Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260325_LH00519_0075_A23NLN3LT4__0ce77ad5--20260331-121018/alignments/recalibrated/1029_J1U-N1-BDNA-1_A23NLN3LT4_1/1029_J1U-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2c/16b0e6eb48e45f7c072aae003b480b/.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/2c/16b0e6eb48e45f7c072aae003b480b/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260325_LH00519_0075_A23NLN3LT4__0ce77ad5--20260331-121018/alignments/recalibrated/1029_J1U-N1-BDNA-1_A23NLN3LT4_1/1029_J1U-N1-BDNA-1_A23NLN3LT4_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: 1029_J1U-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai[W::hts_idx_load3] 
The index file is older than the data file: 1029_J1U-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_J1U-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_J1U-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: 56437314 total, 43795 skipped (flags/unmapped)
Fragments: 28274531 total (28091264 tlen-paired, 2376 hash-paired, 241 singletons, 10708 discordant, 169942 orphans, 7320 too large [>5000 bp], 8098715 duplicates)
Reads: 61482424 total, 34758 skipped (flags/unmapped)
Fragments: 30802729 total (30620563 tlen-paired, 2460 hash-paired, 278 singletons, 7384 discordant, 172044 orphans, 7265 too large [>5000 bp], 8664358 duplicates)
Reads: 60810352 total, 39409 skipped (flags/unmapped)
Fragments: 30468870 total (30252582 tlen-paired, 4040 hash-paired, 236 singletons, 9459 discordant, 202553 orphans, 17996 too large [>5000 bp], 8757708 duplicates)
Reads: 67383338 total, 61978 skipped (flags/unmapped)
Fragments: 33806832 total (33348827 tlen-paired, 3379 hash-paired, 260 singletons, 87086 discordant, 367280 orphans, 37618 too large [>5000 bp], 9737518 duplicates)