Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00519_0072_A23KFG7LT4__d7a6b981--20260322-104015/alignments/recalibrated/1136_19S-N1-BDNA-1_A23KFG7LT4_1/1136_19S-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5c/53d3582a79d0aa74d97ff8607dc78b/.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/5c/53d3582a79d0aa74d97ff8607dc78b/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00519_0072_A23KFG7LT4__d7a6b981--20260322-104015/alignments/recalibrated/1136_19S-N1-BDNA-1_A23KFG7LT4_1/1136_19S-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 1136_19S-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.baiThe index file is older than the data file: 1136_19S-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai

[W::hts_idx_load3] The index file is older than the data file: 1136_19S-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_19S-N1-BDNA-1_A23KFG7LT4_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: 66018905 total, 45177 skipped (flags/unmapped)
Fragments: 33074433 total (32868903 tlen-paired, 2746 hash-paired, 305 singletons, 10388 discordant, 192091 orphans, 8629 too large [>5000 bp], 11103311 duplicates)
Reads: 70178727 total, 37671 skipped (flags/unmapped)
Fragments: 35162369 total (34955092 tlen-paired, 2024 hash-paired, 357 singletons, 7139 discordant, 197757 orphans, 7216 too large [>5000 bp], 11455439 duplicates)
Reads: 77092381 total, 68147 skipped (flags/unmapped)
Fragments: 38692384 total (38137190 tlen-paired, 1804 hash-paired, 353 singletons, 104448 discordant, 448589 orphans, 44204 too large [>5000 bp], 13028736 duplicates)
Reads: 76706244 total, 42652 skipped (flags/unmapped)
Fragments: 38434569 total (38180767 tlen-paired, 2710 hash-paired, 309 singletons, 10994 discordant, 239789 orphans, 17276 too large [>5000 bp], 12910734 duplicates)