Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4b/588ab18bf6cae7a7b750c68e3ecfa2/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00519_0072_A23KFG7LT4__d7a6b981--20260322-104015/alignments/recalibrated/1136_0QS-N1-BDNA-1_A23KFG7LT4_1/1136_0QS-N1-BDNA-1_A23KFG7LT4_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/4b/588ab18bf6cae7a7b750c68e3ecfa2/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00519_0072_A23KFG7LT4__d7a6b981--20260322-104015/alignments/recalibrated/1136_0QS-N1-BDNA-1_A23KFG7LT4_1/1136_0QS-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_0QS-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.baiThe index file is older than the data file: 1136_0QS-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai

[W::hts_idx_load3] The index file is older than the data file: 1136_0QS-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_0QS-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: 77410786 total, 52815 skipped (flags/unmapped)
Fragments: 38785421 total (38536596 tlen-paired, 3047 hash-paired, 324 singletons, 13821 discordant, 231633 orphans, 9543 too large [>5000 bp], 12803827 duplicates)
Reads: 83400270 total, 43673 skipped (flags/unmapped)
Fragments: 41789528 total (41537846 tlen-paired, 3284 hash-paired, 461 singletons, 10261 discordant, 237676 orphans, 7839 too large [>5000 bp], 13438114 duplicates)
Reads: 82576137 total, 46519 skipped (flags/unmapped)
Fragments: 41377336 total (41106777 tlen-paired, 3070 hash-paired, 376 singletons, 12351 discordant, 254762 orphans, 15042 too large [>5000 bp], 13719443 duplicates)
Reads: 91019563 total, 79188 skipped (flags/unmapped)
Fragments: 45675579 total (45034709 tlen-paired, 3117 hash-paired, 460 singletons, 123920 discordant, 513373 orphans, 51525 too large [>5000 bp], 15205208 duplicates)