Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260522_LH00527_0093_A23TY7KLT4__8afaba2b--20260524-103028/alignments/recalibrated/1241_BIUX-N1-BDNA-1_A23TY7KLT4_1/1241_BIUX-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260522_LH00527_0093_A23TY7KLT4__8afaba2b--20260524-103028/alignments/recalibrated/1241_BIUX-N1-BDNA-1_A23TY7KLT4_1/1241_BIUX-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0d/fd0f0c5d6d17eed2ae1711255c8b26/.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/0d/fd0f0c5d6d17eed2ae1711255c8b26/.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_BIUX-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_BIUX-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_BIUX-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_BIUX-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: 74892716 total, 55548 skipped (flags/unmapped)
Fragments: 37526599 total (37275089 tlen-paired, 4182 hash-paired, 280 singletons, 11510 discordant, 235538 orphans, 9894 too large [>5000 bp], 13634020 duplicates)
Reads: 79641701 total, 44476 skipped (flags/unmapped)
Fragments: 39915531 total (39655630 tlen-paired, 2307 hash-paired, 365 singletons, 7711 discordant, 249518 orphans, 8023 too large [>5000 bp], 14258277 duplicates)
Reads: 87483077 total, 83106 skipped (flags/unmapped)
Fragments: 43936422 total (43212289 tlen-paired, 3143 hash-paired, 344 singletons, 137865 discordant, 582781 orphans, 55126 too large [>5000 bp], 16024624 duplicates)
Reads: 86899704 total, 48529 skipped (flags/unmapped)
Fragments: 43552222 total (43251949 tlen-paired, 2950 hash-paired, 279 singletons, 11316 discordant, 285728 orphans, 16369 too large [>5000 bp], 15880207 duplicates)