Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/48/def8ff6013a8176a44008e8a38d4bf/.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/48/def8ff6013a8176a44008e8a38d4bf/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260325_LH00519_0075_A23NLN3LT4__0ce77ad5--20260331-121018/alignments/recalibrated/1136_43M-N1-BDNA-1_A23NLN3LT4_1/1136_43M-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260325_LH00519_0075_A23NLN3LT4__0ce77ad5--20260331-121018/alignments/recalibrated/1136_43M-N1-BDNA-1_A23NLN3LT4_1/1136_43M-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1136_43M-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1136_43M-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_43M-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_43M-N1-BDNA-1_A23NLN3LT4_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: 82001487 total, 58938 skipped (flags/unmapped)
Fragments: 41073720 total (40830466 tlen-paired, 4734 hash-paired, 360 singletons, 12775 discordant, 225385 orphans, 10427 too large [>5000 bp], 13389380 duplicates)
Reads: 88321722 total, 51958 skipped (flags/unmapped)
Fragments: 44246595 total (43976113 tlen-paired, 4207 hash-paired, 290 singletons, 10639 discordant, 255346 orphans, 16105 too large [>5000 bp], 14541024 duplicates)
Reads: 89733255 total, 51569 skipped (flags/unmapped)
Fragments: 44947816 total (44698719 tlen-paired, 3215 hash-paired, 452 singletons, 9206 discordant, 236224 orphans, 11365 too large [>5000 bp], 14363806 duplicates)
Reads: 97037409 total, 80574 skipped (flags/unmapped)
Fragments: 48685735 total (48041715 tlen-paired, 2635 hash-paired, 351 singletons, 123342 discordant, 517692 orphans, 51704 too large [>5000 bp], 16025703 duplicates)