Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4a/4aa8368a6455d83862a9ea76e80167/.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/4a/4aa8368a6455d83862a9ea76e80167/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260508_LH00519_0089_A23TNVNLT4__8afaba2b--20260511-081020/alignments/recalibrated/1241_PIM-N1-BDNA-1_A23TNVNLT4_1/1241_PIM-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260508_LH00519_0089_A23TNVNLT4__8afaba2b--20260511-081020/alignments/recalibrated/1241_PIM-N1-BDNA-1_A23TNVNLT4_1/1241_PIM-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] The index file is older than the data file: 1241_PIM-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 1241_PIM-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
The index file is older than the data file: 1241_PIM-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_PIM-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: 81035524 total, 51870 skipped (flags/unmapped)
Fragments: 40649432 total (40301503 tlen-paired, 2538 hash-paired, 407 singletons, 12247 discordant, 332737 orphans, 8967 too large [>5000 bp], 14640835 duplicates)
Reads: 86986951 total, 47701 skipped (flags/unmapped)
Fragments: 43640291 total (43269064 tlen-paired, 2948 hash-paired, 421 singletons, 8487 discordant, 359371 orphans, 9230 too large [>5000 bp], 15400937 duplicates)
Reads: 96626379 total, 88252 skipped (flags/unmapped)
Fragments: 48631405 total (47505165 tlen-paired, 3569 hash-paired, 359 singletons, 222680 discordant, 899632 orphans, 87654 too large [>5000 bp], 17571585 duplicates)
Reads: 94632064 total, 48440 skipped (flags/unmapped)
Fragments: 47475386 total (47052627 tlen-paired, 2318 hash-paired, 376 singletons, 12427 discordant, 407638 orphans, 20433 too large [>5000 bp], 17196181 duplicates)