Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260522_LH00527_0093_A23TY7KLT4__8afaba2b--20260524-103028/alignments/recalibrated/1241_B34J-N1-BDNA-1_A23TY7KLT4_1/1241_B34J-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5d/0efc5fe9075f4b8a187efb485df74d/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260522_LH00527_0093_A23TY7KLT4__8afaba2b--20260524-103028/alignments/recalibrated/1241_B34J-N1-BDNA-1_A23TY7KLT4_1/1241_B34J-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam
  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/5d/0efc5fe9075f4b8a187efb485df74d/.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_B34J-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_B34J-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_B34J-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_B34J-N1-BDNA-1_A23TY7KLT4_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: 71120229 total, 50189 skipped (flags/unmapped)
Fragments: 35623899 total (35418521 tlen-paired, 3682 hash-paired, 337 singletons, 9346 discordant, 192013 orphans, 7296 too large [>5000 bp], 12009964 duplicates)
Reads: 75944926 total, 44642 skipped (flags/unmapped)
Fragments: 38046453 total (37818773 tlen-paired, 3958 hash-paired, 235 singletons, 7832 discordant, 215655 orphans, 11634 too large [>5000 bp], 12895904 duplicates)
Reads: 76558210 total, 41177 skipped (flags/unmapped)
Fragments: 38351556 total (38141338 tlen-paired, 3051 hash-paired, 290 singletons, 6610 discordant, 200267 orphans, 7239 too large [>5000 bp], 12665467 duplicates)
Reads: 83649532 total, 72095 skipped (flags/unmapped)
Fragments: 41972628 total (41399290 tlen-paired, 3266 hash-paired, 259 singletons, 111211 discordant, 458602 orphans, 45521 too large [>5000 bp], 14243784 duplicates)