Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260508_LH00519_0089_A23TNVNLT4__8afaba2b--20260511-081020/alignments/recalibrated/659_ein-N1-BDNA-1_A23TNVNLT4_1/659_ein-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_ein-N1-BDNA-1_A23TNVNLT4_1/659_ein-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/67/c8cc7deb7bff6ecfabb90d53cc17b1/.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/67/c8cc7deb7bff6ecfabb90d53cc17b1/.command.run
==> 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_ein-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_ein-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_ein-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_ein-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: 98151304 total, 65413 skipped (flags/unmapped)
Fragments: 49290304 total (48753111 tlen-paired, 4043 hash-paired, 515 singletons, 16021 discordant, 516614 orphans, 11206 too large [>5000 bp], 19527075 duplicates)
Reads: 105409864 total, 58814 skipped (flags/unmapped)
Fragments: 52948386 total (52366724 tlen-paired, 2964 hash-paired, 562 singletons, 11566 discordant, 566570 orphans, 10705 too large [>5000 bp], 20598440 duplicates)
Reads: 115063077 total, 61873 skipped (flags/unmapped)
Fragments: 57789476 total (57142953 tlen-paired, 6730 hash-paired, 407 singletons, 16751 discordant, 622635 orphans, 22647 too large [>5000 bp], 23109757 duplicates)
Reads: 118057590 total, 114499 skipped (flags/unmapped)
Fragments: 59558164 total (57736548 tlen-paired, 3458 hash-paired, 476 singletons, 364815 discordant, 1452867 orphans, 140053 too large [>5000 bp], 23654486 duplicates)