Starting /dee2/code/volunteer_pipeline.sh SRR7180063 current disk space = 3058617462784 free memory = 785362048 SRR7180063 SRAfilesize 30ffb38452f7b063b8f94f902aa37e43 SRR7180063.sra SRR7180063.sra file validated SRR7180063 is paired end SRR7180063 is conventional basespace SRR7180063 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR7180063_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 43 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 27.51225 31.0 25.0 33.0 18.0 33.0 2 29.3245 31.0 28.0 33.0 25.0 33.0 3 31.39075 33.0 31.0 33.0 27.0 33.0 4 32.77725 33.0 33.0 33.0 32.0 34.0 5 32.82575 33.0 33.0 33.0 32.0 34.0 6 36.819 38.0 37.0 38.0 35.0 38.0 7 37.1405 38.0 38.0 38.0 36.0 38.0 8 37.39925 38.0 38.0 38.0 37.0 38.0 9 37.4885 38.0 38.0 38.0 37.0 38.0 10-14 37.614149999999995 38.0 38.0 38.0 38.0 38.0 15-19 37.61595 38.0 38.0 38.0 38.0 38.0 20-24 37.599199999999996 38.0 38.0 38.0 38.0 38.0 25-29 37.592 38.0 38.0 38.0 38.0 38.0 30-34 37.564499999999995 38.0 38.0 38.0 38.0 38.0 35-39 37.55225 38.0 38.0 38.0 38.0 38.0 40-44 37.479949999999995 38.0 38.0 38.0 37.8 38.0 45-49 37.47685 38.0 38.0 38.0 37.6 38.0 50-54 37.44445 38.0 38.0 38.0 37.4 38.0 55-59 37.449149999999996 38.0 38.0 38.0 37.0 38.0 60-64 37.44085 38.0 38.0 38.0 37.0 38.0 65-69 37.3374 38.0 38.0 38.0 37.0 38.0 70-74 37.320350000000005 38.0 38.0 38.0 37.0 38.0 75-79 37.2719 38.0 38.0 38.0 37.0 38.0 80-84 37.177049999999994 38.0 38.0 38.0 36.8 38.0 85-89 37.142250000000004 38.0 38.0 38.0 36.4 38.0 90-94 37.1101 38.0 38.0 38.0 36.0 38.0 95-99 36.955149999999996 38.0 38.0 38.0 36.0 38.0 100-104 36.92280000000001 38.0 38.0 38.0 35.6 38.0 105-109 36.8988 38.0 38.0 38.0 36.0 38.0 110-114 36.72795 38.0 38.0 38.0 34.8 38.0 115-119 36.529199999999996 38.0 38.0 38.0 34.4 38.0 120-124 36.436949999999996 38.0 38.0 38.0 34.0 38.0 125-129 36.38265 38.0 38.0 38.0 34.0 38.0 130-134 36.07935 38.0 37.8 38.0 33.6 38.0 135-139 35.8684 38.0 37.4 38.0 32.6 38.0 140-144 35.5501 38.0 36.2 38.0 32.0 38.0 145-149 35.216 38.0 36.0 38.0 31.0 38.0 150-151 32.426875 37.0 33.5 38.0 15.5 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 1.0 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 1.0 13 0.0 14 0.0 15 0.0 16 0.0 17 1.0 18 4.0 19 0.0 20 5.0 21 1.0 22 6.0 23 2.0 24 4.0 25 11.0 26 9.0 27 8.0 28 16.0 29 27.0 30 23.0 31 41.0 32 54.0 33 75.0 34 101.0 35 168.0 36 548.0 37 2894.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 34.78488982161595 16.84155299055614 13.011542497376706 35.362014690451204 2 22.45 21.8 34.625 21.125 3 17.849999999999998 28.95 26.424999999999997 26.775 4 21.775 34.375 23.125 20.724999999999998 5 20.7 36.925000000000004 24.099999999999998 18.275 6 17.8 34.925 26.625 20.65 7 13.825000000000001 21.85 44.85 19.475 8 17.25 24.375 28.449999999999996 29.925 9 18.0 23.05 33.475 25.474999999999998 10-14 20.375 28.355000000000004 27.05 24.22 15-19 19.985 28.43 27.83 23.755000000000003 20-24 19.935 28.845 27.88 23.34 25-29 19.400000000000002 29.165000000000003 27.68 23.755000000000003 30-34 20.3 28.410000000000004 27.860000000000003 23.43 35-39 19.835 28.904999999999998 27.625 23.635 40-44 20.21 28.98 27.224999999999998 23.585 45-49 19.79 28.470000000000002 27.944999999999997 23.794999999999998 50-54 20.18 28.48 27.775 23.565 55-59 20.080000000000002 28.384999999999998 27.834999999999997 23.7 60-64 20.330000000000002 28.38 27.46 23.830000000000002 65-69 20.515 28.455000000000002 27.33 23.7 70-74 20.4 27.98 28.084999999999997 23.535 75-79 20.19 28.444999999999997 27.46 23.905 80-84 20.195 28.16 27.975 23.669999999999998 85-89 19.825 28.235 28.155 23.785 90-94 20.21 28.08 28.315 23.395 95-99 20.62 27.855 27.765 23.76 100-104 20.599999999999998 28.754999999999995 27.24 23.405 105-109 20.195 28.16 27.815 23.830000000000002 110-114 20.44 28.660000000000004 27.810000000000002 23.09 115-119 20.59 28.375 27.634999999999998 23.400000000000002 120-124 20.419999999999998 28.65 27.13 23.799999999999997 125-129 20.355 27.685 28.115000000000002 23.845 130-134 20.665 28.98 27.034999999999997 23.32 135-139 20.674999999999997 28.185 27.450000000000003 23.69 140-144 20.830000000000002 28.754999999999995 26.875 23.54 145-149 21.13 28.175 27.584999999999997 23.11 150-151 20.625 29.225 27.025 23.125 >>END_MODULE >>Per sequence GC content pass #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 0.0 13 0.0 14 0.0 15 0.0 16 0.0 17 0.0 18 0.0 19 0.0 20 1.5 21 2.0 22 1.5 23 1.0 24 2.5 25 5.0 26 4.5 27 4.5 28 6.5 29 12.0 30 16.5 31 22.0 32 32.5 33 39.0 34 48.5 35 72.5 36 98.5 37 111.0 38 129.5 39 174.0 40 212.0 41 226.5 42 243.0 43 262.0 44 286.5 45 289.0 46 277.5 47 268.5 48 230.0 49 185.5 50 157.0 51 133.0 52 113.0 53 91.5 54 60.0 55 46.0 56 37.5 57 22.0 58 18.0 59 17.5 60 12.0 61 7.5 62 5.0 63 3.0 64 3.0 65 2.5 66 2.0 67 2.0 68 1.0 69 0.5 70 0.5 71 0.0 72 0.0 73 0.0 74 0.0 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 pass #Base N-Count 1 4.7 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 0.0 50-54 0.0 55-59 0.0 60-64 0.0 65-69 0.0 70-74 0.0 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 99.8 #Duplication Level Percentage of deduplicated Percentage of total 1 99.79959919839679 99.6 2 0.2004008016032064 0.4 3 0.0 0.0 4 0.0 0.0 5 0.0 0.0 6 0.0 0.0 7 0.0 0.0 8 0.0 0.0 9 0.0 0.0 >10 0.0 0.0 >50 0.0 0.0 >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 pass >>END_MODULE >>Adapter Content pass #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 0.0 0.0 0.0 0.0 0.0 64-65 0.0 0.0 0.0 0.0 0.0 66-67 0.0 0.0 0.0 0.0 0.0 68-69 0.0 0.0 0.0 0.0 0.0 70-71 0.0 0.0 0.0 0.0 0.0 72-73 0.0 0.0 0.0 0.0 0.0 74-75 0.0 0.0 0.0 0.0 0.0 76-77 0.0 0.0 0.0 0.0 0.0 78-79 0.0 0.0 0.0 0.0 0.0 80-81 0.0 0.0 0.0 0.0 0.0 82-83 0.037500000000000006 0.0 0.0 0.0 0.0 84-85 0.075 0.0 0.0 0.0 0.0 86-87 0.075 0.0 0.0 0.0 0.0 88-89 0.1375 0.0 0.0 0.0 0.0 90-91 0.16249999999999998 0.0 0.0 0.0 0.0 92-93 0.25 0.0 0.0 0.0 0.0 94-95 0.3375 0.0 0.0 0.0 0.0 96-97 0.425 0.0 0.0 0.0 0.0 98-99 0.5 0.0 0.0 0.0 0.0 100-101 0.5625 0.0 0.0 0.0 0.0 102-103 0.6 0.0 0.0 0.0 0.0 104-105 0.675 0.0 0.0 0.0 0.0 106-107 0.8625 0.0 0.0 0.0 0.0 108-109 0.9874999999999999 0.0 0.0 0.0 0.0 110-111 1.0499999999999998 0.0 0.0 0.0 0.0 112-113 1.275 0.0 0.0 0.0 0.0 114-115 1.4375 0.0 0.0 0.0 0.0 116-117 1.5750000000000002 0.0 0.0 0.0 0.0 118-119 1.75 0.0 0.0 0.0 0.0 120-121 1.925 0.0 0.0 0.0 0.0 122-123 2.1375 0.0 0.0 0.0 0.0 124-125 2.3375000000000004 0.0 0.0 0.0 0.0 126-127 2.575 0.0 0.0 0.0 0.0 128-129 2.85 0.0 0.0 0.0 0.0 130-131 3.1375 0.0 0.0 0.0 0.0 132-133 3.4125 0.0 0.0 0.0 0.0 134-135 3.7 0.0 0.0 0.0 0.0 136-137 3.95 0.0 0.0 0.0 0.0 138-139 4.3875 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE SRR7180063 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR7180063_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 44 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 32.799 33.0 33.0 34.0 32.0 34.0 2 33.02375 33.0 33.0 34.0 32.0 34.0 3 32.9805 34.0 33.0 34.0 32.0 34.0 4 32.94525 34.0 33.0 34.0 32.0 34.0 5 32.97575 34.0 33.0 34.0 32.0 34.0 6 37.171 38.0 38.0 38.0 37.0 38.0 7 37.174 38.0 38.0 38.0 37.0 38.0 8 37.055 38.0 38.0 38.0 36.0 38.0 9 37.20575 38.0 38.0 38.0 37.0 38.0 10-14 37.16955 38.0 38.0 38.0 37.0 38.0 15-19 37.1194 38.0 38.0 38.0 36.8 38.0 20-24 37.0655 38.0 38.0 38.0 36.4 38.0 25-29 37.1186 38.0 38.0 38.0 37.0 38.0 30-34 37.099349999999994 38.0 38.0 38.0 37.0 38.0 35-39 37.029900000000005 38.0 38.0 38.0 36.6 38.0 40-44 37.008449999999996 38.0 38.0 38.0 36.0 38.0 45-49 37.032700000000006 38.0 38.0 38.0 36.0 38.0 50-54 37.046800000000005 38.0 38.0 38.0 36.0 38.0 55-59 36.8898 38.0 38.0 38.0 35.6 38.0 60-64 36.758 38.0 38.0 38.0 35.0 38.0 65-69 36.857099999999996 38.0 38.0 38.0 35.8 38.0 70-74 36.7549 38.0 38.0 38.0 35.0 38.0 75-79 36.75475 38.0 38.0 38.0 35.0 38.0 80-84 36.624700000000004 38.0 38.0 38.0 34.8 38.0 85-89 36.5152 38.0 38.0 38.0 34.0 38.0 90-94 36.404999999999994 38.0 38.0 38.0 34.0 38.0 95-99 36.28305 38.0 38.0 38.0 34.0 38.0 100-104 36.1502 38.0 37.4 38.0 33.6 38.0 105-109 36.0355 38.0 37.0 38.0 33.2 38.0 110-114 35.9418 38.0 37.2 38.0 33.0 38.0 115-119 35.844649999999994 38.0 37.0 38.0 32.2 38.0 120-124 35.576499999999996 38.0 36.6 38.0 31.0 38.0 125-129 35.35465000000001 38.0 36.0 38.0 30.6 38.0 130-134 34.996599999999994 38.0 35.8 38.0 28.6 38.0 135-139 34.768299999999996 38.0 35.4 38.0 28.0 38.0 140-144 34.2472 38.0 35.0 38.0 24.4 38.0 145-149 33.62650000000001 38.0 35.0 38.0 19.2 38.0 150-151 29.994374999999998 36.5 28.5 38.0 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 3.0 3 3.0 4 0.0 5 0.0 6 1.0 7 0.0 8 0.0 9 1.0 10 1.0 11 1.0 12 2.0 13 0.0 14 2.0 15 2.0 16 1.0 17 3.0 18 4.0 19 6.0 20 6.0 21 12.0 22 9.0 23 16.0 24 11.0 25 16.0 26 14.0 27 26.0 28 27.0 29 36.0 30 45.0 31 54.0 32 84.0 33 100.0 34 163.0 35 241.0 36 642.0 37 2468.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 39.509877469367346 16.504126031507877 15.878969742435608 28.107026756689173 2 26.206551637909474 21.8304576144036 34.48362090522631 17.479369842460617 3 20.330082520630157 26.70667666916729 31.807951987997 21.155288822205552 4 22.95 35.75 22.575 18.725 5 23.40585146286572 37.33433358339585 21.13028257064266 18.12953238309577 6 19.179794948737182 38.03450862715679 23.1807951987997 19.604901225306325 7 18.904726181545385 17.129282320580145 42.5856464116029 21.380345086271568 8 19.929982495623904 23.13078269567392 28.33208302075519 28.60715178794699 9 21.305326331582897 25.256314078519633 28.732183045761438 24.706176544136035 10-14 23.416170808540425 27.43637181859093 26.611330566528324 22.536126806340317 15-19 22.875718929732432 27.97199299824956 28.29707426856714 20.855213803450862 20-24 22.73432417554922 27.96877345743882 28.00380323274784 21.293099134264125 25-29 22.91364205256571 28.35043804755945 27.704630788485606 21.03128911138924 30-34 23.26839284819953 28.35178043772224 27.305053338007713 21.074773376070517 35-39 22.709502806736168 28.598636728147554 27.91700080192462 20.774859663191663 40-44 22.796291656226508 28.0430969681784 28.338762214983714 20.821849160611375 45-49 22.609217835159885 28.173947855677326 28.088875544212584 21.127958764950208 50-54 23.110777694423607 27.796949237309327 28.3520880220055 20.740185046261566 55-59 23.098464769715456 28.464269640446066 28.114217132569884 20.32304845726859 60-64 23.219643928785757 27.1754350870174 28.765753150630125 20.839167833566712 65-69 22.921146057302867 28.23641182059103 28.296414820741038 20.54602730136507 70-74 22.95614780739037 28.23641182059103 28.111405570278514 20.696034801740087 75-79 23.491174558727938 27.58137906895345 28.30141507075354 20.626031301565078 80-84 23.621181059052955 27.85139256962848 27.946397319865994 20.581029051452575 85-89 23.35116755837792 28.0114005700285 28.07640382019101 20.56102805140257 90-94 23.275000000000002 27.92 28.485 20.32 95-99 24.335 28.315 27.6 19.75 100-104 23.315 28.205000000000002 28.035 20.445 105-109 23.98 27.939999999999998 28.005000000000003 20.075000000000003 110-114 23.615 28.050000000000004 27.705000000000002 20.630000000000003 115-119 23.98 28.12 27.534999999999997 20.365 120-124 24.05 29.099999999999998 27.1 19.75 125-129 24.29 27.865000000000002 27.810000000000002 20.035 130-134 23.974999999999998 27.91 27.589999999999996 20.525 135-139 24.154999999999998 28.110000000000003 27.925 19.81 140-144 24.38 27.985 27.55 20.085 145-149 24.145 27.88 27.88 20.095 150-151 25.103137892236532 27.015876984623077 28.353544193024128 19.527440930116263 >>END_MODULE >>Per sequence GC content pass #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 1.0 14 0.5 15 0.5 16 0.5 17 0.5 18 0.5 19 0.5 20 0.5 21 0.5 22 0.5 23 0.5 24 0.5 25 1.0 26 2.5 27 3.5 28 5.0 29 10.0 30 15.0 31 17.5 32 21.0 33 29.0 34 45.5 35 63.0 36 78.0 37 102.5 38 134.0 39 161.5 40 200.5 41 245.5 42 270.5 43 281.5 44 284.5 45 296.0 46 291.5 47 266.0 48 232.5 49 203.0 50 181.0 51 139.5 52 98.0 53 76.5 54 64.0 55 47.5 56 35.0 57 23.0 58 16.5 59 15.5 60 11.0 61 7.0 62 6.0 63 5.0 64 2.5 65 0.5 66 0.5 67 0.5 68 0.5 69 0.5 70 1.0 71 1.0 72 0.0 73 0.0 74 0.0 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 pass #Base N-Count 1 0.025 2 0.025 3 0.025 4 0.0 5 0.025 6 0.025 7 0.025 8 0.025 9 0.025 10-14 0.005 15-19 0.025 20-24 0.08499999999999999 25-29 0.125 30-34 0.165 35-39 0.24 40-44 0.22499999999999998 45-49 0.08499999999999999 50-54 0.025 55-59 0.015 60-64 0.02 65-69 0.005 70-74 0.005 75-79 0.005 80-84 0.005 85-89 0.005 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 0.0125 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 99.5 #Duplication Level Percentage of deduplicated Percentage of total 1 99.57286432160805 99.075 2 0.35175879396984927 0.7000000000000001 3 0.07537688442211055 0.22499999999999998 4 0.0 0.0 5 0.0 0.0 6 0.0 0.0 7 0.0 0.0 8 0.0 0.0 9 0.0 0.0 >10 0.0 0.0 >50 0.0 0.0 >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 pass >>END_MODULE >>Adapter Content pass #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 0.0 0.0 0.0 0.0 0.0 64-65 0.0 0.0 0.0 0.0 0.0 66-67 0.0 0.0 0.0 0.0 0.0 68-69 0.0 0.0 0.0 0.0 0.0 70-71 0.0 0.0 0.0 0.0 0.0 72-73 0.0 0.0 0.0 0.0 0.0 74-75 0.0 0.0 0.0 0.0 0.0 76-77 0.0 0.0 0.0 0.0 0.0 78-79 0.0 0.0 0.0 0.0 0.0 80-81 0.0 0.0 0.0 0.0 0.0 82-83 0.037500000000000006 0.0 0.0 0.0 0.0 84-85 0.075 0.0 0.0 0.0 0.0 86-87 0.075 0.0 0.0 0.0 0.0 88-89 0.1375 0.0 0.0 0.0 0.0 90-91 0.16249999999999998 0.0 0.0 0.0 0.0 92-93 0.25 0.0 0.0 0.0 0.0 94-95 0.3375 0.0 0.0 0.0 0.0 96-97 0.425 0.0 0.0 0.0 0.0 98-99 0.5 0.0 0.0 0.0 0.0 100-101 0.5625 0.0 0.0 0.0 0.0 102-103 0.6 0.0 0.0 0.0 0.0 104-105 0.7 0.0 0.0 0.0 0.0 106-107 0.8875 0.0 0.0 0.0 0.0 108-109 1.0125 0.0 0.0 0.0 0.0 110-111 1.0750000000000002 0.0 0.0 0.0 0.0 112-113 1.3 0.0 0.0 0.0 0.0 114-115 1.4625 0.0 0.0 0.0 0.0 116-117 1.6 0.0 0.0 0.0 0.0 118-119 1.8 0.0 0.0 0.0 0.0 120-121 1.975 0.0 0.0 0.0 0.0 122-123 2.1875 0.0 0.0 0.0 0.0 124-125 2.3875 0.0 0.0 0.0 0.0 126-127 2.575 0.0 0.0 0.0 0.0 128-129 2.85 0.0 0.0 0.0 0.0 130-131 3.1375 0.0 0.0 0.0 0.0 132-133 3.4125 0.0 0.0 0.0 0.0 134-135 3.675 0.0 0.0 0.0 0.0 136-137 3.925 0.0 0.0 0.0 0.0 138-139 4.35 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position ACAGTAT 10 0.006830828 145.0 4 CAGTATA 10 0.006830828 145.0 5 AGTATAC 10 0.006830828 145.0 6 ATACGGG 10 0.006830828 145.0 9 CTCACAG 10 0.006830828 145.0 1 TCACAGT 10 0.006830828 145.0 2 CACAGTA 10 0.006830828 145.0 3 TTTAATG 10 0.006830828 145.0 5 >>END_MODULE Read 856739 spots for SRR7180063.sra Written 856739 spots for SRR7180063.sra Read 856739 spots for SRR7180063.sra Written 856739 spots for SRR7180063.sra Read 856739 spots for SRR7180063.sra Written 856739 spots for SRR7180063.sra Read 856739 spots for SRR7180063.sra Written 856739 spots for SRR7180063.sra Read 856739 spots for SRR7180063.sra Written 856739 spots for SRR7180063.sra Read 856739 spots for SRR7180063.sra Written 856739 spots for SRR7180063.sra Read 856739 spots for SRR7180063.sra Written 856739 spots for SRR7180063.sra Read 856739 spots for SRR7180063.sra Written 856739 spots for SRR7180063.sra Read 856739 spots for SRR7180063.sra Written 856739 spots for SRR7180063.sra Read 856739 spots for SRR7180063.sra Written 856739 spots for SRR7180063.sra Read 856739 spots for SRR7180063.sra Written 856739 spots for SRR7180063.sra Read 856739 spots for SRR7180063.sra Written 856739 spots for SRR7180063.sra Read 856739 spots for SRR7180063.sra Written 856739 spots for SRR7180063.sra Read 856739 spots for SRR7180063.sra Written 856739 spots for SRR7180063.sra Read 856739 spots for SRR7180063.sra Written 856739 spots for SRR7180063.sra Read 856739 spots for SRR7180063.sra Written 856739 spots for SRR7180063.sra Read 856739 spots for SRR7180063.sra Written 856739 spots for SRR7180063.sra Read 856739 spots for SRR7180063.sra Written 856739 spots for SRR7180063.sra Read 856739 spots for SRR7180063.sra Written 856739 spots for SRR7180063.sra Read 856743 spots for SRR7180063.sra Written 856743 spots for SRR7180063.sra SRR ids: ['SRR7180063.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_60vi1d4b SRR7180063.sra spots: 17134784 blocks: [[1, 856739], [856740, 1713478], [1713479, 2570217], [2570218, 3426956], [3426957, 4283695], [4283696, 5140434], [5140435, 5997173], [5997174, 6853912], [6853913, 7710651], [7710652, 8567390], [8567391, 9424129], [9424130, 10280868], [10280869, 11137607], [11137608, 11994346], [11994347, 12851085], [12851086, 13707824], [13707825, 14564563], [14564564, 15421302], [15421303, 16278041], [16278042, 17134784]] SRR7180063 file size 5784715 SRR7180063 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 SRR7180063 SRR7180063_1.fastq SRR7180063_2.fastq Input file: SRR7180063_1.fastq Paired file: SRR7180063_2.fastq trimmed: SRR7180063-trimmed-pair1.fastq, SRR7180063-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 16:14:46 2025 >> started Mon Feb 10 16:15:06 2025 >> done (19.891s) 17134784 read pairs processed; of these: 15677 ( 0.09%) short read pairs filtered out after trimming by size control 15677 ( 0.09%) empty read pairs filtered out after trimming by size control 17103430 (99.82%) read pairs available; of these: 6453895 (37.73%) trimmed read pairs available after processing 10649535 (62.27%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 1 0.00% 19 4 0.00% 20 3 0.00% 21 2 0.00% 22 7 0.00% 23 3 0.00% 24 0 0.00% 25 1 0.00% 26 2 0.00% 27 2 0.00% 28 5 0.00% 29 3 0.00% 30 9 0.00% 31 4 0.00% 32 3 0.00% 33 1 0.00% 34 4 0.00% 35 7 0.00% 36 10 0.00% 37 20 0.00% 38 3 0.00% 39 10 0.00% 40 37 0.00% 41 21 0.00% 42 4 0.00% 43 10 0.00% 44 24 0.00% 45 78 0.00% 46 59 0.00% 47 28 0.00% 48 31 0.00% 49 75 0.00% 50 126 0.00% 51 66 0.00% 52 55 0.00% 53 30 0.00% 54 96 0.00% 55 154 0.00% 56 49 0.00% 57 32 0.00% 58 60 0.00% 59 204 0.00% 60 108 0.00% 61 72 0.00% 62 99 0.00% 63 115 0.00% 64 122 0.00% 65 119 0.00% 66 144 0.00% 67 166 0.00% 68 211 0.00% 69 257 0.00% 70 269 0.00% 71 293 0.00% 72 345 0.00% 73 402 0.00% 74 451 0.00% 75 509 0.00% 76 584 0.00% 77 702 0.00% 78 782 0.00% 79 837 0.00% 80 1002 0.01% 81 1106 0.01% 82 1232 0.01% 83 1418 0.01% 84 2239 0.01% 85 2866 0.02% 86 3056 0.02% 87 3523 0.02% 88 3695 0.02% 89 3876 0.02% 90 4160 0.02% 91 4435 0.03% 92 4821 0.03% 93 5041 0.03% 94 5487 0.03% 95 6050 0.04% 96 6466 0.04% 97 6845 0.04% 98 7157 0.04% 99 7688 0.04% 100 8208 0.05% 101 8634 0.05% 102 9437 0.06% 103 10339 0.06% 104 10576 0.06% 105 11581 0.07% 106 12477 0.07% 107 13288 0.08% 108 13986 0.08% 109 14794 0.09% 110 15694 0.09% 111 16270 0.10% 112 17291 0.10% 113 18491 0.11% 114 19360 0.11% 115 20550 0.12% 116 21664 0.13% 117 22948 0.13% 118 24016 0.14% 119 25682 0.15% 120 26503 0.15% 121 28412 0.17% 122 29549 0.17% 123 29979 0.18% 124 31366 0.18% 125 32690 0.19% 126 34378 0.20% 127 35633 0.21% 128 37438 0.22% 129 38957 0.23% 130 40748 0.24% 131 43161 0.25% 132 45487 0.27% 133 48195 0.28% 134 50500 0.30% 135 53366 0.31% 136 56506 0.33% 137 60132 0.35% 138 63404 0.37% 139 67967 0.40% 140 72829 0.43% 141 79364 0.46% 142 87498 0.51% 143 96494 0.56% 144 110112 0.64% 145 128278 0.75% 146 156998 0.92% 147 204830 1.20% 148 304368 1.78% 149 585472 3.42% 150 3367902 19.69% 151 10649535 62.27% 17103430 reads passed initial QC criterion=sequence-density sequence-density=0.24 sequence-density-rank=1 fanout-score=2.54 fanout-score-rank=26 prefix-density=0.27 prefix-fanout=2.2 sequence=CAGGTGCAGTTTGATCCACA criterion=fanout-score sequence-density=0.01 sequence-density-rank=28 fanout-score=181.59 fanout-score-rank=1 prefix-density=0.16 prefix-fanout=14.1 sequence=CTCCTTCCTCTAAATGATAAGGTTCAGTGGACTTCTCGCGACGTCGCCGGCGGCGAACCGCCCACGTCGCCGCGATCCGAACACTTCACCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGAATTCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCAAAGATTACCCGGGCCTGTCGGCCAAGGCTATAGACTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCTTGGCCTGGAAGGCCATAGTCCCTCTAAGAAGCTGGCCGCGGAGGGTCACCTCCGCATAGCTAGTTAGCAGGCTGAGGTCTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCATGCACCAC criterion=sequence-density sequence-density=0.38 sequence-density-rank=1 fanout-score=2.42 fanout-score-rank=28 prefix-density=0.40 prefix-fanout=2.3 sequence=ATGTACCCTGACTTAGGTTTCTCAGA criterion=fanout-score sequence-density=0.02 sequence-density-rank=31 fanout-score=94.36 fanout-score-rank=1 prefix-density=0.12 prefix-fanout=12.6 sequence=AAGAAAAACAAAAAAGAAATGGATGCCAAAGCTCTCTTCTTCTTTGCCTTGTTGTCCTTCTCAGCTGTGTCGGTCAGGCCGGCATTAGCAGAAAATGAAGAAGACCCTGGTCTTGTTATGAACTTTTACAAGGATACATGCCCTCAAGCTGAGGACATTGTCAAAGAACAAGTTAGACTCCTTTACAAGAGACACAAAAACACTGCATTTTCTTGGCTAAGAAACATCTTCCATGACTGTGCTGTTCAGTCATGTGATGCTTCACTGCTGCTGGACTCAACAAGGAGGACCTTGTCCGAGAAGGAGACAGACAGGAGCTTTGGCCTCAGGAACTTTAGATACTTTGACGATATCAAAGAAGCTGTTGAAAGAGAGTGTCCTGGAGTCGTTTCCTGTGCTGATATTCTTGTCCTGTCTGCTAGAGATGGCATTGTTTCGCTAGGAGGACCTCATATCCCTCTCAAAACTGGAAGAAGGGATGGCAGGAAGAGCAGAGCAGATGTGATCGAGG SRR7180063 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 10 16:16:35 Started mapping on | Feb 10 16:16:35 Finished on | Feb 10 16:19:00 Mapping speed, Million of reads per hour | 424.64 Number of input reads | 17103430 Average input read length | 296 UNIQUE READS: Uniquely mapped reads number | 15820012 Uniquely mapped reads % | 92.50% Average mapped length | 295.89 Number of splices: Total | 15555389 Number of splices: Annotated (sjdb) | 15235598 Number of splices: GT/AG | 15298111 Number of splices: GC/AG | 201252 Number of splices: AT/AC | 11364 Number of splices: Non-canonical | 44662 Mismatch rate per base, % | 0.35% Deletion rate per base | 0.03% Deletion average length | 2.77 Insertion rate per base | 0.02% Insertion average length | 2.64 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 403226 % of reads mapped to multiple loci | 2.36% Number of reads mapped to too many loci | 108738 % of reads mapped to too many loci | 0.64% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 4.37% % of reads unmapped: other | 0.14% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 895526 895526 895526 N_multimapping 403226 403226 403226 N_noFeature 448320 15677205 504064 N_ambiguous 175160 795 87664 UnstrandedReadsAssigned:15196532 PositiveStrandReadsAssigned:142012 NegativeStrandReadsAssigned:15228284 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=150 echo kmer=145 SRR7180063 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: SRR7180063-trimmed-pair1.fastq SRR7180063-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 17,103,430 reads, 15,208,762 reads pseudoaligned [quant] estimated average fragment length: 252.531 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,151 rounds 52401 SRR7180063.ke.tsv 34699 SRR7180063.se.tsv 87100 total ==> SRR7180063.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1766.47 1154 45.507 Potri.005G024800.1.v4.1 1035 783.469 150 13.3367 Potri.004G059700.1.v4.1 961 709.527 14 1.37448 Potri.007G009000.2.v4.1 1416 1164.47 0 0 Potri.003G141000.2.v4.1 2943 2691.47 576 14.9077 Potri.016G087400.1.v4.1 270 77.0281 836 756.024 Potri.015G069301.1.v4.1 564 319.404 0 0 Potri.010G195200.1.v4.1 1773 1521.47 345.606 15.8233 Potri.012G127500.1.v4.1 977 725.501 5607 538.358 ==> SRR7180063.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 155 Potri.001G233950.v4.1 1 Potri.001G122700.v4.1 482 Potri.001G212900.v4.1 0 Potri.001G182400.v4.1 1 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 0 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 545 SRR7180063 completed mapping pipeline successfully