Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260410_LH00527_0075_A23NMNVLT4__0ce77ad5--20260414-073011/alignments/recalibrated/1136_7QF-N1-BDNA-1_A23NMNVLT4_1/1136_7QF-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/41/c4fd37a4e53a659476418e8b8148f9/.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/41/c4fd37a4e53a659476418e8b8148f9/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260410_LH00527_0075_A23NMNVLT4__0ce77ad5--20260414-073011/alignments/recalibrated/1136_7QF-N1-BDNA-1_A23NMNVLT4_1/1136_7QF-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_7QF-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_7QF-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai[W::hts_idx_load3] 
The index file is older than the data file: 1136_7QF-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_7QF-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: 89645351 total, 69065 skipped (flags/unmapped)
Fragments: 44918577 total (44618318 tlen-paired, 3718 hash-paired, 359 singletons, 14921 discordant, 281261 orphans, 10376 too large [>5000 bp], 14629920 duplicates)
Reads: 97236387 total, 62437 skipped (flags/unmapped)
Fragments: 48727327 total (48376012 tlen-paired, 5032 hash-paired, 350 singletons, 12651 discordant, 333282 orphans, 26464 too large [>5000 bp], 16100269 duplicates)
Reads: 97441878 total, 56311 skipped (flags/unmapped)
Fragments: 48828274 total (48525291 tlen-paired, 2280 hash-paired, 453 singletons, 9760 discordant, 290490 orphans, 9981 too large [>5000 bp], 15738785 duplicates)
Reads: 107284135 total, 96376 skipped (flags/unmapped)
Fragments: 53856997 total (53027593 tlen-paired, 3355 hash-paired, 439 singletons, 163724 discordant, 661886 orphans, 68045 too large [>5000 bp], 17810005 duplicates)