Starting /dee2/code/volunteer_pipeline.sh ERR3450088 current disk space = 1542712123392 free memory = 1595976656 ERR3450088 SRAfilesize 949a9c288d9cc8cba03fd9515c85d175 ERR3450088.sra ERR3450088.sra file validated ERR3450088 is paired end ERR3450088 is conventional basespace ERR3450088 read1 length is 101 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR3450088_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 101 %GC 52 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.134 37.0 37.0 37.0 37.0 37.0 2 36.3545 37.0 37.0 37.0 37.0 37.0 3 36.419 37.0 37.0 37.0 37.0 37.0 4 36.551 37.0 37.0 37.0 37.0 37.0 5 36.5205 37.0 37.0 37.0 37.0 37.0 6 36.54 37.0 37.0 37.0 37.0 37.0 7 36.402 37.0 37.0 37.0 37.0 37.0 8 36.501 37.0 37.0 37.0 37.0 37.0 9 36.4945 37.0 37.0 37.0 37.0 37.0 10-11 36.4955 37.0 37.0 37.0 37.0 37.0 12-13 36.50775 37.0 37.0 37.0 37.0 37.0 14-15 36.441 37.0 37.0 37.0 37.0 37.0 16-17 36.439499999999995 37.0 37.0 37.0 37.0 37.0 18-19 36.49325 37.0 37.0 37.0 37.0 37.0 20-21 36.426249999999996 37.0 37.0 37.0 37.0 37.0 22-23 36.40325 37.0 37.0 37.0 37.0 37.0 24-25 36.387249999999995 37.0 37.0 37.0 37.0 37.0 26-27 36.323750000000004 37.0 37.0 37.0 37.0 37.0 28-29 36.328 37.0 37.0 37.0 37.0 37.0 30-31 36.34525 37.0 37.0 37.0 37.0 37.0 32-33 36.32825 37.0 37.0 37.0 37.0 37.0 34-35 36.2955 37.0 37.0 37.0 37.0 37.0 36-37 36.329499999999996 37.0 37.0 37.0 37.0 37.0 38-39 36.294 37.0 37.0 37.0 37.0 37.0 40-41 36.27775 37.0 37.0 37.0 37.0 37.0 42-43 36.294250000000005 37.0 37.0 37.0 37.0 37.0 44-45 36.2705 37.0 37.0 37.0 37.0 37.0 46-47 36.2715 37.0 37.0 37.0 37.0 37.0 48-49 36.186 37.0 37.0 37.0 37.0 37.0 50-51 36.132000000000005 37.0 37.0 37.0 37.0 37.0 52-53 36.1595 37.0 37.0 37.0 37.0 37.0 54-55 36.133250000000004 37.0 37.0 37.0 37.0 37.0 56-57 36.107749999999996 37.0 37.0 37.0 37.0 37.0 58-59 36.04075 37.0 37.0 37.0 37.0 37.0 60-61 36.084999999999994 37.0 37.0 37.0 37.0 37.0 62-63 36.151250000000005 37.0 37.0 37.0 37.0 37.0 64-65 36.03675 37.0 37.0 37.0 37.0 37.0 66-67 36.1055 37.0 37.0 37.0 37.0 37.0 68-69 36.05 37.0 37.0 37.0 37.0 37.0 70-71 36.10275 37.0 37.0 37.0 37.0 37.0 72-73 36.114000000000004 37.0 37.0 37.0 37.0 37.0 74-75 36.171 37.0 37.0 37.0 37.0 37.0 76-77 36.168 37.0 37.0 37.0 37.0 37.0 78-79 36.027 37.0 37.0 37.0 37.0 37.0 80-81 35.96175 37.0 37.0 37.0 37.0 37.0 82-83 35.989000000000004 37.0 37.0 37.0 37.0 37.0 84-85 35.95625 37.0 37.0 37.0 37.0 37.0 86-87 35.97 37.0 37.0 37.0 37.0 37.0 88-89 35.960499999999996 37.0 37.0 37.0 37.0 37.0 90-91 35.99725 37.0 37.0 37.0 37.0 37.0 92-93 35.848 37.0 37.0 37.0 37.0 37.0 94-95 35.8315 37.0 37.0 37.0 37.0 37.0 96-97 35.8395 37.0 37.0 37.0 37.0 37.0 98-99 35.8315 37.0 37.0 37.0 37.0 37.0 100-101 35.7665 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 21 1.0 22 1.0 23 0.0 24 4.0 25 3.0 26 13.0 27 21.0 28 31.0 29 26.0 30 59.0 31 63.0 32 53.0 33 83.0 34 105.0 35 210.0 36 1719.0 37 1608.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 40.286144578313255 10.316265060240964 10.843373493975903 38.55421686746988 2 21.5 12.475 29.849999999999998 36.175000000000004 3 22.075 16.5 25.224999999999998 36.199999999999996 4 28.050000000000004 22.275 19.275000000000002 30.4 5 29.075 25.424999999999997 21.9 23.599999999999998 6 24.05 29.825000000000003 24.15 21.975 7 20.474999999999998 23.150000000000002 36.975 19.400000000000002 8 22.55 21.175 29.225 27.05 9 22.325 22.2 30.4 25.074999999999996 10-11 23.674999999999997 29.15 22.3625 24.8125 12-13 24.525 22.725 25.137500000000003 27.6125 14-15 23.7625 24.887500000000003 24.837500000000002 26.5125 16-17 24.4 24.875 25.2 25.525 18-19 25.0625 24.6 24.625 25.7125 20-21 23.925 25.5375 25.575 24.962500000000002 22-23 24.25 25.112499999999997 24.8125 25.825 24-25 25.25 24.125 24.2375 26.387500000000003 26-27 24.825 23.849999999999998 24.349999999999998 26.974999999999998 28-29 25.0125 24.375 23.125 27.487499999999997 30-31 25.0 23.525 24.4125 27.0625 32-33 24.7 23.7125 24.1625 27.425 34-35 24.712500000000002 23.4875 25.074999999999996 26.724999999999998 36-37 25.224999999999998 23.4625 23.7375 27.575 38-39 25.074999999999996 23.95 24.0375 26.937499999999996 40-41 25.7625 24.3625 23.2125 26.6625 42-43 25.5 23.65 24.425 26.424999999999997 44-45 25.587500000000002 23.3375 24.1875 26.887499999999996 46-47 24.712500000000002 24.637500000000003 24.95 25.7 48-49 25.724999999999998 23.8375 23.425 27.0125 50-51 23.7875 23.5375 24.6125 28.0625 52-53 25.2 24.4375 24.099999999999998 26.2625 54-55 25.0125 24.4 24.125 26.4625 56-57 24.525 23.3375 24.65 27.487499999999997 58-59 24.2625 23.0875 24.474999999999998 28.175 60-61 24.975 23.474999999999998 23.9375 27.6125 62-63 24.762500000000003 23.5375 23.65 28.050000000000004 64-65 25.4625 23.5 24.325 26.7125 66-67 25.05 23.0625 24.474999999999998 27.4125 68-69 24.9125 24.025 23.3875 27.675 70-71 25.637500000000003 23.3625 23.7 27.3 72-73 24.85 22.7625 24.2625 28.125 74-75 25.474999999999998 23.4625 23.45 27.6125 76-77 24.85 24.0125 23.7375 27.400000000000002 78-79 25.637500000000003 23.3625 23.425 27.575 80-81 24.525 24.6875 23.7125 27.075 82-83 25.775 24.0375 23.4875 26.700000000000003 84-85 26.075 23.849999999999998 23.225 26.85 86-87 25.55 23.8875 23.7125 26.85 88-89 25.7 23.9375 23.6125 26.75 90-91 26.3 23.575 22.662499999999998 27.462500000000002 92-93 26.674999999999997 23.200000000000003 23.375 26.75 94-95 25.6 23.7 23.849999999999998 26.85 96-97 24.5125 25.15 23.200000000000003 27.1375 98-99 25.775 23.925 23.575 26.724999999999998 100-101 25.837500000000002 24.775 22.662499999999998 26.724999999999998 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 7.0 1 5.0 2 3.0 3 2.0 4 0.5 5 0.0 6 1.0 7 1.0 8 1.5 9 1.5 10 0.0 11 0.5 12 0.5 13 0.5 14 0.5 15 0.0 16 0.0 17 0.0 18 0.5 19 0.5 20 0.5 21 0.5 22 0.5 23 0.5 24 3.0 25 4.0 26 3.5 27 3.0 28 1.0 29 0.5 30 1.5 31 5.0 32 5.5 33 5.0 34 7.5 35 13.0 36 25.5 37 34.5 38 47.0 39 63.5 40 73.0 41 85.5 42 106.0 43 128.0 44 152.0 45 168.0 46 180.0 47 165.0 48 153.5 49 175.5 50 179.5 51 168.5 52 155.0 53 143.5 54 145.5 55 151.0 56 147.0 57 137.5 58 117.5 59 96.0 60 90.5 61 84.5 62 69.0 63 67.0 64 60.0 65 60.5 66 60.5 67 51.5 68 56.5 69 52.5 70 43.0 71 36.5 72 37.0 73 33.5 74 23.5 75 23.0 76 21.0 77 13.5 78 13.0 79 10.0 80 3.5 81 3.5 82 4.0 83 2.5 84 1.0 85 1.5 86 2.0 87 1.0 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 0.4 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10-11 0.0 12-13 0.0 14-15 0.0 16-17 0.0 18-19 0.0 20-21 0.0 22-23 0.0 24-25 0.0 26-27 0.0 28-29 0.0 30-31 0.0 32-33 0.0 34-35 0.0 36-37 0.0 38-39 0.0 40-41 0.0 42-43 0.0 44-45 0.0 46-47 0.0 48-49 0.0 50-51 0.0 52-53 0.0 54-55 0.0 56-57 0.0 58-59 0.0 60-61 0.0 62-63 0.0 64-65 0.0 66-67 0.0 68-69 0.0 70-71 0.0 72-73 0.0 74-75 0.0 76-77 0.0 78-79 0.0 80-81 0.0 82-83 0.0 84-85 0.0 86-87 0.0 88-89 0.0 90-91 0.0 92-93 0.0 94-95 0.0 96-97 0.0 98-99 0.0 100-101 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 101 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 84.5 #Duplication Level Percentage of deduplicated Percentage of total 1 85.71005917159763 72.425 2 11.597633136094675 19.6 3 1.982248520710059 5.025 4 0.38461538461538464 1.3 5 0.17751479289940827 0.75 6 0.08875739644970414 0.44999999999999996 7 0.0 0.0 8 0.02958579881656805 0.2 9 0.0 0.0 >10 0.02958579881656805 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 CCCGACTGTCCCTATTAATCATTACTCCGATCCCGAAGGCCAACACAATA 10 0.25 No Hit AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 8 0.2 No Hit GGCAGAAATTTGAATGATGCGTCGCCGGCACGAGGGCCGTGCGATCCGTC 6 0.15 No Hit GTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCC 6 0.15 No Hit CTTCAAAGTAACGATGCCGGAGGCACGACCCGGCCAATTAAGGCTAGGAG 6 0.15 No Hit GCATACTTCACCAAGATTAAATTTACCTGGGAACTTGACAACAAGACAAC 5 0.125 No Hit CTTGTTACGACTTCTCCTTCCTCTAAATGATAAGGTTCAATGGACTTCTC 5 0.125 No Hit CTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATT 5 0.125 No Hit GGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGA 5 0.125 No Hit TACGACTTCTCCTTCCTCTAAATGATAAGGTTCAATGGACTTCTCGCGAC 5 0.125 No Hit ATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCTATA 5 0.125 No Hit >>END_MODULE >>Adapter Content warn #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 0.025 0.0 0.0 0.0 0.0 24-25 0.025 0.0 0.0 0.0 0.0 26-27 0.025 0.0 0.0 0.0 0.0 28-29 0.025 0.0 0.0 0.0 0.0 30-31 0.025 0.0 0.0 0.0 0.0 32-33 0.025 0.0 0.0 0.0 0.0 34-35 0.025 0.0 0.0 0.0 0.0 36-37 0.05 0.0 0.0 0.0 0.0 38-39 0.1125 0.0 0.0 0.0 0.0 40-41 0.125 0.0 0.0 0.0 0.0 42-43 0.15 0.0 0.0 0.0 0.0 44-45 0.2 0.0 0.0 0.0 0.0 46-47 0.2375 0.0 0.0 0.0 0.0 48-49 0.3 0.0 0.0 0.0 0.0 50-51 0.3375 0.0 0.0 0.0 0.0 52-53 0.425 0.0 0.0 0.0 0.0 54-55 0.5 0.0 0.0 0.0 0.0 56-57 0.575 0.0 0.0 0.0 0.0 58-59 0.75 0.0 0.0 0.0 0.0 60-61 0.8999999999999999 0.0 0.0 0.0 0.0 62-63 1.0 0.0 0.0 0.0 0.0 64-65 1.2 0.0 0.0 0.0 0.0 66-67 1.4249999999999998 0.0 0.0 0.0 0.0 68-69 1.7125 0.0 0.0 0.0 0.0 70-71 2.0 0.0 0.0 0.0 0.0 72-73 2.325 0.0 0.0 0.0 0.0 74-75 2.6125 0.0 0.0 0.0 0.0 76-77 2.95 0.0 0.0 0.0 0.0 78-79 3.4749999999999996 0.0 0.0 0.0 0.05 80-81 3.9124999999999996 0.0 0.0 0.0 0.05 82-83 4.3 0.0 0.0 0.0 0.05 84-85 4.6 0.0 0.0 0.0 0.05 86-87 5.0125 0.0 0.0 0.0 0.05 88-89 5.5625 0.0 0.0 0.0 0.05 >>END_MODULE >>Kmer Content pass >>END_MODULE ERR3450088 read2 length is 101 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR3450088_2.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 101 %GC 52 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 35.603 37.0 37.0 37.0 37.0 37.0 2 35.5535 37.0 37.0 37.0 37.0 37.0 3 35.694 37.0 37.0 37.0 37.0 37.0 4 35.7725 37.0 37.0 37.0 37.0 37.0 5 35.9635 37.0 37.0 37.0 37.0 37.0 6 35.9475 37.0 37.0 37.0 37.0 37.0 7 35.882 37.0 37.0 37.0 37.0 37.0 8 35.966 37.0 37.0 37.0 37.0 37.0 9 35.961 37.0 37.0 37.0 37.0 37.0 10-11 36.023250000000004 37.0 37.0 37.0 37.0 37.0 12-13 36.005 37.0 37.0 37.0 37.0 37.0 14-15 35.973749999999995 37.0 37.0 37.0 37.0 37.0 16-17 36.01875 37.0 37.0 37.0 37.0 37.0 18-19 35.96625 37.0 37.0 37.0 37.0 37.0 20-21 36.023250000000004 37.0 37.0 37.0 37.0 37.0 22-23 36.06325 37.0 37.0 37.0 37.0 37.0 24-25 35.94825 37.0 37.0 37.0 37.0 37.0 26-27 35.866749999999996 37.0 37.0 37.0 37.0 37.0 28-29 35.86625 37.0 37.0 37.0 37.0 37.0 30-31 35.89375 37.0 37.0 37.0 37.0 37.0 32-33 35.83175 37.0 37.0 37.0 37.0 37.0 34-35 35.875249999999994 37.0 37.0 37.0 37.0 37.0 36-37 35.77875 37.0 37.0 37.0 37.0 37.0 38-39 35.8265 37.0 37.0 37.0 37.0 37.0 40-41 35.7235 37.0 37.0 37.0 37.0 37.0 42-43 35.73075 37.0 37.0 37.0 37.0 37.0 44-45 35.71175 37.0 37.0 37.0 37.0 37.0 46-47 35.6365 37.0 37.0 37.0 37.0 37.0 48-49 35.77875 37.0 37.0 37.0 37.0 37.0 50-51 35.747249999999994 37.0 37.0 37.0 37.0 37.0 52-53 35.81075 37.0 37.0 37.0 37.0 37.0 54-55 35.733000000000004 37.0 37.0 37.0 37.0 37.0 56-57 35.839749999999995 37.0 37.0 37.0 37.0 37.0 58-59 35.75675 37.0 37.0 37.0 37.0 37.0 60-61 35.76275 37.0 37.0 37.0 37.0 37.0 62-63 35.80725 37.0 37.0 37.0 37.0 37.0 64-65 35.692499999999995 37.0 37.0 37.0 37.0 37.0 66-67 35.777 37.0 37.0 37.0 37.0 37.0 68-69 35.657 37.0 37.0 37.0 37.0 37.0 70-71 35.64475 37.0 37.0 37.0 37.0 37.0 72-73 35.6425 37.0 37.0 37.0 37.0 37.0 74-75 35.592375 37.0 37.0 37.0 37.0 37.0 76-77 35.64575 37.0 37.0 37.0 37.0 37.0 78-79 35.582499999999996 37.0 37.0 37.0 37.0 37.0 80-81 35.573499999999996 37.0 37.0 37.0 37.0 37.0 82-83 35.68725 37.0 37.0 37.0 37.0 37.0 84-85 35.58925 37.0 37.0 37.0 37.0 37.0 86-87 35.569500000000005 37.0 37.0 37.0 37.0 37.0 88-89 35.47325 37.0 37.0 37.0 37.0 37.0 90-91 35.526250000000005 37.0 37.0 37.0 37.0 37.0 92-93 35.459500000000006 37.0 37.0 37.0 37.0 37.0 94-95 35.50175 37.0 37.0 37.0 37.0 37.0 96-97 35.389 37.0 37.0 37.0 37.0 37.0 98-99 35.47725 37.0 37.0 37.0 37.0 37.0 100-101 35.4935 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 15 4.0 16 2.0 17 4.0 18 5.0 19 3.0 20 6.0 21 11.0 22 14.0 23 12.0 24 14.0 25 21.0 26 22.0 27 26.0 28 24.0 29 35.0 30 51.0 31 53.0 32 64.0 33 79.0 34 135.0 35 274.0 36 2161.0 37 980.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 42.025 18.025 10.7 29.25 2 26.150000000000002 23.275000000000002 26.825 23.75 3 25.374999999999996 22.975 27.250000000000004 24.4 4 29.675 27.200000000000003 18.525 24.6 5 28.199999999999996 30.95 19.225 21.625 6 24.4 32.05 20.349999999999998 23.200000000000003 7 25.324999999999996 19.925 32.225 22.525000000000002 8 25.75 21.349999999999998 23.025000000000002 29.875 9 26.35 20.825 26.125 26.700000000000003 10-11 27.987499999999997 26.6625 19.537499999999998 25.8125 12-13 29.049999999999997 21.575 22.275 27.1 14-15 26.674999999999997 25.2 22.7125 25.412499999999998 16-17 28.237499999999997 24.349999999999998 22.375 25.0375 18-19 27.725 24.5375 23.3875 24.349999999999998 20-21 26.1 26.1125 22.225 25.5625 22-23 28.925 23.7375 23.0 24.337500000000002 24-25 27.150000000000002 24.925 22.3625 25.5625 26-27 27.275 24.8 22.775000000000002 25.15 28-29 27.5875 24.3 21.625 26.487500000000004 30-31 28.299999999999997 24.65 21.762500000000003 25.2875 32-33 28.199999999999996 23.974999999999998 22.8375 24.9875 34-35 27.775 24.337500000000002 22.3 25.587500000000002 36-37 27.700000000000003 25.162499999999998 21.95 25.1875 38-39 27.825 24.887500000000003 22.7375 24.55 40-41 27.800000000000004 24.45 22.4875 25.2625 42-43 27.8625 24.625 21.9625 25.55 44-45 27.3375 24.587500000000002 23.25 24.825 46-47 28.050000000000004 24.7375 22.650000000000002 24.5625 48-49 27.8625 24.3875 22.9375 24.8125 50-51 26.887499999999996 24.7 22.7 25.7125 52-53 28.749999999999996 23.7 22.95 24.6 54-55 27.462500000000002 23.974999999999998 23.4125 25.15 56-57 27.425 24.7 23.275000000000002 24.6 58-59 28.075 24.5625 22.662499999999998 24.7 60-61 29.362500000000004 23.575 22.7 24.3625 62-63 28.012500000000003 24.7 22.3375 24.95 64-65 28.962500000000002 24.8125 22.4875 23.7375 66-67 28.8375 24.45 21.6125 25.1 68-69 27.925 24.7 22.15 25.224999999999998 70-71 27.875 25.6125 22.7125 23.799999999999997 72-73 27.8125 24.9125 22.725 24.55 74-75 27.415926990873857 25.153144143017876 22.240280035004375 25.19064883110389 76-77 28.925 23.7 22.4625 24.9125 78-79 27.725 25.424999999999997 21.275 25.575 80-81 28.537499999999998 24.5375 22.225 24.7 82-83 28.537499999999998 24.625 22.875 23.962500000000002 84-85 28.125 24.075 23.275000000000002 24.525 86-87 28.599999999999998 23.6625 22.7375 25.0 88-89 28.625 23.8625 23.0 24.5125 90-91 28.249999999999996 23.8125 23.25 24.6875 92-93 28.8625 24.825 23.0625 23.25 94-95 29.3875 24.675 22.237499999999997 23.7 96-97 29.262500000000003 25.162499999999998 22.162499999999998 23.4125 98-99 28.499999999999996 25.1 22.900000000000002 23.5 100-101 28.8375 25.474999999999998 21.425 24.2625 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 0.0 1 1.0 2 1.0 3 0.0 4 1.0 5 1.0 6 0.5 7 0.5 8 0.5 9 1.0 10 2.5 11 3.0 12 1.0 13 0.5 14 2.0 15 2.5 16 1.5 17 1.0 18 1.5 19 1.5 20 2.5 21 2.0 22 0.5 23 0.5 24 1.0 25 1.5 26 1.5 27 2.0 28 1.0 29 1.0 30 2.0 31 3.0 32 6.0 33 8.0 34 10.0 35 17.0 36 19.5 37 25.0 38 42.5 39 60.0 40 81.5 41 94.5 42 111.5 43 130.0 44 145.5 45 163.5 46 160.5 47 155.0 48 154.0 49 156.0 50 160.5 51 150.0 52 151.0 53 166.5 54 151.0 55 141.0 56 133.5 57 118.5 58 113.5 59 89.5 60 79.5 61 79.5 62 75.0 63 77.0 64 74.0 65 68.5 66 67.0 67 63.0 68 59.5 69 56.0 70 51.5 71 45.5 72 43.0 73 46.5 74 35.0 75 22.5 76 16.0 77 11.5 78 9.0 79 6.0 80 5.5 81 4.0 82 3.0 83 5.5 84 4.0 85 1.5 86 2.0 87 1.0 88 1.0 89 1.0 90 0.0 91 0.5 92 1.0 93 1.0 94 1.5 95 1.5 96 1.0 97 2.0 98 2.5 99 2.5 100 8.5 >>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 10-11 0.0 12-13 0.0 14-15 0.0 16-17 0.0 18-19 0.0 20-21 0.0 22-23 0.0 24-25 0.0 26-27 0.0 28-29 0.0 30-31 0.0 32-33 0.0 34-35 0.0 36-37 0.0 38-39 0.0 40-41 0.0 42-43 0.0 44-45 0.0 46-47 0.0 48-49 0.0 50-51 0.0 52-53 0.0 54-55 0.0 56-57 0.0 58-59 0.0 60-61 0.0 62-63 0.0 64-65 0.0 66-67 0.0 68-69 0.0 70-71 0.0 72-73 0.0 74-75 0.0125 76-77 0.0 78-79 0.0 80-81 0.0 82-83 0.0 84-85 0.0 86-87 0.0 88-89 0.0 90-91 0.0 92-93 0.0 94-95 0.0 96-97 0.0 98-99 0.0 100-101 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 101 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 85.575 #Duplication Level Percentage of deduplicated Percentage of total 1 86.473853345019 74.0 2 11.18901548349401 19.15 3 1.9281332164767746 4.95 4 0.23371311714869997 0.8 5 0.11685655857434998 0.5 6 0.0 0.0 7 0.0 0.0 8 0.029214139643587496 0.2 9 0.0 0.0 >10 0.029214139643587496 0.4 >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 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 16 0.4 No Hit GACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTTGATTCTATGGGTG 8 0.2 No Hit GTTTGAGGCAATAACAGGTCTGTGATGCCCTTAGATGTTCTGGGCCGCAC 5 0.125 No Hit TAACATTTCAAGCCCCCGTTTCGAATGGCAGCGAAAGAGAGGGGGAGGGT 5 0.125 No Hit GGCGGGACTACCCGCTGAGTTTAAGCATATAAATAAGCGGAGGAGAAGAA 5 0.125 No Hit CTTACCAGGTCCAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTT 5 0.125 No Hit >>END_MODULE >>Adapter Content warn #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 0.025 0.0 0.0 0.0 0.0 24-25 0.025 0.0 0.0 0.0 0.0 26-27 0.025 0.0 0.0 0.0 0.0 28-29 0.025 0.0 0.0 0.0 0.0 30-31 0.025 0.0 0.0 0.0 0.0 32-33 0.025 0.0 0.0 0.0 0.0 34-35 0.025 0.0 0.0 0.0 0.0 36-37 0.05 0.0 0.0 0.0 0.0 38-39 0.1125 0.0 0.0 0.0 0.0 40-41 0.125 0.0 0.0 0.0 0.0 42-43 0.15 0.0 0.0 0.0 0.0 44-45 0.2 0.0 0.0 0.0 0.0 46-47 0.2375 0.0 0.0 0.0 0.0 48-49 0.3 0.0 0.0 0.0 0.0 50-51 0.3375 0.0 0.0 0.0 0.0 52-53 0.425 0.0 0.0 0.0 0.0 54-55 0.5 0.0 0.0 0.0 0.0 56-57 0.575 0.0 0.0 0.0 0.0 58-59 0.75 0.0 0.0 0.0 0.0 60-61 0.8999999999999999 0.0 0.0 0.0 0.0 62-63 1.025 0.0 0.0 0.0 0.0 64-65 1.225 0.0 0.0 0.0 0.0 66-67 1.4500000000000002 0.0 0.0 0.0 0.0 68-69 1.7374999999999998 0.0 0.0 0.0 0.0 70-71 2.025 0.0 0.0 0.0 0.0 72-73 2.3499999999999996 0.0 0.0 0.0 0.0 74-75 2.6375 0.0 0.0 0.0 0.0 76-77 2.975 0.0 0.0 0.0 0.0 78-79 3.5 0.0 0.0 0.0 0.0 80-81 3.9625 0.0 0.0 0.0 0.0 82-83 4.35 0.0 0.0 0.0 0.0 84-85 4.6625 0.0 0.0 0.0 0.0 86-87 5.0625 0.0 0.0 0.0 0.0 88-89 5.6125 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Read 1678505 spots for ERR3450088.sra Written 1678505 spots for ERR3450088.sra Read 1678505 spots for ERR3450088.sra Written 1678505 spots for ERR3450088.sra Read 1678505 spots for ERR3450088.sra Written 1678505 spots for ERR3450088.sra Read 1678505 spots for ERR3450088.sra Written 1678505 spots for ERR3450088.sra Read 1678505 spots for ERR3450088.sra Written 1678505 spots for ERR3450088.sra Read 1678523 spots for ERR3450088.sra Written 1678523 spots for ERR3450088.sra Read 1678505 spots for ERR3450088.sra Written 1678505 spots for ERR3450088.sra Read 1678505 spots for ERR3450088.sra Written 1678505 spots for ERR3450088.sra Read 1678505 spots for ERR3450088.sra Written 1678505 spots for ERR3450088.sra Read 1678505 spots for ERR3450088.sra Written 1678505 spots for ERR3450088.sra Read 1678505 spots for ERR3450088.sra Written 1678505 spots for ERR3450088.sra Read 1678505 spots for ERR3450088.sra Written 1678505 spots for ERR3450088.sra Read 1678505 spots for ERR3450088.sra Written 1678505 spots for ERR3450088.sra Read 1678505 spots for ERR3450088.sra Written 1678505 spots for ERR3450088.sra Read 1678505 spots for ERR3450088.sra Written 1678505 spots for ERR3450088.sra Read 1678505 spots for ERR3450088.sra Written 1678505 spots for ERR3450088.sra Read 1678505 spots for ERR3450088.sra Written 1678505 spots for ERR3450088.sra Read 1678505 spots for ERR3450088.sra Written 1678505 spots for ERR3450088.sra Read 1678505 spots for ERR3450088.sra Written 1678505 spots for ERR3450088.sra Read 1678505 spots for ERR3450088.sra Written 1678505 spots for ERR3450088.sra SRR ids: ['ERR3450088.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_yygf0rc8 ERR3450088.sra spots: 33570118 blocks: [[1, 1678505], [1678506, 3357010], [3357011, 5035515], [5035516, 6714020], [6714021, 8392525], [8392526, 10071030], [10071031, 11749535], [11749536, 13428040], [13428041, 15106545], [15106546, 16785050], [16785051, 18463555], [18463556, 20142060], [20142061, 21820565], [21820566, 23499070], [23499071, 25177575], [25177576, 26856080], [26856081, 28534585], [28534586, 30213090], [30213091, 31891595], [31891596, 33570118]] ERR3450088 file size 8075779 ERR3450088 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 ERR3450088 ERR3450088_1.fastq ERR3450088_2.fastq Input file: ERR3450088_1.fastq Paired file: ERR3450088_2.fastq trimmed: ERR3450088-trimmed-pair1.fastq, ERR3450088-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 Sat Dec 7 15:05:58 2024 >> started Sat Dec 7 15:06:31 2024 >> done (32.618s) 33570118 read pairs processed; of these: 256 ( 0.00%) short read pairs filtered out after trimming by size control 50762 ( 0.15%) empty read pairs filtered out after trimming by size control 33519100 (99.85%) read pairs available; of these: 3250683 ( 9.70%) trimmed read pairs available after processing 30268417 (90.30%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 43 0.00% 19 74 0.00% 20 229 0.00% 21 596 0.00% 22 701 0.00% 23 364 0.00% 24 376 0.00% 25 482 0.00% 26 774 0.00% 27 1024 0.00% 28 1460 0.00% 29 1872 0.01% 30 2281 0.01% 31 2841 0.01% 32 2885 0.01% 33 2825 0.01% 34 2852 0.01% 35 2867 0.01% 36 3236 0.01% 37 3417 0.01% 38 4160 0.01% 39 4900 0.01% 40 5537 0.02% 41 6642 0.02% 42 7572 0.02% 43 7913 0.02% 44 7353 0.02% 45 7349 0.02% 46 7799 0.02% 47 8498 0.03% 48 9305 0.03% 49 10454 0.03% 50 11308 0.03% 51 13072 0.04% 52 14045 0.04% 53 15183 0.05% 54 15809 0.05% 55 16638 0.05% 56 17140 0.05% 57 18200 0.05% 58 19582 0.06% 59 21152 0.06% 60 23262 0.07% 61 25415 0.08% 62 27555 0.08% 63 29739 0.09% 64 31168 0.09% 65 32440 0.10% 66 33581 0.10% 67 35974 0.11% 68 37293 0.11% 69 39321 0.12% 70 41426 0.12% 71 44617 0.13% 72 48643 0.15% 73 50619 0.15% 74 53259 0.16% 75 55446 0.17% 76 57466 0.17% 77 59088 0.18% 78 61758 0.18% 79 65133 0.19% 80 67231 0.20% 81 69980 0.21% 82 73849 0.22% 83 77190 0.23% 84 80095 0.24% 85 83216 0.25% 86 85138 0.25% 87 89287 0.27% 88 92602 0.28% 89 95456 0.28% 90 97622 0.29% 91 102678 0.31% 92 108102 0.32% 93 110501 0.33% 94 114120 0.34% 95 118200 0.35% 96 119742 0.36% 97 124819 0.37% 98 126995 0.38% 99 128677 0.38% 100 151170 0.45% 101 30268417 90.30% 33519100 reads passed initial QC criterion=sequence-density sequence-density=0.34 sequence-density-rank=1 fanout-score=2.01 fanout-score-rank=27 prefix-density=0.34 prefix-fanout=2.0 sequence=GTATTTAGCCTTG criterion=fanout-score sequence-density=0.08 sequence-density-rank=23 fanout-score=49.18 fanout-score-rank=1 prefix-density=1.14 prefix-fanout=3.5 sequence=GGCGGCGGCGGCCTCGCCGTCGCTGGTGTACTTCCCCAGCTGCGCCAGGGAGTTTGCCTTGGCGCGCAGCAGCAGTGCCTCCTGGGCCGCCGCCACGTTCTCCGGCCGTCCTC criterion=sequence-density sequence-density=0.20 sequence-density-rank=1 fanout-score=2.24 fanout-score-rank=26 prefix-density=0.21 prefix-fanout=2.1 sequence=AGCCAGAGGAAA criterion=fanout-score sequence-density=0.08 sequence-density-rank=27 fanout-score=191.47 fanout-score-rank=1 prefix-density=0.71 prefix-fanout=21.5 sequence=CGGCGGCGGCGC ERR3450088 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 07 15:07:28 Started mapping on | Dec 07 15:07:28 Finished on | Dec 07 15:09:58 Mapping speed, Million of reads per hour | 804.46 Number of input reads | 33519100 Average input read length | 198 UNIQUE READS: Uniquely mapped reads number | 24450929 Uniquely mapped reads % | 72.95% Average mapped length | 197.92 Number of splices: Total | 15526325 Number of splices: Annotated (sjdb) | 14752836 Number of splices: GT/AG | 15321994 Number of splices: GC/AG | 178475 Number of splices: AT/AC | 8924 Number of splices: Non-canonical | 16932 Mismatch rate per base, % | 0.24% Deletion rate per base | 0.01% Deletion average length | 2.13 Insertion rate per base | 0.01% Insertion average length | 1.93 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 1920729 % of reads mapped to multiple loci | 5.73% Number of reads mapped to too many loci | 1209284 % of reads mapped to too many loci | 3.61% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 3.14% % of reads unmapped: other | 14.58% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 7147442 7147442 7147442 N_multimapping 1920729 1920729 1920729 N_noFeature 818436 23563212 1342395 N_ambiguous 448385 3533 89486 UnstrandedReadsAssigned:23184108 PositiveStrandReadsAssigned:884184 NegativeStrandReadsAssigned:23019048 Dataset is classified negative stranded MeadianReadLen=101 20thPercentileLength=101 echo kmer=97 ERR3450088 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: 52,972 [index] number of k-mers: 66,720,672 [index] number of equivalence classes: 111,837 [quant] running in paired-end mode [quant] will process pair 1: ERR3450088-trimmed-pair1.fastq ERR3450088-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 33,519,100 reads, 24,501,029 reads pseudoaligned [quant] estimated average fragment length: 183.84 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,205 rounds 52973 ERR3450088.ke.tsv 35125 ERR3450088.se.tsv 88098 total ==> ERR3450088.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 753.345 0 0 PNS24247 1044 861.16 45.2743 3.17855 PNS24249 1928 1745.16 275.494 9.54419 PNS24246 1044 861.16 45.2743 3.17855 PNS24248 1044 861.16 45.2743 3.17855 PNS24244 1471 1288.16 61.6831 2.89507 PNS24243 293 129.935 3 1.39591 KQK14069 1603 1420.16 3725.48 158.601 KQK14071 474 294.556 210.929 43.2941 ==> ERR3450088.se.tsv <== BRADI_1g14170v3 4079 BRADI_1g53295v3 27 BRADI_1g59795v3 262 BRADI_1g07683v3 0 BRADI_1g00485v3 61 BRADI_1g20270v3 2934 BRADI_1g74790v3 267 BRADI_1g09890v3 6 BRADI_1g77505v3 317 BRADI_1g48960v3 1 ERR3450088 completed mapping pipeline successfully