Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/10/71507f69b9d675829d65044ca51c9e/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260410_LH00527_0075_A23NMNVLT4__0ce77ad5--20260414-073011/alignments/recalibrated/1029_I90-N1-BDNA-1_A23NMNVLT4_1/1029_I90-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
  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/10/71507f69b9d675829d65044ca51c9e/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260410_LH00527_0075_A23NMNVLT4__0ce77ad5--20260414-073011/alignments/recalibrated/1029_I90-N1-BDNA-1_A23NMNVLT4_1/1029_I90-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 1029_I90-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
The index file is older than the data file: 1029_I90-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai[W::hts_idx_load3] 
The index file is older than the data file: 1029_I90-N1-BDNA-1_A23NMNVLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_I90-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: 91514343 total, 63837 skipped (flags/unmapped)
Fragments: 45885781 total (45528648 tlen-paired, 3659 hash-paired, 436 singletons, 12646 discordant, 340392 orphans, 9886 too large [>5000 bp], 13411327 duplicates)
Reads: 97735565 total, 51481 skipped (flags/unmapped)
Fragments: 49012828 total (48642465 tlen-paired, 3299 hash-paired, 456 singletons, 8828 discordant, 357780 orphans, 8332 too large [>5000 bp], 14057713 duplicates)
Reads: 106988665 total, 57511 skipped (flags/unmapped)
Fragments: 53655693 total (53222130 tlen-paired, 4999 hash-paired, 338 singletons, 13242 discordant, 414984 orphans, 17545 too large [>5000 bp], 15942406 duplicates)
Reads: 108775900 total, 92065 skipped (flags/unmapped)
Fragments: 54704338 total (53574747 tlen-paired, 2657 hash-paired, 479 singletons, 221599 discordant, 904856 orphans, 90247 too large [>5000 bp], 16230642 duplicates)