Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fb/4ce1ed8d3c113eacb360c4be481866/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260508_LH00519_0089_A23TNVNLT4__8afaba2b--20260511-081020/alignments/recalibrated/1241_DW4-N1-BDNA-1_A23TNVNLT4_1/1241_DW4-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
  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/fb/4ce1ed8d3c113eacb360c4be481866/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260508_LH00519_0089_A23TNVNLT4__8afaba2b--20260511-081020/alignments/recalibrated/1241_DW4-N1-BDNA-1_A23TNVNLT4_1/1241_DW4-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam
==> 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_DW4-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.baiThe index file is older than the data file: 1241_DW4-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai

[W::hts_idx_load3] The index file is older than the data file: 1241_DW4-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_DW4-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
Deduplicated 94 probes with identical coordinates
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
Loaded 472416 probes across 3366 contigs
Reads: 70820948 total, 47510 skipped (flags/unmapped)
Fragments: 35504417 total (35235226 tlen-paired, 2744 hash-paired, 339 singletons, 12711 discordant, 253397 orphans, 9170 too large [>5000 bp], 12273199 duplicates)
Reads: 75851402 total, 42701 skipped (flags/unmapped)
Fragments: 38034010 total (37729663 tlen-paired, 3827 hash-paired, 307 singletons, 11129 discordant, 289084 orphans, 15036 too large [>5000 bp], 13242488 duplicates)
Reads: 76932451 total, 41152 skipped (flags/unmapped)
Fragments: 38572424 total (38292358 tlen-paired, 2258 hash-paired, 394 singletons, 9739 discordant, 267675 orphans, 7260 too large [>5000 bp], 13102483 duplicates)
Reads: 84301578 total, 79441 skipped (flags/unmapped)
Fragments: 42354818 total (41594242 tlen-paired, 3392 hash-paired, 364 singletons, 149791 discordant, 607029 orphans, 59947 too large [>5000 bp], 14709525 duplicates)