Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4e/8e0f45d63f236e30d4455741749ace/output/Reports/Demultiplex_Stats.csv Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/54/f952a746ed41165c6626d70cdcd334/output/Reports/Demultiplex_Stats.csv Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e5/810c1ed99c9777720a9775fa34a90e/output/Reports/Top_Unknown_Barcodes.csv Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/21/86594e8df030ec1333e6ac02d4e24b/output/Reports/Top_Unknown_Barcodes.csv Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d7/5418e87bf4204107683ccca95a5e98/output/Reports/Demultiplex_Stats.csv Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/52/bb2c0a74896dcc763c7a3539d18407/output/Reports/Top_Unknown_Barcodes.csv Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e5/810c1ed99c9777720a9775fa34a90e/output/Reports/Demultiplex_Stats.csv Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f3/7f0a48d7570689412f68ab8e48090f/output/Reports/Demultiplex_Stats.csv Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4e/8e0f45d63f236e30d4455741749ace/output/Reports/Top_Unknown_Barcodes.csv Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9b/027b7c7c3170a1395d667f586add76/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/38/4328b383c01c3cee1513d81df0b07d/output/Reports/Demultiplex_Stats.csv Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/38/4328b383c01c3cee1513d81df0b07d/output/Reports/Top_Unknown_Barcodes.csv Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d7/5418e87bf4204107683ccca95a5e98/output/Reports/Top_Unknown_Barcodes.csv Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9b/027b7c7c3170a1395d667f586add76/.command.run Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/21/86594e8df030ec1333e6ac02d4e24b/output/Reports/Demultiplex_Stats.csv Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/52/bb2c0a74896dcc763c7a3539d18407/output/Reports/Demultiplex_Stats.csv Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/54/f952a746ed41165c6626d70cdcd334/output/Reports/Top_Unknown_Barcodes.csv Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f3/7f0a48d7570689412f68ab8e48090f/output/Reports/Top_Unknown_Barcodes.csv ==> STAGING COMPLETE (18 inputs) Analyzing demux output from: merged Loading Demultiplex_Stats.csv from: merged/Reports/Demultiplex_Stats.csv Loaded 392 rows from Demultiplex_Stats.csv ================================================================================ 1. % UNDETERMINED PER LANE ================================================================================ Undetermined Summary per Lane: %_Undetermined Undetermined_Reads Total_Reads Lane 1 4.66 201657180 4327821958 2 4.76 204854255 4304734692 3 4.83 209169038 4332980005 4 5.02 214139561 4267817260 5 5.28 224463395 4250454746 6 5.31 224448301 4229151809 7 5.32 227677607 4276187445 8 5.55 234654678 4228210849 ================================================================================ 2. SAMPLES WITH <1000000 READS (NON-NTC) ================================================================================ No samples found with <1000000 reads ================================================================================ 3. NTC SAMPLES WITH >2000000 READS ================================================================================ Found 2 NTC samples with >2000000 reads: SampleID Index # Reads 0 NTC_0001_0001_23KKJ7LT4_1 AGGCAATCGC-ATGAGTCTGT 6189071 1 NTC_0001_0001_23KKJ7LT4_2 GCATCCTACT-GACATCGCGA 5082195 ================================================================================ 4. TOP UNKNOWN BARCODES (>0.05% OF LANE READS) ================================================================================ Loading Top_Unknown_Barcodes.csv from: merged/Reports/Top_Unknown_Barcodes.csv Lane 1 - Found 14 barcodes with >0.05% of lane reads: index index2 # Reads Percentage_of_Lane Percentage_of_Total 7001 CCAGTGCACT GGGGGGGGGG 17071524 0.3945 0.0499 7002 TTGGATTGTC GGGGGGGGGG 9450316 0.2184 0.0276 7003 AATTGGCACA GGGGGGGGGG 6591205 0.1523 0.0193 7004 TGCAACACTA GGGGGGGGGG 6052821 0.1399 0.0177 7005 TCGCATGACA GGGGGGGGGG 4657991 0.1076 0.0136 7006 GAAGCAAGCG GGGGGGGGGG 4287288 0.0991 0.0125 7007 ACAATAGCAC GGGGGGGGGG 3821687 0.0883 0.0112 7008 CCACCTGCTT GGGGGGGGGG 3593237 0.0830 0.0105 7009 GTACGCATCG GGGGGGGGGG 3517495 0.0813 0.0103 7010 CGTACTTAGA GGGGGGGGGG 3034993 0.0701 0.0089 7011 GATCTGTATG GGGGGGGGGG 2345695 0.0542 0.0069 7012 TTACGGACGC GGGGGGGGGG 2312243 0.0534 0.0068 7013 ACTTCCGTTC GGGGGGGGGG 2254874 0.0521 0.0066 7014 CATCAGGCGT GGGGGGGGGG 2216465 0.0512 0.0065 Lane 2 - Found 15 barcodes with >0.05% of lane reads: index index2 # Reads Percentage_of_Lane Percentage_of_Total 1000 CCAGTGCACT GGGGGGGGGG 15691485 0.3645 0.0459 1001 TTGGATTGTC GGGGGGGGGG 8798536 0.2044 0.0257 1002 AATTGGCACA GGGGGGGGGG 6256110 0.1453 0.0183 1003 TGCAACACTA GGGGGGGGGG 5828771 0.1354 0.0170 1004 TCGCATGACA GGGGGGGGGG 4772549 0.1109 0.0139 1005 GAAGCAAGCG GGGGGGGGGG 3884918 0.0902 0.0114 1006 ACAATAGCAC GGGGGGGGGG 3704982 0.0861 0.0108 1007 CCACCTGCTT GGGGGGGGGG 3698399 0.0859 0.0108 1008 GTACGCATCG GGGGGGGGGG 3399116 0.0790 0.0099 1009 CGTACTTAGA GGGGGGGGGG 2858804 0.0664 0.0084 1010 GATCTGTATG GGGGGGGGGG 2495807 0.0580 0.0073 1011 TTACGGACGC GGGGGGGGGG 2429654 0.0564 0.0071 1012 ACTTCCGTTC GGGGGGGGGG 2324597 0.0540 0.0068 1013 AGTACAACTG GGGGGGGGGG 2252124 0.0523 0.0066 1014 CTACAAGTTC GGGGGGGGGG 2158134 0.0501 0.0063 Lane 3 - Found 15 barcodes with >0.05% of lane reads: index index2 # Reads Percentage_of_Lane Percentage_of_Total 6001 CCAGTGCACT GGGGGGGGGG 15180901 0.3504 0.0444 6002 TTGGATTGTC GGGGGGGGGG 8574303 0.1979 0.0251 6003 AATTGGCACA GGGGGGGGGG 6180787 0.1426 0.0181 6004 TGCAACACTA GGGGGGGGGG 5881459 0.1357 0.0172 6005 TCGCATGACA GGGGGGGGGG 4950297 0.1142 0.0145 6006 GAAGCAAGCG GGGGGGGGGG 3987420 0.0920 0.0117 6007 CCACCTGCTT GGGGGGGGGG 3890082 0.0898 0.0114 6008 ACAATAGCAC GGGGGGGGGG 3790102 0.0875 0.0111 6009 GTACGCATCG GGGGGGGGGG 3531683 0.0815 0.0103 6010 CGTACTTAGA GGGGGGGGGG 3094222 0.0714 0.0090 6011 GATCTGTATG GGGGGGGGGG 2591359 0.0598 0.0076 6012 TTACGGACGC GGGGGGGGGG 2511405 0.0580 0.0073 6013 ACTTCCGTTC GGGGGGGGGG 2445214 0.0564 0.0071 6014 AGTACAACTG GGGGGGGGGG 2394711 0.0553 0.0070 6015 CTACAAGTTC GGGGGGGGGG 2273212 0.0525 0.0066 Lane 4 - Found 18 barcodes with >0.05% of lane reads: index index2 # Reads Percentage_of_Lane Percentage_of_Total 3000 CCAGTGCACT GGGGGGGGGG 14615746 0.3425 0.0427 3001 TTGGATTGTC GGGGGGGGGG 8311691 0.1948 0.0243 3002 AATTGGCACA GGGGGGGGGG 6220867 0.1458 0.0182 3003 TGCAACACTA GGGGGGGGGG 6095722 0.1428 0.0178 3004 TCGCATGACA GGGGGGGGGG 5016570 0.1175 0.0147 3005 GAAGCAAGCG GGGGGGGGGG 4337469 0.1016 0.0127 3006 CCACCTGCTT GGGGGGGGGG 4094555 0.0959 0.0120 3007 ACAATAGCAC GGGGGGGGGG 3829519 0.0897 0.0112 3008 GTACGCATCG GGGGGGGGGG 3712787 0.0870 0.0109 3009 CGTACTTAGA GGGGGGGGGG 3433570 0.0805 0.0100 3010 GATCTGTATG GGGGGGGGGG 2995399 0.0702 0.0088 3011 ACTTCCGTTC GGGGGGGGGG 2723886 0.0638 0.0080 3012 TTACGGACGC GGGGGGGGGG 2714440 0.0636 0.0079 3013 AGTACAACTG GGGGGGGGGG 2664015 0.0624 0.0078 3014 CTACAAGTTC GGGGGGGGGG 2471397 0.0579 0.0072 3015 ATAGGCAGTG GGGGGGGGGG 2264720 0.0531 0.0066 3016 TCAATCTAGC GGGGGGGGGG 2260632 0.0530 0.0066 3017 GATGCTAGAA GGGGGGGGGG 2210396 0.0518 0.0065 Lane 5 - Found 19 barcodes with >0.05% of lane reads: index index2 # Reads Percentage_of_Lane Percentage_of_Total 2000 CTCACCAGTT GGGGGGGGGG 9482600 0.2231 0.0277 2001 AATAGACTGC GGGGGGGGGG 8739035 0.2056 0.0255 2002 TAGAAGATCG GGGGGGGGGG 7612531 0.1791 0.0222 2003 AGTCCAGCGT GGGGGGGGGG 7336649 0.1726 0.0214 2004 AGGACGGACA GGGGGGGGGG 7140315 0.1680 0.0209 2005 CGGCATATAC GGGGGGGGGG 4696827 0.1105 0.0137 2006 CAACGTTGAC GGGGGGGGGG 4332297 0.1019 0.0127 2007 CATCACCTAA GGGGGGGGGG 3703435 0.0871 0.0108 2008 CCTGGAATTA GGGGGGGGGG 3293110 0.0775 0.0096 2009 ACGGTCGCAT CGTCATCGAA 3259393 0.0767 0.0095 2010 CCTATGTGTA GGGGGGGGGG 3118628 0.0734 0.0091 2011 GCGCGGTTAA GGGGGGGGGG 2969540 0.0699 0.0087 2012 GCGAAGTAGG CAGGCCATGT 2885608 0.0679 0.0084 2013 GCGACTCGTA GGGGGGGGGG 2876524 0.0677 0.0084 2014 GCGCGGTTAA GTACTCTCTA 2851901 0.0671 0.0083 2015 GCGATGGAAG GGGGGGGGGG 2763468 0.0650 0.0081 2016 ACGGTCGCAT AAGCTATAGC 2747653 0.0646 0.0080 2017 CACGAGTGTC GGGGGGGGGG 2679571 0.0630 0.0078 2018 ACAGAGGCGT GGGGGGGGGG 2389090 0.0562 0.0070 Lane 6 - Found 19 barcodes with >0.05% of lane reads: index index2 # Reads Percentage_of_Lane Percentage_of_Total 5000 CTCACCAGTT GGGGGGGGGG 9976890 0.2359 0.0292 5001 AATAGACTGC GGGGGGGGGG 8859001 0.2095 0.0259 5002 TAGAAGATCG GGGGGGGGGG 8279894 0.1958 0.0242 5003 AGTCCAGCGT GGGGGGGGGG 7888127 0.1865 0.0231 5004 AGGACGGACA GGGGGGGGGG 7882113 0.1864 0.0230 5005 CGGCATATAC GGGGGGGGGG 4700725 0.1112 0.0137 5006 CAACGTTGAC GGGGGGGGGG 4295625 0.1016 0.0126 5007 CATCACCTAA GGGGGGGGGG 3757044 0.0888 0.0110 5008 CCTGGAATTA GGGGGGGGGG 3345085 0.0791 0.0098 5009 ACGGTCGCAT CGTCATCGAA 3322547 0.0786 0.0097 5010 CCTATGTGTA GGGGGGGGGG 2908761 0.0688 0.0085 5011 GCGACTCGTA GGGGGGGGGG 2862085 0.0677 0.0084 5012 GCGCGGTTAA GTACTCTCTA 2842978 0.0672 0.0083 5013 GCGCGGTTAA GGGGGGGGGG 2832696 0.0670 0.0083 5014 GCGAAGTAGG CAGGCCATGT 2827767 0.0669 0.0083 5015 ACGGTCGCAT AAGCTATAGC 2787528 0.0659 0.0081 5016 GCGATGGAAG GGGGGGGGGG 2677435 0.0633 0.0078 5017 CACGAGTGTC GGGGGGGGGG 2521842 0.0596 0.0074 5018 ACAGAGGCGT GGGGGGGGGG 2308460 0.0546 0.0067 Lane 7 - Found 19 barcodes with >0.05% of lane reads: index index2 # Reads Percentage_of_Lane Percentage_of_Total 4000 CTCACCAGTT GGGGGGGGGG 10273297 0.2402 0.0300 4001 AATAGACTGC GGGGGGGGGG 9223699 0.2157 0.0270 4002 TAGAAGATCG GGGGGGGGGG 8675847 0.2029 0.0254 4003 AGTCCAGCGT GGGGGGGGGG 8261550 0.1932 0.0241 4004 AGGACGGACA GGGGGGGGGG 8058779 0.1885 0.0236 4005 CGGCATATAC GGGGGGGGGG 4766496 0.1115 0.0139 4006 CAACGTTGAC GGGGGGGGGG 4356298 0.1019 0.0127 4007 CATCACCTAA GGGGGGGGGG 3820382 0.0893 0.0112 4008 CCTGGAATTA GGGGGGGGGG 3541234 0.0828 0.0103 4009 ACGGTCGCAT CGTCATCGAA 3349088 0.0783 0.0098 4010 GCGACTCGTA GGGGGGGGGG 2970326 0.0695 0.0087 4011 GCGCGGTTAA GGGGGGGGGG 2955530 0.0691 0.0086 4012 CCTATGTGTA GGGGGGGGGG 2933578 0.0686 0.0086 4013 GCGCGGTTAA GTACTCTCTA 2868979 0.0671 0.0084 4014 GCGAAGTAGG CAGGCCATGT 2868818 0.0671 0.0084 4015 GCGATGGAAG GGGGGGGGGG 2862104 0.0669 0.0084 4016 ACGGTCGCAT AAGCTATAGC 2806545 0.0656 0.0082 4017 CACGAGTGTC GGGGGGGGGG 2614985 0.0612 0.0076 4018 ACAGAGGCGT GGGGGGGGGG 2326372 0.0544 0.0068 Lane 8 - Found 19 barcodes with >0.05% of lane reads: index index2 # Reads Percentage_of_Lane Percentage_of_Total 0 CTCACCAGTT GGGGGGGGGG 10762895 0.2545 0.0315 1 AATAGACTGC GGGGGGGGGG 10077705 0.2383 0.0295 2 TAGAAGATCG GGGGGGGGGG 9043631 0.2139 0.0264 3 AGTCCAGCGT GGGGGGGGGG 8606056 0.2035 0.0252 4 AGGACGGACA GGGGGGGGGG 8248868 0.1951 0.0241 5 CGGCATATAC GGGGGGGGGG 4920299 0.1164 0.0144 6 CAACGTTGAC GGGGGGGGGG 4651706 0.1100 0.0136 7 CATCACCTAA GGGGGGGGGG 4109300 0.0972 0.0120 8 CCTGGAATTA GGGGGGGGGG 3652859 0.0864 0.0107 9 ACGGTCGCAT CGTCATCGAA 3290300 0.0778 0.0096 10 CCTATGTGTA GGGGGGGGGG 3157234 0.0747 0.0092 11 GCGACTCGTA GGGGGGGGGG 3068052 0.0726 0.0090 12 GCGCGGTTAA GGGGGGGGGG 3047624 0.0721 0.0089 13 GCGATGGAAG GGGGGGGGGG 2975291 0.0704 0.0087 14 GCGCGGTTAA GTACTCTCTA 2835885 0.0671 0.0083 15 GCGAAGTAGG CAGGCCATGT 2832434 0.0670 0.0083 16 ACGGTCGCAT AAGCTATAGC 2752574 0.0651 0.0080 17 CACGAGTGTC GGGGGGGGGG 2728874 0.0645 0.0080 18 ACAGAGGCGT GGGGGGGGGG 2403712 0.0568 0.0070 ================================================================================ 5. BARCODES WITH HIGH MISMATCH RATES ================================================================================ No barcodes found with >20.0% mismatch rate ================================================================================ FINAL STATUS CHECK ================================================================================ Overall % Undetermined: 5.09% Status: 🔴 FAIL Reason(s): Overall undetermined 5.09% >= 5.0% NTC sample NTC_0001_0001_23KKJ7LT4_1 has 6,189,071 reads > 2,000,000 NTC sample NTC_0001_0001_23KKJ7LT4_2 has 5,082,195 reads > 2,000,000 Thresholds: <5.0% = PASS, 5.0-10.0% = WARNING, >10.0% = FAIL NTC gate: >2,000,000 reads = FAIL === Creating reports in . === QC summary saved to: ./qc_report.csv Detailed QC report saved to: ./qc_report_detailed.txt Fail file created: ./samplesheet_status.fail ================================================================================ QC SUMMARY ================================================================================ Metric Value Total_Reads 34217358764 Total_Samples_Analyzed 97 Number_of_Lanes 8 Global_Percent_Undetermined 5.09% Lanes_Exceeding_Fail_Threshold None Samples_with_Low_Reads 0 NTC_Samples_with_High_Reads 2 Significant_Unknown_Barcodes 138 High_Mismatch_Barcodes 0 Final_Status FAIL ================================================================================ QC Analysis completed successfully! Flowcell Status: FAIL Reports generated: - ./qc_report.csv - ./qc_report_detailed.txt - ./samplesheet_status.fail ================================================================================