Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260323_LH00519_0074_B23KFG5LT4__d7a6b981--20260325-091021/alignments/recalibrated/1136_7DO-N1-BDNA-1_B23KFG5LT4_1/1136_7DO-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260323_LH00519_0074_B23KFG5LT4__d7a6b981--20260325-091021/alignments/recalibrated/1136_7DO-N1-BDNA-1_B23KFG5LT4_1/1136_7DO-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/52/85550987384bce37b3f578d307ff15/.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/52/85550987384bce37b3f578d307ff15/.command.run
==> 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: 1136_7DO-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_7DO-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1136_7DO-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_7DO-N1-BDNA-1_B23KFG5LT4_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: 56748118 total, 40633 skipped (flags/unmapped)
Fragments: 28437615 total (28239635 tlen-paired, 2571 hash-paired, 247 singletons, 10168 discordant, 184994 orphans, 8748 too large [>5000 bp], 10586750 duplicates)
Reads: 60260063 total, 33928 skipped (flags/unmapped)
Fragments: 30200534 total (30001683 tlen-paired, 2469 hash-paired, 257 singletons, 6685 discordant, 189440 orphans, 7382 too large [>5000 bp], 10942088 duplicates)
Reads: 66757372 total, 37235 skipped (flags/unmapped)
Fragments: 33458513 total (33218699 tlen-paired, 3473 hash-paired, 217 singletons, 10018 discordant, 226106 orphans, 14717 too large [>5000 bp], 12453929 duplicates)
Reads: 67150966 total, 58700 skipped (flags/unmapped)
Fragments: 33719725 total (33184539 tlen-paired, 1665 hash-paired, 251 singletons, 101315 discordant, 431955 orphans, 42511 too large [>5000 bp], 12583039 duplicates)