Starting /dee2/code/volunteer_pipeline.sh SRR28623238 current disk space = 3088915263488 free memory = 1475885948 SRR28623238 SRAfilesize 03044a203b2967ed019599d10d60c6d8 SRR28623238.sra SRR28623238.sra file validated SRR28623238 is paired end SRR28623238 is conventional basespace SRR28623238 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR28623238_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 36.49375 37.0 37.0 37.0 37.0 37.0 2 36.447 37.0 37.0 37.0 37.0 37.0 3 36.672 37.0 37.0 37.0 37.0 37.0 4 36.6035 37.0 37.0 37.0 37.0 37.0 5 36.667 37.0 37.0 37.0 37.0 37.0 6 36.718 37.0 37.0 37.0 37.0 37.0 7 36.6185 37.0 37.0 37.0 37.0 37.0 8 36.4085 37.0 37.0 37.0 37.0 37.0 9 36.5725 37.0 37.0 37.0 37.0 37.0 10-14 36.5955 37.0 37.0 37.0 37.0 37.0 15-19 36.5567 37.0 37.0 37.0 37.0 37.0 20-24 36.548300000000005 37.0 37.0 37.0 37.0 37.0 25-29 36.5172 37.0 37.0 37.0 37.0 37.0 30-34 36.4697 37.0 37.0 37.0 37.0 37.0 35-39 36.412400000000005 37.0 37.0 37.0 37.0 37.0 40-44 36.407900000000005 37.0 37.0 37.0 37.0 37.0 45-49 36.3881 37.0 37.0 37.0 37.0 37.0 50-54 36.304199999999994 37.0 37.0 37.0 37.0 37.0 55-59 36.2633 37.0 37.0 37.0 37.0 37.0 60-64 36.3249 37.0 37.0 37.0 37.0 37.0 65-69 36.2713 37.0 37.0 37.0 37.0 37.0 70-74 36.2122 37.0 37.0 37.0 37.0 37.0 75-79 36.145599999999995 37.0 37.0 37.0 37.0 37.0 80-84 36.071600000000004 37.0 37.0 37.0 37.0 37.0 85-89 36.1315 37.0 37.0 37.0 37.0 37.0 90-94 36.0567 37.0 37.0 37.0 37.0 37.0 95-99 35.859500000000004 37.0 37.0 37.0 37.0 37.0 100-104 35.9748 37.0 37.0 37.0 37.0 37.0 105-109 35.921 37.0 37.0 37.0 37.0 37.0 110-114 35.8599 37.0 37.0 37.0 37.0 37.0 115-119 35.8713 37.0 37.0 37.0 37.0 37.0 120-124 35.689499999999995 37.0 37.0 37.0 37.0 37.0 125-129 35.698299999999996 37.0 37.0 37.0 37.0 37.0 130-134 35.7857 37.0 37.0 37.0 37.0 37.0 135-139 35.644099999999995 37.0 37.0 37.0 37.0 37.0 140-144 35.3842 37.0 37.0 37.0 34.6 37.0 145-149 35.3095 37.0 37.0 37.0 32.2 37.0 150-151 35.02975 37.0 37.0 37.0 31.0 37.0 >>END_MODULE >>Per tile sequence quality pass #Tile Base Mean 1101 1 0.0 1101 2 0.0 1101 3 0.0 1101 4 0.0 1101 5 0.0 1101 6 0.0 1101 7 0.0 1101 8 0.0 1101 9 0.0 1101 10-14 0.0 1101 15-19 0.0 1101 20-24 0.0 1101 25-29 0.0 1101 30-34 0.0 1101 35-39 0.0 1101 40-44 0.0 1101 45-49 0.0 1101 50-54 0.0 1101 55-59 0.0 1101 60-64 0.0 1101 65-69 0.0 1101 70-74 0.0 1101 75-79 0.0 1101 80-84 0.0 1101 85-89 0.0 1101 90-94 0.0 1101 95-99 0.0 1101 100-104 0.0 1101 105-109 0.0 1101 110-114 0.0 1101 115-119 0.0 1101 120-124 0.0 1101 125-129 0.0 1101 130-134 0.0 1101 135-139 0.0 1101 140-144 0.0 1101 145-149 0.0 1101 150-151 0.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 21 1.0 22 1.0 23 2.0 24 3.0 25 6.0 26 9.0 27 8.0 28 6.0 29 17.0 30 33.0 31 52.0 32 62.0 33 84.0 34 150.0 35 388.0 36 2930.0 37 248.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 35.68381430363864 12.371392722710164 10.188205771643664 41.75658720200753 2 18.7 15.075 36.425000000000004 29.799999999999997 3 18.275 19.05 28.375 34.300000000000004 4 21.975 27.150000000000002 23.775 27.1 5 24.349999999999998 33.35 23.65 18.65 6 20.9 38.15 22.125 18.825 7 15.425 27.35 40.050000000000004 17.175 8 18.099999999999998 26.25 31.8 23.849999999999998 9 17.4 24.15 33.825 24.625 10-14 19.41 30.814999999999998 27.224999999999998 22.55 15-19 19.545 29.365000000000002 28.4 22.689999999999998 20-24 20.1 28.555000000000003 28.13 23.215 25-29 19.695 29.035 28.249999999999996 23.02 30-34 19.96 28.68 27.529999999999998 23.830000000000002 35-39 19.8 29.375 27.639999999999997 23.185 40-44 19.46 28.92 27.650000000000002 23.97 45-49 20.405 28.310000000000002 27.85 23.435 50-54 20.125 28.955 27.99 22.93 55-59 19.685 29.25 27.900000000000002 23.165 60-64 19.37 29.78 27.13 23.72 65-69 20.46 28.84 27.575 23.125 70-74 20.080000000000002 29.075 27.57 23.275000000000002 75-79 20.355 28.494999999999997 27.765 23.385 80-84 20.13 28.610000000000003 28.015 23.244999999999997 85-89 19.475 29.299999999999997 27.865000000000002 23.36 90-94 19.625 29.345 27.815 23.215 95-99 19.605 29.49 27.415 23.49 100-104 19.794999999999998 29.4 27.575 23.23 105-109 20.29 28.660000000000004 27.375 23.674999999999997 110-114 20.275000000000002 28.725 27.345000000000002 23.655 115-119 20.115 29.17 27.565 23.150000000000002 120-124 20.18 28.560000000000002 27.505000000000003 23.755000000000003 125-129 20.225 29.2 26.87 23.705000000000002 130-134 20.810000000000002 29.49 26.295 23.405 135-139 21.0 28.955 26.179999999999996 23.865 140-144 21.015 29.915000000000003 25.480000000000004 23.59 145-149 20.93 29.244999999999997 26.334999999999997 23.49 150-151 20.7625 28.6875 26.0 24.55 >>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 0.5 15 0.5 16 0.0 17 0.0 18 1.0 19 1.0 20 0.0 21 0.0 22 1.0 23 2.0 24 3.0 25 4.5 26 5.0 27 4.5 28 9.5 29 19.0 30 25.5 31 36.0 32 51.0 33 54.0 34 64.5 35 93.5 36 118.5 37 133.5 38 148.5 39 169.0 40 202.5 41 238.5 42 241.5 43 243.5 44 242.5 45 236.5 46 250.5 47 247.5 48 217.0 49 184.0 50 162.5 51 133.5 52 104.0 53 78.0 54 64.0 55 52.0 56 38.5 57 30.0 58 20.5 59 17.0 60 9.0 61 7.0 62 9.0 63 8.0 64 4.5 65 1.5 66 1.5 67 3.0 68 3.5 69 2.0 70 0.5 71 0.5 72 0.5 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 0.375 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 87.125 #Duplication Level Percentage of deduplicated Percentage of total 1 87.46054519368724 76.2 2 10.731707317073171 18.7 3 1.4347202295552368 3.75 4 0.31563845050215206 1.0999999999999999 5 0.05738880918220947 0.25 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 GTCCAAATTTCACAGACCCGTCAGCTTCTTCTGCCAAAACCTTGTGCGGC 5 0.125 No Hit CAGCAGATTTGGTCACCTTAGCACCAGAGGGATCCTTCTTCTCCACGCTC 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 0.025 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 0.037500000000000006 0.0 0.0 0.0 0.0 70-71 0.075 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 0.125 0.0 0.0 0.0 0.0 78-79 0.1875 0.0 0.0 0.0 0.0 80-81 0.25 0.0 0.0 0.0 0.0 82-83 0.275 0.0 0.0 0.0 0.0 84-85 0.3 0.0 0.0 0.0 0.0 86-87 0.4 0.0 0.0 0.0 0.0 88-89 0.5249999999999999 0.0 0.0 0.0 0.0 90-91 0.675 0.0 0.0 0.0 0.0 92-93 0.8625 0.0 0.0 0.0 0.0 94-95 1.0625 0.0 0.0 0.0 0.0 96-97 1.225 0.0 0.0 0.0 0.0 98-99 1.425 0.0 0.0 0.0 0.0 100-101 1.725 0.0 0.0 0.0 0.0 102-103 1.9125 0.0 0.0 0.0 0.0 104-105 2.1875 0.0 0.0 0.0 0.0 106-107 2.65 0.0 0.0 0.0 0.0 108-109 3.3 0.0 0.0 0.0 0.0 110-111 3.7875 0.0 0.0 0.0 0.0 112-113 4.1 0.0 0.0 0.0 0.0 114-115 4.475 0.0 0.0 0.0 0.0 116-117 4.9 0.0 0.0 0.0 0.0 118-119 5.4625 0.0 0.0 0.0 0.0 120-121 6.012499999999999 0.0 0.0 0.0 0.0 122-123 6.6125 0.0 0.0 0.0 0.0 124-125 7.2 0.0 0.0 0.0 0.0 126-127 8.125 0.0 0.0 0.0 0.0 128-129 8.899999999999999 0.0 0.0 0.0 0.0 130-131 9.6375 0.0 0.0 0.0 0.0 132-133 10.3 0.0 0.0 0.0 0.0 134-135 10.9875 0.0 0.0 0.0 0.0 136-137 11.675 0.0 0.0 0.0 0.0 138-139 12.3875 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE SRR28623238 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR28623238_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 43 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 35.663 37.0 37.0 37.0 37.0 37.0 2 36.194 37.0 37.0 37.0 37.0 37.0 3 36.2975 37.0 37.0 37.0 37.0 37.0 4 36.138 37.0 37.0 37.0 37.0 37.0 5 36.4585 37.0 37.0 37.0 37.0 37.0 6 36.344 37.0 37.0 37.0 37.0 37.0 7 36.314 37.0 37.0 37.0 37.0 37.0 8 36.277 37.0 37.0 37.0 37.0 37.0 9 36.171 37.0 37.0 37.0 37.0 37.0 10-14 36.1302 37.0 37.0 37.0 37.0 37.0 15-19 36.1797 37.0 37.0 37.0 37.0 37.0 20-24 36.1259 37.0 37.0 37.0 37.0 37.0 25-29 36.132400000000004 37.0 37.0 37.0 37.0 37.0 30-34 36.095600000000005 37.0 37.0 37.0 37.0 37.0 35-39 36.0809 37.0 37.0 37.0 37.0 37.0 40-44 35.992399999999996 37.0 37.0 37.0 37.0 37.0 45-49 36.0529 37.0 37.0 37.0 37.0 37.0 50-54 36.016099999999994 37.0 37.0 37.0 37.0 37.0 55-59 35.825399999999995 37.0 37.0 37.0 37.0 37.0 60-64 35.850100000000005 37.0 37.0 37.0 37.0 37.0 65-69 35.898300000000006 37.0 37.0 37.0 37.0 37.0 70-74 35.861900000000006 37.0 37.0 37.0 37.0 37.0 75-79 35.877500000000005 37.0 37.0 37.0 37.0 37.0 80-84 35.7779 37.0 37.0 37.0 37.0 37.0 85-89 35.775 37.0 37.0 37.0 37.0 37.0 90-94 35.6917 37.0 37.0 37.0 37.0 37.0 95-99 35.7204 37.0 37.0 37.0 37.0 37.0 100-104 35.6142 37.0 37.0 37.0 37.0 37.0 105-109 35.5886 37.0 37.0 37.0 37.0 37.0 110-114 35.5424 37.0 37.0 37.0 37.0 37.0 115-119 35.5161 37.0 37.0 37.0 37.0 37.0 120-124 35.471199999999996 37.0 37.0 37.0 37.0 37.0 125-129 34.972300000000004 37.0 37.0 37.0 29.8 37.0 130-134 35.300700000000006 37.0 37.0 37.0 32.2 37.0 135-139 35.178200000000004 37.0 37.0 37.0 27.4 37.0 140-144 35.16369999999999 37.0 37.0 37.0 27.4 37.0 145-149 35.0311 37.0 37.0 37.0 25.0 37.0 150-151 34.746 37.0 37.0 37.0 25.0 37.0 >>END_MODULE >>Per tile sequence quality pass #Tile Base Mean 1101 1 0.0 1101 2 0.0 1101 3 0.0 1101 4 0.0 1101 5 0.0 1101 6 0.0 1101 7 0.0 1101 8 0.0 1101 9 0.0 1101 10-14 0.0 1101 15-19 0.0 1101 20-24 0.0 1101 25-29 0.0 1101 30-34 0.0 1101 35-39 0.0 1101 40-44 0.0 1101 45-49 0.0 1101 50-54 0.0 1101 55-59 0.0 1101 60-64 0.0 1101 65-69 0.0 1101 70-74 0.0 1101 75-79 0.0 1101 80-84 0.0 1101 85-89 0.0 1101 90-94 0.0 1101 95-99 0.0 1101 100-104 0.0 1101 105-109 0.0 1101 110-114 0.0 1101 115-119 0.0 1101 120-124 0.0 1101 125-129 0.0 1101 130-134 0.0 1101 135-139 0.0 1101 140-144 0.0 1101 145-149 0.0 1101 150-151 0.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 14 9.0 15 1.0 16 3.0 17 3.0 18 1.0 19 2.0 20 2.0 21 2.0 22 7.0 23 3.0 24 9.0 25 12.0 26 5.0 27 8.0 28 24.0 29 19.0 30 26.0 31 44.0 32 65.0 33 98.0 34 258.0 35 688.0 36 2475.0 37 236.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 40.5 20.200000000000003 15.024999999999999 24.275 2 26.275 26.5 31.424999999999997 15.8 3 22.625 25.724999999999998 31.525 20.125 4 24.825 32.800000000000004 23.799999999999997 18.575 5 24.3 35.699999999999996 22.7 17.299999999999997 6 21.55 38.6 22.55 17.299999999999997 7 21.375 20.275000000000002 40.35 18.0 8 20.225 27.35 28.075 24.349999999999998 9 21.775 24.95 30.975 22.3 10-14 23.375 28.860000000000003 27.310000000000002 20.455000000000002 15-19 23.185 27.87 28.835 20.11 20-24 22.66 28.22 28.449999999999996 20.669999999999998 25-29 22.97 28.975 27.665 20.39 30-34 22.445 28.585 28.415000000000003 20.555 35-39 23.385 27.794999999999998 28.595 20.225 40-44 23.075000000000003 28.49 27.825 20.61 45-49 23.385 27.675 28.435 20.505000000000003 50-54 23.395 28.349999999999998 28.610000000000003 19.645000000000003 55-59 23.405 28.275 28.15 20.169999999999998 60-64 23.155 28.22 28.95 19.675 65-69 23.255 28.110000000000003 28.52 20.115 70-74 23.115 28.634999999999998 28.375 19.875 75-79 23.68 27.55 28.65 20.119999999999997 80-84 23.48 27.985 28.044999999999998 20.49 85-89 23.62 28.310000000000002 28.225 19.845 90-94 23.425 27.965 28.49 20.119999999999997 95-99 24.01 28.455000000000002 28.139999999999997 19.395 100-104 23.765 28.144999999999996 28.265 19.825 105-109 23.96 28.275 27.62 20.145 110-114 24.38 28.025 28.125 19.470000000000002 115-119 24.265 28.999999999999996 27.73 19.005 120-124 24.515 28.225 28.02 19.24 125-129 24.79 28.375 27.529999999999998 19.305 130-134 24.97 28.854999999999997 27.095000000000002 19.08 135-139 25.94 28.544999999999998 26.72 18.795 140-144 25.705 28.685 26.875 18.735 145-149 26.47 28.084999999999997 26.61 18.834999999999997 150-151 27.05 28.499999999999996 26.35 18.099999999999998 >>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 1.0 7 1.5 8 1.5 9 1.0 10 0.0 11 0.0 12 0.0 13 0.5 14 1.0 15 0.5 16 0.5 17 2.0 18 1.5 19 2.5 20 3.0 21 1.5 22 2.0 23 2.0 24 2.0 25 1.5 26 8.0 27 10.5 28 5.5 29 15.0 30 23.5 31 29.5 32 36.5 33 46.0 34 68.0 35 83.5 36 98.5 37 109.5 38 134.0 39 166.0 40 206.5 41 244.5 42 244.5 43 257.5 44 278.5 45 283.5 46 262.0 47 242.5 48 219.0 49 179.5 50 148.5 51 123.0 52 103.0 53 92.0 54 71.5 55 43.5 56 34.0 57 27.5 58 21.0 59 14.0 60 8.5 61 8.0 62 9.0 63 5.5 64 2.0 65 1.0 66 1.0 67 0.5 68 0.5 69 1.0 70 0.5 71 0.5 72 1.0 73 0.5 74 0.5 75 0.5 76 0.0 77 0.0 78 0.0 79 0.0 80 0.0 81 0.0 82 0.5 83 0.5 84 0.5 85 1.0 86 0.5 87 0.0 88 0.0 89 0.0 90 0.0 91 0.0 92 0.5 93 0.5 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 0.0 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 87.47500000000001 #Duplication Level Percentage of deduplicated Percentage of total 1 87.7965132895113 76.8 2 10.431551871963418 18.25 3 1.4861388968276652 3.9 4 0.22863675335810232 0.8 5 0.05715918833952558 0.25 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 AAGCAATGGCTAAGCTTACAACGGACCAGTTGAGTGAGCCGGGAGCACCA 5 0.125 No Hit GCCAACTTCACCTCCCAAGTTATCATCATGAACCATCCTGGACAGATCGG 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 0.025 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 0.037500000000000006 0.0 0.0 0.0 0.0 70-71 0.075 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 0.125 0.0 0.0 0.0 0.0 78-79 0.1875 0.0 0.0 0.0 0.0 80-81 0.25 0.0 0.0 0.0 0.0 82-83 0.275 0.0 0.0 0.0 0.0 84-85 0.3 0.0 0.0 0.0 0.0 86-87 0.4125 0.0 0.0 0.0 0.0 88-89 0.55 0.0 0.0 0.0 0.0 90-91 0.7 0.0 0.0 0.0 0.0 92-93 0.8875 0.0 0.0 0.0 0.0 94-95 1.0875 0.0 0.0 0.0 0.0 96-97 1.25 0.0 0.0 0.0 0.0 98-99 1.475 0.0 0.0 0.0 0.0 100-101 1.7875 0.0 0.0 0.0 0.0 102-103 2.0125 0.0 0.0 0.0 0.0 104-105 2.2874999999999996 0.0 0.0 0.0 0.0 106-107 2.775 0.0 0.0 0.0 0.0 108-109 3.4000000000000004 0.0 0.0 0.0 0.0 110-111 3.9125 0.0 0.0 0.0 0.0 112-113 4.225 0.0 0.0 0.0 0.0 114-115 4.625 0.0 0.0 0.0 0.0 116-117 5.0 0.0 0.0 0.0 0.0 118-119 5.5875 0.0 0.0 0.0 0.0 120-121 6.137499999999999 0.0 0.0 0.0 0.0 122-123 6.725 0.0 0.0 0.0 0.0 124-125 7.2875 0.0 0.0 0.0 0.0 126-127 8.175 0.0 0.0 0.0 0.0 128-129 8.975000000000001 0.0 0.0 0.0 0.0 130-131 9.6875 0.0 0.0 0.0 0.0 132-133 10.350000000000001 0.0 0.0 0.0 0.0 134-135 11.0 0.0 0.0 0.0 0.0 136-137 11.675 0.0 0.0 0.0 0.0 138-139 12.412500000000001 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TTGAGTT 10 0.006830828 145.0 7 >>END_MODULE Read 1928805 spots for SRR28623238.sra Written 1928805 spots for SRR28623238.sra Read 1928805 spots for SRR28623238.sra Written 1928805 spots for SRR28623238.sra Read 1928805 spots for SRR28623238.sra Written 1928805 spots for SRR28623238.sra Read 1928805 spots for SRR28623238.sra Written 1928805 spots for SRR28623238.sra Read 1928805 spots for SRR28623238.sra Written 1928805 spots for SRR28623238.sra Read 1928805 spots for SRR28623238.sra Written 1928805 spots for SRR28623238.sra Read 1928805 spots for SRR28623238.sra Written 1928805 spots for SRR28623238.sra Read 1928805 spots for SRR28623238.sra Written 1928805 spots for SRR28623238.sra Read 1928805 spots for SRR28623238.sra Written 1928805 spots for SRR28623238.sra Read 1928805 spots for SRR28623238.sra Written 1928805 spots for SRR28623238.sra Read 1928810 spots for SRR28623238.sra Written 1928810 spots for SRR28623238.sra Read 1928805 spots for SRR28623238.sra Written 1928805 spots for SRR28623238.sra Read 1928805 spots for SRR28623238.sra Written 1928805 spots for SRR28623238.sra Read 1928805 spots for SRR28623238.sra Written 1928805 spots for SRR28623238.sra Read 1928805 spots for SRR28623238.sra Written 1928805 spots for SRR28623238.sra Read 1928805 spots for SRR28623238.sra Written 1928805 spots for SRR28623238.sra Read 1928805 spots for SRR28623238.sra Written 1928805 spots for SRR28623238.sra Read 1928805 spots for SRR28623238.sra Written 1928805 spots for SRR28623238.sra Read 1928805 spots for SRR28623238.sra Written 1928805 spots for SRR28623238.sra Read 1928805 spots for SRR28623238.sra Written 1928805 spots for SRR28623238.sra SRR ids: ['SRR28623238.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_dt_gb_hg SRR28623238.sra spots: 38576105 blocks: [[1, 1928805], [1928806, 3857610], [3857611, 5786415], [5786416, 7715220], [7715221, 9644025], [9644026, 11572830], [11572831, 13501635], [13501636, 15430440], [15430441, 17359245], [17359246, 19288050], [19288051, 21216855], [21216856, 23145660], [23145661, 25074465], [25074466, 27003270], [27003271, 28932075], [28932076, 30860880], [30860881, 32789685], [32789686, 34718490], [34718491, 36647295], [36647296, 38576105]] SRR28623238 file size 14246693 SRR28623238 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 SRR28623238 SRR28623238_1.fastq SRR28623238_2.fastq Input file: SRR28623238_1.fastq Paired file: SRR28623238_2.fastq trimmed: SRR28623238-trimmed-pair1.fastq, SRR28623238-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 Thu Feb 13 15:30:19 2025 >> started Thu Feb 13 15:31:07 2025 >> done (48.222s) 38576105 read pairs processed; of these: 20 ( 0.00%) short read pairs filtered out after trimming by size control 26377 ( 0.07%) empty read pairs filtered out after trimming by size control 38549708 (99.93%) read pairs available; of these: 6545114 (16.98%) trimmed read pairs available after processing 32004594 (83.02%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 2 0.00% 19 0 0.00% 20 4 0.00% 21 8 0.00% 22 8 0.00% 23 4 0.00% 24 9 0.00% 25 6 0.00% 26 14 0.00% 27 12 0.00% 28 6 0.00% 29 12 0.00% 30 19 0.00% 31 12 0.00% 32 21 0.00% 33 18 0.00% 34 22 0.00% 35 20 0.00% 36 33 0.00% 37 30 0.00% 38 41 0.00% 39 43 0.00% 40 51 0.00% 41 56 0.00% 42 53 0.00% 43 61 0.00% 44 55 0.00% 45 87 0.00% 46 87 0.00% 47 108 0.00% 48 150 0.00% 49 175 0.00% 50 205 0.00% 51 198 0.00% 52 269 0.00% 53 291 0.00% 54 340 0.00% 55 405 0.00% 56 429 0.00% 57 481 0.00% 58 577 0.00% 59 686 0.00% 60 804 0.00% 61 956 0.00% 62 1084 0.00% 63 1262 0.00% 64 1414 0.00% 65 1652 0.00% 66 1876 0.00% 67 2106 0.01% 68 2378 0.01% 69 2717 0.01% 70 3271 0.01% 71 3787 0.01% 72 4469 0.01% 73 4969 0.01% 74 5772 0.01% 75 6435 0.02% 76 7444 0.02% 77 8002 0.02% 78 8964 0.02% 79 10108 0.03% 80 11196 0.03% 81 12579 0.03% 82 14383 0.04% 83 16326 0.04% 84 18345 0.05% 85 20100 0.05% 86 21567 0.06% 87 23398 0.06% 88 25405 0.07% 89 27400 0.07% 90 29910 0.08% 91 31916 0.08% 92 34564 0.09% 93 37709 0.10% 94 40702 0.11% 95 43572 0.11% 96 46175 0.12% 97 49380 0.13% 98 51296 0.13% 99 53339 0.14% 100 56045 0.15% 101 58553 0.15% 102 61786 0.16% 103 64497 0.17% 104 67513 0.18% 105 71483 0.19% 106 74336 0.19% 107 76927 0.20% 108 79019 0.20% 109 81327 0.21% 110 82907 0.22% 111 86348 0.22% 112 88540 0.23% 113 90706 0.24% 114 94781 0.25% 115 97868 0.25% 116 100010 0.26% 117 102409 0.27% 118 105339 0.27% 119 105518 0.27% 120 108708 0.28% 121 110540 0.29% 122 112379 0.29% 123 114372 0.30% 124 117691 0.31% 125 119762 0.31% 126 122235 0.32% 127 125447 0.33% 128 126151 0.33% 129 127432 0.33% 130 130721 0.34% 131 129979 0.34% 132 132325 0.34% 133 134741 0.35% 134 134362 0.35% 135 137524 0.36% 136 139588 0.36% 137 141270 0.37% 138 142163 0.37% 139 143995 0.37% 140 144864 0.38% 141 146074 0.38% 142 147103 0.38% 143 147581 0.38% 144 148956 0.39% 145 149890 0.39% 146 151128 0.39% 147 153427 0.40% 148 154101 0.40% 149 155150 0.40% 150 155703 0.40% 151 32004594 83.02% 38549708 reads passed initial QC criterion=sequence-density sequence-density=0.14 sequence-density-rank=1 fanout-score=5.10 fanout-score-rank=23 prefix-density=0.21 prefix-fanout=3.2 sequence=TCCTTGTCCTGGATCTTGGCCTT criterion=fanout-score sequence-density=0.02 sequence-density-rank=36 fanout-score=147.03 fanout-score-rank=1 prefix-density=0.16 prefix-fanout=14.0 sequence=TCTCCTTCCTCTAAATGATAAGGTTCAGTGGACTTCTCGCGACGTCGCCGGCGGCGAACCGCCCACGTCGCCGCGATCCGAACACTTCACCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGAATTCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCAAAGATTACCCGGGCCTGTCGGCCAAGGCTATAGACTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCTTGGCCTGGAAGGCCATAGTCCCTCTAAGAAGCTGGCCGCGGAGGGTCACCTCCGCATAGCTAGTTAGCAGGCTGAGGTCTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCATGCACCACCACCCAT criterion=sequence-density sequence-density=0.11 sequence-density-rank=1 fanout-score=2.45 fanout-score-rank=39 prefix-density=0.12 prefix-fanout=2.2 sequence=CCAGACCAGCAGAGG criterion=fanout-score sequence-density=0.07 sequence-density-rank=16 fanout-score=369.76 fanout-score-rank=1 prefix-density=0.83 prefix-fanout=32.7 sequence=AAGAAGAAGAAA SRR28623238 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 13 15:31:52 Started mapping on | Feb 13 15:31:53 Finished on | Feb 13 15:36:25 Mapping speed, Million of reads per hour | 510.22 Number of input reads | 38549708 Average input read length | 293 UNIQUE READS: Uniquely mapped reads number | 36239193 Uniquely mapped reads % | 94.01% Average mapped length | 291.49 Number of splices: Total | 32054048 Number of splices: Annotated (sjdb) | 31311371 Number of splices: GT/AG | 31496509 Number of splices: GC/AG | 432163 Number of splices: AT/AC | 28508 Number of splices: Non-canonical | 96868 Mismatch rate per base, % | 0.41% Deletion rate per base | 0.03% Deletion average length | 2.96 Insertion rate per base | 0.03% Insertion average length | 2.41 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 912580 % of reads mapped to multiple loci | 2.37% Number of reads mapped to too many loci | 178771 % of reads mapped to too many loci | 0.46% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 2.98% % of reads unmapped: other | 0.18% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 1397935 1397935 1397935 N_multimapping 912580 912580 912580 N_noFeature 1508957 35751928 1749120 N_ambiguous 455386 3033 206111 UnstrandedReadsAssigned:34274850 PositiveStrandReadsAssigned:484232 NegativeStrandReadsAssigned:34283962 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=151 echo kmer=147 SRR28623238 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: SRR28623238-trimmed-pair1.fastq SRR28623238-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 38,549,708 reads, 34,671,358 reads pseudoaligned [quant] estimated average fragment length: 225.878 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,101 rounds 52401 SRR28623238.ke.tsv 34699 SRR28623238.se.tsv 87100 total ==> SRR28623238.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1793.12 1464 25.0225 Potri.005G024800.1.v4.1 1035 810.122 417 15.7756 Potri.004G059700.1.v4.1 961 736.132 46 1.91514 Potri.007G009000.2.v4.1 1416 1191.12 0 0 Potri.003G141000.2.v4.1 2943 2718.12 1167.44 13.1634 Potri.016G087400.1.v4.1 270 94.7045 2395.04 775.071 Potri.015G069301.1.v4.1 564 344.207 0 0 Potri.010G195200.1.v4.1 1773 1548.12 48 0.950245 Potri.012G127500.1.v4.1 977 752.127 6699 272.972 ==> SRR28623238.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 2091 Potri.001G233950.v4.1 5 Potri.001G122700.v4.1 707 Potri.001G212900.v4.1 3 Potri.001G182400.v4.1 6 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 0 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 1 SRR28623238 completed mapping pipeline successfully