Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260227_LH00519_0059_B23L5TMLT4__444aee1e--20260301-135529/alignments/recalibrated/1047_C9-N1-BDNA-1_B23L5TMLT4_1/1047_C9-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/1047_C9-N1-BDNA-1_B23L5TMLT4_1/1047_C9-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fe/cbb66aeca366ba55474104a007b924/.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/fe/cbb66aeca366ba55474104a007b924/.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: 1047_C9-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1047_C9-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1047_C9-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1047_C9-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
Loaded 472416 probes across 3366 contigs
Deduplicated 94 probes with identical coordinates
Loaded 472416 probes across 3366 contigs
Reads: 59558506 total, 48866 skipped (flags/unmapped)
Fragments: 29873307 total (29602333 tlen-paired, 4165 hash-paired, 335 singletons, 11267 discordant, 255207 orphans, 9284 too large [>5000 bp], 9561897 duplicates)
Reads: 63557470 total, 38444 skipped (flags/unmapped)
Fragments: 31883121 total (31609040 tlen-paired, 2905 hash-paired, 340 singletons, 7692 discordant, 263144 orphans, 8134 too large [>5000 bp], 10002098 duplicates)
Reads: 68791661 total, 41093 skipped (flags/unmapped)
Fragments: 34512410 total (34188820 tlen-paired, 2808 hash-paired, 337 singletons, 11230 discordant, 309215 orphans, 17650 too large [>5000 bp], 11080212 duplicates)
Reads: 69113022 total, 68522 skipped (flags/unmapped)
Fragments: 34778714 total (33986041 tlen-paired, 3017 hash-paired, 376 singletons, 150792 discordant, 638488 orphans, 62968 too large [>5000 bp], 11151474 duplicates)