[2026-05-27 17:43:47] [miniwdl-eks.task] Staging: downloading command and 0 inputs
cp s3://natera-rnd-pltf-dev-miniwdl-scratch-01/work/48/488943b0a282e82c7a255c5ff936f963/command /tmp/miniwdl_task/command
[2026-05-27 17:43:47] [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/3599846414_sv1.bam downloaded.bam
Completed 95.0 KiB/95.0 KiB (910.4 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/3599846414_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/3599846414_sv1.bam.bai downloaded.bam.bai
Completed 256.0 KiB/1.2 MiB (214.1 KiB/s) with 1 file(s) remaining
Completed 512.0 KiB/1.2 MiB (427.1 KiB/s) with 1 file(s) remaining
Completed 768.0 KiB/1.2 MiB (639.4 KiB/s) with 1 file(s) remaining
Completed 1.0 MiB/1.2 MiB (849.6 KiB/s) with 1 file(s) remaining  
Completed 1.2 MiB/1.2 MiB (1.0 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/3599846414_sv1.bam.bai to ./downloaded.bam.bai
[2026-05-27 17:43:50] [miniwdl-eks.task] Task finished exit_code=0 (3ms)
cp /tmp/miniwdl_task/stdout.txt s3://natera-rnd-pltf-dev-miniwdl-scratch-01/work/48/488943b0a282e82c7a255c5ff936f963/stdout.txt
cp /tmp/miniwdl_task/stderr.txt s3://natera-rnd-pltf-dev-miniwdl-scratch-01/work/48/488943b0a282e82c7a255c5ff936f963/stderr.txt
cp work/downloaded.bam s3://natera-rnd-pltf-dev-miniwdl-scratch-01/work/48/488943b0a282e82c7a255c5ff936f963/work/downloaded.bam
cp work/downloaded.bam.bai s3://natera-rnd-pltf-dev-miniwdl-scratch-01/work/48/488943b0a282e82c7a255c5ff936f963/work/downloaded.bam.bai
cp /tmp/miniwdl_task/timing.json s3://natera-rnd-pltf-dev-miniwdl-scratch-01/work/48/488943b0a282e82c7a255c5ff936f963/timing.json
cp /tmp/miniwdl_task/metrics.json s3://natera-rnd-pltf-dev-miniwdl-scratch-01/work/48/488943b0a282e82c7a255c5ff936f963/metrics.json
cp /tmp/miniwdl_task/exit_code s3://natera-rnd-pltf-dev-miniwdl-scratch-01/work/48/488943b0a282e82c7a255c5ff936f963/exit_code
[2026-05-27 17:43:51] [miniwdl-eks.task] Done exit_code=0 (0ms unstage, 3ms total)