Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260508_LH00519_0089_A23TNVNLT4__8afaba2b--20260511-081020/alignments/recalibrated/1241_XKZ-N1-BDNA-1_A23TNVNLT4_1/1241_XKZ-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bf/254ecef4fddb08d7f9491f4e0e1062/.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/bf/254ecef4fddb08d7f9491f4e0e1062/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260508_LH00519_0089_A23TNVNLT4__8afaba2b--20260511-081020/alignments/recalibrated/1241_XKZ-N1-BDNA-1_A23TNVNLT4_1/1241_XKZ-N1-BDNA-1_A23TNVNLT4_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: 1241_XKZ-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_XKZ-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_XKZ-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_XKZ-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: 79111343 total, 51614 skipped (flags/unmapped)
Fragments: 39672950 total (39351543 tlen-paired, 2661 hash-paired, 326 singletons, 14705 discordant, 303715 orphans, 8935 too large [>5000 bp], 13828791 duplicates)
Reads: 86094710 total, 44180 skipped (flags/unmapped)
Fragments: 43177297 total (42842985 tlen-paired, 2705 hash-paired, 447 singletons, 10079 discordant, 321081 orphans, 8732 too large [>5000 bp], 14821797 duplicates)
Reads: 95034862 total, 80986 skipped (flags/unmapped)
Fragments: 47784743 total (46836052 tlen-paired, 2034 hash-paired, 375 singletons, 184465 discordant, 761817 orphans, 73291 too large [>5000 bp], 16889666 duplicates)
Reads: 92926928 total, 46782 skipped (flags/unmapped)
Fragments: 46609706 total (46232923 tlen-paired, 2981 hash-paired, 327 singletons, 14752 discordant, 358723 orphans, 9892 too large [>5000 bp], 16474128 duplicates)