Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260508_LH00519_0089_A23TNVNLT4__8afaba2b--20260511-081020/alignments/recalibrated/1267_E3-N1-BDNA-1_A23TNVNLT4_1/1267_E3-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260508_LH00519_0089_A23TNVNLT4__8afaba2b--20260511-081020/alignments/recalibrated/1267_E3-N1-BDNA-1_A23TNVNLT4_1/1267_E3-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e6/3436108adc2d1b8dcbb1f9f856001d/.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/e6/3436108adc2d1b8dcbb1f9f856001d/.command.run
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1267_E3-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
Count mode: frac
[W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 1267_E3-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
The index file is older than the data file: 1267_E3-N1-BDNA-1_A23TNVNLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1267_E3-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: 103214623 total, 68801 skipped (flags/unmapped)
Fragments: 51730716 total (51367657 tlen-paired, 5183 hash-paired, 538 singletons, 18244 discordant, 339094 orphans, 12011 too large [>5000 bp], 20772755 duplicates)
Reads: 110507470 total, 58191 skipped (flags/unmapped)
Fragments: 55387047 total (55022452 tlen-paired, 4417 hash-paired, 516 singletons, 12201 discordant, 347461 orphans, 11581 too large [>5000 bp], 21917257 duplicates)
Reads: 121625518 total, 64824 skipped (flags/unmapped)
Fragments: 60960281 total (60527475 tlen-paired, 5269 hash-paired, 434 singletons, 18419 discordant, 408684 orphans, 24625 too large [>5000 bp], 24608670 duplicates)
Reads: 123008956 total, 110370 skipped (flags/unmapped)
Fragments: 61776530 total (60769247 tlen-paired, 3809 hash-paired, 480 singletons, 192506 discordant, 810488 orphans, 78247 too large [>5000 bp], 24991830 duplicates)