Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260410_LH00527_0075_A23NMNVLT4__0ce77ad5--20260414-073011/alignments/recalibrated/1136_61O-N1-BDNA-1_A23NMNVLT4_1/1136_61O-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4e/3df770a70f86129ae2bf9c4034335e/.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/4e/3df770a70f86129ae2bf9c4034335e/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260410_LH00527_0075_A23NMNVLT4__0ce77ad5--20260414-073011/alignments/recalibrated/1136_61O-N1-BDNA-1_A23NMNVLT4_1/1136_61O-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
==> 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: 1136_61O-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_61O-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_61O-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_61O-N1-BDNA-1_A23NMNVLT4_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: 65664629 total, 49248 skipped (flags/unmapped)
Fragments: 32895983 total (32694475 tlen-paired, 2702 hash-paired, 316 singletons, 8137 discordant, 190353 orphans, 7042 too large [>5000 bp], 9884136 duplicates)
Reads: 70789856 total, 40900 skipped (flags/unmapped)
Fragments: 35467556 total (35260432 tlen-paired, 2380 hash-paired, 319 singletons, 5512 discordant, 198913 orphans, 6538 too large [>5000 bp], 10463285 duplicates)
Reads: 71109567 total, 44131 skipped (flags/unmapped)
Fragments: 35632515 total (35389101 tlen-paired, 3965 hash-paired, 218 singletons, 7027 discordant, 232204 orphans, 16414 too large [>5000 bp], 10795905 duplicates)
Reads: 78574458 total, 75327 skipped (flags/unmapped)
Fragments: 39438340 total (38840591 tlen-paired, 2804 hash-paired, 314 singletons, 118372 discordant, 476259 orphans, 49512 too large [>5000 bp], 11967151 duplicates)