Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/79/64466ad83ce64447855967c7d2d067/.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/79/64466ad83ce64447855967c7d2d067/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00519_0072_A23KFG7LT4__d7a6b981--20260322-104015/alignments/recalibrated/1136_0ZS-N1-BDNA-1_A23KFG7LT4_1/1136_0ZS-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00519_0072_A23KFG7LT4__d7a6b981--20260322-104015/alignments/recalibrated/1136_0ZS-N1-BDNA-1_A23KFG7LT4_1/1136_0ZS-N1-BDNA-1_A23KFG7LT4_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: 1136_0ZS-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.baiThe index file is older than the data file: 1136_0ZS-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai

[W::hts_idx_load3] The index file is older than the data file: 1136_0ZS-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_0ZS-N1-BDNA-1_A23KFG7LT4_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: 81043390 total, 56551 skipped (flags/unmapped)
Fragments: 40611842 total (40336760 tlen-paired, 3465 hash-paired, 300 singletons, 13294 discordant, 258023 orphans, 10739 too large [>5000 bp], 14568066 duplicates)
Reads: 85945322 total, 46559 skipped (flags/unmapped)
Fragments: 43070604 total (42795866 tlen-paired, 2844 hash-paired, 421 singletons, 8987 discordant, 262486 orphans, 10231 too large [>5000 bp], 15043100 duplicates)
Reads: 94927641 total, 76305 skipped (flags/unmapped)
Fragments: 47671537 total (46912295 tlen-paired, 2826 hash-paired, 353 singletons, 144144 discordant, 611919 orphans, 60267 too large [>5000 bp], 17199632 duplicates)
Reads: 94287849 total, 50093 skipped (flags/unmapped)
Fragments: 47256513 total (46933080 tlen-paired, 4595 hash-paired, 340 singletons, 13226 discordant, 305272 orphans, 15171 too large [>5000 bp], 16975929 duplicates)