Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00519_0072_A23KFG7LT4__d7a6b981--20260322-104015/alignments/recalibrated/1136_3FG-N1-BDNA-1_A23KFG7LT4_1/1136_3FG-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/59/5807ecb3602d29a5d91e297c3173b0/.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/59/5807ecb3602d29a5d91e297c3173b0/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00519_0072_A23KFG7LT4__d7a6b981--20260322-104015/alignments/recalibrated/1136_3FG-N1-BDNA-1_A23KFG7LT4_1/1136_3FG-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
==> 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: 1136_3FG-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
The index file is older than the data file: 1136_3FG-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 1136_3FG-N1-BDNA-1_A23KFG7LT4_1.recalibrated.bam.baiThe index file is older than the data file: 1136_3FG-N1-BDNA-1_A23KFG7LT4_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: 59097080 total, 41471 skipped (flags/unmapped)
Fragments: 29677533 total (29355424 tlen-paired, 2119 hash-paired, 369 singletons, 9405 discordant, 310216 orphans, 5564 too large [>5000 bp], 10448627 duplicates)
Reads: 62637609 total, 36182 skipped (flags/unmapped)
Fragments: 31455008 total (31124131 tlen-paired, 1623 hash-paired, 377 singletons, 6467 discordant, 322410 orphans, 7099 too large [>5000 bp], 10765036 duplicates)
Reads: 68851113 total, 39306 skipped (flags/unmapped)
Fragments: 34577087 total (34194203 tlen-paired, 2954 hash-paired, 323 singletons, 9267 discordant, 370340 orphans, 14148 too large [>5000 bp], 12181849 duplicates)
Reads: 69929354 total, 67678 skipped (flags/unmapped)
Fragments: 35270096 total (34210126 tlen-paired, 1669 hash-paired, 392 singletons, 207941 discordant, 849968 orphans, 85922 too large [>5000 bp], 12385154 duplicates)