Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260508_LH00519_0089_A23TNVNLT4__8afaba2b--20260511-081020/alignments/recalibrated/1241_IDO-N1-BDNA-1_A23TNVNLT4_1/1241_IDO-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f4/e986bdac874a8de2c4b40b60de265a/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260508_LH00519_0089_A23TNVNLT4__8afaba2b--20260511-081020/alignments/recalibrated/1241_IDO-N1-BDNA-1_A23TNVNLT4_1/1241_IDO-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam
  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/f4/e986bdac874a8de2c4b40b60de265a/.command.run
==> 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: 1241_IDO-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.baiThe index file is older than the data file: 1241_IDO-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai

[W::hts_idx_load3] The index file is older than the data file: 1241_IDO-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_IDO-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: 75818968 total, 53034 skipped (flags/unmapped)
Fragments: 38012678 total (37719090 tlen-paired, 4269 hash-paired, 328 singletons, 12527 discordant, 276464 orphans, 8685 too large [>5000 bp], 14493709 duplicates)
Reads: 81407027 total, 46525 skipped (flags/unmapped)
Fragments: 40821437 total (40494194 tlen-paired, 2991 hash-paired, 306 singletons, 11122 discordant, 312824 orphans, 15379 too large [>5000 bp], 15628164 duplicates)
Reads: 81632109 total, 43672 skipped (flags/unmapped)
Fragments: 40932338 total (40628992 tlen-paired, 2512 hash-paired, 407 singletons, 9225 discordant, 291202 orphans, 7685 too large [>5000 bp], 15274685 duplicates)
Reads: 90247658 total, 81965 skipped (flags/unmapped)
Fragments: 45355510 total (44500660 tlen-paired, 2140 hash-paired, 331 singletons, 170955 discordant, 681424 orphans, 68214 too large [>5000 bp], 17355306 duplicates)