Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/33/fd702fea2da19e1a76e55ea3a0c5c2/.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/33/fd702fea2da19e1a76e55ea3a0c5c2/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260508_LH00519_0089_A23TNVNLT4__8afaba2b--20260511-081020/alignments/recalibrated/1241_BV6H-N1-BDNA-1_A23TNVNLT4_1/1241_BV6H-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/1241_BV6H-N1-BDNA-1_A23TNVNLT4_1/1241_BV6H-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] The index file is older than the data file: 1241_BV6H-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 1241_BV6H-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.baiThe index file is older than the data file: 1241_BV6H-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai

[W::hts_idx_load3] The index file is older than the data file: 1241_BV6H-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
Deduplicated 94 probes with identical coordinates
Loaded 472416 probes across 3366 contigs
Loaded 472416 probes across 3366 contigs
Deduplicated 94 probes with identical coordinates
Loaded 472416 probes across 3366 contigs
Reads: 77231174 total, 54813 skipped (flags/unmapped)
Fragments: 38694859 total (38446068 tlen-paired, 4537 hash-paired, 343 singletons, 14051 discordant, 229860 orphans, 8423 too large [>5000 bp], 13848880 duplicates)
Reads: 82881363 total, 48174 skipped (flags/unmapped)
Fragments: 41528774 total (41251969 tlen-paired, 4951 hash-paired, 280 singletons, 12225 discordant, 259349 orphans, 17635 too large [>5000 bp], 14985068 duplicates)
Reads: 84208780 total, 46448 skipped (flags/unmapped)
Fragments: 42190737 total (41940992 tlen-paired, 3936 hash-paired, 412 singletons, 10183 discordant, 235214 orphans, 8242 too large [>5000 bp], 14861982 duplicates)
Reads: 91417564 total, 81595 skipped (flags/unmapped)
Fragments: 45872316 total (45242474 tlen-paired, 4429 hash-paired, 358 singletons, 119570 discordant, 505485 orphans, 48590 too large [>5000 bp], 16634907 duplicates)