Starting /dee2/code/volunteer_pipeline.sh SRR23047995 current disk space = 3050080202752 free memory = 1298109140 SRR23047995 SRAfilesize 1a72174abf094683f48ae8b8b6f55c70 SRR23047995.sra SRR23047995.sra file validated SRR23047995 is paired end SRR23047995 is conventional basespace SRR23047995 read1 length is 150 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR23047995_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 150 %GC 44 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.11075 37.0 37.0 37.0 37.0 37.0 2 36.257 37.0 37.0 37.0 37.0 37.0 3 36.3625 37.0 37.0 37.0 37.0 37.0 4 36.3515 37.0 37.0 37.0 37.0 37.0 5 36.3795 37.0 37.0 37.0 37.0 37.0 6 36.3275 37.0 37.0 37.0 37.0 37.0 7 36.3375 37.0 37.0 37.0 37.0 37.0 8 36.304 37.0 37.0 37.0 37.0 37.0 9 36.3145 37.0 37.0 37.0 37.0 37.0 10-14 36.3991 37.0 37.0 37.0 37.0 37.0 15-19 36.3426 37.0 37.0 37.0 37.0 37.0 20-24 36.2941 37.0 37.0 37.0 37.0 37.0 25-29 36.24640000000001 37.0 37.0 37.0 37.0 37.0 30-34 36.2148 37.0 37.0 37.0 37.0 37.0 35-39 36.1734 37.0 37.0 37.0 37.0 37.0 40-44 36.1001 37.0 37.0 37.0 37.0 37.0 45-49 36.1053 37.0 37.0 37.0 37.0 37.0 50-54 36.066500000000005 37.0 37.0 37.0 37.0 37.0 55-59 36.0502 37.0 37.0 37.0 37.0 37.0 60-64 36.0274 37.0 37.0 37.0 37.0 37.0 65-69 36.0342 37.0 37.0 37.0 37.0 37.0 70-74 36.0155 37.0 37.0 37.0 37.0 37.0 75-79 36.0089 37.0 37.0 37.0 37.0 37.0 80-84 35.992399999999996 37.0 37.0 37.0 37.0 37.0 85-89 35.9735 37.0 37.0 37.0 37.0 37.0 90-94 35.9032 37.0 37.0 37.0 37.0 37.0 95-99 35.8447 37.0 37.0 37.0 37.0 37.0 100-104 35.819900000000004 37.0 37.0 37.0 37.0 37.0 105-109 35.781600000000005 37.0 37.0 37.0 37.0 37.0 110-114 35.781099999999995 37.0 37.0 37.0 37.0 37.0 115-119 35.7692 37.0 37.0 37.0 37.0 37.0 120-124 35.7243 37.0 37.0 37.0 37.0 37.0 125-129 35.6952 37.0 37.0 37.0 37.0 37.0 130-134 35.7714 37.0 37.0 37.0 37.0 37.0 135-139 35.7153 37.0 37.0 37.0 37.0 37.0 140-144 35.5141 37.0 37.0 37.0 37.0 37.0 145-149 35.567899999999995 37.0 37.0 37.0 37.0 37.0 150 35.7235 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 23 1.0 24 1.0 25 4.0 26 4.0 27 7.0 28 13.0 29 17.0 30 27.0 31 54.0 32 97.0 33 139.0 34 185.0 35 472.0 36 2810.0 37 169.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 38.25671941723185 8.11353931173072 10.123084652097463 43.506656618939964 2 20.175 12.375 37.95 29.5 3 24.8 15.75 22.625 36.825 4 26.224999999999998 25.3 17.95 30.525000000000002 5 23.45 28.825 24.2 23.525 6 19.775000000000002 31.8 27.700000000000003 20.724999999999998 7 13.125 26.125 42.775 17.974999999999998 8 19.225 21.525 34.175 25.074999999999996 9 17.875 23.525 35.699999999999996 22.900000000000002 10-14 20.27 29.145 27.67 22.915 15-19 19.97 28.16 28.910000000000004 22.96 20-24 20.47 27.305 29.175 23.05 25-29 20.495 27.61 28.165000000000003 23.73 30-34 20.044999999999998 27.715 28.494999999999997 23.745 35-39 20.755000000000003 27.74 27.779999999999998 23.724999999999998 40-44 20.265 27.74 28.03 23.965 45-49 20.29 27.68 27.650000000000002 24.38 50-54 20.44 27.67 27.98 23.91 55-59 20.419999999999998 28.075 28.050000000000004 23.455000000000002 60-64 20.18 28.04 27.779999999999998 24.0 65-69 20.14 28.175 28.13 23.555 70-74 20.87 27.650000000000002 27.975 23.505000000000003 75-79 20.645 28.07 27.884999999999998 23.400000000000002 80-84 21.035 27.589999999999996 27.87 23.505000000000003 85-89 21.11 27.994999999999997 27.345000000000002 23.549999999999997 90-94 20.46 27.85 27.815 23.875 95-99 20.555 26.71 28.665000000000003 24.07 100-104 20.825 28.299999999999997 27.485 23.39 105-109 21.145 26.965 28.12 23.77 110-114 21.044999999999998 27.915 27.73 23.31 115-119 21.3 27.48 28.04 23.18 120-124 21.165 27.0 27.595 24.240000000000002 125-129 20.48 27.625 27.87 24.025 130-134 20.990000000000002 26.974999999999998 28.225 23.810000000000002 135-139 20.785 27.27 28.13 23.815 140-144 21.55 26.665 27.91 23.875 145-149 20.69 27.24 28.07 24.0 150 18.95 28.95 28.075 24.025 >>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 0.5 16 0.5 17 0.0 18 0.0 19 0.0 20 0.0 21 0.0 22 0.5 23 0.5 24 1.5 25 2.5 26 3.0 27 8.0 28 10.0 29 12.0 30 13.5 31 19.0 32 27.0 33 36.0 34 47.5 35 52.5 36 68.5 37 91.0 38 112.5 39 146.0 40 188.5 41 227.0 42 246.0 43 271.0 44 278.5 45 262.5 46 264.0 47 260.5 48 244.0 49 205.5 50 162.0 51 149.5 52 127.0 53 100.5 54 91.5 55 69.5 56 50.0 57 42.5 58 31.5 59 19.0 60 11.5 61 8.5 62 9.0 63 6.0 64 2.5 65 2.0 66 3.5 67 4.5 68 3.0 69 1.0 70 1.0 71 1.0 72 0.5 73 0.5 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 0.475 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 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 150 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 90.45 #Duplication Level Percentage of deduplicated Percentage of total 1 90.32614704256495 81.69999999999999 2 8.927584300718628 16.150000000000002 3 0.6357103372028745 1.725 4 0.08291873963515754 0.3 5 0.027639579878385848 0.125 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 warn #Sequence Count Percentage Possible Source CCATGTGCAAGTGCCGTTCACATGGAACCTTTCCCCTCTTCGGCCTTCAA 5 0.125 No Hit >>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 0.0 0.0 0.0 0.0 0.0 84-85 0.0 0.0 0.0 0.0 0.0 86-87 0.0 0.0 0.0 0.0 0.0 88-89 0.0 0.0 0.0 0.0 0.0 90-91 0.0 0.0 0.0 0.0 0.0 92-93 0.0 0.0 0.0 0.0 0.0 94-95 0.0 0.0 0.0 0.0 0.0 96-97 0.0 0.0 0.0 0.0 0.0 98-99 0.0 0.0 0.0 0.0 0.0 100-101 0.0 0.0 0.0 0.0 0.0 102-103 0.0 0.0 0.0 0.0 0.0 104-105 0.0 0.0 0.0 0.0 0.0 106-107 0.0 0.0 0.0 0.0 0.0 108-109 0.0 0.0 0.0 0.0 0.0 110-111 0.0 0.0 0.0 0.0 0.0 112-113 0.0 0.0 0.0 0.0 0.0 114-115 0.0 0.0 0.0 0.0 0.0 116-117 0.0 0.0 0.0 0.0 0.0 118-119 0.0 0.0 0.0 0.0 0.0 120-121 0.0 0.0 0.0 0.0 0.0 122-123 0.0 0.0 0.0 0.0 0.0 124-125 0.0 0.0 0.0 0.0 0.0 126-127 0.0 0.0 0.0 0.0 0.0 128-129 0.0 0.0 0.0 0.0 0.0 130-131 0.0 0.0 0.0 0.0 0.0 132-133 0.0 0.0 0.0 0.0 0.0 134-135 0.0 0.0 0.0 0.0 0.0 136-137 0.0 0.0 0.0 0.0 0.0 138 0.0 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TGACCAT 10 0.006973645 144.0 3 CCGGTTC 10 0.006973645 144.0 1 CATAATT 10 0.006973645 144.0 7 AAAAAAA 70 1.9314211E-6 18.514284 75-79 >>END_MODULE SRR23047995 read2 length is 150 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR23047995_2.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 150 %GC 44 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 35.4695 37.0 37.0 37.0 37.0 37.0 2 35.89 37.0 37.0 37.0 37.0 37.0 3 35.8055 37.0 37.0 37.0 37.0 37.0 4 36.0105 37.0 37.0 37.0 37.0 37.0 5 36.054 37.0 37.0 37.0 37.0 37.0 6 35.9085 37.0 37.0 37.0 37.0 37.0 7 35.9365 37.0 37.0 37.0 37.0 37.0 8 36.0005 37.0 37.0 37.0 37.0 37.0 9 35.974 37.0 37.0 37.0 37.0 37.0 10-14 36.086 37.0 37.0 37.0 37.0 37.0 15-19 35.9911 37.0 37.0 37.0 37.0 37.0 20-24 35.913799999999995 37.0 37.0 37.0 37.0 37.0 25-29 35.974599999999995 37.0 37.0 37.0 37.0 37.0 30-34 35.839600000000004 37.0 37.0 37.0 37.0 37.0 35-39 35.8554 37.0 37.0 37.0 37.0 37.0 40-44 35.882400000000004 37.0 37.0 37.0 37.0 37.0 45-49 35.8136 37.0 37.0 37.0 37.0 37.0 50-54 35.707300000000004 37.0 37.0 37.0 37.0 37.0 55-59 35.74640000000001 37.0 37.0 37.0 37.0 37.0 60-64 35.6421 37.0 37.0 37.0 37.0 37.0 65-69 35.6708 37.0 37.0 37.0 37.0 37.0 70-74 35.55329999999999 37.0 37.0 37.0 37.0 37.0 75-79 35.6565 37.0 37.0 37.0 37.0 37.0 80-84 35.533100000000005 37.0 37.0 37.0 37.0 37.0 85-89 35.506899999999995 37.0 37.0 37.0 37.0 37.0 90-94 35.444 37.0 37.0 37.0 37.0 37.0 95-99 35.39209999999999 37.0 37.0 37.0 37.0 37.0 100-104 35.4083 37.0 37.0 37.0 34.6 37.0 105-109 35.21 37.0 37.0 37.0 29.8 37.0 110-114 35.319599999999994 37.0 37.0 37.0 29.8 37.0 115-119 35.1572 37.0 37.0 37.0 29.8 37.0 120-124 35.1511 37.0 37.0 37.0 27.4 37.0 125-129 35.240300000000005 37.0 37.0 37.0 29.8 37.0 130-134 35.190599999999996 37.0 37.0 37.0 27.4 37.0 135-139 34.8966 37.0 37.0 37.0 25.0 37.0 140-144 34.9728 37.0 37.0 37.0 25.0 37.0 145-149 35.0059 37.0 37.0 37.0 25.0 37.0 150 35.213 37.0 37.0 37.0 25.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 21 1.0 22 5.0 23 9.0 24 13.0 25 8.0 26 7.0 27 13.0 28 23.0 29 28.0 30 44.0 31 58.0 32 96.0 33 183.0 34 270.0 35 854.0 36 2301.0 37 87.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 35.978701825557806 20.968559837728197 14.02129817444219 29.031440162271803 2 20.0 34.475 31.225 14.299999999999999 3 20.25 32.725 25.8 21.224999999999998 4 24.15 36.325 20.375 19.15 5 24.55 38.475 21.7 15.275 6 20.625 39.050000000000004 23.799999999999997 16.525000000000002 7 18.125 22.650000000000002 40.45 18.775 8 21.8 24.224999999999998 29.475 24.5 9 23.35 24.275 29.099999999999998 23.275000000000002 10-14 23.615 29.28 25.465 21.64 15-19 22.79 29.709999999999997 27.065 20.435 20-24 23.119999999999997 29.470000000000002 26.455000000000002 20.955 25-29 23.5 28.970000000000002 26.479999999999997 21.05 30-34 22.645 29.385 26.615 21.355 35-39 23.47 28.93 26.545 21.055 40-44 23.215 29.575000000000003 26.25 20.96 45-49 22.78 28.205000000000002 27.43 21.584999999999997 50-54 22.67 29.330000000000002 26.36 21.64 55-59 23.515 28.095 26.77 21.62 60-64 23.45 28.64 26.545 21.365000000000002 65-69 23.369999999999997 28.499999999999996 27.295 20.835 70-74 23.465 29.160000000000004 26.565 20.810000000000002 75-79 23.155 28.24 26.875 21.73 80-84 22.915 28.32 26.395000000000003 22.37 85-89 23.715 28.22 26.72 21.345 90-94 23.54 28.645 26.695 21.12 95-99 23.105 28.73 26.565 21.6 100-104 23.815 28.439999999999998 26.240000000000002 21.505 105-109 23.474999999999998 28.38 27.115000000000002 21.029999999999998 110-114 23.635 28.07 27.12 21.175 115-119 23.87 28.485 27.065 20.580000000000002 120-124 23.724999999999998 27.875 27.43 20.97 125-129 23.98 27.145000000000003 27.0 21.875 130-134 23.405 28.335 27.115000000000002 21.145 135-139 24.365000000000002 28.17 27.034999999999997 20.43 140-144 23.855 27.97 27.115000000000002 21.060000000000002 145-149 23.515 27.855 27.18 21.45 150 23.799999999999997 27.825 27.0 21.375 >>END_MODULE >>Per sequence GC content pass #GC Content Count 0 0.0 1 0.5 2 0.5 3 0.0 4 0.0 5 0.0 6 0.0 7 0.5 8 0.5 9 0.5 10 0.5 11 0.0 12 0.5 13 1.5 14 1.5 15 0.5 16 1.0 17 1.5 18 0.5 19 0.0 20 0.5 21 0.5 22 0.5 23 1.5 24 2.5 25 3.0 26 3.5 27 3.5 28 4.5 29 8.5 30 11.5 31 13.0 32 20.5 33 33.0 34 49.5 35 60.0 36 82.5 37 97.5 38 112.5 39 171.0 40 200.5 41 228.0 42 259.5 43 261.0 44 270.0 45 274.0 46 278.5 47 265.5 48 247.0 49 208.0 50 158.0 51 145.0 52 117.0 53 86.0 54 71.0 55 58.0 56 41.0 57 29.5 58 29.0 59 22.0 60 14.5 61 8.5 62 8.0 63 8.0 64 4.0 65 2.5 66 2.0 67 2.0 68 3.5 69 2.0 70 0.5 71 1.0 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 0.5 96 0.5 97 0.0 98 0.5 99 0.5 100 1.0 >>END_MODULE >>Per base N content pass #Base N-Count 1 1.4000000000000001 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 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 150 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 90.85 #Duplication Level Percentage of deduplicated Percentage of total 1 90.83654375343974 82.525 2 8.365437534397358 15.2 3 0.6879471656576774 1.875 4 0.1100715465052284 0.4 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 0.0 0.0 0.0 0.0 0.0 84-85 0.0 0.0 0.0 0.0 0.0 86-87 0.0 0.0 0.0 0.0 0.0 88-89 0.0 0.0 0.0 0.0 0.0 90-91 0.0 0.0 0.0 0.0 0.0 92-93 0.0 0.0 0.0 0.0 0.0 94-95 0.0 0.0 0.0 0.0 0.0 96-97 0.0 0.0 0.0 0.0 0.0 98-99 0.0 0.0 0.0 0.0 0.0 100-101 0.0 0.0 0.0 0.0 0.0 102-103 0.0 0.0 0.0 0.0 0.0 104-105 0.0 0.0 0.0 0.0 0.0 106-107 0.0 0.0 0.0 0.0 0.0 108-109 0.0 0.0 0.0 0.0 0.0 110-111 0.0 0.0 0.0 0.0 0.0 112-113 0.0 0.0 0.0 0.0 0.0 114-115 0.0 0.0 0.0 0.0 0.0 116-117 0.0 0.0 0.0 0.0 0.0 118-119 0.0 0.0 0.0 0.0 0.0 120-121 0.0 0.0 0.0 0.0 0.0 122-123 0.0 0.0 0.0 0.0 0.0 124-125 0.0 0.0 0.0 0.0 0.0 126-127 0.0 0.0 0.0 0.0 0.0 128-129 0.0 0.0 0.0 0.0 0.0 130-131 0.0 0.0 0.0 0.0 0.0 132-133 0.0 0.0 0.0 0.0 0.0 134-135 0.0 0.0 0.0 0.0 0.0 136-137 0.0 0.0 0.0 0.0 0.0 138 0.0 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TGACCAT 10 0.0069754543 143.9875 3 GAACCCT 10 0.0069754543 143.9875 6 ACCCTTG 10 0.0069754543 143.9875 8 GCAGAAC 10 0.0069754543 143.9875 3 >>END_MODULE Read 1856265 spots for SRR23047995.sra Written 1856265 spots for SRR23047995.sra Read 1856265 spots for SRR23047995.sra Written 1856265 spots for SRR23047995.sra Read 1856265 spots for SRR23047995.sra Written 1856265 spots for SRR23047995.sra Read 1856265 spots for SRR23047995.sra Written 1856265 spots for SRR23047995.sra Read 1856265 spots for SRR23047995.sra Written 1856265 spots for SRR23047995.sra Read 1856265 spots for SRR23047995.sra Written 1856265 spots for SRR23047995.sra Read 1856265 spots for SRR23047995.sra Written 1856265 spots for SRR23047995.sra Read 1856265 spots for SRR23047995.sra Written 1856265 spots for SRR23047995.sra Read 1856265 spots for SRR23047995.sra Written 1856265 spots for SRR23047995.sra Read 1856265 spots for SRR23047995.sra Written 1856265 spots for SRR23047995.sra Read 1856265 spots for SRR23047995.sra Written 1856265 spots for SRR23047995.sra Read 1856265 spots for SRR23047995.sra Written 1856265 spots for SRR23047995.sra Read 1856278 spots for SRR23047995.sra Written 1856278 spots for SRR23047995.sra Read 1856265 spots for SRR23047995.sra Written 1856265 spots for SRR23047995.sra Read 1856265 spots for SRR23047995.sra Written 1856265 spots for SRR23047995.sra Read 1856265 spots for SRR23047995.sra Written 1856265 spots for SRR23047995.sra Read 1856265 spots for SRR23047995.sra Written 1856265 spots for SRR23047995.sra Read 1856265 spots for SRR23047995.sra Written 1856265 spots for SRR23047995.sra Read 1856265 spots for SRR23047995.sra Written 1856265 spots for SRR23047995.sra Read 1856265 spots for SRR23047995.sra Written 1856265 spots for SRR23047995.sra SRR ids: ['SRR23047995.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_mrqp0ny3 SRR23047995.sra spots: 37125313 blocks: [[1, 1856265], [1856266, 3712530], [3712531, 5568795], [5568796, 7425060], [7425061, 9281325], [9281326, 11137590], [11137591, 12993855], [12993856, 14850120], [14850121, 16706385], [16706386, 18562650], [18562651, 20418915], [20418916, 22275180], [22275181, 24131445], [24131446, 25987710], [25987711, 27843975], [27843976, 29700240], [29700241, 31556505], [31556506, 33412770], [33412771, 35269035], [35269036, 37125313]] SRR23047995 file size 12522594 SRR23047995 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 SRR23047995 SRR23047995_1.fastq SRR23047995_2.fastq Input file: SRR23047995_1.fastq Paired file: SRR23047995_2.fastq trimmed: SRR23047995-trimmed-pair1.fastq, SRR23047995-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 Wed Feb 12 07:07:48 2025 >> started Wed Feb 12 07:08:29 2025 >> done (40.235s) 37125313 read pairs processed; of these: 0 ( 0.00%) short read pairs filtered out after trimming by size control 0 ( 0.00%) empty read pairs filtered out after trimming by size control 37125313 (100.00%) read pairs available; of these: 88385 ( 0.24%) trimmed read pairs available after processing 37036928 (99.76%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 20 1 0.00% 21 1 0.00% 22 0 0.00% 23 4 0.00% 24 1 0.00% 25 2 0.00% 26 1 0.00% 27 1 0.00% 28 4 0.00% 29 2 0.00% 30 2 0.00% 31 3 0.00% 32 4 0.00% 33 3 0.00% 34 5 0.00% 35 1 0.00% 36 6 0.00% 37 4 0.00% 38 6 0.00% 39 6 0.00% 40 8 0.00% 41 2 0.00% 42 7 0.00% 43 6 0.00% 44 8 0.00% 45 6 0.00% 46 8 0.00% 47 10 0.00% 48 6 0.00% 49 13 0.00% 50 7 0.00% 51 5 0.00% 52 8 0.00% 53 9 0.00% 54 13 0.00% 55 14 0.00% 56 11 0.00% 57 16 0.00% 58 11 0.00% 59 18 0.00% 60 25 0.00% 61 8 0.00% 62 15 0.00% 63 13 0.00% 64 15 0.00% 65 17 0.00% 66 11 0.00% 67 17 0.00% 68 19 0.00% 69 20 0.00% 70 13 0.00% 71 15 0.00% 72 13 0.00% 73 22 0.00% 74 16 0.00% 75 25 0.00% 76 10 0.00% 77 20 0.00% 78 19 0.00% 79 17 0.00% 80 18 0.00% 81 22 0.00% 82 18 0.00% 83 27 0.00% 84 30 0.00% 85 19 0.00% 86 21 0.00% 87 22 0.00% 88 20 0.00% 89 21 0.00% 90 27 0.00% 91 20 0.00% 92 19 0.00% 93 18 0.00% 94 18 0.00% 95 13 0.00% 96 19 0.00% 97 14 0.00% 98 20 0.00% 99 17 0.00% 100 23 0.00% 101 20 0.00% 102 24 0.00% 103 23 0.00% 104 29 0.00% 105 24 0.00% 106 28 0.00% 107 33 0.00% 108 28 0.00% 109 24 0.00% 110 35 0.00% 111 25 0.00% 112 16 0.00% 113 23 0.00% 114 20 0.00% 115 24 0.00% 116 21 0.00% 117 23 0.00% 118 34 0.00% 119 14 0.00% 120 29 0.00% 121 46 0.00% 122 44 0.00% 123 46 0.00% 124 42 0.00% 125 23 0.00% 126 12 0.00% 127 20 0.00% 128 28 0.00% 129 16 0.00% 130 26 0.00% 131 40 0.00% 132 39 0.00% 133 41 0.00% 134 39 0.00% 135 32 0.00% 136 40 0.00% 137 42 0.00% 138 0 0.00% 139 0 0.00% 140 14 0.00% 141 98 0.00% 142 83 0.00% 143 129 0.00% 144 0 0.00% 145 285 0.00% 146 20154 0.05% 147 20920 0.06% 148 21745 0.06% 149 22885 0.06% 150 37036928 99.76% 37125313 reads passed initial QC criterion=sequence-density sequence-density=0.25 sequence-density-rank=1 fanout-score=2.00 fanout-score-rank=39 prefix-density=0.25 prefix-fanout=2.0 sequence=TGGCCACGGTCTAGACGGCGCCCACCGCCAGGTGAGGCTGCGGCCCACACAGTGTAAGGGCAATTGTTTCGGATTTCGAAGGTGGCTGCATTAGTAGAGATGATGAGAAGGCTAAAGAGGAGGGAGGAGGTGAGAAATTTGGTTAAGTG criterion=fanout-score sequence-density=0.01 sequence-density-rank=39 fanout-score=224.20 fanout-score-rank=1 prefix-density=0.12 prefix-fanout=10.9 sequence=TCCTTCCTCTAAATGATAAGGTTCAGTGGACTTCTCGCGACGTCGCCGGCGGCGAACCGCCCACGTCGCCGCGATCCGAACACTTCACCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGAATTCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCAAAGATTACCCGGGCCTGTCGGCCAAGGCTATAGACTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCTTGGCCTGGAAGGCCATAGTCCCTCTAAGAAGCTGGCCGCGGAGGGTCACCTCCGCATAGCTAGTTAGCAGGCTGAGGTCTCGTTCGTTAAC criterion=sequence-density sequence-density=0.35 sequence-density-rank=1 fanout-score=2.34 fanout-score-rank=32 prefix-density=0.37 prefix-fanout=2.2 sequence=ACCAAATTTCTCACCTCCTCCCTCCTCTTTAGCCTTCTCATCATCTCTACTAATGCAGCCACCTTCGAAATCCGAAACAATTGCCCTTACACTGTGTGGGCCGCAGCCTCACCTGGCGGTGGGCGCCGTCTAGACCGTGGCCA criterion=fanout-score sequence-density=0.02 sequence-density-rank=30 fanout-score=146.94 fanout-score-rank=1 prefix-density=0.19 prefix-fanout=18.2 sequence=CAAGAAGATCAACTGTCTCTCTGCCTGGTTTGTATTCCAAGAAATGGAGAAAGTCCAAAAGCTCCTTTGTGTGGCTCTATTGCTTGCAGTACTAGCCATAGCAAGCAATATTGCGAATGCCCAGAGTACCATATGCAAAATGCCTGTTGCTGGCCTAATGTCATGCAAGCCTTCTGTAACTCCTCCTAACCCTACCGCACCCTCGGCAGACTGCTGCTCGGCACTTTCGCATGCTGACATAAACTGCCTTTGCTCCTACAAAAATTCCAACCTGCTCCCTTCC SRR23047995 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 12 07:09:12 Started mapping on | Feb 12 07:09:12 Finished on | Feb 12 07:12:29 Mapping speed, Million of reads per hour | 678.43 Number of input reads | 37125313 Average input read length | 299 UNIQUE READS: Uniquely mapped reads number | 35186802 Uniquely mapped reads % | 94.78% Average mapped length | 298.98 Number of splices: Total | 34274798 Number of splices: Annotated (sjdb) | 33589973 Number of splices: GT/AG | 33735483 Number of splices: GC/AG | 441971 Number of splices: AT/AC | 31153 Number of splices: Non-canonical | 66191 Mismatch rate per base, % | 0.28% Deletion rate per base | 0.02% Deletion average length | 3.02 Insertion rate per base | 0.01% Insertion average length | 2.05 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 994397 % of reads mapped to multiple loci | 2.68% Number of reads mapped to too many loci | 410838 % of reads mapped to too many loci | 1.11% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.15% % of reads unmapped: other | 0.29% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 944114 944114 944114 N_multimapping 994397 994397 994397 N_noFeature 997689 34873247 1142326 N_ambiguous 355280 2503 184590 UnstrandedReadsAssigned:33833833 PositiveStrandReadsAssigned:311052 NegativeStrandReadsAssigned:33859886 Dataset is classified negative stranded MeadianReadLen=150 20thPercentileLength=150 echo kmer=145 SRR23047995 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: SRR23047995-trimmed-pair1.fastq SRR23047995-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 37,125,313 reads, 34,626,206 reads pseudoaligned [quant] estimated average fragment length: 294.841 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,248 rounds 52401 SRR23047995.ke.tsv 34699 SRR23047995.se.tsv 87100 total ==> SRR23047995.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1724.16 5374 80.1391 Potri.005G024800.1.v4.1 1035 741.159 1255 43.5368 Potri.004G059700.1.v4.1 961 667.175 151 5.81917 Potri.007G009000.2.v4.1 1416 1122.16 0 0 Potri.003G141000.2.v4.1 2943 2649.16 1508.22 14.6379 Potri.016G087400.1.v4.1 270 47.7355 1233 664.119 Potri.015G069301.1.v4.1 564 272.227 0 0 Potri.010G195200.1.v4.1 1773 1479.16 1101.94 19.1543 Potri.012G127500.1.v4.1 977 683.17 12948 487.302 ==> SRR23047995.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 3 Potri.001G233950.v4.1 1 Potri.001G122700.v4.1 674 Potri.001G212900.v4.1 0 Potri.001G182400.v4.1 0 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 4 Potri.001G416900.v4.1 2 Potri.001G452600.v4.1 1911 SRR23047995 completed mapping pipeline successfully