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-resume bding-main-2026-05-11t16-48-57z
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
{"samtools":["659_7h_normal",["659_7h_normal.stats"],"659_bCu_normal",["659_bCu_normal.stats"],"659_8h_normal",["659_8h_normal.stats"],"659_3g_normal",["659_3g_normal.stats"],"659_1q_normal",["659_1q_normal.stats"],"659_b69_normal",["659_b69_normal.stats"],"659_b6L_normal",["659_b6L_normal.stats"],"659_91_normal",["659_91_normal.stats"],"659_b6q_normal",["659_b6q_normal.stats"],"659_bD1_normal",["659_bD1_normal.stats"],"659_1q_tumor",["659_1q_tumor.stats"],"659_b6L_tumor",["659_b6L_tumor.stats"],"659_b6q_tumor",["659_b6q_tumor.stats"],"659_3g_tumor",["659_3g_tumor.stats"],"659_b69_tumor",["659_b69_tumor.stats"],"659_bCu_tumor",["659_bCu_tumor.stats"],"659_bD1_tumor",["659_bD1_tumor.stats"],"659_7h_tumor",["659_7h_tumor.stats"],"659_91_tumor",["659_91_tumor.stats"],"659_8h_tumor",["659_8h_tumor.stats"]],"mosdepth":["659_7h_normal",["659_7h_normal.mosdepth.summary.txt"],"659_bCu_normal",["659_bCu_normal.mosdepth.summary.txt"],"659_1q_normal",["659_1q_normal.mosdepth.summary.txt"],"659_3g_normal",["659_3g_normal.mosdepth.summary.txt"],"659_8h_normal",["659_8h_normal.mosdepth.summary.txt"],"659_b69_normal",["659_b69_normal.mosdepth.summary.txt"],"659_b6L_normal",["659_b6L_normal.mosdepth.summary.txt"],"659_91_normal",["659_91_normal.mosdepth.summary.txt"],"659_b6q_normal",["659_b6q_normal.mosdepth.summary.txt"],"659_bD1_normal",["659_bD1_normal.mosdepth.summary.txt"],"659_b6L_tumor",["659_b6L_tumor.mosdepth.summary.txt"],"659_1q_tumor",["659_1q_tumor.mosdepth.summary.txt"],"659_b6q_tumor",["659_b6q_tumor.mosdepth.summary.txt"],"659_b69_tumor",["659_b69_tumor.mosdepth.summary.txt"],"659_3g_tumor",["659_3g_tumor.mosdepth.summary.txt"],"659_bCu_tumor",["659_bCu_tumor.mosdepth.summary.txt"],"659_bD1_tumor",["659_bD1_tumor.mosdepth.summary.txt"],"659_7h_tumor",["659_7h_tumor.mosdepth.summary.txt"],"659_91_tumor",["659_91_tumor.mosdepth.summary.txt"],"659_8h_tumor",["659_8h_tumor.mosdepth.summary.txt"]],"sentieon_insert":["659_7h_normal",["659_7h_normal.sentieon.insert_size_metrics"],"659_bCu_normal",["659_bCu_normal.sentieon.insert_size_metrics"],"659_3g_normal",["659_3g_normal.sentieon.insert_size_metrics"],"659_8h_normal",["659_8h_normal.sentieon.insert_size_metrics"],"659_b69_normal",["659_b69_normal.sentieon.insert_size_metrics"],"659_1q_normal",["659_1q_normal.sentieon.insert_size_metrics"],"659_b6L_normal",["659_b6L_normal.sentieon.insert_size_metrics"],"659_bD1_normal",["659_bD1_normal.sentieon.insert_size_metrics"],"659_91_normal",["659_91_normal.sentieon.insert_size_metrics"],"659_b6q_normal",["659_b6q_normal.sentieon.insert_size_metrics"],"659_b6L_tumor",["659_b6L_tumor.sentieon.insert_size_metrics"],"659_1q_tumor",["659_1q_tumor.sentieon.insert_size_metrics"],"659_b6q_tumor",["659_b6q_tumor.sentieon.insert_size_metrics"],"659_3g_tumor",["659_3g_tumor.sentieon.insert_size_metrics"],"659_b69_tumor",["659_b69_tumor.sentieon.insert_size_metrics"],"659_bCu_tumor",["659_bCu_tumor.sentieon.insert_size_metrics"],"659_bD1_tumor",["659_bD1_tumor.sentieon.insert_size_metrics"],"659_7h_tumor",["659_7h_tumor.sentieon.insert_size_metrics"],"659_91_tumor",["659_91_tumor.sentieon.insert_size_metrics"],"659_8h_tumor",["659_8h_tumor.sentieon.insert_size_metrics"]],"sentieon_hs":["659_7h_normal",["659_7h_normal_altera_v3_targets_postQC_hg38.sentieon.hs_metrics","659_7h_normal_xgen-exome-hyb-panel-v2_AND_altera_v3_probes_short_hg38_AND_cdx_spike_custom30off4x_hg38_AND_foresight_clarity_footprint.sentieon.hs_metrics","659_7h_normal_xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_AND_foresight_clarity.sentieon.hs_metrics","659_7h_normal_altera_v3_targets_coding_postQC_hg38.sentieon.hs_metrics","659_7h_normal_altera_v3_targets_noncoding_postQC_hg38.sentieon.hs_metrics","659_7h_normal_xgen-exome-hyb-panel-v2-targets-hg38_minus_altera_v3_targets_postQC_hg38.sentieon.hs_metrics","659_7h_normal_foresight_clarity_targets_hg38.sentieon.hs_metrics","659_7h_normal_FINAL_hotspot_list_07302025_hg38_sorted.sentieon.hs_metrics"],"659_bCu_normal",["659_bCu_normal_xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_AND_foresight_clarity.sentieon.hs_metrics","659_bCu_normal_xgen-exome-hyb-panel-v2_AND_altera_v3_probes_short_hg38_AND_cdx_spike_custom30off4x_hg38_AND_foresight_clarity_footprint.sentieon.hs_metrics","659_bCu_normal_altera_v3_targets_coding_postQC_hg38.sentieon.hs_metrics","659_bCu_normal_altera_v3_targets_postQC_hg38.sentieon.hs_metrics","659_bCu_normal_altera_v3_targets_noncoding_postQC_hg38.sentieon.hs_metrics","659_bCu_normal_xgen-exome-hyb-panel-v2-targets-hg38_minus_altera_v3_targets_postQC_hg38.sentieon.hs_metrics","659_bCu_normal_FINAL_hotspot_list_07302025_hg38_sorted.sentieon.hs_metrics","659_bCu_normal_foresight_clarity_targets_hg38.sentieon.hs_metrics"],"659_8h_normal",["659_8h_normal_altera_v3_targets_coding_postQC_hg38.sentieon.hs_metrics","659_8h_normal_altera_v3_targets_postQC_hg38.sentieon.hs_metrics","659_8h_normal_xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_AND_foresight_clarity.sentieon.hs_metrics","659_8h_normal_xgen-exome-hyb-panel-v2_AND_altera_v3_probes_short_hg38_AND_cdx_spike_custom30off4x_hg38_AND_foresight_clarity_footprint.sentieon.hs_metrics","659_8h_normal_xgen-exome-hyb-panel-v2-targets-hg38_minus_altera_v3_targets_postQC_hg38.sentieon.hs_metrics","659_8h_normal_FINAL_hotspot_list_07302025_hg38_sorted.sentieon.hs_metrics","659_8h_normal_altera_v3_targets_noncoding_postQC_hg38.sentieon.hs_metrics","659_8h_normal_foresight_clarity_targets_hg38.sentieon.hs_metrics"],"659_b6q_normal",["659_b6q_normal_xgen-exome-hyb-panel-v2-targets-hg38_minus_altera_v3_targets_postQC_hg38.sentieon.hs_metrics","659_b6q_normal_xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_AND_foresight_clarity.sentieon.hs_metrics","659_b6q_normal_xgen-exome-hyb-panel-v2_AND_altera_v3_probes_short_hg38_AND_cdx_spike_custom30off4x_hg38_AND_foresight_clarity_footprint.sentieon.hs_metrics","659_b6q_normal_altera_v3_targets_postQC_hg38.sentieon.hs_metrics","659_b6q_normal_altera_v3_targets_noncoding_postQC_hg38.sentieon.hs_metrics","659_b6q_normal_FINAL_hotspot_list_07302025_hg38_sorted.sentieon.hs_metrics","659_b6q_normal_altera_v3_targets_coding_postQC_hg38.sentieon.hs_metrics","659_b6q_normal_foresight_clarity_targets_hg38.sentieon.hs_metrics"],"659_3g_normal",["659_3g_normal_xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_AND_foresight_clarity.sentieon.hs_metrics","659_3g_normal_altera_v3_targets_postQC_hg38.sentieon.hs_metrics","659_3g_normal_altera_v3_targets_coding_postQC_hg38.sentieon.hs_metrics","659_3g_normal_altera_v3_targets_noncoding_postQC_hg38.sentieon.hs_metrics","659_3g_normal_FINAL_hotspot_list_07302025_hg38_sorted.sentieon.hs_metrics","659_3g_normal_foresight_clarity_targets_hg38.sentieon.hs_metrics","659_3g_normal_xgen-exome-hyb-panel-v2-targets-hg38_minus_altera_v3_targets_postQC_hg38.sentieon.hs_metrics","659_3g_normal_xgen-exome-hyb-panel-v2_AND_altera_v3_probes_short_hg38_AND_cdx_spike_custom30off4x_hg38_AND_foresight_clarity_footprint.sentieon.hs_metrics"],"659_1q_normal",["659_1q_normal_altera_v3_targets_postQC_hg38.sentieon.hs_metrics","659_1q_normal_altera_v3_targets_coding_postQC_hg38.sentieon.hs_metrics","659_1q_normal_xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_AND_foresight_clarity.sentieon.hs_metrics","659_1q_normal_xgen-exome-hyb-panel-v2_AND_altera_v3_probes_short_hg38_AND_cdx_spike_custom30off4x_hg38_AND_foresight_clarity_footprint.sentieon.hs_metrics","659_1q_normal_xgen-exome-hyb-panel-v2-targets-hg38_minus_altera_v3_targets_postQC_hg38.sentieon.hs_metrics","659_1q_normal_altera_v3_targets_noncoding_postQC_hg38.sentieon.hs_metrics","659_1q_normal_FINAL_hotspot_list_07302025_hg38_sorted.sentieon.hs_metrics","659_1q_normal_foresight_clarity_targets_hg38.sentieon.hs_metrics"],"659_b69_normal",["659_b69_normal_xgen-exome-hyb-panel-v2_AND_altera_v3_probes_short_hg38_AND_cdx_spike_custom30off4x_hg38_AND_foresight_clarity_footprint.sentieon.hs_metrics","659_b69_normal_xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_AND_foresight_clarity.sentieon.hs_metrics","659_b69_normal_altera_v3_targets_coding_postQC_hg38.sentieon.hs_metrics","659_b69_normal_altera_v3_targets_postQC_hg38.sentieon.hs_metrics","659_b69_normal_xgen-exome-hyb-panel-v2-targets-hg38_minus_altera_v3_targets_postQC_hg38.sentieon.hs_metrics","659_b69_normal_FINAL_hotspot_list_07302025_hg38_sorted.sentieon.hs_metrics","659_b69_normal_altera_v3_targets_noncoding_postQC_hg38.sentieon.hs_metrics","659_b69_normal_foresight_clarity_targets_hg38.sentieon.hs_metrics"],"659_b6L_normal",["659_b6L_normal_altera_v3_targets_postQC_hg38.sentieon.hs_metrics","659_b6L_normal_xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_AND_foresight_clarity.sentieon.hs_metrics","659_b6L_normal_xgen-exome-hyb-panel-v2_AND_altera_v3_probes_short_hg38_AND_cdx_spike_custom30off4x_hg38_AND_foresight_clarity_footprint.sentieon.hs_metrics","659_b6L_normal_altera_v3_targets_coding_postQC_hg38.sentieon.hs_metrics","659_b6L_normal_altera_v3_targets_noncoding_postQC_hg38.sentieon.hs_metrics","659_b6L_normal_xgen-exome-hyb-panel-v2-targets-hg38_minus_altera_v3_targets_postQC_hg38.sentieon.hs_metrics","659_b6L_normal_FINAL_hotspot_list_07302025_hg38_sorted.sentieon.hs_metrics","659_b6L_normal_foresight_clarity_targets_hg38.sentieon.hs_metrics"],"659_91_normal",["659_91_normal_altera_v3_targets_coding_postQC_hg38.sentieon.hs_metrics","659_91_normal_altera_v3_targets_noncoding_postQC_hg38.sentieon.hs_metrics","659_91_normal_xgen-exome-hyb-panel-v2-targets-hg38_minus_altera_v3_targets_postQC_hg38.sentieon.hs_metrics","659_91_normal_foresight_clarity_targets_hg38.sentieon.hs_metrics","659_91_normal_xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_AND_foresight_clarity.sentieon.hs_metrics","659_91_normal_xgen-exome-hyb-panel-v2_AND_altera_v3_probes_short_hg38_AND_cdx_spike_custom30off4x_hg38_AND_foresight_clarity_footprint.sentieon.hs_metrics","659_91_normal_altera_v3_targets_postQC_hg38.sentieon.hs_metrics","659_91_normal_FINAL_hotspot_list_07302025_hg38_sorted.sentieon.hs_metrics"],"659_bD1_normal",["659_bD1_normal_xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_AND_foresight_clarity.sentieon.hs_metrics","659_bD1_normal_xgen-exome-hyb-panel-v2_AND_altera_v3_probes_short_hg38_AND_cdx_spike_custom30off4x_hg38_AND_foresight_clarity_footprint.sentieon.hs_metrics","659_bD1_normal_altera_v3_targets_postQC_hg38.sentieon.hs_metrics","659_bD1_normal_altera_v3_targets_coding_postQC_hg38.sentieon.hs_metrics","659_bD1_normal_xgen-exome-hyb-panel-v2-targets-hg38_minus_altera_v3_targets_postQC_hg38.sentieon.hs_metrics","659_bD1_normal_FINAL_hotspot_list_07302025_hg38_sorted.sentieon.hs_metrics","659_bD1_normal_foresight_clarity_targets_hg38.sentieon.hs_metrics","659_bD1_normal_altera_v3_targets_noncoding_postQC_hg38.sentieon.hs_metrics"],"659_1q_tumor",["659_1q_tumor_altera_v3_targets_coding_postQC_hg38.sentieon.hs_metrics","659_1q_tumor_xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_AND_foresight_clarity.sentieon.hs_metrics","659_1q_tumor_xgen-exome-hyb-panel-v2_AND_altera_v3_probes_short_hg38_AND_cdx_spike_custom30off4x_hg38_AND_foresight_clarity_footprint.sentieon.hs_metrics","659_1q_tumor_altera_v3_targets_postQC_hg38.sentieon.hs_metrics","659_1q_tumor_altera_v3_targets_noncoding_postQC_hg38.sentieon.hs_metrics","659_1q_tumor_xgen-exome-hyb-panel-v2-targets-hg38_minus_altera_v3_targets_postQC_hg38.sentieon.hs_metrics","659_1q_tumor_FINAL_hotspot_list_07302025_hg38_sorted.sentieon.hs_metrics","659_1q_tumor_foresight_clarity_targets_hg38.sentieon.hs_metrics"],"659_b6L_tumor",["659_b6L_tumor_xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_AND_foresight_clarity.sentieon.hs_metrics","659_b6L_tumor_xgen-exome-hyb-panel-v2_AND_altera_v3_probes_short_hg38_AND_cdx_spike_custom30off4x_hg38_AND_foresight_clarity_footprint.sentieon.hs_metrics","659_b6L_tumor_altera_v3_targets_postQC_hg38.sentieon.hs_metrics","659_b6L_tumor_altera_v3_targets_coding_postQC_hg38.sentieon.hs_metrics","659_b6L_tumor_altera_v3_targets_noncoding_postQC_hg38.sentieon.hs_metrics","659_b6L_tumor_xgen-exome-hyb-panel-v2-targets-hg38_minus_altera_v3_targets_postQC_hg38.sentieon.hs_metrics","659_b6L_tumor_FINAL_hotspot_list_07302025_hg38_sorted.sentieon.hs_metrics","659_b6L_tumor_foresight_clarity_targets_hg38.sentieon.hs_metrics"],"659_3g_tumor",["659_3g_tumor_xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_AND_foresight_clarity.sentieon.hs_metrics","659_3g_tumor_xgen-exome-hyb-panel-v2_AND_altera_v3_probes_short_hg38_AND_cdx_spike_custom30off4x_hg38_AND_foresight_clarity_footprint.sentieon.hs_metrics","659_3g_tumor_altera_v3_targets_coding_postQC_hg38.sentieon.hs_metrics","659_3g_tumor_altera_v3_targets_postQC_hg38.sentieon.hs_metrics","659_3g_tumor_xgen-exome-hyb-panel-v2-targets-hg38_minus_altera_v3_targets_postQC_hg38.sentieon.hs_metrics","659_3g_tumor_FINAL_hotspot_list_07302025_hg38_sorted.sentieon.hs_metrics","659_3g_tumor_altera_v3_targets_noncoding_postQC_hg38.sentieon.hs_metrics","659_3g_tumor_foresight_clarity_targets_hg38.sentieon.hs_metrics"],"659_b6q_tumor",["659_b6q_tumor_xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_AND_foresight_clarity.sentieon.hs_metrics","659_b6q_tumor_altera_v3_targets_postQC_hg38.sentieon.hs_metrics","659_b6q_tumor_xgen-exome-hyb-panel-v2_AND_altera_v3_probes_short_hg38_AND_cdx_spike_custom30off4x_hg38_AND_foresight_clarity_footprint.sentieon.hs_metrics","659_b6q_tumor_altera_v3_targets_coding_postQC_hg38.sentieon.hs_metrics","659_b6q_tumor_altera_v3_targets_noncoding_postQC_hg38.sentieon.hs_metrics","659_b6q_tumor_xgen-exome-hyb-panel-v2-targets-hg38_minus_altera_v3_targets_postQC_hg38.sentieon.hs_metrics","659_b6q_tumor_foresight_clarity_targets_hg38.sentieon.hs_metrics","659_b6q_tumor_FINAL_hotspot_list_07302025_hg38_sorted.sentieon.hs_metrics"],"659_b69_tumor",["659_b69_tumor_xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_AND_foresight_clarity.sentieon.hs_metrics","659_b69_tumor_xgen-exome-hyb-panel-v2_AND_altera_v3_probes_short_hg38_AND_cdx_spike_custom30off4x_hg38_AND_foresight_clarity_footprint.sentieon.hs_metrics","659_b69_tumor_altera_v3_targets_postQC_hg38.sentieon.hs_metrics","659_b69_tumor_altera_v3_targets_noncoding_postQC_hg38.sentieon.hs_metrics","659_b69_tumor_xgen-exome-hyb-panel-v2-targets-hg38_minus_altera_v3_targets_postQC_hg38.sentieon.hs_metrics","659_b69_tumor_altera_v3_targets_coding_postQC_hg38.sentieon.hs_metrics","659_b69_tumor_foresight_clarity_targets_hg38.sentieon.hs_metrics","659_b69_tumor_FINAL_hotspot_list_07302025_hg38_sorted.sentieon.hs_metrics"],"659_bCu_tumor",["659_bCu_tumor_xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_AND_foresight_clarity.sentieon.hs_metrics","659_bCu_tumor_altera_v3_targets_postQC_hg38.sentieon.hs_metrics","659_bCu_tumor_xgen-exome-hyb-panel-v2_AND_altera_v3_probes_short_hg38_AND_cdx_spike_custom30off4x_hg38_AND_foresight_clarity_footprint.sentieon.hs_metrics","659_bCu_tumor_altera_v3_targets_coding_postQC_hg38.sentieon.hs_metrics","659_bCu_tumor_altera_v3_targets_noncoding_postQC_hg38.sentieon.hs_metrics","659_bCu_tumor_FINAL_hotspot_list_07302025_hg38_sorted.sentieon.hs_metrics","659_bCu_tumor_xgen-exome-hyb-panel-v2-targets-hg38_minus_altera_v3_targets_postQC_hg38.sentieon.hs_metrics","659_bCu_tumor_foresight_clarity_targets_hg38.sentieon.hs_metrics"],"659_bD1_tumor",["659_bD1_tumor_altera_v3_targets_coding_postQC_hg38.sentieon.hs_metrics","659_bD1_tumor_altera_v3_targets_postQC_hg38.sentieon.hs_metrics","659_bD1_tumor_xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_AND_foresight_clarity.sentieon.hs_metrics","659_bD1_tumor_xgen-exome-hyb-panel-v2_AND_altera_v3_probes_short_hg38_AND_cdx_spike_custom30off4x_hg38_AND_foresight_clarity_footprint.sentieon.hs_metrics","659_bD1_tumor_altera_v3_targets_noncoding_postQC_hg38.sentieon.hs_metrics","659_bD1_tumor_FINAL_hotspot_list_07302025_hg38_sorted.sentieon.hs_metrics","659_bD1_tumor_foresight_clarity_targets_hg38.sentieon.hs_metrics","659_bD1_tumor_xgen-exome-hyb-panel-v2-targets-hg38_minus_altera_v3_targets_postQC_hg38.sentieon.hs_metrics"],"659_7h_tumor",["659_7h_tumor_xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_AND_foresight_clarity.sentieon.hs_metrics","659_7h_tumor_xgen-exome-hyb-panel-v2_AND_altera_v3_probes_short_hg38_AND_cdx_spike_custom30off4x_hg38_AND_foresight_clarity_footprint.sentieon.hs_metrics","659_7h_tumor_altera_v3_targets_postQC_hg38.sentieon.hs_metrics","659_7h_tumor_altera_v3_targets_noncoding_postQC_hg38.sentieon.hs_metrics","659_7h_tumor_altera_v3_targets_coding_postQC_hg38.sentieon.hs_metrics","659_7h_tumor_xgen-exome-hyb-panel-v2-targets-hg38_minus_altera_v3_targets_postQC_hg38.sentieon.hs_metrics","659_7h_tumor_FINAL_hotspot_list_07302025_hg38_sorted.sentieon.hs_metrics","659_7h_tumor_foresight_clarity_targets_hg38.sentieon.hs_metrics"],"659_91_tumor",["659_91_tumor_altera_v3_targets_coding_postQC_hg38.sentieon.hs_metrics","659_91_tumor_altera_v3_targets_postQC_hg38.sentieon.hs_metrics","659_91_tumor_FINAL_hotspot_list_07302025_hg38_sorted.sentieon.hs_metrics","659_91_tumor_foresight_clarity_targets_hg38.sentieon.hs_metrics","659_91_tumor_xgen-exome-hyb-panel-v2_AND_altera_v3_probes_short_hg38_AND_cdx_spike_custom30off4x_hg38_AND_foresight_clarity_footprint.sentieon.hs_metrics","659_91_tumor_xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_AND_foresight_clarity.sentieon.hs_metrics","659_91_tumor_xgen-exome-hyb-panel-v2-targets-hg38_minus_altera_v3_targets_postQC_hg38.sentieon.hs_metrics","659_91_tumor_altera_v3_targets_noncoding_postQC_hg38.sentieon.hs_metrics"],"659_8h_tumor",["659_8h_tumor_xgen-exome-hyb-panel-v2_AND_altera_v3_probes_short_hg38_AND_cdx_spike_custom30off4x_hg38_AND_foresight_clarity_footprint.sentieon.hs_metrics","659_8h_tumor_altera_v3_targets_coding_postQC_hg38.sentieon.hs_metrics","659_8h_tumor_xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_AND_foresight_clarity.sentieon.hs_metrics","659_8h_tumor_altera_v3_targets_noncoding_postQC_hg38.sentieon.hs_metrics","659_8h_tumor_altera_v3_targets_postQC_hg38.sentieon.hs_metrics","659_8h_tumor_FINAL_hotspot_list_07302025_hg38_sorted.sentieon.hs_metrics","659_8h_tumor_foresight_clarity_targets_hg38.sentieon.hs_metrics","659_8h_tumor_xgen-exome-hyb-panel-v2-targets-hg38_minus_altera_v3_targets_postQC_hg38.sentieon.hs_metrics"]],"seqtool":["659_7h_normal",["659_7h_normal_full_basic_stats.tsv"],"659_bCu_normal",["659_bCu_normal_full_basic_stats.tsv"],"659_3g_normal",["659_3g_normal_full_basic_stats.tsv"],"659_91_normal",["659_91_normal_full_basic_stats.tsv"],"659_8h_normal",["659_8h_normal_full_basic_stats.tsv"],"659_b69_normal",["659_b69_normal_full_basic_stats.tsv"],"659_bD1_normal",["659_bD1_normal_full_basic_stats.tsv"],"659_b6L_normal",["659_b6L_normal_full_basic_stats.tsv"],"659_1q_normal",["659_1q_normal_full_basic_stats.tsv"],"659_b6q_normal",["659_b6q_normal_full_basic_stats.tsv"],"659_1q_tumor",["659_1q_tumor_full_basic_stats.tsv"],"659_b6L_tumor",["659_b6L_tumor_full_basic_stats.tsv"],"659_3g_tumor",["659_3g_tumor_full_basic_stats.tsv"],"659_b6q_tumor",["659_b6q_tumor_full_basic_stats.tsv"],"659_b69_tumor",["659_b69_tumor_full_basic_stats.tsv"],"659_bD1_tumor",["659_bD1_tumor_full_basic_stats.tsv"],"659_bCu_tumor",["659_bCu_tumor_full_basic_stats.tsv"],"659_7h_tumor",["659_7h_tumor_full_basic_stats.tsv"],"659_91_tumor",["659_91_tumor_full_basic_stats.tsv"],"659_8h_tumor",["659_8h_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/31/a0e299cfd5b4eb3861b482a76f54ae
Container:
292967571998.dkr.ecr.us-west-2.amazonaws.com/daq/aggregate_postdedup_qc:1.8.0
Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`
Workflow
- Language / Cluster
- Nextflow / pltf-dev
- Session ID
- 3da2dcf2-369b-4fc3-a38e-5cfb85107593
- 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
- $62.77
- Outputs
- 0 B
- Started
- May 11, 2026 9:49 AM
- Completed
- May 11, 2026 11:48 AM
- Duration
- 1h 59m
- Post-workflow Transfer
- 21s
- Exit Status
- 2
- Peak Tasks / CPU / Mem
- 75 / 1,851 / 8.6 TB