identical coordinates
Loaded 472416 probes across 3366 contigs
Loaded 472416 probes across 3366 contigs
Reads: 86164144 total, 68869 skipped (flags/unmapped)
Fragments: 43206803 total (42841636 tlen-paired, 6290 hash-paired, 442 singletons, 15698 discordant, 342737 orphans, 12424 too large [>5000 bp], 15702413 duplicates)
Reads: 90408897 total, 55792 skipped (flags/unmapped)
Fragments: 45339305 total (44979877 tlen-paired, 4653 hash-paired, 481 singletons, 10668 discordant, 343626 orphans, 9301 too large [>5000 bp], 16197628 duplicates)
Reads: 100653845 total, 104130 skipped (flags/unmapped)
Fragments: 50612951 total (49563780 tlen-paired, 5270 hash-paired, 447 singletons, 199392 discordant, 844062 orphans, 84161 too large [>5000 bp], 18461965 duplicates)
Reads: 99949349 total, 64753 skipped (flags/unmapped)
Fragments: 50127158 total (49696051 tlen-paired, 7243 hash-paired, 417 singletons, 15886 discordant, 407561 orphans, 19129 too large [>5000 bp], 18295451 duplicates)