Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260318_LH00166_0269_A23H3W5LT3__d7a6b981--20260320-054016/alignments/recalibrated/1136_4HJ-N1-BDNA-1_A23H3W5LT3_1/1136_4HJ-N1-BDNA-1_A23H3W5LT3_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/be/c8235f103149a9f5d316ecd1f53be4/.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/be/c8235f103149a9f5d316ecd1f53be4/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260318_LH00166_0269_A23H3W5LT3__d7a6b981--20260320-054016/alignments/recalibrated/1136_4HJ-N1-BDNA-1_A23H3W5LT3_1/1136_4HJ-N1-BDNA-1_A23H3W5LT3_1.recalibrated.bam.bai
==> 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: 1136_4HJ-N1-BDNA-1_A23H3W5LT3_1.recalibrated.bam.baiThe index file is older than the data file: 1136_4HJ-N1-BDNA-1_A23H3W5LT3_1.recalibrated.bam.bai

[W::hts_idx_load3] The index file is older than the data file: 1136_4HJ-N1-BDNA-1_A23H3W5LT3_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_4HJ-N1-BDNA-1_A23H3W5LT3_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: 97788290 total, 73300 skipped (flags/unmapped)
Fragments: 49026395 total (48628782 tlen-paired, 16406 hash-paired, 6298 singletons, 8847 discordant, 366062 orphans, 17280 too large [>5000 bp], 11207207 duplicates)
Reads: 96951167 total, 82115 skipped (flags/unmapped)
Fragments: 48598462 total (48224183 tlen-paired, 17319 hash-paired, 6170 singletons, 9580 discordant, 341210 orphans, 9754 too large [>5000 bp], 11193617 duplicates)
Reads: 108677133 total, 126062 skipped (flags/unmapped)
Fragments: 54650300 total (53472368 tlen-paired, 18968 hash-paired, 7067 singletons, 225779 discordant, 926118 orphans, 91828 too large [>5000 bp], 12474078 duplicates)
Reads: 107736919 total, 74359 skipped (flags/unmapped)
Fragments: 54016242 total (53596677 tlen-paired, 18690 hash-paired, 6721 singletons, 7585 discordant, 386569 orphans, 11683 too large [>5000 bp], 12328480 duplicates)