Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260325_LH00519_0075_A23NLN3LT4__0ce77ad5--20260331-121018/alignments/recalibrated/1136_4JY-N1-BDNA-1_A23NLN3LT4_1/1136_4JY-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_4JY-N1-BDNA-1_A23NLN3LT4_1/1136_4JY-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/94/e0e3118df327d4a48c8af4db80f171/.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/94/e0e3118df327d4a48c8af4db80f171/.command.run
==> 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_4JY-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_4JY-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_4JY-N1-BDNA-1_A23NLN3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_4JY-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: 89302130 total, 63744 skipped (flags/unmapped)
Fragments: 44749218 total (44447609 tlen-paired, 3441 hash-paired, 369 singletons, 16216 discordant, 281583 orphans, 10951 too large [>5000 bp], 14893618 duplicates)
Reads: 95955344 total, 54094 skipped (flags/unmapped)
Fragments: 48081652 total (47777103 tlen-paired, 4367 hash-paired, 456 singletons, 11080 discordant, 288646 orphans, 13524 too large [>5000 bp], 15713035 duplicates)
Reads: 105441370 total, 94246 skipped (flags/unmapped)
Fragments: 52933670 total (52135341 tlen-paired, 2470 hash-paired, 402 singletons, 149783 discordant, 645674 orphans, 62930 too large [>5000 bp], 17783676 duplicates)
Reads: 104894080 total, 57672 skipped (flags/unmapped)
Fragments: 52571369 total (52203292 tlen-paired, 6006 hash-paired, 379 singletons, 16391 discordant, 345301 orphans, 19675 too large [>5000 bp], 17617088 duplicates)