Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7f/6687d52650339cb1c94ae8b41b3dd9/output/Reports/Demultiplex_Stats.csv Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c4/8b7f9d07e68f27df7b12ae7350cade/output/Reports/Demultiplex_Stats.csv Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9d/ce78f9f8193f9ecab120d2b7e794eb/output/Reports/Top_Unknown_Barcodes.csv Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/30/ef24e3f720f913318492730b2a67af/output/Reports/Top_Unknown_Barcodes.csv Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d6/b6f145d94963c0ee1016fe19b8a489/output/Reports/Demultiplex_Stats.csv Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a6/4a29eaa1e088963c9238fb1e53496d/output/Reports/Top_Unknown_Barcodes.csv Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9d/ce78f9f8193f9ecab120d2b7e794eb/output/Reports/Demultiplex_Stats.csv Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1a/7f5a6546d30c77cd88d39bbf82f441/output/Reports/Demultiplex_Stats.csv Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7f/6687d52650339cb1c94ae8b41b3dd9/output/Reports/Top_Unknown_Barcodes.csv Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e1/af6bff549163c72f8635b35ec794ec/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2c/312e06c0766ce417359ddc3aff9a95/output/Reports/Demultiplex_Stats.csv Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2c/312e06c0766ce417359ddc3aff9a95/output/Reports/Top_Unknown_Barcodes.csv Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d6/b6f145d94963c0ee1016fe19b8a489/output/Reports/Top_Unknown_Barcodes.csv Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e1/af6bff549163c72f8635b35ec794ec/.command.run Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/30/ef24e3f720f913318492730b2a67af/output/Reports/Demultiplex_Stats.csv Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a6/4a29eaa1e088963c9238fb1e53496d/output/Reports/Demultiplex_Stats.csv Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c4/8b7f9d07e68f27df7b12ae7350cade/output/Reports/Top_Unknown_Barcodes.csv Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1a/7f5a6546d30c77cd88d39bbf82f441/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 6.12 250334217 4090325735 2 7.00 285165933 4074910534 3 6.21 253916096 4088175087 4 6.11 248089917 4059169203 5 6.55 268356261 4095544764 6 6.47 265289440 4099623814 7 6.78 278776905 4109400122 8 6.76 279032115 4129288043 ================================================================================ 2. SAMPLES WITH <1000000 READS (NON-NTC) ================================================================================ No samples found with <1000000 reads ================================================================================ 3. NTC SAMPLES WITH >2000000 READS ================================================================================ No NTC samples found with >2000000 reads ================================================================================ 4. TOP UNKNOWN BARCODES (>0.05% OF LANE READS) ================================================================================ Loading Top_Unknown_Barcodes.csv from: merged/Reports/Top_Unknown_Barcodes.csv Lane 1 - Found 17 barcodes with >0.05% of lane reads: index index2 # Reads Percentage_of_Lane Percentage_of_Total 4000 AGCCTCTGCT GGGGGGGGGG 15462051 0.3780 0.0472 4001 GCATTCCTTC GGGGGGGGGG 6799376 0.1662 0.0208 4002 GCAGAAGTCT GGGGGGGGGG 6410016 0.1567 0.0196 4003 GATAGATCAG GGGGGGGGGG 6303578 0.1541 0.0192 4004 TCACCGTGGT GGGGGGGGGG 5979060 0.1462 0.0183 4005 CGGATCATTA GGGGGGGGGG 4890689 0.1196 0.0149 4006 TGTGATCGCG GGGGGGGGGG 4725038 0.1155 0.0144 4007 GATTCTTAGC GGGGGGGGGG 4442279 0.1086 0.0136 4008 AGCACCAGTC GGGGGGGGGG 3933604 0.0962 0.0120 4009 GCGACAATAT GGGGGGGGGG 3606282 0.0882 0.0110 4010 ATCGAGAGAC GGGGGGGGGG 3575489 0.0874 0.0109 4011 CTAGACGAGC GGGGGGGGGG 3425352 0.0837 0.0105 4012 CCACTCAACG GGGGGGGGGG 2883641 0.0705 0.0088 4013 GCGAAGAATT GGGGGGGGGG 2872728 0.0702 0.0088 4014 GTGTTCCTTC GAGCCTGCTT 2779782 0.0680 0.0085 4015 ATCTAACCTG GGGGGGGGGG 2283440 0.0558 0.0070 4016 CAACTACCGC GGGGGGGGGG 2195123 0.0537 0.0067 Lane 2 - Found 16 barcodes with >0.05% of lane reads: index index2 # Reads Percentage_of_Lane Percentage_of_Total 7000 AGCCTCTGCT GGGGGGGGGG 13801734 0.3387 0.0421 7001 GCATTCCTTC GGGGGGGGGG 6088094 0.1494 0.0186 7002 GATAGATCAG GGGGGGGGGG 5722551 0.1404 0.0175 7003 GCAGAAGTCT GGGGGGGGGG 5716443 0.1403 0.0175 7004 TCACCGTGGT GGGGGGGGGG 5433855 0.1333 0.0166 7005 CGGATCATTA GGGGGGGGGG 4351064 0.1068 0.0133 7006 TGTGATCGCG GGGGGGGGGG 4190213 0.1028 0.0128 7007 GATTCTTAGC GGGGGGGGGG 4160605 0.1021 0.0127 7008 GCGACAATAT GGGGGGGGGG 3629263 0.0891 0.0111 7009 AGCACCAGTC GGGGGGGGGG 3615647 0.0887 0.0110 7010 ATCGAGAGAC GGGGGGGGGG 3338464 0.0819 0.0102 7011 CTAGACGAGC GGGGGGGGGG 3281278 0.0805 0.0100 7012 GCGAAGAATT GGGGGGGGGG 2703105 0.0663 0.0083 7013 CCACTCAACG GGGGGGGGGG 2671012 0.0655 0.0082 7014 GTGTTCCTTC GAGCCTGCTT 2654142 0.0651 0.0081 7015 ATCTAACCTG GGGGGGGGGG 2143704 0.0526 0.0065 Lane 3 - Found 20 barcodes with >0.05% of lane reads: index index2 # Reads Percentage_of_Lane Percentage_of_Total 5000 AGCCTCTGCT GGGGGGGGGG 13354033 0.3267 0.0408 5001 GCATTCCTTC GGGGGGGGGG 5879199 0.1438 0.0180 5002 GCAGAAGTCT GGGGGGGGGG 5775924 0.1413 0.0176 5003 GATAGATCAG GGGGGGGGGG 5684881 0.1391 0.0174 5004 TCACCGTGGT GGGGGGGGGG 5241177 0.1282 0.0160 5005 CGGATCATTA GGGGGGGGGG 4394200 0.1075 0.0134 5006 GATTCTTAGC GGGGGGGGGG 4241888 0.1038 0.0130 5007 TGTGATCGCG GGGGGGGGGG 4086498 0.1000 0.0125 5008 GCGACAATAT GGGGGGGGGG 3959008 0.0968 0.0121 5009 AGCACCAGTC GGGGGGGGGG 3720865 0.0910 0.0114 5010 CTAGACGAGC GGGGGGGGGG 3542724 0.0867 0.0108 5011 ATCGAGAGAC GGGGGGGGGG 3431575 0.0839 0.0105 5012 GCGAAGAATT GGGGGGGGGG 3037634 0.0743 0.0093 5013 CCACTCAACG GGGGGGGGGG 2940399 0.0719 0.0090 5014 GTGTTCCTTC GAGCCTGCTT 2835712 0.0694 0.0087 5015 ATCTAACCTG GGGGGGGGGG 2392837 0.0585 0.0073 5016 CGCACATTAC GGGGGGGGGG 2224352 0.0544 0.0068 5017 CAACTACCGC GGGGGGGGGG 2171869 0.0531 0.0066 5018 GATTGGCGAT GGGGGGGGGG 2155948 0.0527 0.0066 5019 GTAATACTCG GGGGGGGGGG 2052798 0.0502 0.0063 Lane 4 - Found 19 barcodes with >0.05% of lane reads: index index2 # Reads Percentage_of_Lane Percentage_of_Total 6000 AGCCTCTGCT GGGGGGGGGG 13111254 0.3230 0.0400 6001 GCATTCCTTC GGGGGGGGGG 5785178 0.1425 0.0177 6002 GCAGAAGTCT GGGGGGGGGG 5613130 0.1383 0.0171 6003 GATAGATCAG GGGGGGGGGG 5466637 0.1347 0.0167 6004 TCACCGTGGT GGGGGGGGGG 5065498 0.1248 0.0155 6005 CGGATCATTA GGGGGGGGGG 4308240 0.1061 0.0132 6006 TGTGATCGCG GGGGGGGGGG 4150257 0.1022 0.0127 6007 GATTCTTAGC GGGGGGGGGG 3893699 0.0959 0.0119 6008 AGCACCAGTC GGGGGGGGGG 3702627 0.0912 0.0113 6009 GCGACAATAT GGGGGGGGGG 3452816 0.0851 0.0105 6010 CTAGACGAGC GGGGGGGGGG 3401747 0.0838 0.0104 6011 ATCGAGAGAC GGGGGGGGGG 3169982 0.0781 0.0097 6012 GCGAAGAATT GGGGGGGGGG 3151401 0.0776 0.0096 6013 CCACTCAACG GGGGGGGGGG 2927500 0.0721 0.0089 6014 GTGTTCCTTC GAGCCTGCTT 2871127 0.0707 0.0088 6015 ATCTAACCTG GGGGGGGGGG 2388460 0.0588 0.0073 6016 GATTGGCGAT GGGGGGGGGG 2243153 0.0553 0.0069 6017 CAACTACCGC GGGGGGGGGG 2233873 0.0550 0.0068 6018 CGCACATTAC GGGGGGGGGG 2145749 0.0529 0.0066 Lane 5 - Found 14 barcodes with >0.05% of lane reads: index index2 # Reads Percentage_of_Lane Percentage_of_Total 0 GTCGACTCCT GGGGGGGGGG 28213535 0.6889 0.0862 1 CCTCTGTCAT GGGGGGGGGG 21211324 0.5179 0.0648 2 TTGTGAAGGC GGGGGGGGGG 17124222 0.4181 0.0523 3 CTTCGGAATC GGGGGGGGGG 9047527 0.2209 0.0276 4 GCAGATGTAA GGGGGGGGGG 6508182 0.1589 0.0199 5 CAACCATACA GGGGGGGGGG 6450505 0.1575 0.0197 6 TTGCAATGCG GGGGGGGGGG 5469904 0.1336 0.0167 7 CATTATCGCT GGGGGGGGGG 5383290 0.1314 0.0164 8 AACATAAGGC GGGGGGGGGG 3805274 0.0929 0.0116 9 CGGATTGATC GGGGGGGGGG 3792311 0.0926 0.0116 10 ACTTAGATCG GGGGGGGGGG 2963370 0.0724 0.0090 11 AACCGGCCTT GGGGGGGGGG 2671844 0.0652 0.0082 12 AGGTATTCGG AGATCTCGGT 2576643 0.0629 0.0079 13 AAGAGTACGA GGGGGGGGGG 2185456 0.0534 0.0067 Lane 6 - Found 13 barcodes with >0.05% of lane reads: index index2 # Reads Percentage_of_Lane Percentage_of_Total 1000 GTCGACTCCT GGGGGGGGGG 31161329 0.7601 0.0952 1001 CCTCTGTCAT GGGGGGGGGG 20161615 0.4918 0.0616 1002 TTGTGAAGGC GGGGGGGGGG 18902057 0.4611 0.0577 1003 CTTCGGAATC GGGGGGGGGG 9912851 0.2418 0.0303 1004 CAACCATACA GGGGGGGGGG 5813006 0.1418 0.0178 1005 TTGCAATGCG GGGGGGGGGG 5404782 0.1318 0.0165 1006 CATTATCGCT GGGGGGGGGG 5307486 0.1295 0.0162 1007 GCAGATGTAA GGGGGGGGGG 5050759 0.1232 0.0154 1008 AACATAAGGC GGGGGGGGGG 3620816 0.0883 0.0111 1009 CGGATTGATC GGGGGGGGGG 3458507 0.0844 0.0106 1010 ACTTAGATCG GGGGGGGGGG 3057781 0.0746 0.0093 1011 AACCGGCCTT GGGGGGGGGG 2391704 0.0583 0.0073 1012 AGGTATTCGG AGATCTCGGT 2384264 0.0582 0.0073 Lane 7 - Found 14 barcodes with >0.05% of lane reads: index index2 # Reads Percentage_of_Lane Percentage_of_Total 2000 GTCGACTCCT GGGGGGGGGG 33418063 0.8132 0.1021 2001 CCTCTGTCAT GGGGGGGGGG 22375267 0.5445 0.0683 2002 TTGTGAAGGC GGGGGGGGGG 20975773 0.5104 0.0641 2003 CTTCGGAATC GGGGGGGGGG 10655032 0.2593 0.0325 2004 CAACCATACA GGGGGGGGGG 6528282 0.1589 0.0199 2005 TTGCAATGCG GGGGGGGGGG 6130695 0.1492 0.0187 2006 GCAGATGTAA GGGGGGGGGG 5931573 0.1443 0.0181 2007 CATTATCGCT GGGGGGGGGG 5737349 0.1396 0.0175 2008 AACATAAGGC GGGGGGGGGG 4069480 0.0990 0.0124 2009 CGGATTGATC GGGGGGGGGG 3947189 0.0961 0.0121 2010 ACTTAGATCG GGGGGGGGGG 3385918 0.0824 0.0103 2011 AACCGGCCTT GGGGGGGGGG 2644753 0.0644 0.0081 2012 AGGTATTCGG AGATCTCGGT 2070736 0.0504 0.0063 2013 AAGAGTACGA GGGGGGGGGG 2058586 0.0501 0.0063 Lane 8 - Found 13 barcodes with >0.05% of lane reads: index index2 # Reads Percentage_of_Lane Percentage_of_Total 3000 GTCGACTCCT GGGGGGGGGG 34256889 0.8296 0.1046 3001 CCTCTGTCAT GGGGGGGGGG 22855710 0.5535 0.0698 3002 TTGTGAAGGC GGGGGGGGGG 21380948 0.5178 0.0653 3003 CTTCGGAATC GGGGGGGGGG 11044249 0.2675 0.0337 3004 TTGCAATGCG GGGGGGGGGG 6330099 0.1533 0.0193 3005 CAACCATACA GGGGGGGGGG 6312569 0.1529 0.0193 3006 GCAGATGTAA GGGGGGGGGG 5877037 0.1423 0.0179 3007 CATTATCGCT GGGGGGGGGG 5828140 0.1411 0.0178 3008 AACATAAGGC GGGGGGGGGG 4069191 0.0985 0.0124 3009 CGGATTGATC GGGGGGGGGG 3901058 0.0945 0.0119 3010 ACTTAGATCG GGGGGGGGGG 3521385 0.0853 0.0108 3011 AACCGGCCTT GGGGGGGGGG 2574437 0.0623 0.0079 3012 AAGAGTACGA GGGGGGGGGG 2103096 0.0509 0.0064 ================================================================================ 5. BARCODES WITH HIGH MISMATCH RATES ================================================================================ ⚠️ WARNING: 4 sample(s) with >20.0% mismatch rate: Lane SampleID ... # Reads Mismatch_Rate 374 2 FFPE_V4_0001_RNA_0001_B23LG7FLT4_1 ... 69597426 27.97 276 3 FFPE_V4_0001_RNA_0001_B23LG7FLT4_1 ... 70368438 26.90 325 4 FFPE_V4_0001_RNA_0001_B23LG7FLT4_1 ... 69620090 26.32 227 1 FFPE_V4_0001_RNA_0001_B23LG7FLT4_1 ... 70409954 25.77 [4 rows x 5 columns] Mismatch Rate Summary: Average mismatch rate: 3.21% Maximum mismatch rate: 27.97% Samples with >20.0% mismatch: 4 ================================================================================ FINAL STATUS CHECK ================================================================================ Overall % Undetermined: 6.50% Status: 🟡 WARNING Reason(s): Overall undetermined 6.50% >= 5.0% 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 Warning file created: ./samplesheet_status.warning ================================================================================ QC SUMMARY ================================================================================ Metric Value Total_Reads 32746437302 Total_Samples_Analyzed 97 Number_of_Lanes 8 Global_Percent_Undetermined 6.50% Lanes_Exceeding_Fail_Threshold None Samples_with_Low_Reads 0 NTC_Samples_with_High_Reads 0 Significant_Unknown_Barcodes 126 High_Mismatch_Barcodes 4 Final_Status WARNING ================================================================================ QC Analysis completed successfully! Flowcell Status: WARNING Reports generated: - ./qc_report.csv - ./qc_report_detailed.txt - ./samplesheet_status.warning ================================================================================