Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00519_0072_A23KFG7LT4__d7a6b981--20260322-104015/alignments/recalibrated/1136_23Q-N1-BDNA-1_A23KFG7LT4_1/1136_23Q-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ce/2fef20f5f6f9b94cd848fb029d61c4/.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/ce/2fef20f5f6f9b94cd848fb029d61c4/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00519_0072_A23KFG7LT4__d7a6b981--20260322-104015/alignments/recalibrated/1136_23Q-N1-BDNA-1_A23KFG7LT4_1/1136_23Q-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] The index file is older than the data file: 1136_23Q-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_23Q-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 1136_23Q-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.baiThe index file is older than the data file: 1136_23Q-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: 104253500 total, 67345 skipped (flags/unmapped)
Fragments: 52264262 total (51877031 tlen-paired, 4297 hash-paired, 397 singletons, 18301 discordant, 364236 orphans, 11132 too large [>5000 bp], 19591286 duplicates)
Reads: 111733263 total, 59691 skipped (flags/unmapped)
Fragments: 56016690 total (55614800 tlen-paired, 3374 hash-paired, 561 singletons, 13454 discordant, 384501 orphans, 12627 too large [>5000 bp], 20528000 duplicates)
Reads: 111025486 total, 60443 skipped (flags/unmapped)
Fragments: 55658214 total (55265708 tlen-paired, 4529 hash-paired, 432 singletons, 15504 discordant, 372041 orphans, 10544 too large [>5000 bp], 20907821 duplicates)
Reads: 122415131 total, 103954 skipped (flags/unmapped)
Fragments: 61504383 total (60415754 tlen-paired, 3604 hash-paired, 494 singletons, 214604 discordant, 869927 orphans, 86416 too large [>5000 bp], 23111809 duplicates)