Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260508_LH00519_0089_A23TNVNLT4__8afaba2b--20260511-081020/alignments/recalibrated/659_eaQ-N1-BDNA-1_A23TNVNLT4_1/659_eaQ-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a3/15b81ac19138370b507549c896708c/.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/a3/15b81ac19138370b507549c896708c/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260508_LH00519_0089_A23TNVNLT4__8afaba2b--20260511-081020/alignments/recalibrated/659_eaQ-N1-BDNA-1_A23TNVNLT4_1/659_eaQ-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: 659_eaQ-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_eaQ-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_eaQ-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_eaQ-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: 109696597 total, 66989 skipped (flags/unmapped)
Fragments: 54976932 total (54607042 tlen-paired, 5443 hash-paired, 523 singletons, 15825 discordant, 348099 orphans, 12183 too large [>5000 bp], 20386318 duplicates)
Reads: 117181112 total, 55602 skipped (flags/unmapped)
Fragments: 58735138 total (58355473 tlen-paired, 3290 hash-paired, 552 singletons, 10921 discordant, 364902 orphans, 10344 too large [>5000 bp], 21424175 duplicates)
Reads: 127840115 total, 60985 skipped (flags/unmapped)
Fragments: 64078633 total (63628165 tlen-paired, 4521 hash-paired, 469 singletons, 15921 discordant, 429557 orphans, 25945 too large [>5000 bp], 23944596 duplicates)
Reads: 130235553 total, 111103 skipped (flags/unmapped)
Fragments: 65416263 total (64319738 tlen-paired, 4294 hash-paired, 540 singletons, 212813 discordant, 878878 orphans, 85671 too large [>5000 bp], 24427767 duplicates)