[2026-05-27 17:43:30] [miniwdl-eks.task] Staging: downloading command and 0 inputs
cp s3://natera-rnd-pltf-dev-miniwdl-scratch-01/work/e3/e3d4f0eee0d38503e26bdaca1f4e9d2a/command /tmp/miniwdl_task/command
[2026-05-27 17:43:30] [miniwdl-eks.task] Staging completed (0 inputs, 0ms) s5cmd=workers:256,concurrency:10,cpus:192
+ aws s3 cp s3://natera-platform-sandbox/pipeline-outputs/flowcell-runs/20251022_LH00519_0039_A235GK3LT3/1009-update-cnv-caller-with-specificity-fix_5b02bb_251024165007/bams/3599846437_sv1.bam downloaded.bam
Completed 77.0 KiB/77.0 KiB (366.7 KiB/s) with 1 file(s) remaining
download: s3://natera-platform-sandbox/pipeline-outputs/flowcell-runs/20251022_LH00519_0039_A235GK3LT3/1009-update-cnv-caller-with-specificity-fix_5b02bb_251024165007/bams/3599846437_sv1.bam to ./downloaded.bam
+ aws s3 cp s3://natera-platform-sandbox/pipeline-outputs/flowcell-runs/20251022_LH00519_0039_A235GK3LT3/1009-update-cnv-caller-with-specificity-fix_5b02bb_251024165007/bams/3599846437_sv1.bam.bai downloaded.bam.bai
Completed 256.0 KiB/1.2 MiB (679.1 KiB/s) with 1 file(s) remaining
Completed 512.0 KiB/1.2 MiB (1.3 MiB/s) with 1 file(s) remaining  
Completed 768.0 KiB/1.2 MiB (1.9 MiB/s) with 1 file(s) remaining  
Completed 1.0 MiB/1.2 MiB (2.4 MiB/s) with 1 file(s) remaining    
Completed 1.2 MiB/1.2 MiB (2.8 MiB/s) with 1 file(s) remaining    
download: s3://natera-platform-sandbox/pipeline-outputs/flowcell-runs/20251022_LH00519_0039_A235GK3LT3/1009-update-cnv-caller-with-specificity-fix_5b02bb_251024165007/bams/3599846437_sv1.bam.bai to ./downloaded.bam.bai
[2026-05-27 17:43:32] [miniwdl-eks.task] Task finished exit_code=0 (2ms)
cp /tmp/miniwdl_task/stdout.txt s3://natera-rnd-pltf-dev-miniwdl-scratch-01/work/e3/e3d4f0eee0d38503e26bdaca1f4e9d2a/stdout.txt
cp /tmp/miniwdl_task/stderr.txt s3://natera-rnd-pltf-dev-miniwdl-scratch-01/work/e3/e3d4f0eee0d38503e26bdaca1f4e9d2a/stderr.txt
cp work/downloaded.bam s3://natera-rnd-pltf-dev-miniwdl-scratch-01/work/e3/e3d4f0eee0d38503e26bdaca1f4e9d2a/work/downloaded.bam
cp work/downloaded.bam.bai s3://natera-rnd-pltf-dev-miniwdl-scratch-01/work/e3/e3d4f0eee0d38503e26bdaca1f4e9d2a/work/downloaded.bam.bai
cp /tmp/miniwdl_task/timing.json s3://natera-rnd-pltf-dev-miniwdl-scratch-01/work/e3/e3d4f0eee0d38503e26bdaca1f4e9d2a/timing.json
cp /tmp/miniwdl_task/metrics.json s3://natera-rnd-pltf-dev-miniwdl-scratch-01/work/e3/e3d4f0eee0d38503e26bdaca1f4e9d2a/metrics.json
cp /tmp/miniwdl_task/exit_code s3://natera-rnd-pltf-dev-miniwdl-scratch-01/work/e3/e3d4f0eee0d38503e26bdaca1f4e9d2a/exit_code
[2026-05-27 17:43:34] [miniwdl-eks.task] Done exit_code=0 (1ms unstage, 3ms total)