Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260508_LH00519_0089_A23TNVNLT4__8afaba2b--20260511-081020/alignments/recalibrated/1241_B1B5-N1-BDNA-1_A23TNVNLT4_1/1241_B1B5-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260508_LH00519_0089_A23TNVNLT4__8afaba2b--20260511-081020/alignments/recalibrated/1241_B1B5-N1-BDNA-1_A23TNVNLT4_1/1241_B1B5-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7d/05b44c9fc4469531bcce6444e1677c/.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/7d/05b44c9fc4469531bcce6444e1677c/.command.run
==> 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: 1241_B1B5-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 1241_B1B5-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
The index file is older than the data file: 1241_B1B5-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_B1B5-N1-BDNA-1_A23TNVNLT4_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: 39412371 total, 41604 skipped (flags/unmapped)
Fragments: 20083852 total (19270192 tlen-paired, 1655 hash-paired, 244 singletons, 3630 discordant, 808131 orphans, 5719 too large [>5000 bp], 10138194 duplicates)
Reads: 41334104 total, 38245 skipped (flags/unmapped)
Fragments: 21106116 total (20175058 tlen-paired, 1468 hash-paired, 325 singletons, 2669 discordant, 926596 orphans, 5274 too large [>5000 bp], 10538900 duplicates)
Reads: 46466526 total, 39549 skipped (flags/unmapped)
Fragments: 23696313 total (22697962 tlen-paired, 2348 hash-paired, 185 singletons, 4012 discordant, 991806 orphans, 13171 too large [>5000 bp], 12219551 duplicates)
Reads: 50399963 total, 78762 skipped (flags/unmapped)
Fragments: 26226104 total (22864696 tlen-paired, 1949 hash-paired, 323 singletons, 694358 discordant, 2664778 orphans, 267047 too large [>5000 bp], 12770122 duplicates)