Starting /dee2/code/volunteer_pipeline.sh SRR12670103 current disk space = 3057574379520 free memory = 1471502912 SRR12670103 SRAfilesize 259df8637090f47b8d5724296ea70459 SRR12670103.sra SRR12670103.sra file validated SRR12670103 is paired end SRR12670103 is conventional basespace SRR12670103 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12670103_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 44 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.558 37.0 37.0 37.0 37.0 37.0 2 36.36175 37.0 37.0 37.0 37.0 37.0 3 36.6395 37.0 37.0 37.0 37.0 37.0 4 36.582 37.0 37.0 37.0 37.0 37.0 5 36.65 37.0 37.0 37.0 37.0 37.0 6 36.6815 37.0 37.0 37.0 37.0 37.0 7 36.5225 37.0 37.0 37.0 37.0 37.0 8 36.6235 37.0 37.0 37.0 37.0 37.0 9 36.6575 37.0 37.0 37.0 37.0 37.0 10-14 36.6558 37.0 37.0 37.0 37.0 37.0 15-19 36.625600000000006 37.0 37.0 37.0 37.0 37.0 20-24 36.599000000000004 37.0 37.0 37.0 37.0 37.0 25-29 36.562 37.0 37.0 37.0 37.0 37.0 30-34 36.5156 37.0 37.0 37.0 37.0 37.0 35-39 36.5384 37.0 37.0 37.0 37.0 37.0 40-44 36.519999999999996 37.0 37.0 37.0 37.0 37.0 45-49 36.5106 37.0 37.0 37.0 37.0 37.0 50-54 36.4585 37.0 37.0 37.0 37.0 37.0 55-59 36.4624 37.0 37.0 37.0 37.0 37.0 60-64 36.418 37.0 37.0 37.0 37.0 37.0 65-69 36.3941 37.0 37.0 37.0 37.0 37.0 70-74 36.325300000000006 37.0 37.0 37.0 37.0 37.0 75-79 36.3942 37.0 37.0 37.0 37.0 37.0 80-84 36.370799999999996 37.0 37.0 37.0 37.0 37.0 85-89 36.3012 37.0 37.0 37.0 37.0 37.0 90-94 36.348800000000004 37.0 37.0 37.0 37.0 37.0 95-99 36.211200000000005 37.0 37.0 37.0 37.0 37.0 100-104 36.2799 37.0 37.0 37.0 37.0 37.0 105-109 36.213699999999996 37.0 37.0 37.0 37.0 37.0 110-114 36.142900000000004 37.0 37.0 37.0 37.0 37.0 115-119 36.155100000000004 37.0 37.0 37.0 37.0 37.0 120-124 36.0772 37.0 37.0 37.0 37.0 37.0 125-129 35.978 37.0 37.0 37.0 37.0 37.0 130-134 35.9864 37.0 37.0 37.0 37.0 37.0 135-139 35.903999999999996 37.0 37.0 37.0 37.0 37.0 140-144 35.6964 37.0 37.0 37.0 37.0 37.0 145-149 35.511 37.0 37.0 37.0 37.0 37.0 150-151 35.295249999999996 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 18 1.0 19 0.0 20 0.0 21 0.0 22 0.0 23 1.0 24 1.0 25 2.0 26 3.0 27 4.0 28 10.0 29 14.0 30 19.0 31 32.0 32 57.0 33 81.0 34 129.0 35 271.0 36 2969.0 37 406.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 42.475 10.424999999999999 6.9 40.2 2 17.94036582310198 12.703583061889251 38.286143823603105 31.069907291405663 3 16.825000000000003 17.7 28.9 36.575 4 21.675 25.424999999999997 24.725 28.175 5 21.025 32.1 25.6 21.275 6 20.625 34.050000000000004 25.95 19.375 7 16.35 24.975 42.525 16.150000000000002 8 18.075 25.25 31.65 25.025 9 18.975 23.35 33.6 24.075 10-14 19.384999999999998 29.585 28.185 22.845 15-19 19.57 28.425 27.625 24.38 20-24 20.345 28.34 27.334999999999997 23.98 25-29 20.125 28.155 27.55 24.169999999999998 30-34 20.119999999999997 28.65 27.834999999999997 23.395 35-39 19.945 28.51 27.365000000000002 24.18 40-44 20.375 28.310000000000002 27.634999999999998 23.68 45-49 20.61 28.854999999999997 26.974999999999998 23.56 50-54 20.630000000000003 28.360000000000003 27.034999999999997 23.974999999999998 55-59 20.200000000000003 28.12 27.644999999999996 24.035 60-64 20.835 27.85 28.235 23.080000000000002 65-69 20.255000000000003 28.439999999999998 27.83 23.474999999999998 70-74 20.41 28.315 27.07 24.205 75-79 20.51 27.705000000000002 27.42 24.365000000000002 80-84 20.76 28.199999999999996 27.584999999999997 23.455000000000002 85-89 20.955 28.194999999999997 27.165 23.685000000000002 90-94 20.5 28.144999999999996 27.73 23.625 95-99 21.275 27.744999999999997 27.310000000000002 23.669999999999998 100-104 21.005 28.449999999999996 27.145000000000003 23.400000000000002 105-109 21.21 28.799999999999997 27.139999999999997 22.85 110-114 20.835 28.515 27.29 23.36 115-119 21.51 27.985 27.700000000000003 22.805 120-124 21.27 28.095 26.655 23.98 125-129 20.95 28.660000000000004 26.38 24.01 130-134 21.6 28.485 26.365 23.549999999999997 135-139 21.795 28.375 26.009999999999998 23.82 140-144 22.15 27.815 26.555 23.48 145-149 22.64 27.93 25.990000000000002 23.44 150-151 21.775 27.8875 25.662499999999998 24.675 >>END_MODULE >>Per sequence GC content pass #GC Content Count 0 1.0 1 0.5 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 1.0 20 1.5 21 1.0 22 0.5 23 2.0 24 2.5 25 1.0 26 4.0 27 9.0 28 12.0 29 12.5 30 13.5 31 19.5 32 30.5 33 37.0 34 44.5 35 68.0 36 92.0 37 107.0 38 124.5 39 150.5 40 170.0 41 189.0 42 219.5 43 251.5 44 286.5 45 273.5 46 250.5 47 250.0 48 241.5 49 213.5 50 186.0 51 163.5 52 119.5 53 98.0 54 82.5 55 67.0 56 57.5 57 37.5 58 29.0 59 30.5 60 19.0 61 6.5 62 4.5 63 4.0 64 3.0 65 3.5 66 3.5 67 1.5 68 0.5 69 0.5 70 0.5 71 0.5 72 0.0 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 pass #Base N-Count 1 0.0 2 0.22499999999999998 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 80.85 #Duplication Level Percentage of deduplicated Percentage of total 1 81.88002473716759 66.2 2 13.883735312306742 22.45 3 3.1230674087816945 7.575 4 0.927643784786642 3.0 5 0.15460729746444032 0.625 6 0.030921459492888066 0.15 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 ATCAGCAGTCCTTGTCAGCACTGACAAGAAGTAATATTGTTTCCCATCGA 6 0.15 No Hit GGGAGAAATATGAACTCAAACAAAGCTAAATGCCCTTCATAATAAGCATT 5 0.125 No Hit CTTGGAGATGTGAACAACAAGCTTGTCCATGAAAGCAGGAGCAATGTAGA 5 0.125 No Hit GCCTTCTTGAAGTCGGTATGTGTCACCTTCATGCGCCGCTCTCGTAAAGC 5 0.125 No Hit CCCCAATCACTTGCAGTATTCCTTTGTTTATTATCAATTCTACAACGAAA 5 0.125 No Hit GAACTAAACAATGGGTCTGCAGCAGAGAAACCAAGACCACGGAGGCTGGT 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 0.0125 0.0 0.0 0.0 0.0 44-45 0.037500000000000006 0.0 0.0 0.0 0.0 46-47 0.05 0.0 0.0 0.0 0.0 48-49 0.05 0.0 0.0 0.0 0.0 50-51 0.05 0.0 0.0 0.0 0.0 52-53 0.05 0.0 0.0 0.0 0.0 54-55 0.05 0.0 0.0 0.0 0.0 56-57 0.05 0.0 0.0 0.0 0.0 58-59 0.15 0.0 0.0 0.0 0.0 60-61 0.15 0.0 0.0 0.0 0.0 62-63 0.2 0.0 0.0 0.0 0.0 64-65 0.2 0.0 0.0 0.0 0.0 66-67 0.225 0.0 0.0 0.0 0.0 68-69 0.225 0.0 0.0 0.0 0.0 70-71 0.25 0.0 0.0 0.0 0.0 72-73 0.275 0.0 0.0 0.0 0.0 74-75 0.36250000000000004 0.0 0.0 0.0 0.0 76-77 0.4625 0.0 0.0 0.0 0.0 78-79 0.5125 0.0 0.0 0.0 0.0 80-81 0.5874999999999999 0.0 0.0 0.0 0.0 82-83 0.65 0.0 0.0 0.0 0.0 84-85 0.7625 0.0 0.0 0.0 0.0 86-87 0.9375 0.0 0.0 0.0 0.0 88-89 1.15 0.0 0.0 0.0 0.0 90-91 1.3625 0.0 0.0 0.0 0.0 92-93 1.6375 0.0 0.0 0.0 0.0 94-95 2.0375 0.0 0.0 0.0 0.0 96-97 2.2875 0.0 0.0 0.0 0.0 98-99 2.7375 0.0 0.0 0.0 0.0 100-101 3.1875 0.0 0.0 0.0 0.0 102-103 3.425 0.0 0.0 0.0 0.0 104-105 3.9625 0.0 0.0 0.0 0.0 106-107 4.4625 0.0 0.0 0.0 0.0 108-109 4.875 0.0 0.0 0.0 0.0 110-111 5.5 0.0 0.0 0.0 0.0 112-113 5.925 0.0 0.0 0.0 0.0 114-115 6.3 0.0 0.0 0.0 0.0 116-117 6.7875 0.0 0.0 0.0 0.0 118-119 7.300000000000001 0.0 0.0 0.0 0.0 120-121 7.925 0.0 0.0 0.0 0.0 122-123 8.4875 0.0 0.0 0.0 0.0 124-125 9.462499999999999 0.0 0.0 0.0 0.0 126-127 10.1375 0.0 0.0 0.0 0.0 128-129 10.925 0.0 0.0 0.0 0.0 130-131 11.45 0.0 0.0 0.0 0.0 132-133 11.975 0.0 0.0 0.0 0.0 134-135 12.5625 0.0 0.0 0.0 0.0 136-137 13.225 0.0 0.0 0.0 0.0 138-139 13.975 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position CCACGAA 10 0.006830828 145.0 1 CCTGAAA 10 0.006830828 145.0 8 CACGAAA 10 0.006830828 145.0 2 ACGAAAG 10 0.006830828 145.0 3 >>END_MODULE SRR12670103 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12670103_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 36.2645 37.0 37.0 37.0 37.0 37.0 2 36.082 37.0 37.0 37.0 37.0 37.0 3 36.236 37.0 37.0 37.0 37.0 37.0 4 36.2125 37.0 37.0 37.0 37.0 37.0 5 36.3675 37.0 37.0 37.0 37.0 37.0 6 36.303 37.0 37.0 37.0 37.0 37.0 7 36.36 37.0 37.0 37.0 37.0 37.0 8 36.4205 37.0 37.0 37.0 37.0 37.0 9 36.2225 37.0 37.0 37.0 37.0 37.0 10-14 36.339299999999994 37.0 37.0 37.0 37.0 37.0 15-19 36.2915 37.0 37.0 37.0 37.0 37.0 20-24 36.2582 37.0 37.0 37.0 37.0 37.0 25-29 36.1949 37.0 37.0 37.0 37.0 37.0 30-34 36.1836 37.0 37.0 37.0 37.0 37.0 35-39 36.189800000000005 37.0 37.0 37.0 37.0 37.0 40-44 36.1362 37.0 37.0 37.0 37.0 37.0 45-49 36.123 37.0 37.0 37.0 37.0 37.0 50-54 36.068799999999996 37.0 37.0 37.0 37.0 37.0 55-59 36.1048 37.0 37.0 37.0 37.0 37.0 60-64 36.0309 37.0 37.0 37.0 37.0 37.0 65-69 35.9652 37.0 37.0 37.0 37.0 37.0 70-74 36.028800000000004 37.0 37.0 37.0 37.0 37.0 75-79 35.9716 37.0 37.0 37.0 37.0 37.0 80-84 35.938300000000005 37.0 37.0 37.0 37.0 37.0 85-89 35.9221 37.0 37.0 37.0 37.0 37.0 90-94 35.9019 37.0 37.0 37.0 37.0 37.0 95-99 35.852 37.0 37.0 37.0 37.0 37.0 100-104 35.8223 37.0 37.0 37.0 37.0 37.0 105-109 35.7047 37.0 37.0 37.0 37.0 37.0 110-114 35.691500000000005 37.0 37.0 37.0 37.0 37.0 115-119 35.7815 37.0 37.0 37.0 37.0 37.0 120-124 35.657 37.0 37.0 37.0 37.0 37.0 125-129 35.5884 37.0 37.0 37.0 37.0 37.0 130-134 35.4577 37.0 37.0 37.0 37.0 37.0 135-139 35.361399999999996 37.0 37.0 37.0 37.0 37.0 140-144 35.330200000000005 37.0 37.0 37.0 37.0 37.0 145-149 35.0615 37.0 37.0 37.0 29.8 37.0 150-151 34.77825 37.0 37.0 37.0 25.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 12 2.0 13 2.0 14 1.0 15 6.0 16 0.0 17 2.0 18 0.0 19 3.0 20 1.0 21 2.0 22 6.0 23 8.0 24 8.0 25 1.0 26 10.0 27 4.0 28 10.0 29 14.0 30 17.0 31 30.0 32 72.0 33 101.0 34 202.0 35 576.0 36 2674.0 37 248.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 39.85 22.15 10.375 27.625 2 26.775 26.724999999999998 30.15 16.35 3 19.725 28.1 31.775 20.4 4 23.35 33.900000000000006 23.825 18.925 5 24.925 36.175000000000004 22.325 16.575 6 21.625 38.65 22.5 17.224999999999998 7 19.725 22.225 38.725 19.325 8 21.7 25.624999999999996 28.749999999999996 23.925 9 21.45 23.25 30.65 24.65 10-14 23.365 28.560000000000002 26.61 21.465 15-19 22.665 27.894999999999996 28.52 20.919999999999998 20-24 22.7 28.910000000000004 27.55 20.84 25-29 23.255 28.24 27.634999999999998 20.87 30-34 22.900000000000002 28.095 28.299999999999997 20.705000000000002 35-39 22.695 28.29 27.694999999999997 21.32 40-44 23.05 28.425 27.43 21.095 45-49 23.13 28.384999999999998 27.750000000000004 20.735 50-54 23.535 28.005000000000003 27.215 21.245 55-59 22.939999999999998 28.134999999999998 27.644999999999996 21.279999999999998 60-64 23.35 27.735 27.715 21.2 65-69 23.325000000000003 28.315 27.325 21.035 70-74 23.65 27.93 27.575 20.845 75-79 23.325000000000003 28.16 27.375 21.14 80-84 23.24 28.634999999999998 27.42 20.705000000000002 85-89 23.39 28.555000000000003 27.12 20.935000000000002 90-94 23.89 27.48 28.08 20.549999999999997 95-99 23.945 29.005 26.245 20.805 100-104 24.474999999999998 28.799999999999997 26.229999999999997 20.495 105-109 24.21 27.565 27.88 20.345 110-114 24.9 27.455000000000002 26.865 20.78 115-119 25.11 27.815 27.169999999999998 19.905 120-124 25.629999999999995 27.54 26.779999999999998 20.05 125-129 25.905 28.605000000000004 25.755 19.735 130-134 26.26 27.97 26.365 19.405 135-139 26.240000000000002 28.084999999999997 26.305 19.37 140-144 26.900000000000002 27.689999999999998 26.27 19.139999999999997 145-149 27.139999999999997 27.955000000000002 26.290000000000003 18.615000000000002 150-151 29.849999999999998 26.8375 25.75 17.5625 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 0.0 1 0.0 2 0.0 3 0.0 4 0.0 5 0.5 6 0.5 7 0.0 8 0.0 9 0.0 10 0.0 11 0.0 12 0.0 13 0.5 14 0.5 15 0.0 16 0.0 17 0.0 18 1.0 19 1.0 20 0.5 21 1.0 22 2.0 23 2.0 24 1.5 25 2.5 26 5.0 27 6.5 28 6.5 29 12.0 30 14.5 31 20.0 32 30.0 33 37.5 34 56.0 35 66.0 36 80.0 37 103.5 38 137.0 39 166.0 40 183.0 41 224.5 42 275.5 43 270.5 44 257.0 45 270.5 46 258.0 47 238.5 48 221.5 49 208.5 50 172.5 51 142.5 52 122.5 53 81.0 54 67.0 55 62.5 56 49.5 57 37.5 58 27.5 59 19.0 60 11.5 61 9.0 62 5.5 63 4.0 64 2.0 65 3.5 66 2.5 67 1.0 68 1.5 69 1.0 70 1.0 71 0.5 72 0.0 73 0.5 74 1.5 75 1.5 76 1.0 77 0.5 78 0.5 79 1.5 80 1.0 81 0.0 82 0.0 83 0.0 84 0.5 85 0.5 86 0.0 87 0.0 88 0.0 89 1.0 90 1.0 91 0.5 92 0.5 93 0.0 94 0.0 95 0.0 96 0.0 97 0.0 98 0.0 99 0.5 100 1.0 >>END_MODULE >>Per base N content pass #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 0.0 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 80.875 #Duplication Level Percentage of deduplicated Percentage of total 1 82.41112828438949 66.64999999999999 2 13.508500772797527 21.85 3 2.7820710973724885 6.75 4 0.9891808346213292 3.2 5 0.1545595054095827 0.625 6 0.061823802163833076 0.3 7 0.030911901081916538 0.17500000000000002 8 0.030911901081916538 0.2 9 0.0 0.0 >10 0.030911901081916538 0.25 >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 AGAACACATTCATACTCCAAGTCTTTTAGTTCATCCATTTAAGCTTAATC 10 0.25 No Hit AGAGAACACATTCATACTCCAAGTCTTTTAGTTCATCCATTTAAGCTTAA 8 0.2 No Hit AACACATTCATACTCCAAGTCTTTTAGTTCATCCATTTAAGCTTAATCAA 7 0.17500000000000002 No Hit CAGAGAACACATTCATACTCCAAGTCTTTTAGTTCATCCATTTAAGCTTA 6 0.15 No Hit GCACTCACTGTGCTCATTGGTGCTGCTGCCCTTGGCTCAAAGGTTGCTCC 6 0.15 No Hit GGAAGATTGAATTCCCTCTTCCTGATATCAAAACAAGGAGGCGTATCTTC 5 0.125 No Hit TGACTATGTTCATCAGAAAGGGCTCCAGAAAGGAGATAAAGTTATCTTGA 5 0.125 No Hit AGAAGGATGAGGAAGTTCGATCCATGGCCAGTATTCTTCAAGAGAGAATG 5 0.125 No Hit ATTTTTCAGTATGAAAGCTTTTGTGATAGCTATTCTTATAGCTACCATTG 5 0.125 No Hit CTTTTCCTTTTAGTCCACACAACTTCTCTCACAAAACAGTCCACAAACAC 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 0.0125 0.0 0.0 0.0 0.0 44-45 0.037500000000000006 0.0 0.0 0.0 0.0 46-47 0.05 0.0 0.0 0.0 0.0 48-49 0.05 0.0 0.0 0.0 0.0 50-51 0.05 0.0 0.0 0.0 0.0 52-53 0.05 0.0 0.0 0.0 0.0 54-55 0.05 0.0 0.0 0.0 0.0 56-57 0.05 0.0 0.0 0.0 0.0 58-59 0.15 0.0 0.0 0.0 0.0 60-61 0.15 0.0 0.0 0.0 0.0 62-63 0.2 0.0 0.0 0.0 0.0 64-65 0.2 0.0 0.0 0.0 0.0 66-67 0.225 0.0 0.0 0.0 0.0 68-69 0.225 0.0 0.0 0.0 0.0 70-71 0.25 0.0 0.0 0.0 0.0 72-73 0.275 0.0 0.0 0.0 0.0 74-75 0.36250000000000004 0.0 0.0 0.0 0.0 76-77 0.4625 0.0 0.0 0.0 0.0 78-79 0.5125 0.0 0.0 0.0 0.0 80-81 0.5874999999999999 0.0 0.0 0.0 0.0 82-83 0.6375 0.0 0.0 0.0 0.0 84-85 0.7375 0.0 0.0 0.0 0.0 86-87 0.9125000000000001 0.0 0.0 0.0 0.0 88-89 1.1375 0.0 0.0 0.0 0.0 90-91 1.3375 0.0 0.0 0.0 0.0 92-93 1.6125 0.0 0.0 0.0 0.0 94-95 2.0125 0.0 0.0 0.0 0.0 96-97 2.2625 0.0 0.0 0.0 0.0 98-99 2.7125 0.0 0.0 0.0 0.0 100-101 3.1625 0.0 0.0 0.0 0.0 102-103 3.3875 0.0 0.0 0.0 0.0 104-105 3.9125 0.0 0.0 0.0 0.0 106-107 4.4125 0.0 0.0 0.0 0.0 108-109 4.7875 0.0 0.0 0.0 0.0 110-111 5.3875 0.0 0.0 0.0 0.0 112-113 5.8 0.0 0.0 0.0 0.0 114-115 6.2125 0.0 0.0 0.0 0.0 116-117 6.7125 0.0 0.0 0.0 0.0 118-119 7.2125 0.0 0.0 0.0 0.0 120-121 7.824999999999999 0.0 0.0 0.0 0.0 122-123 8.3875 0.0 0.0 0.0 0.0 124-125 9.3875 0.0 0.0 0.0 0.0 126-127 10.0625 0.0 0.0 0.0 0.0 128-129 10.825 0.0 0.0 0.0 0.0 130-131 11.350000000000001 0.0 0.0 0.0 0.0 132-133 11.875 0.0 0.0 0.0 0.0 134-135 12.462499999999999 0.0 0.0 0.0 0.0 136-137 13.125 0.0 0.0 0.0 0.0 138-139 13.875 0.0 0.0 0.0375 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position ACTCTCT 10 0.006830828 145.0 5 TCTGCGA 10 0.006830828 145.0 9 >>END_MODULE Read 596630 spots for SRR12670103.sra Written 596630 spots for SRR12670103.sra Read 596630 spots for SRR12670103.sra Written 596630 spots for SRR12670103.sra Read 596630 spots for SRR12670103.sra Written 596630 spots for SRR12670103.sra Read 596630 spots for SRR12670103.sra Written 596630 spots for SRR12670103.sra Read 596630 spots for SRR12670103.sra Written 596630 spots for SRR12670103.sra Read 596630 spots for SRR12670103.sra Written 596630 spots for SRR12670103.sra Read 596630 spots for SRR12670103.sra Written 596630 spots for SRR12670103.sra Read 596630 spots for SRR12670103.sra Written 596630 spots for SRR12670103.sra Read 596630 spots for SRR12670103.sra Written 596630 spots for SRR12670103.sra Read 596630 spots for SRR12670103.sra Written 596630 spots for SRR12670103.sra Read 596630 spots for SRR12670103.sra Written 596630 spots for SRR12670103.sra Read 596630 spots for SRR12670103.sra Written 596630 spots for SRR12670103.sra Read 596630 spots for SRR12670103.sra Written 596630 spots for SRR12670103.sra Read 596630 spots for SRR12670103.sra Written 596630 spots for SRR12670103.sra Read 596630 spots for SRR12670103.sra Written 596630 spots for SRR12670103.sra Read 596639 spots for SRR12670103.sra Written 596639 spots for SRR12670103.sra Read 596630 spots for SRR12670103.sra Written 596630 spots for SRR12670103.sra Read 596630 spots for SRR12670103.sra Written 596630 spots for SRR12670103.sra Read 596630 spots for SRR12670103.sra Written 596630 spots for SRR12670103.sra Read 596630 spots for SRR12670103.sra Written 596630 spots for SRR12670103.sra SRR ids: ['SRR12670103.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_8nb1t9og SRR12670103.sra spots: 11932609 blocks: [[1, 596630], [596631, 1193260], [1193261, 1789890], [1789891, 2386520], [2386521, 2983150], [2983151, 3579780], [3579781, 4176410], [4176411, 4773040], [4773041, 5369670], [5369671, 5966300], [5966301, 6562930], [6562931, 7159560], [7159561, 7756190], [7756191, 8352820], [8352821, 8949450], [8949451, 9546080], [9546081, 10142710], [10142711, 10739340], [10739341, 11335970], [11335971, 11932609]] SRR12670103 file size 4033522 SRR12670103 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 SRR12670103 SRR12670103_1.fastq SRR12670103_2.fastq Input file: SRR12670103_1.fastq Paired file: SRR12670103_2.fastq trimmed: SRR12670103-trimmed-pair1.fastq, SRR12670103-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 23:00:39 2025 >> started Mon Feb 10 23:00:52 2025 >> done (13.213s) 11932609 read pairs processed; of these: 97 ( 0.00%) short read pairs filtered out after trimming by size control 7711 ( 0.06%) empty read pairs filtered out after trimming by size control 11924801 (99.93%) read pairs available; of these: 2250688 (18.87%) trimmed read pairs available after processing 9674113 (81.13%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 5 0.00% 19 5 0.00% 20 15 0.00% 21 12 0.00% 22 20 0.00% 23 27 0.00% 24 33 0.00% 25 48 0.00% 26 72 0.00% 27 61 0.00% 28 74 0.00% 29 84 0.00% 30 83 0.00% 31 85 0.00% 32 91 0.00% 33 106 0.00% 34 104 0.00% 35 109 0.00% 36 115 0.00% 37 130 0.00% 38 132 0.00% 39 146 0.00% 40 152 0.00% 41 171 0.00% 42 194 0.00% 43 190 0.00% 44 179 0.00% 45 200 0.00% 46 230 0.00% 47 252 0.00% 48 292 0.00% 49 303 0.00% 50 360 0.00% 51 380 0.00% 52 428 0.00% 53 429 0.00% 54 507 0.00% 55 468 0.00% 56 521 0.00% 57 600 0.01% 58 664 0.01% 59 879 0.01% 60 891 0.01% 61 1026 0.01% 62 1075 0.01% 63 1256 0.01% 64 1285 0.01% 65 1390 0.01% 66 1526 0.01% 67 1638 0.01% 68 1885 0.02% 69 2155 0.02% 70 2526 0.02% 71 2725 0.02% 72 3116 0.03% 73 3528 0.03% 74 3724 0.03% 75 4160 0.03% 76 4302 0.04% 77 4654 0.04% 78 4979 0.04% 79 5706 0.05% 80 6072 0.05% 81 7148 0.06% 82 7777 0.07% 83 8554 0.07% 84 9321 0.08% 85 9772 0.08% 86 10245 0.09% 87 10730 0.09% 88 11543 0.10% 89 12078 0.10% 90 13177 0.11% 91 14182 0.12% 92 14987 0.13% 93 16865 0.14% 94 18036 0.15% 95 18842 0.16% 96 18893 0.16% 97 19940 0.17% 98 19950 0.17% 99 20780 0.17% 100 21865 0.18% 101 22254 0.19% 102 23584 0.20% 103 24828 0.21% 104 26309 0.22% 105 27019 0.23% 106 27613 0.23% 107 27903 0.23% 108 27741 0.23% 109 28771 0.24% 110 28453 0.24% 111 29934 0.25% 112 30853 0.26% 113 31772 0.27% 114 33530 0.28% 115 34275 0.29% 116 34785 0.29% 117 35027 0.29% 118 34977 0.29% 119 34426 0.29% 120 34943 0.29% 121 35815 0.30% 122 36995 0.31% 123 38487 0.32% 124 39258 0.33% 125 39395 0.33% 126 40545 0.34% 127 40001 0.34% 128 39762 0.33% 129 40151 0.34% 130 40256 0.34% 131 40277 0.34% 132 40699 0.34% 133 42406 0.36% 134 43125 0.36% 135 44344 0.37% 136 44845 0.38% 137 44803 0.38% 138 44680 0.37% 139 45114 0.38% 140 44569 0.37% 141 44502 0.37% 142 45417 0.38% 143 45737 0.38% 144 46905 0.39% 145 47770 0.40% 146 49067 0.41% 147 48333 0.41% 148 49157 0.41% 149 47698 0.40% 150 48318 0.41% 151 9674113 81.13% 11924801 reads passed initial QC criterion=sequence-density sequence-density=0.69 sequence-density-rank=1 fanout-score=2.00 fanout-score-rank=29 prefix-density=0.66 prefix-fanout=2.0 sequence=GTCTCGACGATGCCAGCAGTGTAGCTGCTTCCCTTCTTGACACACTGGGTCTTGTCAGCGCAGTCGCAGGTGTCGCAGGTGCTAGACATGATGATTGATTGATTAAGCTTAAATGGATGAACTAAAAGACTTGGAGTATGAATGTGTTCTCTGTGTA criterion=fanout-score sequence-density=0.01 sequence-density-rank=34 fanout-score=58.65 fanout-score-rank=1 prefix-density=0.08 prefix-fanout=6.1 sequence=AAACAGAATATTTACTTTTAGCGCAAGTTTCAATTCATGAGCTCGTTACATCACAAGTTAACATTACAAGCCAATAGTCCCAGCACAGAAAAAACTCTTTTGTTGCTCACTTTCCGGGAACGAAGTTTGTGGCATATGCCCAGGCGTTGTTGTTTACTGGGTCAGAAAGGTGGTCAGCCAGGTTCTCCAGTGGTCCCTTTCCGGTCACAATGGCCTGGACAAAGAATCCGAACATTGAGAACATAGCCAA criterion=sequence-density sequence-density=0.53 sequence-density-rank=1 fanout-score=2.10 fanout-score-rank=30 prefix-density=0.53 prefix-fanout=2.1 sequence=TGTAAGAGATGGCTTCCTC criterion=fanout-score sequence-density=0.01 sequence-density-rank=36 fanout-score=52.32 fanout-score-rank=1 prefix-density=0.08 prefix-fanout=4.1 sequence=TGGCCATGTAAAACACAATATTTTTCAGTATGAAAGCTTTAGTGATAGCTATTCTTATAGCTACCATTGCCTTCTCTCCCTTATCCATGGCAGCTCGAGAATTGGTCGACTATGGAAAAGATAGCGTTACCGTCAATATCCCATCAACTGGCGATGTATCATCTAGAAGCCAGCCTCCTACCTATGCCCCACGAACTGGCAGTGGATGTAGCATTTACCAACGAGATTGTCCTAAGAAAAAACCTTGTAATCCTTACAAGCGTAGCTGCCATCGCCCTTGAAAATGAAAGAGTAGTTTGATTTGGGTCCATTATCTAGTGGTAAAAGCTGTGAGCTCAAAGCACCAGGGCTATCTATTACTTTCATTTCCATTACCAATGTAATTATATGGTCGTTGGAAATTAAATAAAAGCTCCGAGTGAGCCATGGCAGATATGCATATGCTACAGGTTTCCTTTAGTACTATTGCAATCCTGTAAATGTTACCTATGAACGTTTTGTAGTCTTTTTA SRR12670103 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 10 23:01:45 Started mapping on | Feb 10 23:01:46 Finished on | Feb 10 23:03:09 Mapping speed, Million of reads per hour | 517.22 Number of input reads | 11924801 Average input read length | 291 UNIQUE READS: Uniquely mapped reads number | 11121088 Uniquely mapped reads % | 93.26% Average mapped length | 289.56 Number of splices: Total | 11097249 Number of splices: Annotated (sjdb) | 10849097 Number of splices: GT/AG | 10866013 Number of splices: GC/AG | 181276 Number of splices: AT/AC | 6224 Number of splices: Non-canonical | 43736 Mismatch rate per base, % | 0.36% Deletion rate per base | 0.03% Deletion average length | 2.95 Insertion rate per base | 0.02% Insertion average length | 2.38 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 275807 % of reads mapped to multiple loci | 2.31% Number of reads mapped to too many loci | 35283 % of reads mapped to too many loci | 0.30% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 3.98% % of reads unmapped: other | 0.15% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 527906 527906 527906 N_multimapping 275807 275807 275807 N_noFeature 411959 10930116 476427 N_ambiguous 193269 654 66449 UnstrandedReadsAssigned:10515860 PositiveStrandReadsAssigned:190318 NegativeStrandReadsAssigned:10578212 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=151 echo kmer=147 SRR12670103 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: SRR12670103-trimmed-pair1.fastq SRR12670103-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 11,924,801 reads, 10,582,800 reads pseudoaligned [quant] estimated average fragment length: 224.246 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 971 rounds 52401 SRR12670103.ke.tsv 34699 SRR12670103.se.tsv 87100 total ==> SRR12670103.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1794.75 455 20.5756 Potri.005G024800.1.v4.1 1035 811.754 315 31.4943 Potri.004G059700.1.v4.1 961 737.791 2 0.22001 Potri.007G009000.2.v4.1 1416 1192.75 0 0 Potri.003G141000.2.v4.1 2943 2719.75 610 18.2032 Potri.016G087400.1.v4.1 270 98.0634 541 447.751 Potri.015G069301.1.v4.1 564 348.58 0 0 Potri.010G195200.1.v4.1 1773 1549.75 89.8894 4.70752 Potri.012G127500.1.v4.1 977 753.76 107 11.5212 ==> SRR12670103.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 223 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 178 Potri.001G212900.v4.1 34 Potri.001G182400.v4.1 0 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 2 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 8 SRR12670103 completed mapping pipeline successfully