Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/24/86fbbb9e928afd2b0a2c802791572d/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260508_LH00519_0089_A23TNVNLT4__8afaba2b--20260511-081020/alignments/recalibrated/659_fap-N1-BDNA-1_A23TNVNLT4_1/659_fap-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam
  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/24/86fbbb9e928afd2b0a2c802791572d/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260508_LH00519_0089_A23TNVNLT4__8afaba2b--20260511-081020/alignments/recalibrated/659_fap-N1-BDNA-1_A23TNVNLT4_1/659_fap-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 659_fap-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_fap-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 659_fap-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_fap-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: 96043934 total, 67081 skipped (flags/unmapped)
Fragments: 48152275 total (47782426 tlen-paired, 4329 hash-paired, 417 singletons, 15175 discordant, 349928 orphans, 11324 too large [>5000 bp], 17685429 duplicates)
Reads: 102836053 total, 57763 skipped (flags/unmapped)
Fragments: 51560501 total (51181042 tlen-paired, 4241 hash-paired, 495 singletons, 10514 discordant, 364209 orphans, 10996 too large [>5000 bp], 18723105 duplicates)
Reads: 113049969 total, 61777 skipped (flags/unmapped)
Fragments: 56685762 total (56246284 tlen-paired, 4456 hash-paired, 390 singletons, 15334 discordant, 419298 orphans, 18178 too large [>5000 bp], 21116963 duplicates)
Reads: 115123489 total, 106312 skipped (flags/unmapped)
Fragments: 57868278 total (56754713 tlen-paired, 3523 hash-paired, 493 singletons, 217939 discordant, 891610 orphans, 86362 too large [>5000 bp], 21516022 duplicates)