Starting /dee2/code/volunteer_pipeline.sh SRR7230765 current disk space = 3057463136256 free memory = 1514296020 SRR7230765 SRAfilesize c817818dafccb57e365a94e7e792dc86 SRR7230765.sra SRR7230765.sra file validated SRR7230765 is paired end SRR7230765 is conventional basespace SRR7230765 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR7230765_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 151 %GC 46 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 33.47325 34.0 34.0 34.0 33.0 34.0 2 33.51125 34.0 34.0 34.0 33.0 34.0 3 33.5985 34.0 34.0 34.0 33.0 34.0 4 33.55 34.0 34.0 34.0 33.0 34.0 5 33.543 34.0 34.0 34.0 33.0 34.0 6 37.28175 38.0 38.0 38.0 36.0 38.0 7 37.43375 38.0 38.0 38.0 37.0 38.0 8 37.5095 38.0 38.0 38.0 37.0 38.0 9 37.5355 38.0 38.0 38.0 38.0 38.0 10-14 37.516000000000005 38.0 38.0 38.0 37.8 38.0 15-19 37.4849 38.0 38.0 38.0 38.0 38.0 20-24 37.313199999999995 38.0 38.0 38.0 37.2 38.0 25-29 37.13680000000001 38.0 38.0 38.0 36.6 38.0 30-34 37.032349999999994 38.0 38.0 38.0 36.4 38.0 35-39 36.969500000000004 38.0 38.0 38.0 36.2 38.0 40-44 36.66775 38.0 38.0 38.0 35.4 38.0 45-49 36.77925 38.0 38.0 38.0 35.0 38.0 50-54 36.928200000000004 38.0 38.0 38.0 35.6 38.0 55-59 37.023900000000005 38.0 38.0 38.0 36.6 38.0 60-64 36.9952 38.0 38.0 38.0 36.2 38.0 65-69 37.03150000000001 38.0 38.0 38.0 36.4 38.0 70-74 33.6039 38.0 36.6 38.0 15.6 38.0 75-79 33.8057 38.0 37.4 38.0 21.4 38.0 80-84 35.57000000000001 38.0 38.0 38.0 31.2 38.0 85-89 36.23965 38.0 38.0 38.0 35.2 38.0 90-94 36.24665 38.0 38.0 38.0 35.0 38.0 95-99 36.2734 38.0 38.0 38.0 35.0 38.0 100-104 36.1281 38.0 38.0 38.0 34.6 38.0 105-109 35.9482 38.0 38.0 38.0 34.0 38.0 110-114 35.60965 38.0 37.6 38.0 32.2 38.0 115-119 34.576899999999995 38.0 35.8 38.0 25.8 38.0 120-124 35.2174 38.0 37.2 38.0 31.0 38.0 125-129 34.671049999999994 38.0 35.8 38.0 26.4 38.0 130-134 34.51355 38.0 35.4 38.0 26.2 38.0 135-139 34.7913 38.0 36.0 38.0 28.6 38.0 140-144 34.106950000000005 38.0 35.2 38.0 24.2 38.0 145-149 33.641450000000006 38.0 33.4 38.0 22.8 38.0 150-151 30.18 35.5 28.5 38.0 8.5 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 6 1.0 7 1.0 8 2.0 9 4.0 10 2.0 11 0.0 12 2.0 13 2.0 14 6.0 15 8.0 16 5.0 17 4.0 18 29.0 19 30.0 20 9.0 21 8.0 22 11.0 23 7.0 24 9.0 25 13.0 26 15.0 27 18.0 28 16.0 29 21.0 30 40.0 31 47.0 32 67.0 33 101.0 34 204.0 35 397.0 36 738.0 37 2183.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 41.3 12.475 11.025 35.199999999999996 2 21.6 17.95 33.7 26.75 3 19.175 21.8 27.55 31.474999999999998 4 22.475 28.299999999999997 23.0 26.224999999999998 5 25.15 32.95 22.45 19.45 6 19.650000000000002 30.525000000000002 27.474999999999998 22.35 7 13.325000000000001 23.0 43.974999999999994 19.7 8 16.975 23.175 32.65 27.200000000000003 9 18.675 22.25 32.725 26.35 10-14 20.27 28.294999999999998 25.729999999999997 25.705 15-19 19.741974197419744 27.277727772777276 27.4977497749775 25.48254825482548 20-24 20.215 27.975 26.474999999999998 25.335 25-29 20.095 27.315 27.35 25.240000000000002 30-34 19.32 28.1 26.529999999999998 26.05 35-39 20.478790003505782 27.991185456002405 26.939450092652876 24.590574447838932 40-44 20.74088946892882 27.532376267443027 26.80955727336613 24.91717699026202 45-49 21.661914052729 26.70468757816799 26.92981139626795 24.70358697283506 50-54 20.95 27.415 26.435 25.2 55-59 19.75 26.66 28.194999999999997 25.395 60-64 20.07 26.32 28.060000000000002 25.55 65-69 20.13 27.915 26.545 25.41 70-74 19.573675269877803 28.554989314482988 26.198695818948988 25.672639596690228 75-79 19.787872294836085 28.942575530319264 25.4017570173559 25.86779515748875 80-84 20.016306563391765 28.414186710150837 26.46249490419894 25.107011822258457 85-89 20.788404634134107 27.824865840814482 25.06143738402126 26.325292141030143 90-94 21.22 26.26 26.889999999999997 25.629999999999995 95-99 20.724999999999998 27.339999999999996 27.134999999999998 24.8 100-104 20.849999999999998 28.02 25.900000000000002 25.230000000000004 105-109 20.68 26.995 26.345000000000002 25.979999999999997 110-114 20.915 27.43 25.22 26.435 115-119 20.794999999999998 28.060000000000002 25.805 25.34 120-124 20.935000000000002 27.584999999999997 25.5 25.979999999999997 125-129 20.915 27.1 26.57 25.415 130-134 21.765 27.985 24.82 25.430000000000003 135-139 21.69 28.025 24.73 25.555 140-144 21.89 28.465 23.625 26.02 145-149 21.265 28.139999999999997 24.66 25.935000000000002 150-151 21.4125 28.6125 24.375 25.6 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 1.0 1 1.5 2 2.0 3 2.0 4 1.0 5 0.5 6 2.0 7 1.5 8 0.0 9 0.5 10 0.5 11 0.0 12 0.5 13 0.5 14 0.0 15 1.0 16 1.5 17 1.5 18 1.0 19 0.0 20 0.5 21 0.5 22 0.5 23 2.0 24 4.5 25 8.5 26 8.5 27 7.5 28 11.5 29 21.0 30 32.0 31 44.0 32 45.0 33 52.5 34 80.0 35 94.5 36 107.5 37 108.5 38 127.0 39 148.0 40 149.0 41 161.0 42 163.5 43 161.0 44 173.5 45 169.5 46 155.5 47 151.5 48 142.0 49 146.5 50 145.5 51 130.0 52 151.0 53 191.0 54 199.0 55 180.0 56 120.0 57 90.0 58 88.5 59 68.0 60 52.5 61 41.5 62 28.5 63 11.5 64 3.5 65 1.0 66 0.5 67 0.5 68 0.5 69 0.0 70 0.0 71 0.5 72 0.5 73 0.5 74 0.5 75 0.0 76 0.0 77 0.0 78 0.0 79 0.0 80 0.0 81 0.0 82 0.0 83 0.0 84 0.0 85 0.0 86 0.0 87 0.0 88 0.0 89 0.0 90 0.0 91 0.0 92 0.0 93 0.0 94 0.0 95 0.0 96 0.0 97 0.0 98 0.0 99 0.0 100 0.0 >>END_MODULE >>Per base N content warn #Base N-Count 1 0.0 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10-14 0.0 15-19 0.01 20-24 0.0 25-29 0.0 30-34 0.0 35-39 0.165 40-44 0.38999999999999996 45-49 0.055 50-54 0.0 55-59 0.0 60-64 0.0 65-69 0.0 70-74 8.755 75-79 6.660000000000001 80-84 1.8800000000000001 85-89 0.305 90-94 0.0 95-99 0.0 100-104 0.0 105-109 0.0 110-114 0.0 115-119 0.0 120-124 0.0 125-129 0.0 130-134 0.0 135-139 0.0 140-144 0.0 145-149 0.0 150-151 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 83.22500000000001 #Duplication Level Percentage of deduplicated Percentage of total 1 91.16851907479725 75.875 2 5.016521477921298 8.35 3 1.742264944427756 4.35 4 0.8110543706818865 2.7 5 0.45058576148993695 1.875 6 0.24031240612796637 1.2 7 0.18023430459597475 1.05 8 0.15019525382997898 1.0 9 0.030039050765995796 0.22499999999999998 >10 0.18023430459597475 1.975 >50 0.030039050765995796 1.4000000000000001 >100 0.0 0.0 >500 0.0 0.0 >1k 0.0 0.0 >5k 0.0 0.0 >10k+ 0.0 0.0 >>END_MODULE >>Overrepresented sequences fail #Sequence Count Percentage Possible Source GATCGGAAGAGCACACGTCTGAACTCCAGTCACCAAAAGATCTCGTATGC 56 1.4000000000000001 TruSeq Adapter, Index 7 (97% over 37bp) GTCGGTTCGGTCCTCCAGTTAGTGTTACCCAACCTTCAACCTGCCCATGG 18 0.44999999999999996 No Hit GGCCAACATAGCCTTCTCCGTCCCCCCTTCGCAGTAACACCAAGTACAGG 15 0.375 No Hit GTCAGCATTCGCACTTCTGATACCTCCAGCATGCCTCACAGCACACCTTC 14 0.35000000000000003 No Hit CTTCGCAGTAACACCAAGTACAGGAATATTAACCTGTTTCCCATCGACTA 12 0.3 No Hit CCACGCTTTCGCACCTGAGCGTCAGTCTTCGTCCAGGGGGCCGCCTTCGC 10 0.25 No Hit CCCCACTGCTGCCTCCCGTAGGAGTCTGGACCGTGTCTCAGTTCCAGTGT 10 0.25 No Hit GTCCCCCCTTCGCAGTAACACCAAGTACAGGAATATTAACCTGTTTCCCA 9 0.22499999999999998 No Hit GCCAGCTGGTATCTTCGACTGATTTCAGCTCCACGAGCAAGTCGCTTCAC 8 0.2 No Hit CCGGTATTCCTCCAGATCTCTACGCATTTCACCGCTACACCTGGAATTCT 8 0.2 No Hit GCCTTATGTGATAGATGCCTCTTTAAAATATCTAAGTGCTGGGGTTATGA 8 0.2 No Hit GCCAACATAGCCTTCTCCGTCCCCCCTTCGCAGTAACACCAAGTACAGGA 8 0.2 No Hit CCCACTGCTGCCTCCCGTAGGAGTCTGGACCGTGTCTCAGTTCCAGTGTG 8 0.2 No Hit CCCGGTTCGCCTCATTAACCTATGGATTCAGTTAATGATAGTGTGTCGAA 7 0.17500000000000002 No Hit GGGGATTTCACATCTGACTTAACAAACCGCCTGCGTGCGCTTTACGCCCA 7 0.17500000000000002 No Hit GCTGCTTCTAAGCCAACATCCTGGCTGTCTGGGCCTTCCCACATCGTTTC 7 0.17500000000000002 No Hit GTTGATTTCTTTTCCTCGGGGTACTTAGATGTTTCAGTTCCCCCGGTTCG 7 0.17500000000000002 No Hit CCCCTTCGCAGTAACACCAAGTACAGGAATATTAACCTGTTTCCCATCGA 7 0.17500000000000002 No Hit CAGTAATTCCGATTAACGCTTGCACCCTCCGTATTACCGCGGCTGCTGGC 7 0.17500000000000002 No Hit GTGCTTCTTCTGCGGGTAACGTCAATGAGCAAAGGTATTAACTTTACTCC 6 0.15 No Hit CCCCCTTCGCAGTAACACCAAGTACAGGAATATTAACCTGTTTCCCATCG 6 0.15 No Hit GGCTGGTCATCCTCTCAGACCAGCTAGGGATCGTCGCCTAGGTGAGCCGT 6 0.15 No Hit CGGGAACGTATTCACCGTGGCATTCTGATCCACGATTACTAGCGATTCCG 6 0.15 No Hit GCCTCATTAACCTATGGATTCAGTTAATGATAGTGTGTCGAAACACACTG 6 0.15 No Hit GCCGGTGCTTCTTCTGCGGGTAACGTCAATGAGCAAAGGTATTAACTTTA 6 0.15 No Hit CGGGGATTTCACATCTGACTTAACAAACCGCCTGCGTGCGCTTTACGCCC 6 0.15 No Hit AGTAATTCCGATTAACGCTTGCACCCTCCGTATTACCGCGGCTGCTGGCA 6 0.15 No Hit CCGGTTCGCCTCATTAACCTATGGATTCAGTTAATGATAGTGTGTCGAAA 5 0.125 No Hit ATTCCGATTAACGCTTGCACCCTCCGTATTACCGCGGCTGCTGGCACGGA 5 0.125 No Hit GATTAACGCTTGCACCCTCCGTATTACCGCGGCTGCTGGCACGGAGTTAG 5 0.125 No Hit GTTCGGTCCTCCAGTTAGTGTTACCCAACCTTCAACCTGCCCATGGCTAG 5 0.125 No Hit GTCAGTCAGGAGTATTTAGCCTTGGAGGATGGTCCCCCCATATTCAGACA 5 0.125 No Hit ACGAGACTCAAGCTTGCCAGTATCAGATGCAGTTCCCAGGTTGAGCCCGG 5 0.125 No Hit TTCCGATTAACGCTTGCACCCTCCGTATTACCGCGGCTGCTGGCACGGAG 5 0.125 No Hit CTTGGTCTTCCGGCGAGCGGGCTTTTCACCCGCTTTATCGTTACTTATGT 5 0.125 No Hit CCCTTCGCAGTAACACCAAGTACAGGAATATTAACCTGTTTCCCATCGAC 5 0.125 No Hit GTTATGAGTAGGGATGAGCATAAACCAACAACTCTCAAAGAAGATGGGAA 5 0.125 No Hit CTTTGGTCTTGCGACGTTATGCGGTATTAGCTACCGTTTCCAGTAGTTAT 5 0.125 No Hit GCGCCATTGTAGCACGTGTGTAGCCCTGGTCGTAAGGGCCATGATGACTT 5 0.125 No Hit CCCATATTCAGACAGGATACCACGTGTCCCGCCCTACTCATCGAGCTCAC 5 0.125 No Hit AGGAGATGTTGGAACTCTACCAATTGGAGCTTTCTTAGCTGTCTTAGCAG 5 0.125 No Hit GTTCGCCTCATTAACCTATGGATTCAGTTAATGATAGTGTGTCGAAACAC 5 0.125 No Hit >>END_MODULE >>Adapter Content fail #Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence SOLID Small RNA Adapter 1 0.0 0.0 0.0 0.0 0.0 2 0.0 0.0 0.0 0.0 0.0 3 0.0 0.0 0.0 0.0 0.0 4 0.0 0.0 0.0 0.0 0.0 5 0.0 0.0 0.0 0.0 0.0 6 0.0 0.0 0.0 0.0 0.0 7 0.0 0.0 0.0 0.0 0.0 8 0.0 0.0 0.0 0.0 0.0 9 0.0 0.0 0.0 0.0 0.0 10-11 0.0 0.0 0.0 0.0 0.0 12-13 0.0 0.0 0.0 0.0 0.0 14-15 0.0 0.0 0.0 0.0 0.0 16-17 0.0 0.0 0.0 0.0 0.0 18-19 0.0 0.0 0.0 0.0 0.0 20-21 0.0 0.0 0.0 0.0 0.0 22-23 0.0 0.0 0.0 0.0 0.0 24-25 0.0 0.0 0.0 0.0 0.0 26-27 0.0 0.0 0.0 0.0 0.0 28-29 0.0 0.0 0.0 0.0 0.0 30-31 0.0 0.0 0.0 0.0 0.0 32-33 0.0 0.0 0.0 0.0 0.0 34-35 0.0 0.0 0.0 0.0 0.0 36-37 0.0 0.0 0.0 0.0 0.0 38-39 0.0 0.0 0.0 0.0 0.0 40-41 0.0 0.0 0.0 0.0 0.0 42-43 0.0 0.0 0.0 0.0 0.0 44-45 0.0 0.0 0.0 0.0 0.0 46-47 0.0 0.0 0.0 0.0 0.0 48-49 0.0 0.0 0.0 0.0 0.0 50-51 0.0 0.0 0.0 0.0 0.0 52-53 0.0 0.0 0.0 0.0 0.0 54-55 0.0 0.0 0.0 0.0 0.0 56-57 0.0 0.0 0.0 0.0 0.0 58-59 0.0 0.0 0.0 0.0 0.0 60-61 0.0 0.0 0.0 0.0 0.0 62-63 0.025 0.0 0.0 0.0 0.0 64-65 0.025 0.0 0.0 0.0 0.0 66-67 0.025 0.0 0.0 0.0 0.0 68-69 0.025 0.0 0.0 0.0 0.0 70-71 0.05 0.0 0.0 0.0 0.0 72-73 0.075 0.0 0.0 0.0 0.0 74-75 0.1 0.0 0.0 0.0 0.0 76-77 0.1 0.0 0.0 0.0 0.0 78-79 0.2375 0.0 0.0 0.0 0.0 80-81 0.3375 0.0 0.0 0.0 0.0 82-83 0.42500000000000004 0.0 0.0 0.0 0.0 84-85 0.5249999999999999 0.0 0.0 0.0 0.0 86-87 0.675 0.0 0.0 0.0 0.0 88-89 0.725 0.0 0.0 0.0 0.0 90-91 0.95 0.0 0.0 0.0 0.0 92-93 1.3 0.0 0.0 0.0 0.0 94-95 1.5 0.0 0.0 0.0 0.0 96-97 1.75 0.0 0.0 0.0 0.0 98-99 2.1625 0.0 0.0 0.0 0.0 100-101 2.3875 0.0 0.0 0.0 0.0 102-103 2.7625 0.0 0.0 0.0 0.0 104-105 3.1625 0.0 0.0 0.0 0.0 106-107 3.5374999999999996 0.0 0.0 0.0 0.0 108-109 4.125 0.0 0.0 0.0 0.0 110-111 4.925 0.0 0.0 0.0 0.0 112-113 5.675 0.0 0.0 0.0 0.0 114-115 6.425 0.0 0.0 0.0 0.0 116-117 6.95 0.0 0.0 0.0 0.0 118-119 7.5625 0.0 0.0 0.0 0.0 120-121 8.5125 0.0 0.0 0.0 0.0 122-123 9.3625 0.0 0.0 0.0 0.0 124-125 10.337499999999999 0.0 0.0 0.0 0.0 126-127 11.1625 0.0 0.0 0.0 0.0 128-129 12.0375 0.0 0.0 0.0 0.0 130-131 13.337499999999999 0.0 0.0 0.0 0.0 132-133 14.3125 0.0 0.0 0.0 0.0 134-135 15.325 0.0 0.0 0.0 0.0 136-137 16.35 0.0 0.0 0.0 0.0 138-139 17.4125 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TAATTCA 10 0.0071056043 143.1 9 AGATCGG 90 0.0053686644 11.13 135-139 >>END_MODULE SRR7230765 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR7230765_2.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 151 %GC 46 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 32.83475 34.0 33.0 34.0 32.0 34.0 2 33.03175 34.0 33.0 34.0 33.0 34.0 3 33.04 34.0 33.0 34.0 33.0 34.0 4 32.956 34.0 33.0 34.0 33.0 34.0 5 32.9675 34.0 33.0 34.0 33.0 34.0 6 36.96225 38.0 38.0 38.0 37.0 38.0 7 36.972 38.0 38.0 38.0 37.0 38.0 8 36.9795 38.0 38.0 38.0 37.0 38.0 9 36.93325 38.0 38.0 38.0 37.0 38.0 10-14 36.62695 38.0 38.0 38.0 35.8 38.0 15-19 36.92835 38.0 38.0 38.0 37.0 38.0 20-24 36.93730000000001 38.0 38.0 38.0 37.0 38.0 25-29 36.91935 38.0 38.0 38.0 37.2 38.0 30-34 36.90675 38.0 38.0 38.0 37.2 38.0 35-39 36.700900000000004 38.0 38.0 38.0 36.4 38.0 40-44 36.76345 38.0 38.0 38.0 36.8 38.0 45-49 36.642399999999995 38.0 38.0 38.0 36.4 38.0 50-54 36.73075 38.0 38.0 38.0 37.0 38.0 55-59 36.4901 38.0 38.0 38.0 36.0 38.0 60-64 36.75575 38.0 38.0 38.0 36.8 38.0 65-69 36.4996 38.0 38.0 38.0 36.2 38.0 70-74 35.9947 38.0 38.0 38.0 35.4 38.0 75-79 36.078700000000005 38.0 38.0 38.0 35.4 38.0 80-84 36.071000000000005 38.0 38.0 38.0 35.2 38.0 85-89 36.05815 38.0 38.0 38.0 35.2 38.0 90-94 36.02465 38.0 38.0 38.0 35.0 38.0 95-99 35.9028 38.0 38.0 38.0 34.6 38.0 100-104 35.737350000000006 38.0 38.0 38.0 34.0 38.0 105-109 35.6682 38.0 38.0 38.0 33.8 38.0 110-114 35.46025 38.0 38.0 38.0 33.0 38.0 115-119 35.45455 38.0 38.0 38.0 33.4 38.0 120-124 35.1342 38.0 38.0 38.0 31.4 38.0 125-129 34.956649999999996 38.0 37.4 38.0 30.2 38.0 130-134 34.6985 38.0 36.4 38.0 28.2 38.0 135-139 34.35985 38.0 36.0 38.0 26.2 38.0 140-144 33.7848 38.0 35.4 38.0 21.2 38.0 145-149 32.3176 38.0 32.4 38.0 10.2 38.0 150-151 27.058374999999998 34.5 16.5 38.0 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 18.0 3 3.0 4 10.0 5 7.0 6 1.0 7 3.0 8 3.0 9 3.0 10 5.0 11 6.0 12 7.0 13 2.0 14 7.0 15 10.0 16 19.0 17 40.0 18 5.0 19 2.0 20 6.0 21 8.0 22 6.0 23 13.0 24 11.0 25 16.0 26 13.0 27 11.0 28 20.0 29 31.0 30 33.0 31 47.0 32 47.0 33 70.0 34 116.0 35 184.0 36 487.0 37 2730.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 44.67656682607601 16.53662219984898 14.170651900327208 24.6161590737478 2 28.675 22.325 27.900000000000002 21.099999999999998 3 24.025 25.2 29.4 21.375 4 28.000000000000004 32.800000000000004 19.625 19.575 5 27.925 35.375 19.2 17.5 6 23.474999999999998 35.425000000000004 21.625 19.475 7 21.775 19.425 36.875 21.925 8 24.175 24.349999999999998 24.725 26.75 9 26.1 24.55 25.974999999999998 23.375 10-14 26.650000000000002 27.01 23.615 22.725 15-19 26.905 26.02 25.22 21.855 20-24 27.529999999999998 27.11 24.48 20.880000000000003 25-29 25.645 28.605000000000004 25.16 20.59 30-34 26.93 27.250000000000004 25.130000000000003 20.69 35-39 26.325 26.195 26.179999999999996 21.3 40-44 27.705000000000002 26.745 25.535000000000004 20.015 45-49 26.276494463095656 26.537054667535198 26.0710527634414 21.115398105927742 50-54 25.93316298411744 26.63460093191042 26.709754997745378 20.722481086226765 55-59 25.710555388169126 27.146730943055136 27.227076428643166 19.91563724013257 60-64 25.955000000000002 27.29 26.009999999999998 20.745 65-69 26.376158276984725 27.878787878787882 25.704983721512647 20.040070122714752 70-74 26.053293112116645 28.45148315736551 26.01307189542484 19.482151835093013 75-79 25.335 27.49 26.240000000000002 20.935000000000002 80-84 26.695 27.250000000000004 25.905 20.150000000000002 85-89 26.669999999999998 26.834999999999997 26.195 20.3 90-94 26.665 27.310000000000002 26.305 19.72 95-99 26.195 27.575 26.365 19.865 100-104 26.490000000000002 27.779999999999998 26.224999999999998 19.505 105-109 25.924999999999997 28.299999999999997 25.71 20.064999999999998 110-114 26.555 28.18 25.665 19.6 115-119 26.650000000000002 28.505000000000003 25.674999999999997 19.17 120-124 26.38 27.985 26.13 19.505 125-129 26.185000000000002 28.185 26.055 19.575 130-134 27.93 27.735 24.87 19.465 135-139 27.189999999999998 28.610000000000003 25.019999999999996 19.18 140-144 27.665 28.15 25.174999999999997 19.009999999999998 145-149 28.16 28.255000000000003 24.73 18.855 150-151 29.2 28.537499999999998 24.1875 18.075 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 0.0 1 0.0 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10 0.0 11 0.0 12 0.5 13 0.5 14 0.0 15 0.0 16 0.0 17 0.5 18 0.5 19 0.5 20 0.5 21 0.5 22 1.0 23 1.0 24 1.5 25 1.5 26 1.5 27 3.0 28 4.0 29 9.0 30 10.5 31 13.0 32 20.5 33 23.0 34 40.5 35 59.5 36 75.5 37 94.5 38 110.0 39 119.0 40 141.0 41 153.5 42 161.0 43 168.0 44 163.0 45 166.0 46 169.5 47 171.0 48 174.0 49 195.0 50 199.0 51 174.5 52 175.5 53 205.0 54 224.0 55 203.5 56 146.5 57 103.0 58 83.5 59 67.0 60 47.0 61 40.5 62 37.5 63 21.0 64 7.0 65 2.0 66 1.5 67 1.0 68 0.5 69 1.0 70 0.5 71 0.5 72 1.0 73 1.0 74 1.0 75 1.0 76 0.5 77 0.0 78 0.0 79 0.0 80 0.0 81 0.0 82 0.0 83 0.0 84 0.0 85 0.0 86 0.0 87 0.0 88 0.0 89 0.0 90 0.0 91 0.0 92 0.0 93 0.0 94 0.0 95 0.0 96 0.0 97 0.0 98 0.0 99 0.0 100 0.0 >>END_MODULE >>Per base N content pass #Base N-Count 1 0.675 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10-14 0.0 15-19 0.0 20-24 0.0 25-29 0.0 30-34 0.0 35-39 0.0 40-44 0.0 45-49 0.215 50-54 0.20500000000000002 55-59 0.43 60-64 0.0 65-69 0.17500000000000002 70-74 0.5499999999999999 75-79 0.0 80-84 0.0 85-89 0.0 90-94 0.0 95-99 0.0 100-104 0.0 105-109 0.0 110-114 0.0 115-119 0.0 120-124 0.0 125-129 0.0 130-134 0.0 135-139 0.0 140-144 0.0 145-149 0.0 150-151 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 84.375 #Duplication Level Percentage of deduplicated Percentage of total 1 91.4074074074074 77.125 2 5.777777777777778 9.75 3 1.0074074074074073 2.55 4 0.8592592592592593 2.9000000000000004 5 0.3259259259259259 1.375 6 0.2074074074074074 1.05 7 0.05925925925925926 0.35000000000000003 8 0.02962962962962963 0.2 9 0.02962962962962963 0.22499999999999998 >10 0.26666666666666666 3.15 >50 0.02962962962962963 1.325 >100 0.0 0.0 >500 0.0 0.0 >1k 0.0 0.0 >5k 0.0 0.0 >10k+ 0.0 0.0 >>END_MODULE >>Overrepresented sequences fail #Sequence Count Percentage Possible Source GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCG 53 1.325 Illumina Single End PCR Primer 1 (100% over 50bp) CTCAGATTGAACGCTGGCGGCAGGCCTAACACATGCAAGTCGAACGGTAA 25 0.625 No Hit GCCTGATGCAGCCATGCCGCGTGTATGAAGAAGGCCTTCGGGTTGTAAAG 24 0.6 No Hit GCGACTTATATTCTGTAGCAAGGTTAACCGAATAGGGGAGCCGAAGGGAA 14 0.35000000000000003 No Hit GGTGGATGCCCTGGCAGTCAGAGGCGATGAAGGACGTGCTAATCTGCGAT 12 0.3 No Hit GGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCCATGCCGCGTGTA 11 0.27499999999999997 No Hit GTTTGATCATGGCTCAGATTGAACGCTGGCGGCAGGCCTAACACATGCAA 10 0.25 No Hit GCTGAAAGCCCTAACTTAATGGACGGGAGGTATCCCAATAGGAGGTTTCC 10 0.25 No Hit GGTGAGTCGACCCCTAAGGCGAGGCCGAAAGGCGTAGTCGATGGGAAACA 10 0.25 No Hit CGGGAACTCAAAGGAGACTGCCAGTGATAAACTGGAGGAAGGTGGGGATG 10 0.25 No Hit GGATGCCCTGGCAGTCAGAGGCGATGAAGGACGTGCTAATCTGCGATAAG 9 0.22499999999999998 No Hit ACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCA 8 0.2 No Hit GGGAAACCGAGTCTTAACTGGGCGTTAAGTTGCAGGGTATAGACCCGAAA 7 0.17500000000000002 No Hit ATTGAACGCTGGCGGCAGGCCTAACACATGCAAGTCGAACGGTAACAGGA 7 0.17500000000000002 No Hit GTGAAATCCCCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTT 6 0.15 No Hit GTCGACCCCTAAGGCGAGGCCGAAAGGCGTAGTCGATGGGAAACAGGTTA 6 0.15 No Hit GGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGC 6 0.15 No Hit GCCTAACACATGCAAGTCGAACGGTAACAGGAAGAAGCTTGCTTCTTTGC 6 0.15 No Hit GGGAGACACACGGCGGGTGCTAACGTCCGTCGTGAAGAGGGAAACAACCC 6 0.15 No Hit CGTACACGGTGGATGCCCTGGCAGTCAGAGGCGATGAAGGACGTGCTAAT 6 0.15 No Hit GCACAATGGGCGCAAGCCTGATGCAGCCATGCCGCGTGTATGAAGAAGGC 6 0.15 No Hit GCGTACACGGTGGATGCCCTGGCAGTCAGAGGCGATGAAGGACGTGCTAA 5 0.125 No Hit GTCCAACGTTAATCGGGGCAGGGTGAGTCGACCCCTAAGGCGAGGCCGAA 5 0.125 No Hit GCCCGCTCGCCGGAAGACCAAGGGTTCCTGTCCAACGTTAATCGGGGCAG 5 0.125 No Hit GGCAGGGTGAGTCGACCCCTAAGGCGAGGCCGAAAGGCGTAGTCGATGGG 5 0.125 No Hit GTGAGTCGACCCCTAAGGCGAGGCCGAAAGGCGTAGTCGATGGGAAACAG 5 0.125 No Hit GTTTAAGCGTGTAGGCTGGTTTTCCAGGCAAATCCGGAAAATCAAGGCTG 5 0.125 No Hit GTGAAAAGCCCGCTCGCCGGAAGACCAAGGGTTCCTGTCCAACGTTAATC 5 0.125 No Hit GCCTGATGGAGGGGGATAACTACTGGAAACGGTAGCTAATACCGCATAAC 5 0.125 No Hit GCGAGCGAACGGGGAGCAGCCCAGAGCCTGAATCAGTGTGTGTGTTAGTG 5 0.125 No Hit GGGAACTCAAAGGAGACTGCCAGTGATAAACTGGAGGAAGGTGGGGATGA 5 0.125 No Hit GTTTAATTCGATGCAACGCGAAGAACCTTACCTGGTCTTGACATCCACGG 5 0.125 No Hit >>END_MODULE >>Adapter Content fail #Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence SOLID Small RNA Adapter 1 0.0 0.0 0.0 0.0 0.0 2 0.0 0.0 0.0 0.0 0.0 3 0.0 0.0 0.0 0.0 0.0 4 0.0 0.0 0.0 0.0 0.0 5 0.0 0.0 0.0 0.0 0.0 6 0.0 0.0 0.0 0.0 0.0 7 0.0 0.0 0.0 0.0 0.0 8 0.0 0.0 0.0 0.0 0.0 9 0.0 0.0 0.0 0.0 0.0 10-11 0.0 0.0 0.0 0.0 0.0 12-13 0.0 0.0 0.0 0.0 0.0 14-15 0.0 0.0 0.0 0.0 0.0 16-17 0.0 0.0 0.0 0.0 0.0 18-19 0.0 0.0 0.0 0.0 0.0 20-21 0.0 0.0 0.0 0.0 0.0 22-23 0.0 0.0 0.0 0.0 0.0 24-25 0.0 0.0 0.0 0.0 0.0 26-27 0.0 0.0 0.0 0.0 0.0 28-29 0.0 0.0 0.0 0.0 0.0 30-31 0.0 0.0 0.0 0.0 0.0 32-33 0.0 0.0 0.0 0.0 0.0 34-35 0.0 0.0 0.0 0.0 0.0 36-37 0.0 0.0 0.0 0.0 0.0 38-39 0.0 0.0 0.0 0.0 0.0 40-41 0.0 0.0 0.0 0.0 0.0 42-43 0.0 0.0 0.0 0.0 0.0 44-45 0.0 0.0 0.0 0.0 0.0 46-47 0.0 0.0 0.0 0.0 0.0 48-49 0.0 0.0 0.0 0.0 0.0 50-51 0.0 0.0 0.0 0.0 0.0 52-53 0.0 0.0 0.0 0.0 0.0 54-55 0.0 0.0 0.0 0.0 0.0 56-57 0.0 0.0 0.0 0.0 0.0 58-59 0.0 0.0 0.0 0.0 0.0 60-61 0.0 0.0 0.0 0.0 0.0 62-63 0.037500000000000006 0.0 0.0 0.0 0.0 64-65 0.05 0.0 0.0 0.0 0.0 66-67 0.05 0.0 0.0 0.0 0.0 68-69 0.05 0.0 0.0 0.0 0.0 70-71 0.0875 0.0 0.0 0.0 0.0 72-73 0.15 0.0 0.0 0.0 0.0 74-75 0.175 0.0 0.0 0.0 0.0 76-77 0.175 0.0 0.0 0.0 0.0 78-79 0.32499999999999996 0.0 0.0 0.0 0.0 80-81 0.4375 0.0 0.0 0.0 0.0 82-83 0.5375 0.0 0.0 0.0 0.0 84-85 0.6375 0.0 0.0 0.0 0.0 86-87 0.7625 0.0 0.0 0.0 0.0 88-89 0.8 0.0 0.0 0.0 0.0 90-91 1.025 0.0 0.0 0.0 0.0 92-93 1.4 0.0 0.0 0.0 0.0 94-95 1.6125 0.0 0.0 0.0 0.0 96-97 1.9124999999999999 0.0 0.0 0.0 0.0 98-99 2.3875 0.0 0.0 0.0 0.0 100-101 2.6125 0.0 0.0 0.0 0.0 102-103 2.975 0.0 0.0 0.0 0.0 104-105 3.4000000000000004 0.0 0.0 0.0 0.0 106-107 3.7625 0.0 0.0 0.0 0.0 108-109 4.45 0.0 0.0 0.0 0.0 110-111 5.262499999999999 0.0 0.0 0.0 0.0 112-113 6.05 0.0 0.0 0.0 0.0 114-115 6.8125 0.0 0.0 0.0 0.0 116-117 7.387499999999999 0.0 0.0 0.0 0.0 118-119 7.9875 0.0 0.0 0.0 0.0 120-121 8.9375 0.0 0.0 0.0 0.0 122-123 9.7625 0.0 0.0 0.0 0.0 124-125 10.675 0.0 0.0 0.0 0.0 126-127 11.5125 0.0 0.0 0.0 0.0 128-129 12.350000000000001 0.0 0.0 0.0 0.0 130-131 13.662500000000001 0.0 0.0 0.0 0.0 132-133 14.725 0.0 0.0 0.0 0.0 134-135 15.775 0.0 0.0 0.0 0.0 136-137 16.7875 0.0 0.0 0.0 0.0 138-139 17.8 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position AAGAGTG 35 0.0033465917 61.98214 145 AGATCGG 95 0.0074195447 10.656579 135-139 >>END_MODULE Read 561407 spots for SRR7230765.sra Written 561407 spots for SRR7230765.sra Read 561407 spots for SRR7230765.sra Written 561407 spots for SRR7230765.sra Read 561407 spots for SRR7230765.sra Written 561407 spots for SRR7230765.sra Read 561407 spots for SRR7230765.sra Written 561407 spots for SRR7230765.sra Read 561407 spots for SRR7230765.sra Written 561407 spots for SRR7230765.sra Read 561407 spots for SRR7230765.sra Written 561407 spots for SRR7230765.sra Read 561407 spots for SRR7230765.sra Written 561407 spots for SRR7230765.sra Read 561407 spots for SRR7230765.sra Written 561407 spots for SRR7230765.sra Read 561407 spots for SRR7230765.sra Written 561407 spots for SRR7230765.sra Read 561407 spots for SRR7230765.sra Written 561407 spots for SRR7230765.sra Read 561407 spots for SRR7230765.sra Written 561407 spots for SRR7230765.sra Read 561407 spots for SRR7230765.sra Written 561407 spots for SRR7230765.sra Read 561407 spots for SRR7230765.sra Written 561407 spots for SRR7230765.sra Read 561407 spots for SRR7230765.sra Written 561407 spots for SRR7230765.sra Read 561407 spots for SRR7230765.sra Written 561407 spots for SRR7230765.sra Read 561407 spots for SRR7230765.sra Written 561407 spots for SRR7230765.sra Read 561407 spots for SRR7230765.sra Written 561407 spots for SRR7230765.sra Read 561407 spots for SRR7230765.sra Written 561407 spots for SRR7230765.sra Read 561407 spots for SRR7230765.sra Written 561407 spots for SRR7230765.sra Read 561410 spots for SRR7230765.sra Written 561410 spots for SRR7230765.sra SRR ids: ['SRR7230765.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_ndw3qjtx SRR7230765.sra spots: 11228143 blocks: [[1, 561407], [561408, 1122814], [1122815, 1684221], [1684222, 2245628], [2245629, 2807035], [2807036, 3368442], [3368443, 3929849], [3929850, 4491256], [4491257, 5052663], [5052664, 5614070], [5614071, 6175477], [6175478, 6736884], [6736885, 7298291], [7298292, 7859698], [7859699, 8421105], [8421106, 8982512], [8982513, 9543919], [9543920, 10105326], [10105327, 10666733], [10666734, 11228143]] SRR7230765 file size 3783148 SRR7230765 completed basic pipeline successfully skewer v0.2.2 [April 4, 2016] COMMAND LINE: skewer -f sanger -l 18 -q 10 -k inf -t 20 -o SRR7230765 SRR7230765_1.fastq SRR7230765_2.fastq Input file: SRR7230765_1.fastq Paired file: SRR7230765_2.fastq trimmed: SRR7230765-trimmed-pair1.fastq, SRR7230765-trimmed-pair2.fastq Parameters used: -- 3' end adapter sequence (-x): AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -- paired 3' end adapter sequence (-y): AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA -- maximum error ratio allowed (-r): 0.100 -- maximum indel error ratio allowed (-d): 0.030 -- end quality threshold (-q): 10 -- minimum read length allowed after trimming (-l): 18 -- file format (-f): Sanger/Illumina 1.8+ FASTQ -- number of concurrent threads (-t): 20 Mon Feb 10 23:44:54 2025 >> started Mon Feb 10 23:45:08 2025 >> done (14.051s) 11228143 read pairs processed; of these: 26237 ( 0.23%) short read pairs filtered out after trimming by size control 156065 ( 1.39%) empty read pairs filtered out after trimming by size control 11045841 (98.38%) read pairs available; of these: 5960292 (53.96%) trimmed read pairs available after processing 5085549 (46.04%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 3 0.00% 19 8 0.00% 20 7 0.00% 21 7 0.00% 22 11 0.00% 23 18 0.00% 24 16 0.00% 25 7 0.00% 26 17 0.00% 27 18 0.00% 28 32 0.00% 29 20 0.00% 30 22 0.00% 31 67 0.00% 32 43 0.00% 33 23 0.00% 34 39 0.00% 35 44 0.00% 36 49 0.00% 37 46 0.00% 38 66 0.00% 39 64 0.00% 40 72 0.00% 41 83 0.00% 42 99 0.00% 43 100 0.00% 44 106 0.00% 45 141 0.00% 46 143 0.00% 47 193 0.00% 48 208 0.00% 49 247 0.00% 50 246 0.00% 51 298 0.00% 52 326 0.00% 53 326 0.00% 54 343 0.00% 55 386 0.00% 56 399 0.00% 57 457 0.00% 58 437 0.00% 59 558 0.01% 60 713 0.01% 61 786 0.01% 62 888 0.01% 63 869 0.01% 64 1030 0.01% 65 1241 0.01% 66 1674 0.02% 67 2122 0.02% 68 2633 0.02% 69 7954 0.07% 70 15453 0.14% 71 9347 0.08% 72 5664 0.05% 73 4154 0.04% 74 3687 0.03% 75 3739 0.03% 76 3761 0.03% 77 4423 0.04% 78 4790 0.04% 79 6029 0.05% 80 6206 0.06% 81 6542 0.06% 82 7543 0.07% 83 8764 0.08% 84 12200 0.11% 85 12392 0.11% 86 14732 0.13% 87 14720 0.13% 88 16349 0.15% 89 17032 0.15% 90 17634 0.16% 91 18433 0.17% 92 18861 0.17% 93 21776 0.20% 94 21120 0.19% 95 23880 0.22% 96 24827 0.22% 97 24935 0.23% 98 25394 0.23% 99 28135 0.25% 100 29597 0.27% 101 28510 0.26% 102 30963 0.28% 103 33378 0.30% 104 36750 0.33% 105 41347 0.37% 106 37759 0.34% 107 37156 0.34% 108 40373 0.37% 109 47182 0.43% 110 45493 0.41% 111 41800 0.38% 112 44444 0.40% 113 50791 0.46% 114 47717 0.43% 115 51755 0.47% 116 51917 0.47% 117 48252 0.44% 118 51394 0.47% 119 51943 0.47% 120 55472 0.50% 121 53891 0.49% 122 57904 0.52% 123 59188 0.54% 124 60776 0.55% 125 59372 0.54% 126 60576 0.55% 127 61199 0.55% 128 61833 0.56% 129 63372 0.57% 130 66955 0.61% 131 66052 0.60% 132 67577 0.61% 133 72372 0.66% 134 74150 0.67% 135 76058 0.69% 136 76233 0.69% 137 82295 0.75% 138 82139 0.74% 139 81650 0.74% 140 80509 0.73% 141 90259 0.82% 142 86839 0.79% 143 91894 0.83% 144 98091 0.89% 145 107289 0.97% 146 120141 1.09% 147 143851 1.30% 148 186627 1.69% 149 327110 2.96% 150 2011870 18.21% 151 5085549 46.04% 11045841 reads passed initial QC criterion=sequence-density sequence-density=0.80 sequence-density-rank=1 fanout-score=3.95 fanout-score-rank=26 prefix-density=2.41 prefix-fanout=1.3 sequence=CACTCGTCAGCGAAACAGCAAGCTGTTTCCTGTTACC criterion=fanout-score sequence-density=0.01 sequence-density-rank=40 fanout-score=42.38 fanout-score-rank=1 prefix-density=0.04 prefix-fanout=8.3 sequence=TTTTTTTTTCGCATATAACCACATTCAAATTGACCTCCCTCAGGAAGCTAAGAAATACTATCTCGGCAATAGGATTGTAGCCCAGGATGAGTCCCTCAGCGTGACGCAGTAAACTAGTAGCATCCCGATCTTTTCCCTATCTAATTCACCTCCTATTAGGAGCCGATCGTGCTTGTGCGCCGGCAAAACTTTTCAGGCGAATTTCCGCCCCTGGCGCTCTAGGCTACTACGTGCGCGATATGACAAGTTAACAAGACGGCGCAGGTTGATGCTTCCAATAAACATGATCTTTCTGCTCCGCTGAGAAGTACACCTTTTTGCTAGCATCTCGCACGGCAAGAGCGATTGCCGAGCTTAGAGCGTATCTTCCGGGATCGGGCAAAGGGGCAACTCGAGCTAATCTCCCCAGCGGCTAGCATGTGTAGTGCGCCATATCATATCCAAGATAGTGTAGGACTCGTCGCATTGGATGACGATGCCTAGTACTGTGCGCCAATTAGGTCGTCATTGC criterion=sequence-density sequence-density=3.07 sequence-density-rank=1 fanout-score=2.15 fanout-score-rank=33 prefix-density=3.19 prefix-fanout=2.1 sequence=GCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTAGCTAATACCGCATAACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCGGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACGGCTCACCTAGGCGACGATCCCTAGCTGGTCTGAGAGGATGACCAGCCACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCCATGCCGCGTGTATGAAGAAGGCCTTCGGGTTGTAAAGTACTTTCAGCGGGGAGGAAGGGAGTAAAGTTAATACCTTTGCTCATTGACGTTACCCGCAGAAGAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATG criterion=fanout-score sequence-density=0.06 sequence-density-rank=31 fanout-score=14.93 fanout-score-rank=1 prefix-density=0.71 prefix-fanout=1.3 sequence=CACAGGTGGTCTTGATGGGTGCCGTTGAGGGTTACAGAATTGCTGGCGGGCCACTCGGTGAGGTAACTGACCCAATCTACCCAGGTGGAAGCTTCGACCCACTGGGCTTGGCTGACGATCCCGAAGCATTCGCTGAGTTGAAGGTGAAGGAAC Potential 3prime adapter identified. Now checking if in reference sequence /dee2/code/volunteer_pipeline.sh: line 905: -f: command not found /dee2/code/volunteer_pipeline.sh: line 906: -f: command not found Adapter seq not found in reference. Now shuffling file before clipping skewer v0.2.2 [April 4, 2016] COMMAND LINE: skewer -f sanger -l 18 -t 20 -x CACTCGTCAGCGAAACAGCAAGCTGTTTCCTGTTACC -y GCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTAGCTAATACCGCATAACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCGGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACGGCTCACCTAGGCGACGATCCCTAGCTGGTCTGAGAGGATGACCAGCCACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCCATGCCGCGTGTATGAAGAAGGCCTTCGGGTTGTAAAGTACTTTCAGCGGGGAGGAAGGGAGTAAAGTTAATACCTTTGCTCATTGACGTTACCCGCAGAAGAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATG -o SRR7230765 SRR7230765_1.fastq SRR7230765_2.fastq Input file: SRR7230765_1.fastq Paired file: SRR7230765_2.fastq trimmed: SRR7230765-trimmed-pair1.fastq, SRR7230765-trimmed-pair2.fastq Parameters used: -- 3' end adapter sequence (-x): CACTCGTCAGCGAAACAGCAAGCTGTTTCCTGTTACC -- paired 3' end adapter sequence (-y): GCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGGGGATAACTACT -- maximum error ratio allowed (-r): 0.100 -- maximum indel error ratio allowed (-d): 0.030 -- minimum read length allowed after trimming (-l): 18 -- file format (-f): Sanger/Illumina 1.8+ FASTQ -- number of concurrent threads (-t): 20 Mon Feb 10 23:46:11 2025 >> started Mon Feb 10 23:46:16 2025 >> done (5.822s) 3681947 read pairs processed; of these: 39 ( 0.00%) short read pairs filtered out after trimming by size control 231 ( 0.01%) empty read pairs filtered out after trimming by size control 3681677 (99.99%) read pairs available; of these: 1429 ( 0.04%) trimmed read pairs available after processing 3680248 (99.96%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 2 0.00% 19 3 0.00% 20 2 0.00% 21 2 0.00% 22 4 0.00% 23 7 0.00% 24 4 0.00% 25 2 0.00% 26 11 0.00% 27 9 0.00% 28 14 0.00% 29 2 0.00% 30 9 0.00% 31 24 0.00% 32 15 0.00% 33 8 0.00% 34 4 0.00% 35 15 0.00% 36 20 0.00% 37 12 0.00% 38 24 0.00% 39 19 0.00% 40 25 0.00% 41 23 0.00% 42 33 0.00% 43 28 0.00% 44 39 0.00% 45 49 0.00% 46 41 0.00% 47 72 0.00% 48 70 0.00% 49 78 0.00% 50 87 0.00% 51 109 0.00% 52 109 0.00% 53 111 0.00% 54 121 0.00% 55 129 0.00% 56 140 0.00% 57 137 0.00% 58 155 0.00% 59 187 0.01% 60 230 0.01% 61 274 0.01% 62 293 0.01% 63 302 0.01% 64 342 0.01% 65 446 0.01% 66 581 0.02% 67 714 0.02% 68 900 0.02% 69 2705 0.07% 70 5180 0.14% 71 3116 0.08% 72 1894 0.05% 73 1395 0.04% 74 1196 0.03% 75 1197 0.03% 76 1269 0.03% 77 1459 0.04% 78 1564 0.04% 79 2043 0.06% 80 2078 0.06% 81 2189 0.06% 82 2527 0.07% 83 2974 0.08% 84 4066 0.11% 85 4154 0.11% 86 4824 0.13% 87 4943 0.13% 88 5368 0.15% 89 5633 0.15% 90 5846 0.16% 91 6108 0.17% 92 6345 0.17% 93 7252 0.20% 94 7165 0.19% 95 7895 0.21% 96 8255 0.22% 97 8201 0.22% 98 8413 0.23% 99 9260 0.25% 100 9820 0.27% 101 9505 0.26% 102 10426 0.28% 103 11140 0.30% 104 12357 0.34% 105 13875 0.38% 106 12619 0.34% 107 12234 0.33% 108 13426 0.36% 109 15795 0.43% 110 15133 0.41% 111 13839 0.38% 112 14713 0.40% 113 17109 0.46% 114 15745 0.43% 115 17359 0.47% 116 17331 0.47% 117 16261 0.44% 118 17205 0.47% 119 17189 0.47% 120 18459 0.50% 121 17981 0.49% 122 19253 0.52% 123 19522 0.53% 124 20242 0.55% 125 19863 0.54% 126 20203 0.55% 127 20278 0.55% 128 20293 0.55% 129 21336 0.58% 130 22295 0.61% 131 22207 0.60% 132 22692 0.62% 133 24042 0.65% 134 24735 0.67% 135 25152 0.68% 136 25354 0.69% 137 27614 0.75% 138 27189 0.74% 139 27134 0.74% 140 26754 0.73% 141 30160 0.82% 142 28946 0.79% 143 30336 0.82% 144 32687 0.89% 145 35876 0.97% 146 40177 1.09% 147 47619 1.29% 148 62604 1.70% 149 108974 2.96% 150 671031 18.23% 151 1695037 46.04% criterion=sequence-density sequence-density=0.81 sequence-density-rank=1 fanout-score=3.90 fanout-score-rank=27 prefix-density=2.40 prefix-fanout=1.3 sequence=CACTCGTCAGCGAAACAGCAAGCTGTTTCCTGTTACC criterion=fanout-score sequence-density=0.01 sequence-density-rank=43 fanout-score=41.66 fanout-score-rank=1 prefix-density=0.04 prefix-fanout=7.5 sequence=TTTTTTTTTCGCATATAACCACATTCAAATTGACCTCCCTCAGGAAGCTAAGAAATACTATCTCGGCAATAGGATTGTAGCCCAGGATGAGTCCCTCAGCGTGACGCAGTAAACTAGTAGCATCCCGATCTTTTCCCTATCTAATTCACCTCCTATTAGGAGCCGATCGTGCTTGTGCGCCGGCAAAACTTTTCAGGCGAATTTCCGCCCCTGGCGCTCTAGGCTACTACGTGCGCGATATGACAAGTTAACAAGACGGCGCAGGTTGATGCTTCCAATAAACATGATCTTTCTGCTCCGCTGAGAAGTACACCTTTTTGCTAGCATCTCGCACGGCAAGAGCGATTGCCGAGCTTAGAGCGTATCTTCCGGGATCGGGCAAAGGGGCAACTCGAGCTAATCTCCCCAGCGGCTAGCATGTGTAGTGCGCCATATCATATCCAAGATAGTGTAGGACTCGTCGCATTGGATGACGATGCCTAGTACTGTGCGCCAATTAGGTCGTCATTGC criterion=sequence-density sequence-density=3.06 sequence-density-rank=1 fanout-score=2.14 fanout-score-rank=33 prefix-density=3.18 prefix-fanout=2.1 sequence=GCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTAGCTAATACCGCATAACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCGGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACGGCTCACCTAGGCGACGATCCCTAGCTGGTCTGAGAGGATGACCAGCCACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCCATGCCGCGTGTATGAAGAAGGCCTTCGGGTTGTAAAGTACTTTCAGCGGGGAGGAAGGGAGTAAAGTTAATACCTTTGCTCATTGACGTTACCCGCAGAAGAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATG criterion=fanout-score sequence-density=0.01 sequence-density-rank=42 fanout-score=18.67 fanout-score-rank=1 prefix-density=0.10 prefix-fanout=1.0 sequence=CCGGCGCACGCCACAGGCGTCATACTTCCCAAGAAGCGGCCATAGCCCAGATGCGAGGTGGAAAAGTCACACTAGAGCGACACCAACATCGTTACGCTTACACACCGGACGCTTGGATCAGTGGGAAGTGCTCACGCGCGGAGCCCACTGGGCGAACAGCAACGTTATAACGGCCACTCAGTGGTTCGTCACGCGCAGCCCCGGGTTCGTCCCCTATAAGGGCCTAGTACCTTTCGAGCCCCGCGCGTACTAGGCAGATAAGAACCCTCCAGCTCGGGGCCTCAAACCGATATTCCATGTGGGCCAACTGCCATGTTGTGTCCAGTCGCTATCGGAGTAGCCGCGCTGGTGCCACACGACTACAACCCTCGTAATAGGGCTGCGTGCGTCCTAAATACACTCGCTGTTGAGATACTAAAATTATCTGTGGATTGCCGGCATTGAGCCCACGGTAAACCCCAAATACATAAGTGTATAATGTCTCGGACCCGTCGCAACGGTTGTTAATATG SRR7230765 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 10 23:47:33 Started mapping on | Feb 10 23:47:33 Finished on | Feb 10 23:54:58 Mapping speed, Million of reads per hour | 89.36 Number of input reads | 11045571 Average input read length | 284 UNIQUE READS: Uniquely mapped reads number | 5948053 Uniquely mapped reads % | 53.85% Average mapped length | 286.39 Number of splices: Total | 3710368 Number of splices: Annotated (sjdb) | 3616162 Number of splices: GT/AG | 3624135 Number of splices: GC/AG | 67183 Number of splices: AT/AC | 3234 Number of splices: Non-canonical | 15816 Mismatch rate per base, % | 0.39% Deletion rate per base | 0.04% Deletion average length | 2.52 Insertion rate per base | 0.03% Insertion average length | 2.04 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 160721 % of reads mapped to multiple loci | 1.46% Number of reads mapped to too many loci | 60149 % of reads mapped to too many loci | 0.54% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 43.54% % of reads unmapped: other | 0.61% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 4954981 4954981 4954981 N_multimapping 160721 160721 160721 N_noFeature 185469 5776818 238597 N_ambiguous 165354 515 47096 UnstrandedReadsAssigned:5597230 PositiveStrandReadsAssigned:170720 NegativeStrandReadsAssigned:5662360 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=135 echo kmer=131 SRR7230765 Starting Kallisto paired end mapping to ensembl reference transcriptome [quant] fragment length distribution will be estimated from the data [index] k-mer length: 31 [index] number of targets: 52,400 [index] number of k-mers: 62,057,036 [index] number of equivalence classes: 130,681 [quant] running in paired-end mode [quant] will process pair 1: SRR7230765-trimmed-pair1.fastq SRR7230765-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 11,045,571 reads, 5,815,574 reads pseudoaligned [quant] estimated average fragment length: 192.997 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,133 rounds 52401 SRR7230765.ke.tsv 34699 SRR7230765.se.tsv 87100 total ==> SRR7230765.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1826 155 12.1615 Potri.005G024800.1.v4.1 1035 843.003 19 3.22911 Potri.004G059700.1.v4.1 961 769.016 0 0 Potri.007G009000.2.v4.1 1416 1224 0 0 Potri.003G141000.2.v4.1 2943 2751 294 15.3114 Potri.016G087400.1.v4.1 270 98.5071 169 245.797 Potri.015G069301.1.v4.1 564 372.925 0 0 Potri.010G195200.1.v4.1 1773 1581 0 0 Potri.012G127500.1.v4.1 977 785.003 75 13.6882 ==> SRR7230765.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 471 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 234 Potri.001G212900.v4.1 10 Potri.001G182400.v4.1 0 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 0 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 9 SRR7230765 completed mapping pipeline successfully