Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6b/c09a21e90e5f33967874bc76bfe6e3/.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/6b/c09a21e90e5f33967874bc76bfe6e3/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260508_LH00519_0089_A23TNVNLT4__8afaba2b--20260511-081020/alignments/recalibrated/659_eTs-N1-BDNA-1_A23TNVNLT4_1/659_eTs-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260508_LH00519_0089_A23TNVNLT4__8afaba2b--20260511-081020/alignments/recalibrated/659_eTs-N1-BDNA-1_A23TNVNLT4_1/659_eTs-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
==> 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: 659_eTs-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.baiThe index file is older than the data file: 659_eTs-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai

[W::hts_idx_load3] The index file is older than the data file: 659_eTs-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_eTs-N1-BDNA-1_A23TNVNLT4_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: 67143583 total, 44293 skipped (flags/unmapped)
Fragments: 33691805 total (33381702 tlen-paired, 3513 hash-paired, 298 singletons, 9842 discordant, 296450 orphans, 6214 too large [>5000 bp], 12387096 duplicates)
Reads: 71806346 total, 37979 skipped (flags/unmapped)
Fragments: 36036584 total (35692834 tlen-paired, 1953 hash-paired, 264 singletons, 8174 discordant, 333359 orphans, 14411 too large [>5000 bp], 13273784 duplicates)
Reads: 72497352 total, 37778 skipped (flags/unmapped)
Fragments: 36383329 total (36053655 tlen-paired, 2093 hash-paired, 348 singletons, 6933 discordant, 320300 orphans, 6782 too large [>5000 bp], 13029270 duplicates)
Reads: 80127907 total, 72048 skipped (flags/unmapped)
Fragments: 40345491 total (39339667 tlen-paired, 2836 hash-paired, 335 singletons, 204773 discordant, 797880 orphans, 81546 too large [>5000 bp], 14824594 duplicates)