Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/22/2f505000e63dd433392448dd2be15e/output/Reports/Demultiplex_Stats.csv Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b2/86ac2d4c08fe04ac76ae64862384fe/output/Reports/Demultiplex_Stats.csv Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9f/d4b6ded03ac588f4eef476047b95b7/output/Reports/Top_Unknown_Barcodes.csv Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e3/26aee8f5b70ad55c1e86d31729c8ef/output/Reports/Top_Unknown_Barcodes.csv Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0b/83897806aa184cda898f58e2bb4de5/output/Reports/Demultiplex_Stats.csv Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9f/d4b6ded03ac588f4eef476047b95b7/output/Reports/Demultiplex_Stats.csv Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2b/98ae5f3d58c012b6cc34893b6e1f7b/output/Reports/Top_Unknown_Barcodes.csv Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f5/3551e479dcb8cccf231b019a09a639/output/Reports/Demultiplex_Stats.csv Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/22/2f505000e63dd433392448dd2be15e/output/Reports/Top_Unknown_Barcodes.csv Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2e/521c0c9b251f6a8822e18c4a4a85a8/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/76/a84f795908538c7918b7dc4787c102/output/Reports/Demultiplex_Stats.csv Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/76/a84f795908538c7918b7dc4787c102/output/Reports/Top_Unknown_Barcodes.csv Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0b/83897806aa184cda898f58e2bb4de5/output/Reports/Top_Unknown_Barcodes.csv Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2e/521c0c9b251f6a8822e18c4a4a85a8/.command.run Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e3/26aee8f5b70ad55c1e86d31729c8ef/output/Reports/Demultiplex_Stats.csv Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2b/98ae5f3d58c012b6cc34893b6e1f7b/output/Reports/Demultiplex_Stats.csv Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b2/86ac2d4c08fe04ac76ae64862384fe/output/Reports/Top_Unknown_Barcodes.csv Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f5/3551e479dcb8cccf231b019a09a639/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 5.52 221059769 4004297187 2 5.90 225513465 3822265332 3 5.35 200487374 3746919997 4 5.32 200329565 3768247701 5 4.74 171826374 3628757465 6 4.75 184145712 3874163237 7 4.94 190151678 3850667784 8 5.09 202217613 3974555505 ================================================================================ 2. SAMPLES WITH <1000000 READS (NON-NTC) ================================================================================ No samples found with <1000000 reads ================================================================================ 3. NTC SAMPLES WITH >2000000 READS ================================================================================ Found 1 NTC samples with >2000000 reads: SampleID Index # Reads 0 NTC_0001_0001_23KMKGLT4_1 GATCTGTATG-ATCGAAGAGC 3096639 ================================================================================ 4. TOP UNKNOWN BARCODES (>0.05% OF LANE READS) ================================================================================ Loading Top_Unknown_Barcodes.csv from: merged/Reports/Top_Unknown_Barcodes.csv Lane 1 - Found 23 barcodes with >0.05% of lane reads: index index2 # Reads Percentage_of_Lane Percentage_of_Total 4001 CTCACCAGTT GGGGGGGGGG 8458630 0.2112 0.0276 4002 TAGAAGATCG GGGGGGGGGG 7394299 0.1847 0.0241 4003 AGTCCAGCGT GGGGGGGGGG 7306092 0.1825 0.0238 4004 AATAGACTGC GGGGGGGGGG 5668678 0.1416 0.0185 4005 AGGACGGACA GGGGGGGGGG 4620766 0.1154 0.0151 4006 GCGAAGTAGG CAGGCCATGT 4572171 0.1142 0.0149 4007 CATCACCTAA GGGGGGGGGG 4463209 0.1115 0.0146 4008 ACGGTCGCAT CGTCATCGAA 4368466 0.1091 0.0142 4009 CCTGGAATTA GGGGGGGGGG 3811715 0.0952 0.0124 4010 CGGCATATAC GGGGGGGGGG 3713173 0.0927 0.0121 4011 GCGACTCGTA ACCATTGTGT 3307477 0.0826 0.0108 4012 GCGACTCGTA GGGGGGGGGG 3287995 0.0821 0.0107 4013 CAACGTTGAC GGGGGGGGGG 3189964 0.0797 0.0104 4014 ATGATCAACG GGGGGGGGGG 3151810 0.0787 0.0103 4015 AGGCAGCCAT GGGGGGGGGG 3149692 0.0787 0.0103 4016 TGTTACAGAG CGTCATCGAA 2979753 0.0744 0.0097 4017 ACGGTCGCAT AAGCTATAGC 2870719 0.0717 0.0094 4018 GCGCGGTTAA GGGGGGGGGG 2790916 0.0697 0.0091 4019 TTCAGATCCA GGGGGGGGGG 2789274 0.0697 0.0091 4020 GCGCGGTTAA GTACTCTCTA 2722580 0.0680 0.0089 4021 CCTATGTGTA GGGGGGGGGG 2607642 0.0651 0.0085 4022 CCTGGAATTA TGTGTACCAG 2290216 0.0572 0.0075 4023 CCTGGAATTA GTACTCTCTA 2016250 0.0504 0.0066 Lane 2 - Found 22 barcodes with >0.05% of lane reads: index index2 # Reads Percentage_of_Lane Percentage_of_Total 5001 CTCACCAGTT GGGGGGGGGG 6725259 0.1759 0.0219 5002 AGTCCAGCGT GGGGGGGGGG 5750923 0.1505 0.0188 5003 TAGAAGATCG GGGGGGGGGG 5489139 0.1436 0.0179 5004 AATAGACTGC GGGGGGGGGG 4332307 0.1133 0.0141 5005 GCGAAGTAGG CAGGCCATGT 4076991 0.1067 0.0133 5006 ACGGTCGCAT CGTCATCGAA 3904348 0.1021 0.0127 5007 CATCACCTAA GGGGGGGGGG 3517635 0.0920 0.0115 5008 AGGACGGACA GGGGGGGGGG 3494155 0.0914 0.0114 5009 CCTGGAATTA GGGGGGGGGG 3012663 0.0788 0.0098 5010 CGGCATATAC GGGGGGGGGG 2945794 0.0771 0.0096 5011 GCGACTCGTA ACCATTGTGT 2944708 0.0770 0.0096 5012 TGTTACAGAG CGTCATCGAA 2654226 0.0694 0.0087 5013 ACGGTCGCAT AAGCTATAGC 2577659 0.0674 0.0084 5014 CAACGTTGAC GGGGGGGGGG 2488362 0.0651 0.0081 5015 AGGCAGCCAT GGGGGGGGGG 2463579 0.0645 0.0080 5016 GCGACTCGTA GGGGGGGGGG 2438677 0.0638 0.0080 5017 GCGCGGTTAA GTACTCTCTA 2432896 0.0637 0.0079 5018 ATGATCAACG GGGGGGGGGG 2432085 0.0636 0.0079 5019 TTCAGATCCA GGGGGGGGGG 2168461 0.0567 0.0071 5020 GCGCGGTTAA GGGGGGGGGG 2101575 0.0550 0.0069 5021 CCTATGTGTA GGGGGGGGGG 2076137 0.0543 0.0068 5022 CCTGGAATTA TGTGTACCAG 2056470 0.0538 0.0067 Lane 3 - Found 22 barcodes with >0.05% of lane reads: index index2 # Reads Percentage_of_Lane Percentage_of_Total 1001 CTCACCAGTT GGGGGGGGGG 6353099 0.1696 0.0207 1002 AGTCCAGCGT GGGGGGGGGG 5195636 0.1387 0.0169 1003 TAGAAGATCG GGGGGGGGGG 4880808 0.1303 0.0159 1004 GCGAAGTAGG CAGGCCATGT 4151455 0.1108 0.0135 1005 AATAGACTGC GGGGGGGGGG 4031237 0.1076 0.0131 1006 ACGGTCGCAT CGTCATCGAA 3987944 0.1064 0.0130 1007 CATCACCTAA GGGGGGGGGG 3349193 0.0894 0.0109 1008 AGGACGGACA GGGGGGGGGG 3196524 0.0853 0.0104 1009 GCGACTCGTA ACCATTGTGT 3006908 0.0803 0.0098 1010 CGGCATATAC GGGGGGGGGG 2881372 0.0769 0.0094 1011 CCTGGAATTA GGGGGGGGGG 2827073 0.0755 0.0092 1012 TGTTACAGAG CGTCATCGAA 2704405 0.0722 0.0088 1013 ACGGTCGCAT AAGCTATAGC 2627111 0.0701 0.0086 1014 GCGCGGTTAA GTACTCTCTA 2496230 0.0666 0.0081 1015 AGGCAGCCAT GGGGGGGGGG 2457459 0.0656 0.0080 1016 CAACGTTGAC GGGGGGGGGG 2412657 0.0644 0.0079 1017 ATGATCAACG GGGGGGGGGG 2345782 0.0626 0.0076 1018 GCGACTCGTA GGGGGGGGGG 2318844 0.0619 0.0076 1019 CCTATGTGTA GGGGGGGGGG 2111070 0.0563 0.0069 1020 TTCAGATCCA GGGGGGGGGG 2107300 0.0562 0.0069 1021 CCTGGAATTA TGTGTACCAG 2081886 0.0556 0.0068 1022 GCGCGGTTAA GGGGGGGGGG 2033531 0.0543 0.0066 Lane 4 - Found 23 barcodes with >0.05% of lane reads: index index2 # Reads Percentage_of_Lane Percentage_of_Total 6001 CTCACCAGTT GGGGGGGGGG 6049099 0.1605 0.0197 6002 AGTCCAGCGT GGGGGGGGGG 4946219 0.1313 0.0161 6003 TAGAAGATCG GGGGGGGGGG 4612384 0.1224 0.0150 6004 GCGAAGTAGG CAGGCCATGT 4281644 0.1136 0.0140 6005 ACGGTCGCAT CGTCATCGAA 4068746 0.1080 0.0133 6006 AATAGACTGC GGGGGGGGGG 3800972 0.1009 0.0124 6007 CATCACCTAA GGGGGGGGGG 3251052 0.0863 0.0106 6008 GCGACTCGTA ACCATTGTGT 3071285 0.0815 0.0100 6009 AGGACGGACA GGGGGGGGGG 3021813 0.0802 0.0099 6010 CGGCATATAC GGGGGGGGGG 2816660 0.0747 0.0092 6011 TGTTACAGAG CGTCATCGAA 2757669 0.0732 0.0090 6012 CCTGGAATTA GGGGGGGGGG 2725624 0.0723 0.0089 6013 ACGGTCGCAT AAGCTATAGC 2687520 0.0713 0.0088 6014 GCGCGGTTAA GTACTCTCTA 2562849 0.0680 0.0084 6015 AGGCAGCCAT GGGGGGGGGG 2398519 0.0637 0.0078 6016 CAACGTTGAC GGGGGGGGGG 2344071 0.0622 0.0076 6017 ATGATCAACG GGGGGGGGGG 2256026 0.0599 0.0074 6018 GCGACTCGTA GGGGGGGGGG 2234566 0.0593 0.0073 6019 CCTGGAATTA TGTGTACCAG 2126765 0.0564 0.0069 6020 CCTATGTGTA GGGGGGGGGG 2114862 0.0561 0.0069 6021 TTCAGATCCA GGGGGGGGGG 2042821 0.0542 0.0067 6022 GCGCGGTTAA GGGGGGGGGG 1980505 0.0526 0.0065 6023 CCTGGAATTA GTACTCTCTA 1892375 0.0502 0.0062 Lane 5 - Found 9 barcodes with >0.05% of lane reads: index index2 # Reads Percentage_of_Lane Percentage_of_Total 0 CCAGTGCACT GGGGGGGGGG 8539896 0.2353 0.0278 1 TTGGATTGTC GGGGGGGGGG 4910547 0.1353 0.0160 2 CATCAGGCGT GGGGGGGGGG 4439230 0.1223 0.0145 3 ACAATAGCAC GGGGGGGGGG 3094884 0.0853 0.0101 4 AATTGGCACA GGGGGGGGGG 2733163 0.0753 0.0089 5 GTACGCATCG GGGGGGGGGG 2701236 0.0744 0.0088 6 TGCAACACTA GGGGGGGGGG 2660121 0.0733 0.0087 7 GAAGCAAGCG GGGGGGGGGG 1876059 0.0517 0.0061 8 CCACCTGCTT GGGGGGGGGG 1827986 0.0504 0.0060 Lane 6 - Found 10 barcodes with >0.05% of lane reads: index index2 # Reads Percentage_of_Lane Percentage_of_Total 2001 CCAGTGCACT GGGGGGGGGG 11955380 0.3086 0.0390 2002 TTGGATTGTC GGGGGGGGGG 6822504 0.1761 0.0222 2003 CATCAGGCGT GGGGGGGGGG 6072888 0.1568 0.0198 2004 ACAATAGCAC GGGGGGGGGG 4081883 0.1054 0.0133 2005 AATTGGCACA GGGGGGGGGG 3718466 0.0960 0.0121 2006 GTACGCATCG GGGGGGGGGG 3573840 0.0922 0.0117 2007 TGCAACACTA GGGGGGGGGG 3383154 0.0873 0.0110 2008 GAAGCAAGCG GGGGGGGGGG 2685584 0.0693 0.0088 2009 CCACCTGCTT GGGGGGGGGG 2217437 0.0572 0.0072 2010 TCGCATGACA GGGGGGGGGG 2075737 0.0536 0.0068 Lane 7 - Found 11 barcodes with >0.05% of lane reads: index index2 # Reads Percentage_of_Lane Percentage_of_Total 3001 CCAGTGCACT GGGGGGGGGG 12520817 0.3252 0.0408 3002 TTGGATTGTC GGGGGGGGGG 7190619 0.1867 0.0234 3003 CATCAGGCGT GGGGGGGGGG 6398853 0.1662 0.0209 3004 ACAATAGCAC GGGGGGGGGG 4262477 0.1107 0.0139 3005 AATTGGCACA GGGGGGGGGG 3935036 0.1022 0.0128 3006 GTACGCATCG GGGGGGGGGG 3781413 0.0982 0.0123 3007 TGCAACACTA GGGGGGGGGG 3522018 0.0915 0.0115 3008 GAAGCAAGCG GGGGGGGGGG 2870324 0.0745 0.0094 3009 CCACCTGCTT GGGGGGGGGG 2310566 0.0600 0.0075 3010 TCGCATGACA GGGGGGGGGG 2172931 0.0564 0.0071 3011 AGTACAACTG GGGGGGGGGG 1973818 0.0513 0.0064 Lane 8 - Found 12 barcodes with >0.05% of lane reads: index index2 # Reads Percentage_of_Lane Percentage_of_Total 7001 CCAGTGCACT GGGGGGGGGG 13808902 0.3474 0.0450 7002 TTGGATTGTC GGGGGGGGGG 8055516 0.2027 0.0263 7003 CATCAGGCGT GGGGGGGGGG 7292412 0.1835 0.0238 7004 ACAATAGCAC GGGGGGGGGG 4755613 0.1197 0.0155 7005 AATTGGCACA GGGGGGGGGG 4462422 0.1123 0.0145 7006 GTACGCATCG GGGGGGGGGG 4370742 0.1100 0.0143 7007 TGCAACACTA GGGGGGGGGG 3938302 0.0991 0.0128 7008 GAAGCAAGCG GGGGGGGGGG 3465446 0.0872 0.0113 7009 CCACCTGCTT GGGGGGGGGG 2611613 0.0657 0.0085 7010 TCGCATGACA GGGGGGGGGG 2436248 0.0613 0.0079 7011 AGTACAACTG GGGGGGGGGG 2300837 0.0579 0.0075 7012 GCCGTGAACA GGGGGGGGGG 2057642 0.0518 0.0067 ================================================================================ 5. BARCODES WITH HIGH MISMATCH RATES ================================================================================ No barcodes found with >20.0% mismatch rate ================================================================================ FINAL STATUS CHECK ================================================================================ Overall % Undetermined: 5.20% Status: 🔴 FAIL Reason(s): Overall undetermined 5.20% >= 5.0% NTC sample NTC_0001_0001_23KMKGLT4_1 has 3,096,639 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 30669874208 Total_Samples_Analyzed 97 Number_of_Lanes 8 Global_Percent_Undetermined 5.20% Lanes_Exceeding_Fail_Threshold None Samples_with_Low_Reads 0 NTC_Samples_with_High_Reads 1 Significant_Unknown_Barcodes 132 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 ================================================================================