Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260323_LH00519_0074_B23KFG5LT4__d7a6b981--20260325-091021/alignments/recalibrated/659_cTi-N1-BDNA-1_B23KFG5LT4_1/659_cTi-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/87/8dca56e541c16833cf71e69a355dad/.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/87/8dca56e541c16833cf71e69a355dad/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260323_LH00519_0074_B23KFG5LT4__d7a6b981--20260325-091021/alignments/recalibrated/659_cTi-N1-BDNA-1_B23KFG5LT4_1/659_cTi-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
[W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 659_cTi-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.baiThe index file is older than the data file: 659_cTi-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai

Count mode: frac
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 659_cTi-N1-BDNA-1_B23KFG5LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_cTi-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
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: 73754345 total, 57989 skipped (flags/unmapped)
Fragments: 36963251 total (36692528 tlen-paired, 3037 hash-paired, 425 singletons, 15408 discordant, 251853 orphans, 11066 too large [>5000 bp], 14647579 duplicates)
Reads: 87370898 total, 51933 skipped (flags/unmapped)
Fragments: 43793820 total (43459917 tlen-paired, 4475 hash-paired, 281 singletons, 15781 discordant, 313366 orphans, 22486 too large [>5000 bp], 17442239 duplicates)
Reads: 78435341 total, 48342 skipped (flags/unmapped)
Fragments: 39309324 total (39042037 tlen-paired, 2717 hash-paired, 380 singletons, 10539 discordant, 253651 orphans, 11191 too large [>5000 bp], 15284165 duplicates)
Reads: 88221441 total, 79824 skipped (flags/unmapped)
Fragments: 44300161 total (43601895 tlen-paired, 3830 hash-paired, 327 singletons, 130723 discordant, 563386 orphans, 52504 too large [>5000 bp], 17696283 duplicates)