[2026-05-27 17:44:59] [miniwdl-eks.task] Staging: downloading command and 5 inputs
cp s3://natera-rnd-pltf-dev-miniwdl-scratch-01/work/7e/7ea65e5ea9912f06cc13e35427106243/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/1a/1a45cc81125b8356f169ca877403a34c/work/downloaded.bam.bai /tmp/miniwdl_task/work/_miniwdl_inputs/0/downloaded.bam.bai
cp s3://natera-rnd-pltf-dev-miniwdl-scratch-01/work/1a/1a45cc81125b8356f169ca877403a34c/work/downloaded.bam /tmp/miniwdl_task/work/_miniwdl_inputs/0/downloaded.bam
[2026-05-27 17:45:02] [miniwdl-eks.task] Staging completed (5 inputs, 3389ms) s5cmd=workers:256,concurrency:10,cpus:192
++ 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'
+ 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
Current Conda environment: bedtools
+ 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'
+ echo 'bedtools multicov -q 0 -bams /tmp/miniwdl_task/work/_miniwdl_inputs/0/downloaded.bam -bed concatenated.bed > 3574108912_sv1_multicov_output.tsv'
+ bedtools multicov -q 0 -bams /tmp/miniwdl_task/work/_miniwdl_inputs/0/downloaded.bam -bed concatenated.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
bedtools multicov -q 0 -bams /tmp/miniwdl_task/work/_miniwdl_inputs/0/downloaded.bam -bed concatenated.bed > 3574108912_sv1_multicov_output.tsv
[W::hts_idx_load2] The index file is older than the data file: /tmp/miniwdl_task/work/_miniwdl_inputs/0/downloaded.bam.bai
[2026-05-27 17:45:03] [miniwdl-eks.task] Task finished exit_code=0 (1138ms)
cp /tmp/miniwdl_task/stdout.txt s3://natera-rnd-pltf-dev-miniwdl-scratch-01/work/7e/7ea65e5ea9912f06cc13e35427106243/stdout.txt
cp /tmp/miniwdl_task/stderr.txt s3://natera-rnd-pltf-dev-miniwdl-scratch-01/work/7e/7ea65e5ea9912f06cc13e35427106243/stderr.txt
cp work/3574108912_sv1_multicov_output.tsv s3://natera-rnd-pltf-dev-miniwdl-scratch-01/work/7e/7ea65e5ea9912f06cc13e35427106243/work/3574108912_sv1_multicov_output.tsv
cp work/_miniwdl_inputs/0/smn_hg38.bed s3://natera-rnd-pltf-dev-miniwdl-scratch-01/work/7e/7ea65e5ea9912f06cc13e35427106243/work/_miniwdl_inputs/0/smn_hg38.bed
cp work/concatenated.bed s3://natera-rnd-pltf-dev-miniwdl-scratch-01/work/7e/7ea65e5ea9912f06cc13e35427106243/work/concatenated.bed
cp work/_miniwdl_inputs/0/cyp21_hg38.bed s3://natera-rnd-pltf-dev-miniwdl-scratch-01/work/7e/7ea65e5ea9912f06cc13e35427106243/work/_miniwdl_inputs/0/cyp21_hg38.bed
cp work/_miniwdl_inputs/0/gba_hg38.bed s3://natera-rnd-pltf-dev-miniwdl-scratch-01/work/7e/7ea65e5ea9912f06cc13e35427106243/work/_miniwdl_inputs/0/gba_hg38.bed
cp work/_miniwdl_inputs/0/downloaded.bam.bai s3://natera-rnd-pltf-dev-miniwdl-scratch-01/work/7e/7ea65e5ea9912f06cc13e35427106243/work/_miniwdl_inputs/0/downloaded.bam.bai
cp work/_miniwdl_inputs/0/downloaded.bam s3://natera-rnd-pltf-dev-miniwdl-scratch-01/work/7e/7ea65e5ea9912f06cc13e35427106243/work/_miniwdl_inputs/0/downloaded.bam
cp /tmp/miniwdl_task/timing.json s3://natera-rnd-pltf-dev-miniwdl-scratch-01/work/7e/7ea65e5ea9912f06cc13e35427106243/timing.json
cp /tmp/miniwdl_task/metrics.json s3://natera-rnd-pltf-dev-miniwdl-scratch-01/work/7e/7ea65e5ea9912f06cc13e35427106243/metrics.json
cp /tmp/miniwdl_task/exit_code s3://natera-rnd-pltf-dev-miniwdl-scratch-01/work/7e/7ea65e5ea9912f06cc13e35427106243/exit_code
[2026-05-27 17:45:08] [miniwdl-eks.task] Done exit_code=0 (4578ms unstage, 9107ms total)