Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/74/dba24e14bb2299317f6859a44ac9a9/.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/74/dba24e14bb2299317f6859a44ac9a9/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260325_LH00519_0075_A23NLN3LT4__0ce77ad5--20260331-121018/alignments/recalibrated/1136_51O-N1-BDNA-1_A23NLN3LT4_1/1136_51O-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260325_LH00519_0075_A23NLN3LT4__0ce77ad5--20260331-121018/alignments/recalibrated/1136_51O-N1-BDNA-1_A23NLN3LT4_1/1136_51O-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
==> 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_51O-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_51O-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_51O-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_51O-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: 77587394 total, 41386 skipped (flags/unmapped)
Fragments: 38919592 total (38590087 tlen-paired, 1953 hash-paired, 285 singletons, 9538 discordant, 317729 orphans, 12419 too large [>5000 bp], 13930797 duplicates)
Reads: 66189799 total, 46383 skipped (flags/unmapped)
Fragments: 33195696 total (32917977 tlen-paired, 2649 hash-paired, 274 singletons, 9954 discordant, 264842 orphans, 8570 too large [>5000 bp], 11827537 duplicates)
Reads: 70499781 total, 37830 skipped (flags/unmapped)
Fragments: 35361901 total (35075201 tlen-paired, 1948 hash-paired, 366 singletons, 6647 discordant, 277739 orphans, 8127 too large [>5000 bp], 12351691 duplicates)
Reads: 78729780 total, 70958 skipped (flags/unmapped)
Fragments: 39609285 total (38735353 tlen-paired, 1911 hash-paired, 278 singletons, 171371 discordant, 700372 orphans, 70451 too large [>5000 bp], 14166994 duplicates)