[2026-05-27 17:44:35] [miniwdl-eks.task] Staging: downloading command and 5 inputs
cp s3://natera-rnd-pltf-dev-miniwdl-scratch-01/work/ce/ce1ad9c5e4f74823df903b48e6330669/command /tmp/miniwdl_task/command
cp s3://natera-platform-sandbox/pipeline-resources/germline_pipeline/allele_specific_expression_beds/hg38/gba_hg38.bed /tmp/miniwdl_task/work/_miniwdl_inputs/0/gba_hg38.bed
cp s3://natera-platform-sandbox/pipeline-resources/germline_pipeline/allele_specific_expression_beds/hg38/cyp21_hg38.bed /tmp/miniwdl_task/work/_miniwdl_inputs/0/cyp21_hg38.bed
cp s3://natera-platform-sandbox/pipeline-resources/germline_pipeline/allele_specific_expression_beds/hg38/smn_hg38.bed /tmp/miniwdl_task/work/_miniwdl_inputs/0/smn_hg38.bed
cp s3://natera-rnd-pltf-dev-miniwdl-scratch-01/work/20/20611b0f06fd372e4e0f66cda75c300a/work/downloaded.bam.bai /tmp/miniwdl_task/work/_miniwdl_inputs/0/downloaded.bam.bai
cp s3://natera-rnd-pltf-dev-miniwdl-scratch-01/work/20/20611b0f06fd372e4e0f66cda75c300a/work/downloaded.bam /tmp/miniwdl_task/work/_miniwdl_inputs/0/downloaded.bam
[2026-05-27 17:44:35] [miniwdl-eks.task] Staging completed (5 inputs, 317ms) s5cmd=workers:256,concurrency:10,cpus:72
++ conda info --envs
++ local cmd=info
++ case "$cmd" in
++ __conda_exe info --envs
++ grep '*'
++ awk '{print $1}'
++ /opt/conda/bin/conda info --envs
+ echo 'Current Conda environment: bedtools'
Current Conda environment: bedtools
+ filtered_beds=
+ for bed_file in /tmp/miniwdl_task/work/_miniwdl_inputs/0/smn_hg38.bed /tmp/miniwdl_task/work/_miniwdl_inputs/0/gba_hg38.bed /tmp/miniwdl_task/work/_miniwdl_inputs/0/cyp21_hg38.bed
+ [[ /tmp/miniwdl_task/work/_miniwdl_inputs/0/smn_hg38.bed == *_hg38.bed ]]
+ [[ /tmp/miniwdl_task/work/_miniwdl_inputs/0/smn_hg38.bed != *_exon_info_hg38.bed ]]
+ filtered_beds=' /tmp/miniwdl_task/work/_miniwdl_inputs/0/smn_hg38.bed'
+ for bed_file in /tmp/miniwdl_task/work/_miniwdl_inputs/0/smn_hg38.bed /tmp/miniwdl_task/work/_miniwdl_inputs/0/gba_hg38.bed /tmp/miniwdl_task/work/_miniwdl_inputs/0/cyp21_hg38.bed
+ [[ /tmp/miniwdl_task/work/_miniwdl_inputs/0/gba_hg38.bed == *_hg38.bed ]]
+ [[ /tmp/miniwdl_task/work/_miniwdl_inputs/0/gba_hg38.bed != *_exon_info_hg38.bed ]]
+ filtered_beds=' /tmp/miniwdl_task/work/_miniwdl_inputs/0/smn_hg38.bed /tmp/miniwdl_task/work/_miniwdl_inputs/0/gba_hg38.bed'
+ for bed_file in /tmp/miniwdl_task/work/_miniwdl_inputs/0/smn_hg38.bed /tmp/miniwdl_task/work/_miniwdl_inputs/0/gba_hg38.bed /tmp/miniwdl_task/work/_miniwdl_inputs/0/cyp21_hg38.bed
+ [[ /tmp/miniwdl_task/work/_miniwdl_inputs/0/cyp21_hg38.bed == *_hg38.bed ]]
+ [[ /tmp/miniwdl_task/work/_miniwdl_inputs/0/cyp21_hg38.bed != *_exon_info_hg38.bed ]]
+ filtered_beds=' /tmp/miniwdl_task/work/_miniwdl_inputs/0/smn_hg38.bed /tmp/miniwdl_task/work/_miniwdl_inputs/0/gba_hg38.bed /tmp/miniwdl_task/work/_miniwdl_inputs/0/cyp21_hg38.bed'
+ cat /tmp/miniwdl_task/work/_miniwdl_inputs/0/smn_hg38.bed /tmp/miniwdl_task/work/_miniwdl_inputs/0/gba_hg38.bed /tmp/miniwdl_task/work/_miniwdl_inputs/0/cyp21_hg38.bed
+ echo 'Concatenated BED files:  /tmp/miniwdl_task/work/_miniwdl_inputs/0/smn_hg38.bed /tmp/miniwdl_task/work/_miniwdl_inputs/0/gba_hg38.bed /tmp/miniwdl_task/work/_miniwdl_inputs/0/cyp21_hg38.bed'
Concatenated BED files:  /tmp/miniwdl_task/work/_miniwdl_inputs/0/smn_hg38.bed /tmp/miniwdl_task/work/_miniwdl_inputs/0/gba_hg38.bed /tmp/miniwdl_task/work/_miniwdl_inputs/0/cyp21_hg38.bed
+ echo 'bedtools multicov -q 0 -bams /tmp/miniwdl_task/work/_miniwdl_inputs/0/downloaded.bam -bed concatenated.bed > 3579491586_sv1_multicov_output.tsv'
bedtools multicov -q 0 -bams /tmp/miniwdl_task/work/_miniwdl_inputs/0/downloaded.bam -bed concatenated.bed > 3579491586_sv1_multicov_output.tsv
+ bedtools multicov -q 0 -bams /tmp/miniwdl_task/work/_miniwdl_inputs/0/downloaded.bam -bed concatenated.bed
[2026-05-27 17:44:36] [miniwdl-eks.task] Task finished exit_code=0 (665ms)
cp /tmp/miniwdl_task/stdout.txt s3://natera-rnd-pltf-dev-miniwdl-scratch-01/work/ce/ce1ad9c5e4f74823df903b48e6330669/stdout.txt
cp /tmp/miniwdl_task/stderr.txt s3://natera-rnd-pltf-dev-miniwdl-scratch-01/work/ce/ce1ad9c5e4f74823df903b48e6330669/stderr.txt
cp work/3579491586_sv1_multicov_output.tsv s3://natera-rnd-pltf-dev-miniwdl-scratch-01/work/ce/ce1ad9c5e4f74823df903b48e6330669/work/3579491586_sv1_multicov_output.tsv
cp work/_miniwdl_inputs/0/cyp21_hg38.bed s3://natera-rnd-pltf-dev-miniwdl-scratch-01/work/ce/ce1ad9c5e4f74823df903b48e6330669/work/_miniwdl_inputs/0/cyp21_hg38.bed
cp work/_miniwdl_inputs/0/downloaded.bam s3://natera-rnd-pltf-dev-miniwdl-scratch-01/work/ce/ce1ad9c5e4f74823df903b48e6330669/work/_miniwdl_inputs/0/downloaded.bam
cp work/concatenated.bed s3://natera-rnd-pltf-dev-miniwdl-scratch-01/work/ce/ce1ad9c5e4f74823df903b48e6330669/work/concatenated.bed
cp work/_miniwdl_inputs/0/smn_hg38.bed s3://natera-rnd-pltf-dev-miniwdl-scratch-01/work/ce/ce1ad9c5e4f74823df903b48e6330669/work/_miniwdl_inputs/0/smn_hg38.bed
cp work/_miniwdl_inputs/0/gba_hg38.bed s3://natera-rnd-pltf-dev-miniwdl-scratch-01/work/ce/ce1ad9c5e4f74823df903b48e6330669/work/_miniwdl_inputs/0/gba_hg38.bed
cp work/_miniwdl_inputs/0/downloaded.bam.bai s3://natera-rnd-pltf-dev-miniwdl-scratch-01/work/ce/ce1ad9c5e4f74823df903b48e6330669/work/_miniwdl_inputs/0/downloaded.bam.bai
cp /tmp/miniwdl_task/timing.json s3://natera-rnd-pltf-dev-miniwdl-scratch-01/work/ce/ce1ad9c5e4f74823df903b48e6330669/timing.json
cp /tmp/miniwdl_task/metrics.json s3://natera-rnd-pltf-dev-miniwdl-scratch-01/work/ce/ce1ad9c5e4f74823df903b48e6330669/metrics.json
cp /tmp/miniwdl_task/exit_code s3://natera-rnd-pltf-dev-miniwdl-scratch-01/work/ce/ce1ad9c5e4f74823df903b48e6330669/exit_code
[2026-05-27 17:44:37] [miniwdl-eks.task] Done exit_code=0 (406ms unstage, 1390ms total)