[2026-05-27 17:41:40] [miniwdl-eks.task] Staging: downloading command and 8 inputs
cp s3://natera-rnd-pltf-dev-miniwdl-scratch-01/work/4b/4bd7ebe95c7976fac18588c301a4331f/command /tmp/miniwdl_task/command
cp s3://natera-rnd-pltf-dev-miniwdl-scratch-01/work/4b/4bd7ebe95c7976fac18588c301a4331f/inputs/tmpx6bg2ozh /tmp/miniwdl_task/work/_miniwdl_inputs/0/tmpx6bg2ozh
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/smn_exon_info_hg38_v1.bed /tmp/miniwdl_task/work/_miniwdl_inputs/0/smn_exon_info_hg38_v1.bed
cp s3://natera-rnd-pltf-dev-miniwdl-scratch-01/work/b2/b2370ffc5f508c9dfb9aeec2df0f3d78/work/samples.json /tmp/miniwdl_task/work/_miniwdl_inputs/0/samples.json
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-platform-sandbox/pipeline-resources/germline_pipeline/allele_specific_expression_beds/hg38/gba_exon_info_hg38.bed /tmp/miniwdl_task/work/_miniwdl_inputs/0/gba_exon_info_hg38.bed
cp s3://natera-platform-sandbox/pipeline-resources/germline_pipeline/allele_specific_expression_beds/hg38/cyp21_exon_info_hg38.bed /tmp/miniwdl_task/work/_miniwdl_inputs/0/cyp21_exon_info_hg38.bed
[2026-05-27 17:41:41] [miniwdl-eks.task] Staging completed (8 inputs, 513ms) s5cmd=workers:256,concurrency:5,cpus:2
+ cgp allele_specific_exp_plots validate-callers-with-samples --callers-json /tmp/miniwdl_task/work/_miniwdl_inputs/0/tmpx6bg2ozh --samples-json /tmp/miniwdl_task/work/_miniwdl_inputs/0/samples.json
2026-05-27 17:41:43,369 mt-fe976158003c43d6bdb3b82aaca2727a-6v7fw cgp.__main__:<module>:16 [INFO]: Successfully loaded `validation` tools into `cgp` tools
2026-05-27 17:41:43,386 mt-fe976158003c43d6bdb3b82aaca2727a-6v7fw cgp.__main__:<module>:25 [INFO]: Successfully loaded `tmb` tools into `cgp` tools
2026-05-27 17:41:44,107 mt-fe976158003c43d6bdb3b82aaca2727a-6v7fw cgp.__main__:<module>:34 [INFO]: Successfully loaded `snv_indel_tools` tools into `cgp` tools
2026-05-27 17:41:44,704 mt-fe976158003c43d6bdb3b82aaca2727a-6v7fw cgp.__main__:<module>:43 [INFO]: Successfully loaded `germlinesnvtools` tools into `cgp` tools
2026-05-27 17:41:44,814 mt-fe976158003c43d6bdb3b82aaca2727a-6v7fw cgp.__main__:<module>:52 [INFO]: Successfully loaded `pbconfirmatoryspecialcases` tools into `cgp` tools
2026-05-27 17:41:44,817 mt-fe976158003c43d6bdb3b82aaca2727a-6v7fw cgp.__main__:<module>:61 [INFO]: Successfully loaded `germline_cnvtools` tools into `cgp` tools
2026-05-27 17:41:44,827 mt-fe976158003c43d6bdb3b82aaca2727a-6v7fw cgp.__main__:<module>:70 [INFO]: Successfully loaded `qPCR_cnvtools` tools into `cgp` tools
2026-05-27 17:41:44,833 mt-fe976158003c43d6bdb3b82aaca2727a-6v7fw cgp.__main__:<module>:79 [INFO]: Successfully loaded `germlinespecialcases` tools into `cgp` tools
2026-05-27 17:41:44,833 mt-fe976158003c43d6bdb3b82aaca2727a-6v7fw cgp.__main__:<module>:88 [INFO]: Successfully loaded `vcf_annotation` tools into `cgp` tools
2026-05-27 17:41:44,857 mt-fe976158003c43d6bdb3b82aaca2727a-6v7fw cgp.__main__:<module>:97 [INFO]: Successfully loaded `regression_testing` tools into `cgp` tools
2026-05-27 17:41:44,983 mt-fe976158003c43d6bdb3b82aaca2727a-6v7fw cgp.__main__:<module>:106 [INFO]: Successfully loaded `reflex_rate_calc` tools into `cgp` tools
2026-05-27 17:41:44,985 mt-fe976158003c43d6bdb3b82aaca2727a-6v7fw cgp.__main__:<module>:115 [INFO]: Successfully loaded `igv_tools` tools into `cgp` tools
2026-05-27 17:41:45,024 mt-fe976158003c43d6bdb3b82aaca2727a-6v7fw cgp.__main__:<module>:124 [INFO]: Successfully loaded `qc_tools` tools into `cgp` tools
2026-05-27 17:41:45,032 mt-fe976158003c43d6bdb3b82aaca2727a-6v7fw cgp.__main__:<module>:133 [INFO]: Successfully loaded `qc_tools` tools into `cgp` tools
2026-05-27 17:41:45,033 mt-fe976158003c43d6bdb3b82aaca2727a-6v7fw cgp.__main__:<module>:142 [INFO]: Successfully loaded `sanger_qc_tools` tools into `cgp` tools
2026-05-27 17:41:45,036 mt-fe976158003c43d6bdb3b82aaca2727a-6v7fw cgp.__main__:<module>:151 [INFO]: Successfully loaded `illumina_str` tools into `cgp` tools
2026-05-27 17:41:45,036 mt-fe976158003c43d6bdb3b82aaca2727a-6v7fw cgp.__main__:<module>:160 [INFO]: Successfully loaded `utils` tools into `cgp` tools
2026-05-27 17:41:45,075 mt-fe976158003c43d6bdb3b82aaca2727a-6v7fw cgp.__main__:<module>:169 [INFO]: Successfully loaded `allele_specific_exp_plots` tools into `cgp` tools
2026-05-27 17:41:45,075 mt-fe976158003c43d6bdb3b82aaca2727a-6v7fw cgp.__main__:main:200 [INFO]: Running command: cgp-tools allele_specific_exp_plots validate-callers-with-samples --callers-json /tmp/miniwdl_task/work/_miniwdl_inputs/0/tmpx6bg2ozh --samples-json /tmp/miniwdl_task/work/_miniwdl_inputs/0/samples.json
2026-05-27 17:41:45,429 mt-fe976158003c43d6bdb3b82aaca2727a-6v7fw cgp.__main__:main:203 [INFO]: Completed successfully.
[2026-05-27 17:41:45] [miniwdl-eks.task] Task finished exit_code=0 (4313ms)
cp /tmp/miniwdl_task/stdout.txt s3://natera-rnd-pltf-dev-miniwdl-scratch-01/work/4b/4bd7ebe95c7976fac18588c301a4331f/stdout.txt
cp /tmp/miniwdl_task/stderr.txt s3://natera-rnd-pltf-dev-miniwdl-scratch-01/work/4b/4bd7ebe95c7976fac18588c301a4331f/stderr.txt
cp work/_miniwdl_inputs/0/cyp21_exon_info_hg38.bed s3://natera-rnd-pltf-dev-miniwdl-scratch-01/work/4b/4bd7ebe95c7976fac18588c301a4331f/work/_miniwdl_inputs/0/cyp21_exon_info_hg38.bed
cp work/_miniwdl_inputs/0/gba_hg38.bed s3://natera-rnd-pltf-dev-miniwdl-scratch-01/work/4b/4bd7ebe95c7976fac18588c301a4331f/work/_miniwdl_inputs/0/gba_hg38.bed
cp work/_miniwdl_inputs/0/smn_hg38.bed s3://natera-rnd-pltf-dev-miniwdl-scratch-01/work/4b/4bd7ebe95c7976fac18588c301a4331f/work/_miniwdl_inputs/0/smn_hg38.bed
cp work/_miniwdl_inputs/0/gba_exon_info_hg38.bed s3://natera-rnd-pltf-dev-miniwdl-scratch-01/work/4b/4bd7ebe95c7976fac18588c301a4331f/work/_miniwdl_inputs/0/gba_exon_info_hg38.bed
cp work/_miniwdl_inputs/0/tmpx6bg2ozh s3://natera-rnd-pltf-dev-miniwdl-scratch-01/work/4b/4bd7ebe95c7976fac18588c301a4331f/work/_miniwdl_inputs/0/tmpx6bg2ozh
cp work/_miniwdl_inputs/0/cyp21_hg38.bed s3://natera-rnd-pltf-dev-miniwdl-scratch-01/work/4b/4bd7ebe95c7976fac18588c301a4331f/work/_miniwdl_inputs/0/cyp21_hg38.bed
cp work/_miniwdl_inputs/0/smn_exon_info_hg38_v1.bed s3://natera-rnd-pltf-dev-miniwdl-scratch-01/work/4b/4bd7ebe95c7976fac18588c301a4331f/work/_miniwdl_inputs/0/smn_exon_info_hg38_v1.bed
cp work/_miniwdl_inputs/0/samples.json s3://natera-rnd-pltf-dev-miniwdl-scratch-01/work/4b/4bd7ebe95c7976fac18588c301a4331f/work/_miniwdl_inputs/0/samples.json
cp /tmp/miniwdl_task/timing.json s3://natera-rnd-pltf-dev-miniwdl-scratch-01/work/4b/4bd7ebe95c7976fac18588c301a4331f/timing.json
cp /tmp/miniwdl_task/metrics.json s3://natera-rnd-pltf-dev-miniwdl-scratch-01/work/4b/4bd7ebe95c7976fac18588c301a4331f/metrics.json
cp /tmp/miniwdl_task/exit_code s3://natera-rnd-pltf-dev-miniwdl-scratch-01/work/4b/4bd7ebe95c7976fac18588c301a4331f/exit_code
[2026-05-27 17:41:46] [miniwdl-eks.task] Done exit_code=0 (461ms unstage, 5288ms total)