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-resume bding-main-2026-05-08t22-31-41z
Error Report
Error executing process > 'DAQ:AGGREGATE_POSTDEDUP_QC (postdedup_qc_aggregation)'
Caused by:
Process `DAQ:AGGREGATE_POSTDEDUP_QC (postdedup_qc_aggregation)` terminated with an error exit status (2)
Command executed:
# Write manifest JSON file
cat << 'EOF' > manifest.json
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ts.tsv"],"659_cFT_tumor",["659_cFT_tumor_full_basic_stats.tsv"],"659_ezg_tumor",["659_ezg_tumor_full_basic_stats.tsv"],"659_b6L_tumor",["659_b6L_tumor_full_basic_stats.tsv"],"659_buj_tumor",["659_buj_tumor_full_basic_stats.tsv"],"659_3g_tumor",["659_3g_tumor_full_basic_stats.tsv"],"659_ejY_tumor",["659_ejY_tumor_full_basic_stats.tsv"],"659_eZ4_tumor",["659_eZ4_tumor_full_basic_stats.tsv"],"659_eNS_tumor",["659_eNS_tumor_full_basic_stats.tsv"],"659_esc_tumor",["659_esc_tumor_full_basic_stats.tsv"],"659_b69_tumor",["659_b69_tumor_full_basic_stats.tsv"],"659_btT_tumor",["659_btT_tumor_full_basic_stats.tsv"],"659_bgw_tumor",["659_bgw_tumor_full_basic_stats.tsv"],"659_Em_tumor",["659_Em_tumor_full_basic_stats.tsv"],"659_R1_tumor",["659_R1_tumor_full_basic_stats.tsv"],"659_csY_tumor",["659_csY_tumor_full_basic_stats.tsv"],"659_de0_tumor",["659_de0_tumor_full_basic_stats.tsv"],"659_dhR_tumor",["659_dhR_tumor_full_basic_stats.tsv"],"659_hv_tumor",["659_hv_tumor_full_basic_stats.tsv"],"659_drH_tumor",["659_drH_tumor_full_basic_stats.tsv"],"659_cRB_tumor",["659_cRB_tumor_full_basic_stats.tsv"],"659_bUW_tumor",["659_bUW_tumor_full_basic_stats.tsv"],"659_bmI_tumor",["659_bmI_tumor_full_basic_stats.tsv"],"659_dHy_tumor",["659_dHy_tumor_full_basic_stats.tsv"],"659_e0S_tumor",["659_e0S_tumor_full_basic_stats.tsv"],"659_bR4_tumor",["659_bR4_tumor_full_basic_stats.tsv"],"659_dAn_tumor",["659_dAn_tumor_full_basic_stats.tsv"],"659_eZ3_tumor",["659_eZ3_tumor_full_basic_stats.tsv"],"659_bhK_tumor",["659_bhK_tumor_full_basic_stats.tsv"],"659_1q_tumor",["659_1q_tumor_full_basic_stats.tsv"],"659_eEE_tumor",["659_eEE_tumor_full_basic_stats.tsv"],"659_dYT_tumor",["659_dYT_tumor_full_basic_stats.tsv"],"659_bTq_tumor",["659_bTq_tumor_full_basic_stats.tsv"],"659_cTS_tumor",["659_cTS_tumor_full_basic_stats.tsv"],"659_d13_tumor",["659_d13_tumor_full_basic_stats.tsv"],"659_Jq_tumor",["659_Jq_tumor_full_basic_stats.tsv"],"659_epG_tumor",["659_epG_tumor_full_basic_stats.tsv"],"659_cst_tumor",["659_cst_tumor_full_basic_stats.tsv"],"659_bCu_tumor",["659_bCu_tumor_full_basic_stats.tsv"],"659_cuO_tumor",["659_cuO_tumor_full_basic_stats.tsv"],"659_Kh_tumor",["659_Kh_tumor_full_basic_stats.tsv"],"659_ecd_tumor",["659_ecd_tumor_full_basic_stats.tsv"],"659_bHx_tumor",["659_bHx_tumor_full_basic_stats.tsv"],"659_pO_tumor",["659_pO_tumor_full_basic_stats.tsv"],"659_cAa_tumor",["659_cAa_tumor_full_basic_stats.tsv"],"659_dLs_tumor",["659_dLs_tumor_full_basic_stats.tsv"],"659_cRa_tumor",["659_cRa_tumor_full_basic_stats.tsv"],"659_bPW_tumor",["659_bPW_tumor_full_basic_stats.tsv"],"659_bDa_tumor",["659_bDa_tumor_full_basic_stats.tsv"],"659_cit_tumor",["659_cit_tumor_full_basic_stats.tsv"],"659_eRe_tumor",["659_eRe_tumor_full_basic_stats.tsv"],"659_bvq_tumor",["659_bvq_tumor_full_basic_stats.tsv"],"659_wQ_tumor",["659_wQ_tumor_full_basic_stats.tsv"],"659_cfy_tumor",["659_cfy_tumor_full_basic_stats.tsv"],"659_cwR_tumor",["659_cwR_tumor_full_basic_stats.tsv"],"659_dhS_tumor",["659_dhS_tumor_full_basic_stats.tsv"],"659_sv_tumor",["659_sv_tumor_full_basic_stats.tsv"],"659_b6q_tumor",["659_b6q_tumor_full_basic_stats.tsv"],"659_e6r_tumor",["659_e6r_tumor_full_basic_stats.tsv"],"659_bjq_tumor",["659_bjq_tumor_full_basic_stats.tsv"],"659_kM_tumor",["659_kM_tumor_full_basic_stats.tsv"],"659_ddv_tumor",["659_ddv_tumor_full_basic_stats.tsv"],"659_uv_tumor",["659_uv_tumor_full_basic_stats.tsv"],"659_7h_tumor",["659_7h_tumor_full_basic_stats.tsv"],"659_cAd_tumor",["659_cAd_tumor_full_basic_stats.tsv"],"659_bD1_tumor",["659_bD1_tumor_full_basic_stats.tsv"],"659_dts_tumor",["659_dts_tumor_full_basic_stats.tsv"],"659_dvY_tumor",["659_dvY_tumor_full_basic_stats.tsv"],"659_c6S_tumor",["659_c6S_tumor_full_basic_stats.tsv"],"659_Mt_tumor",["659_Mt_tumor_full_basic_stats.tsv"],"659_drZ_tumor",["659_drZ_tumor_full_basic_stats.tsv"],"659_bnZ_tumor",["659_bnZ_tumor_full_basic_stats.tsv"],"659_mK_tumor",["659_mK_tumor_full_basic_stats.tsv"],"659_Yr_tumor",["659_Yr_tumor_full_basic_stats.tsv"],"659_cCU_tumor",["659_cCU_tumor_full_basic_stats.tsv"],"659_eKx_tumor",["659_eKx_tumor_full_basic_stats.tsv"],"659_djb_tumor",["659_djb_tumor_full_basic_stats.tsv"],"659_ebP_tumor",["659_ebP_tumor_full_basic_stats.tsv"],"659_cAr_tumor",["659_cAr_tumor_full_basic_stats.tsv"],"659_cd9_tumor",["659_cd9_tumor_full_basic_stats.tsv"],"659_QC_tumor",["659_QC_tumor_full_basic_stats.tsv"],"659_91_tumor",["659_91_tumor_full_basic_stats.tsv"],"659_bwh_tumor",["659_bwh_tumor_full_basic_stats.tsv"],"659_bu4_tumor",["659_bu4_tumor_full_basic_stats.tsv"],"659_d0M_tumor",["659_d0M_tumor_full_basic_stats.tsv"],"659_dQk_tumor",["659_dQk_tumor_full_basic_stats.tsv"],"659_dm4_tumor",["659_dm4_tumor_full_basic_stats.tsv"],"659_8h_tumor",["659_8h_tumor_full_basic_stats.tsv"],"659_btj_tumor",["659_btj_tumor_full_basic_stats.tsv"]]}
EOF
cat << 'EOF' > panel_mapping.json
{"xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_AND_foresight_clarity.bed":"all_targets","xgen-exome-hyb-panel-v2_AND_altera_v3_probes_short_hg38_AND_cdx_spike_custom30off4x_hg38_AND_foresight_clarity_footprint.bed":"all_probes","altera_v3_targets_postQC_hg38.bed":"boosted_depth","altera_v3_targets_coding_postQC_hg38.bed":"coding_depth","altera_v3_targets_noncoding_postQC_hg38.bed":"noncoding_depth","xgen-exome-hyb-panel-v2-targets-hg38_minus_altera_v3_targets_postQC_hg38.bed":"non_boosted_depth","FINAL_hotspot_list_07302025_hg38_sorted.bed":"hotspot_depth","foresight_clarity_targets_hg38.bed":"foresight_depth"}
EOF
# Run aggregation script (outputs single JSON)
aggregate_qc_metrics.py \
--mode postdedup \
--manifest manifest.json \
--panel-mapping panel_mapping.json \
--files-dir . \
--output postdedup_qc.json \
--no-summary
cat <<-END_VERSIONS > versions.yml
"DAQ:AGGREGATE_POSTDEDUP_QC":
python: $(python --version | sed 's/Python //g')
aggregate_qc_metrics: 1.0.0
END_VERSIONS
Command exit status:
2
Command output:
(empty)
Command error:
usage: aggregate_qc_metrics.py [-h] --manifest MANIFEST
[--files-dir FILES_DIR] --output OUTPUT
aggregate_qc_metrics.py: error: unrecognized arguments: --mode postdedup --panel-mapping panel_mapping.json --no-summary
Work dir:
s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/09/c69ce611bf48fdb811d1dbe682263e
Container:
292967571998.dkr.ecr.us-west-2.amazonaws.com/daq/aggregate_postdedup_qc:1.8.0
Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`
Workflow
- Language / Cluster
- Nextflow / pltf-dev
- Session ID
- dde4a944-6ebc-43cb-8556-3db39fe5fcf6
- Source
- /code/main.nf
- Work Dir
- s3://natera-rnd-pltf-dev-nextflow-scratch-01/work
- Submitted By
- bding
- Resumed
- No
Cost and Runtime
- Status
- failed
- Cost
- $524.55
- Outputs
- 8.9 TB
- Started
- May 08, 2026 3:32 PM
- Completed
- May 08, 2026 6:05 PM
- Duration
- 2h 33m
- Post-workflow Transfer
- 12s
- Exit Status
- 2
- Peak Tasks / CPU / Mem
- 489 / 11,892 / 53.5 TB