Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3e/6f91c529f218b34ddb8b69d72de6f1/.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/3e/6f91c529f218b34ddb8b69d72de6f1/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00527_0067_B23KGCJLT4__d7a6b981--20260322-105015/alignments/recalibrated/659_d01-N1-BDNA-1_B23KGCJLT4_1/659_d01-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00527_0067_B23KGCJLT4__d7a6b981--20260322-105015/alignments/recalibrated/659_d01-N1-BDNA-1_B23KGCJLT4_1/659_d01-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam
==> 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: 659_d01-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 659_d01-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
The index file is older than the data file: 659_d01-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_d01-N1-BDNA-1_B23KGCJLT4_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: 69368308 total, 42285 skipped (flags/unmapped)
Fragments: 34753208 total (34544084 tlen-paired, 2540 hash-paired, 367 singletons, 8799 discordant, 197418 orphans, 8696 too large [>5000 bp], 11750524 duplicates)
Reads: 65042562 total, 50414 skipped (flags/unmapped)
Fragments: 32586264 total (32369575 tlen-paired, 3484 hash-paired, 315 singletons, 13079 discordant, 199811 orphans, 9873 too large [>5000 bp], 11188198 duplicates)
Reads: 76081320 total, 66650 skipped (flags/unmapped)
Fragments: 38179487 total (37651653 tlen-paired, 2316 hash-paired, 346 singletons, 97908 discordant, 427264 orphans, 41653 too large [>5000 bp], 13245077 duplicates)
Reads: 75835547 total, 46157 skipped (flags/unmapped)
Fragments: 37999098 total (37755372 tlen-paired, 4153 hash-paired, 283 singletons, 12683 discordant, 226607 orphans, 9042 too large [>5000 bp], 13143606 duplicates)