Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260508_LH00519_0089_A23TNVNLT4__8afaba2b--20260511-081020/alignments/recalibrated/1241_DTD-N1-BDNA-1_A23TNVNLT4_1/1241_DTD-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e9/5b08bc27754f8ed41fc42e51b3a44b/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260508_LH00519_0089_A23TNVNLT4__8afaba2b--20260511-081020/alignments/recalibrated/1241_DTD-N1-BDNA-1_A23TNVNLT4_1/1241_DTD-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
  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/e9/5b08bc27754f8ed41fc42e51b3a44b/.command.run
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1241_DTD-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_DTD-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
Count mode: frac
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1241_DTD-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_DTD-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: 83942833 total, 50512 skipped (flags/unmapped)
Fragments: 42193287 total (41672229 tlen-paired, 2729 hash-paired, 459 singletons, 7502 discordant, 510368 orphans, 8287 too large [>5000 bp], 17107277 duplicates)
Reads: 77577729 total, 55060 skipped (flags/unmapped)
Fragments: 38979814 total (38513785 tlen-paired, 2383 hash-paired, 372 singletons, 10487 discordant, 452787 orphans, 8100 too large [>5000 bp], 16143520 duplicates)
Reads: 91606647 total, 51515 skipped (flags/unmapped)
Fragments: 46039543 total (45459220 tlen-paired, 3716 hash-paired, 339 singletons, 11161 discordant, 565107 orphans, 20746 too large [>5000 bp], 19103264 duplicates)
Reads: 94080897 total, 103846 skipped (flags/unmapped)
Fragments: 47529823 total (45842637 tlen-paired, 3072 hash-paired, 393 singletons, 340579 discordant, 1343142 orphans, 130470 too large [>5000 bp], 19522172 duplicates)