Starting /dee2/code/volunteer_pipeline.sh ERR3450058 current disk space = 1543039766528 free memory = 1602559112 ERR3450058 SRAfilesize 354b91f2c5f4a1ab1d0bc9e3fe23e8cf ERR3450058.sra ERR3450058.sra file validated ERR3450058 is paired end ERR3450058 is conventional basespace ERR3450058 read1 length is 101 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR3450058_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 36.154 37.0 37.0 37.0 37.0 37.0 2 36.32 37.0 37.0 37.0 37.0 37.0 3 36.2775 37.0 37.0 37.0 37.0 37.0 4 36.4075 37.0 37.0 37.0 37.0 37.0 5 36.3965 37.0 37.0 37.0 37.0 37.0 6 36.4275 37.0 37.0 37.0 37.0 37.0 7 36.469 37.0 37.0 37.0 37.0 37.0 8 36.49 37.0 37.0 37.0 37.0 37.0 9 36.4805 37.0 37.0 37.0 37.0 37.0 10-11 36.48825 37.0 37.0 37.0 37.0 37.0 12-13 36.444 37.0 37.0 37.0 37.0 37.0 14-15 36.43825 37.0 37.0 37.0 37.0 37.0 16-17 36.488 37.0 37.0 37.0 37.0 37.0 18-19 36.4065 37.0 37.0 37.0 37.0 37.0 20-21 36.40375 37.0 37.0 37.0 37.0 37.0 22-23 36.41525 37.0 37.0 37.0 37.0 37.0 24-25 36.445750000000004 37.0 37.0 37.0 37.0 37.0 26-27 36.33825 37.0 37.0 37.0 37.0 37.0 28-29 36.41375 37.0 37.0 37.0 37.0 37.0 30-31 36.33325 37.0 37.0 37.0 37.0 37.0 32-33 36.37025 37.0 37.0 37.0 37.0 37.0 34-35 36.304500000000004 37.0 37.0 37.0 37.0 37.0 36-37 36.22775 37.0 37.0 37.0 37.0 37.0 38-39 36.326750000000004 37.0 37.0 37.0 37.0 37.0 40-41 36.2905 37.0 37.0 37.0 37.0 37.0 42-43 36.25425 37.0 37.0 37.0 37.0 37.0 44-45 36.224500000000006 37.0 37.0 37.0 37.0 37.0 46-47 36.1635 37.0 37.0 37.0 37.0 37.0 48-49 36.194 37.0 37.0 37.0 37.0 37.0 50-51 36.245999999999995 37.0 37.0 37.0 37.0 37.0 52-53 36.199 37.0 37.0 37.0 37.0 37.0 54-55 36.179 37.0 37.0 37.0 37.0 37.0 56-57 36.135000000000005 37.0 37.0 37.0 37.0 37.0 58-59 36.1965 37.0 37.0 37.0 37.0 37.0 60-61 36.073 37.0 37.0 37.0 37.0 37.0 62-63 36.07525 37.0 37.0 37.0 37.0 37.0 64-65 36.0695 37.0 37.0 37.0 37.0 37.0 66-67 36.085499999999996 37.0 37.0 37.0 37.0 37.0 68-69 36.135 37.0 37.0 37.0 37.0 37.0 70-71 36.06075 37.0 37.0 37.0 37.0 37.0 72-73 36.051500000000004 37.0 37.0 37.0 37.0 37.0 74-75 36.0975 37.0 37.0 37.0 37.0 37.0 76-77 36.141000000000005 37.0 37.0 37.0 37.0 37.0 78-79 36.14675 37.0 37.0 37.0 37.0 37.0 80-81 36.12125 37.0 37.0 37.0 37.0 37.0 82-83 36.068749999999994 37.0 37.0 37.0 37.0 37.0 84-85 36.065 37.0 37.0 37.0 37.0 37.0 86-87 36.03775 37.0 37.0 37.0 37.0 37.0 88-89 36.115750000000006 37.0 37.0 37.0 37.0 37.0 90-91 36.08075 37.0 37.0 37.0 37.0 37.0 92-93 36.055499999999995 37.0 37.0 37.0 37.0 37.0 94-95 36.039249999999996 37.0 37.0 37.0 37.0 37.0 96-97 36.08125 37.0 37.0 37.0 37.0 37.0 98-99 36.00175 37.0 37.0 37.0 37.0 37.0 100-101 35.97575 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 21 1.0 22 3.0 23 0.0 24 6.0 25 13.0 26 10.0 27 23.0 28 21.0 29 26.0 30 43.0 31 49.0 32 57.0 33 81.0 34 101.0 35 194.0 36 1758.0 37 1614.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 41.27382146439318 9.854563691073219 10.882647943831495 37.9889669007021 2 21.85 13.925 27.900000000000002 36.325 3 23.849999999999998 17.1 23.849999999999998 35.199999999999996 4 29.849999999999998 22.425 17.125 30.599999999999998 5 27.150000000000002 28.299999999999997 21.075 23.474999999999998 6 24.349999999999998 30.099999999999998 22.7 22.85 7 20.575 22.1 37.425000000000004 19.900000000000002 8 23.625 19.5 29.799999999999997 27.075 9 22.575 21.95 30.45 25.025 10-11 23.7125 28.549999999999997 21.7375 26.0 12-13 24.575 22.6375 25.124999999999996 27.6625 14-15 23.1875 25.387500000000003 24.875 26.55 16-17 23.7125 24.0625 25.2625 26.9625 18-19 24.9875 25.8125 23.8125 25.387500000000003 20-21 24.325 24.712500000000002 24.8125 26.150000000000002 22-23 24.1375 24.587500000000002 24.5125 26.7625 24-25 24.4125 24.375 24.1625 27.05 26-27 23.8875 24.2375 23.9375 27.9375 28-29 25.45 24.325 22.9875 27.237499999999997 30-31 23.799999999999997 23.8875 24.337500000000002 27.975 32-33 24.6 24.1375 24.224999999999998 27.037499999999998 34-35 24.775 23.875 24.5125 26.8375 36-37 24.65 24.15 24.4125 26.787499999999998 38-39 25.275 24.4125 23.4375 26.875 40-41 24.712500000000002 24.462500000000002 23.962500000000002 26.8625 42-43 24.75 24.15 24.8625 26.237500000000004 44-45 25.55 23.4625 24.6625 26.325 46-47 26.05 24.0125 24.099999999999998 25.837500000000002 48-49 25.4875 22.8375 23.0 28.675 50-51 24.275 24.4375 24.3 26.987499999999997 52-53 25.4875 23.6875 24.0 26.825 54-55 25.0125 23.6625 23.7625 27.5625 56-57 25.4875 23.425 24.025 27.0625 58-59 25.7 24.3875 23.974999999999998 25.937500000000004 60-61 25.1 24.3125 23.525 27.0625 62-63 24.15 23.4375 24.3125 28.1 64-65 24.8625 23.6625 24.725 26.75 66-67 26.424999999999997 23.5875 23.625 26.3625 68-69 23.575 23.8375 24.1125 28.475 70-71 26.687499999999996 23.625 23.125 26.5625 72-73 26.887499999999996 24.0 22.475 26.637499999999996 74-75 25.324999999999996 23.400000000000002 24.3875 26.887499999999996 76-77 25.15 23.9875 23.65 27.212500000000002 78-79 26.2625 23.95 23.1625 26.625 80-81 24.337500000000002 24.3625 23.150000000000002 28.15 82-83 25.85 24.2875 22.075 27.787499999999998 84-85 25.9875 24.3625 22.5625 27.0875 86-87 25.275 24.275 24.462500000000002 25.9875 88-89 25.4875 23.0625 24.0125 27.437499999999996 90-91 25.674999999999997 24.8125 22.5875 26.924999999999997 92-93 26.4625 23.9 22.8875 26.75 94-95 25.4375 24.725 22.1875 27.650000000000002 96-97 24.9875 24.5375 22.375 28.1 98-99 25.05 23.1375 23.799999999999997 28.012500000000003 100-101 25.275 25.2 22.7625 26.7625 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 10.0 1 6.0 2 1.0 3 0.5 4 1.0 5 0.5 6 0.0 7 1.0 8 1.0 9 1.5 10 2.5 11 1.0 12 0.5 13 0.5 14 0.0 15 0.5 16 1.0 17 1.5 18 1.0 19 0.5 20 0.5 21 0.5 22 1.5 23 1.5 24 1.0 25 0.5 26 0.5 27 0.5 28 3.0 29 4.0 30 3.5 31 7.0 32 7.0 33 6.0 34 8.0 35 16.0 36 27.5 37 37.5 38 42.5 39 54.0 40 71.5 41 91.0 42 120.5 43 140.0 44 144.0 45 141.5 46 167.0 47 185.0 48 174.0 49 173.5 50 168.5 51 156.0 52 149.0 53 150.5 54 141.0 55 130.0 56 137.0 57 123.0 58 102.5 59 98.0 60 87.0 61 81.0 62 83.5 63 72.5 64 62.5 65 66.5 66 60.0 67 56.5 68 56.5 69 52.0 70 52.0 71 48.0 72 39.5 73 35.0 74 29.5 75 25.5 76 24.5 77 17.5 78 10.5 79 7.5 80 5.5 81 3.5 82 3.5 83 2.5 84 1.0 85 1.5 86 1.5 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 0.3 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 87.5 #Duplication Level Percentage of deduplicated Percentage of total 1 89.0 77.875 2 9.171428571428573 16.05 3 1.0571428571428572 2.775 4 0.4 1.4000000000000001 5 0.2285714285714286 1.0 6 0.08571428571428572 0.44999999999999996 7 0.028571428571428574 0.17500000000000002 8 0.0 0.0 9 0.0 0.0 >10 0.028571428571428574 0.27499999999999997 >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 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 11 0.27499999999999997 No Hit GCTTTGAGCACTCTAATTTCTTCAAAGTAACGATGCCGGAGGCACGACCC 7 0.17500000000000002 No Hit GTCCCCTCTCTTTTCGAAGCTGTTTTGAATAAGCCGCAGCCTTTGCGTCT 6 0.15 No Hit GCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGC 6 0.15 No Hit GTCGAGTTATCATGAATCATCGGATCAGCGAGCAAAGCCCGCGTCAGCCT 6 0.15 No Hit TTACGACTTCTCCTTCCTCTAAATGATAAGGTTCAATGGACTTCTCGCGA 5 0.125 No Hit CGGTATTGTTATTTATTGTCACTACCTCCCCGTGTCAGGATTGGGTAATT 5 0.125 No Hit CTTTTATCTAATAAATGCGCCCCTCCCAGAAGTCGGGGTTTGTTGCACGT 5 0.125 No Hit CCCGACTGTCCCTATTAATCATTACTCCGATCCCGAAGGCCAACACAATA 5 0.125 No Hit CAGCCTTTTATCTAATAAATGCGCCCCTCCCAGAAGTCGGGGTTTGTTGC 5 0.125 No Hit GGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTC 5 0.125 No Hit CATGAATCATCGGATCAGCGAGCAAAGCCCGCGTCAGCCTTTTATCTAAT 5 0.125 No Hit CCCATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCT 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 0.0125 0.0 0.0 0.0 0.0 32-33 0.05 0.0 0.0 0.0 0.0 34-35 0.11249999999999999 0.0 0.0 0.0 0.0 36-37 0.16249999999999998 0.0 0.0 0.0 0.0 38-39 0.175 0.0 0.0 0.0 0.0 40-41 0.1875 0.0 0.0 0.0 0.0 42-43 0.2375 0.0 0.0 0.0 0.0 44-45 0.3 0.0 0.0 0.0 0.0 46-47 0.3125 0.0 0.0 0.0 0.0 48-49 0.3375 0.0 0.0 0.0 0.0 50-51 0.35 0.0 0.0 0.0 0.0 52-53 0.4 0.0 0.0 0.0 0.0 54-55 0.4875 0.0 0.0 0.0 0.0 56-57 0.5625 0.0 0.0 0.0 0.0 58-59 0.7 0.0 0.0 0.0 0.0 60-61 0.8125 0.0 0.0 0.0 0.0 62-63 0.925 0.0 0.0 0.0 0.0 64-65 1.0375 0.0 0.0 0.0 0.0 66-67 1.1625 0.0 0.0 0.0 0.0 68-69 1.3375 0.0 0.0 0.0 0.0 70-71 1.55 0.0 0.0 0.0 0.0 72-73 1.85 0.0 0.0 0.0 0.0 74-75 2.0 0.0 0.0 0.0 0.0 76-77 2.2249999999999996 0.0 0.0 0.0 0.0 78-79 2.5 0.0 0.0 0.0 0.0 80-81 2.7874999999999996 0.0 0.0 0.0 0.0 82-83 3.2625 0.0 0.0 0.0 0.0 84-85 3.575 0.0 0.0 0.0 0.0 86-87 3.9000000000000004 0.0 0.0 0.0 0.0 88-89 4.175 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE ERR3450058 read2 length is 101 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR3450058_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 35.673 37.0 37.0 37.0 37.0 37.0 2 35.92025 37.0 37.0 37.0 37.0 37.0 3 35.8705 37.0 37.0 37.0 37.0 37.0 4 36.0185 37.0 37.0 37.0 37.0 37.0 5 36.007 37.0 37.0 37.0 37.0 37.0 6 36.0125 37.0 37.0 37.0 37.0 37.0 7 35.977 37.0 37.0 37.0 37.0 37.0 8 36.1025 37.0 37.0 37.0 37.0 37.0 9 36.022 37.0 37.0 37.0 37.0 37.0 10-11 36.01675 37.0 37.0 37.0 37.0 37.0 12-13 36.013 37.0 37.0 37.0 37.0 37.0 14-15 35.99875 37.0 37.0 37.0 37.0 37.0 16-17 36.08525 37.0 37.0 37.0 37.0 37.0 18-19 36.041 37.0 37.0 37.0 37.0 37.0 20-21 35.9905 37.0 37.0 37.0 37.0 37.0 22-23 36.01375 37.0 37.0 37.0 37.0 37.0 24-25 35.86925 37.0 37.0 37.0 37.0 37.0 26-27 36.0025 37.0 37.0 37.0 37.0 37.0 28-29 35.9585 37.0 37.0 37.0 37.0 37.0 30-31 35.98725 37.0 37.0 37.0 37.0 37.0 32-33 35.89175 37.0 37.0 37.0 37.0 37.0 34-35 35.8485 37.0 37.0 37.0 37.0 37.0 36-37 35.798249999999996 37.0 37.0 37.0 37.0 37.0 38-39 35.737 37.0 37.0 37.0 37.0 37.0 40-41 35.76225 37.0 37.0 37.0 37.0 37.0 42-43 35.759625 37.0 37.0 37.0 37.0 37.0 44-45 35.737375 37.0 37.0 37.0 37.0 37.0 46-47 35.7265 37.0 37.0 37.0 37.0 37.0 48-49 35.71925 37.0 37.0 37.0 37.0 37.0 50-51 35.70575 37.0 37.0 37.0 37.0 37.0 52-53 35.785250000000005 37.0 37.0 37.0 37.0 37.0 54-55 35.665499999999994 37.0 37.0 37.0 37.0 37.0 56-57 35.65475 37.0 37.0 37.0 37.0 37.0 58-59 35.607749999999996 37.0 37.0 37.0 37.0 37.0 60-61 35.58475 37.0 37.0 37.0 37.0 37.0 62-63 35.6445 37.0 37.0 37.0 37.0 37.0 64-65 35.584 37.0 37.0 37.0 37.0 37.0 66-67 35.70125 37.0 37.0 37.0 37.0 37.0 68-69 35.59325 37.0 37.0 37.0 37.0 37.0 70-71 35.52575 37.0 37.0 37.0 37.0 37.0 72-73 35.505125 37.0 37.0 37.0 37.0 37.0 74-75 35.464124999999996 37.0 37.0 37.0 37.0 37.0 76-77 35.534499999999994 37.0 37.0 37.0 37.0 37.0 78-79 35.51925 37.0 37.0 37.0 37.0 37.0 80-81 35.39475 37.0 37.0 37.0 37.0 37.0 82-83 35.411500000000004 37.0 37.0 37.0 37.0 37.0 84-85 35.534 37.0 37.0 37.0 37.0 37.0 86-87 35.63675 37.0 37.0 37.0 37.0 37.0 88-89 35.589749999999995 37.0 37.0 37.0 37.0 37.0 90-91 35.569500000000005 37.0 37.0 37.0 37.0 37.0 92-93 35.681125 37.0 37.0 37.0 37.0 37.0 94-95 35.701 37.0 37.0 37.0 37.0 37.0 96-97 35.609750000000005 37.0 37.0 37.0 37.0 37.0 98-99 35.5245 37.0 37.0 37.0 37.0 37.0 100-101 35.493 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 13 1.0 14 1.0 15 3.0 16 1.0 17 4.0 18 2.0 19 4.0 20 9.0 21 11.0 22 8.0 23 11.0 24 11.0 25 22.0 26 19.0 27 21.0 28 34.0 29 27.0 30 42.0 31 57.0 32 77.0 33 89.0 34 131.0 35 342.0 36 2223.0 37 850.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 40.725 16.375 12.225 30.675 2 27.581895473868467 22.780695173793447 25.78144536134033 23.85596399099775 3 25.474999999999998 24.125 26.025 24.375 4 28.475 28.425 18.5 24.6 5 31.075000000000003 28.875 17.4 22.650000000000002 6 23.075000000000003 32.775 21.175 22.975 7 25.8 19.475 31.05 23.674999999999997 8 25.724999999999998 20.200000000000003 23.674999999999997 30.4 9 26.05 22.5 25.474999999999998 25.974999999999998 10-11 28.8625 27.0875 19.162499999999998 24.887500000000003 12-13 28.475 22.0125 22.375 27.1375 14-15 27.0 24.7 22.825 25.474999999999998 16-17 27.325 24.712500000000002 22.7375 25.224999999999998 18-19 27.625 24.55 22.375 25.45 20-21 27.200000000000003 24.224999999999998 23.1125 25.4625 22-23 27.3375 24.775 22.6875 25.2 24-25 27.675 24.675 23.0125 24.637500000000003 26-27 26.487500000000004 24.65 23.6625 25.2 28-29 27.537499999999998 24.5625 21.7875 26.1125 30-31 27.250000000000004 24.8 22.912499999999998 25.0375 32-33 27.5875 24.125 23.8875 24.4 34-35 27.325 24.525 22.3125 25.837500000000002 36-37 28.175 24.575 21.45 25.8 38-39 27.3 24.825 23.200000000000003 24.675 40-41 27.750000000000004 24.125 22.7 25.424999999999997 42-43 27.61595199399925 23.615451931491435 24.04050506313289 24.72809101137642 44-45 27.378422302787847 24.103012876609576 23.777972246530815 24.74059257407176 46-47 27.200000000000003 22.8 23.3125 26.687499999999996 48-49 26.887499999999996 25.0375 22.900000000000002 25.174999999999997 50-51 27.787499999999998 24.625 22.775000000000002 24.8125 52-53 26.5375 24.1125 24.0125 25.337500000000002 54-55 26.5375 24.2625 23.4875 25.7125 56-57 25.974999999999998 25.25 23.9375 24.837500000000002 58-59 27.8875 23.5625 23.0625 25.4875 60-61 27.537499999999998 24.2625 22.9875 25.2125 62-63 26.8375 24.45 24.125 24.587500000000002 64-65 27.437499999999996 24.325 23.1125 25.124999999999996 66-67 26.55 23.7375 23.6625 26.05 68-69 25.424999999999997 25.912499999999998 22.875 25.7875 70-71 27.375 24.087500000000002 23.6125 24.925 72-73 27.765970746343292 24.04050506313289 23.32791598949869 24.86560820102513 74-75 26.428303537942245 24.24053006625828 23.415426928366045 25.91573946743343 76-77 26.974999999999998 23.875 23.4125 25.7375 78-79 27.037499999999998 24.15 23.4875 25.324999999999996 80-81 26.375 23.825 24.7375 25.0625 82-83 27.200000000000003 24.05 22.900000000000002 25.85 84-85 26.437500000000004 23.9 23.2875 26.375 86-87 26.937499999999996 24.25 22.8125 26.0 88-89 29.099999999999998 24.637500000000003 22.45 23.8125 90-91 28.15 24.825 23.1875 23.8375 92-93 28.328541067633456 25.51568946118265 22.665333166645834 23.49043630453807 94-95 29.275000000000002 23.7625 22.6 24.3625 96-97 28.575 24.5 22.1 24.825 98-99 28.675 23.575 23.375 24.375 100-101 30.325000000000003 23.525 22.900000000000002 23.25 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 0.0 1 0.0 2 0.5 3 1.0 4 1.5 5 1.0 6 1.5 7 3.0 8 1.5 9 2.0 10 2.5 11 1.0 12 0.5 13 1.0 14 2.0 15 1.5 16 2.0 17 3.0 18 1.5 19 1.0 20 3.5 21 4.0 22 2.0 23 0.5 24 0.5 25 0.5 26 0.0 27 2.0 28 3.5 29 3.0 30 2.5 31 1.5 32 4.0 33 7.5 34 9.0 35 18.0 36 27.5 37 33.5 38 49.5 39 61.5 40 72.0 41 91.5 42 124.0 43 143.0 44 137.0 45 139.5 46 152.0 47 173.5 48 173.0 49 165.5 50 160.0 51 143.5 52 145.0 53 160.0 54 150.0 55 125.0 56 120.5 57 116.0 58 97.5 59 78.0 60 77.0 61 82.5 62 81.0 63 77.5 64 67.5 65 68.5 66 73.0 67 68.0 68 68.5 69 64.0 70 56.0 71 49.0 72 38.5 73 28.5 74 32.0 75 30.5 76 26.0 77 24.0 78 15.0 79 13.5 80 9.0 81 3.0 82 3.5 83 3.0 84 1.0 85 0.5 86 0.0 87 1.0 88 2.0 89 1.5 90 0.5 91 0.0 92 0.0 93 0.5 94 0.5 95 0.5 96 0.5 97 0.0 98 0.0 99 0.0 100 2.0 >>END_MODULE >>Per base N content pass #Base N-Count 1 0.0 2 0.025 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 0.0125 44-45 0.0125 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 0.0125 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 0.0125 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 88.775 #Duplication Level Percentage of deduplicated Percentage of total 1 89.66488313151225 79.60000000000001 2 8.842579555054913 15.7 3 0.9574767671078569 2.55 4 0.36609405801182765 1.3 5 0.08448324415657561 0.375 6 0.056322162771050406 0.3 7 0.028161081385525203 0.17500000000000002 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 GCGATTTGTCTGGTTAATTCCGTTAACGAACGAGACCTCAGCCTGCTAAC 7 0.17500000000000002 No Hit GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 6 0.15 No Hit CTACATATGAGCACCAGGATACTTCCTTCAGTACTGTAGTGCCCATCGAG 6 0.15 No Hit CCTGCCAGTAGTCATATGCTTGTCTCAAAGATTAAGCCATGCATGTGCAA 5 0.125 No Hit CTTGGATTTATGAAAGACGAACAACTGCGAAAGCATTTGCCAAGGATGTT 5 0.125 No Hit CTTACCAGGTCCAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTT 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 0.0125 0.0 0.0 0.0 0.0 32-33 0.05 0.0 0.0 0.0 0.0 34-35 0.11249999999999999 0.0 0.0 0.0 0.0 36-37 0.16249999999999998 0.0 0.0 0.0 0.0 38-39 0.175 0.0 0.0 0.0 0.0 40-41 0.1875 0.0 0.0 0.0 0.0 42-43 0.2375 0.0 0.0 0.0 0.0 44-45 0.3 0.0 0.0 0.0 0.0 46-47 0.3125 0.0 0.0 0.0 0.0 48-49 0.3375 0.0 0.0 0.0 0.0 50-51 0.35 0.0 0.0 0.0 0.0 52-53 0.4 0.0 0.0 0.0 0.0 54-55 0.4875 0.0 0.0 0.0 0.0 56-57 0.5625 0.0 0.0 0.0 0.0 58-59 0.7 0.0 0.0 0.0 0.0 60-61 0.8125 0.0 0.0 0.0 0.0 62-63 0.9375 0.0 0.0 0.0 0.0 64-65 1.0625 0.0 0.0 0.0 0.0 66-67 1.1875 0.0 0.0 0.0 0.0 68-69 1.3625 0.0 0.0 0.0 0.0 70-71 1.575 0.0 0.0 0.0 0.0 72-73 1.875 0.0 0.0 0.0 0.0 74-75 2.025 0.0 0.0 0.0 0.0 76-77 2.25 0.0 0.0 0.0 0.0 78-79 2.5 0.0 0.0 0.0 0.0 80-81 2.7874999999999996 0.0 0.0 0.0 0.0 82-83 3.25 0.0 0.0 0.0 0.0 84-85 3.55 0.0 0.0 0.0 0.0 86-87 3.875 0.0 0.0 0.0 0.0 88-89 4.15 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Read 694486 spots for ERR3450058.sra Written 694486 spots for ERR3450058.sra Read 694486 spots for ERR3450058.sra Written 694486 spots for ERR3450058.sra Read 694486 spots for ERR3450058.sra Written 694486 spots for ERR3450058.sra Read 694486 spots for ERR3450058.sra Written 694486 spots for ERR3450058.sra Read 694486 spots for ERR3450058.sra Written 694486 spots for ERR3450058.sra Read 694486 spots for ERR3450058.sra Written 694486 spots for ERR3450058.sra Read 694486 spots for ERR3450058.sra Written 694486 spots for ERR3450058.sra Read 694486 spots for ERR3450058.sra Written 694486 spots for ERR3450058.sra Read 694486 spots for ERR3450058.sra Written 694486 spots for ERR3450058.sra Read 694486 spots for ERR3450058.sra Written 694486 spots for ERR3450058.sra Read 694486 spots for ERR3450058.sra Written 694486 spots for ERR3450058.sra Read 694486 spots for ERR3450058.sra Written 694486 spots for ERR3450058.sra Read 694486 spots for ERR3450058.sra Written 694486 spots for ERR3450058.sra Read 694486 spots for ERR3450058.sra Written 694486 spots for ERR3450058.sra Read 694486 spots for ERR3450058.sra Written 694486 spots for ERR3450058.sra Read 694486 spots for ERR3450058.sra Written 694486 spots for ERR3450058.sra Read 694486 spots for ERR3450058.sra Written 694486 spots for ERR3450058.sra Read 694488 spots for ERR3450058.sra Written 694488 spots for ERR3450058.sra Read 694486 spots for ERR3450058.sra Written 694486 spots for ERR3450058.sra Read 694486 spots for ERR3450058.sra Written 694486 spots for ERR3450058.sra SRR ids: ['ERR3450058.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_8qkl2c9x ERR3450058.sra spots: 13889722 blocks: [[1, 694486], [694487, 1388972], [1388973, 2083458], [2083459, 2777944], [2777945, 3472430], [3472431, 4166916], [4166917, 4861402], [4861403, 5555888], [5555889, 6250374], [6250375, 6944860], [6944861, 7639346], [7639347, 8333832], [8333833, 9028318], [9028319, 9722804], [9722805, 10417290], [10417291, 11111776], [11111777, 11806262], [11806263, 12500748], [12500749, 13195234], [13195235, 13889722]] ERR3450058 file size 3328652 ERR3450058 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 ERR3450058 ERR3450058_1.fastq ERR3450058_2.fastq Input file: ERR3450058_1.fastq Paired file: ERR3450058_2.fastq trimmed: ERR3450058-trimmed-pair1.fastq, ERR3450058-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 14:11:12 2024 >> started Sat Dec 7 14:11:24 2024 >> done (12.139s) 13889722 read pairs processed; of these: 110 ( 0.00%) short read pairs filtered out after trimming by size control 15186 ( 0.11%) empty read pairs filtered out after trimming by size control 13874426 (99.89%) read pairs available; of these: 1020325 ( 7.35%) trimmed read pairs available after processing 12854101 (92.65%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 11 0.00% 19 25 0.00% 20 79 0.00% 21 192 0.00% 22 220 0.00% 23 107 0.00% 24 85 0.00% 25 142 0.00% 26 210 0.00% 27 271 0.00% 28 417 0.00% 29 545 0.00% 30 666 0.00% 31 841 0.01% 32 870 0.01% 33 759 0.01% 34 798 0.01% 35 826 0.01% 36 863 0.01% 37 989 0.01% 38 1130 0.01% 39 1296 0.01% 40 1526 0.01% 41 1899 0.01% 42 2039 0.01% 43 2089 0.02% 44 1907 0.01% 45 1893 0.01% 46 2097 0.02% 47 2240 0.02% 48 2465 0.02% 49 2844 0.02% 50 3042 0.02% 51 3471 0.03% 52 3715 0.03% 53 4099 0.03% 54 4296 0.03% 55 4389 0.03% 56 4681 0.03% 57 4896 0.04% 58 5322 0.04% 59 5850 0.04% 60 6285 0.05% 61 7019 0.05% 62 7742 0.06% 63 8172 0.06% 64 8784 0.06% 65 9023 0.07% 66 9471 0.07% 67 10133 0.07% 68 10759 0.08% 69 11039 0.08% 70 11800 0.09% 71 13075 0.09% 72 14287 0.10% 73 14833 0.11% 74 15553 0.11% 75 16483 0.12% 76 17357 0.13% 77 17717 0.13% 78 18334 0.13% 79 19588 0.14% 80 20309 0.15% 81 21189 0.15% 82 22885 0.16% 83 23815 0.17% 84 24827 0.18% 85 26306 0.19% 86 27100 0.20% 87 28020 0.20% 88 29434 0.21% 89 31149 0.22% 90 31732 0.23% 91 34118 0.25% 92 35891 0.26% 93 36724 0.26% 94 38461 0.28% 95 39831 0.29% 96 41067 0.30% 97 42537 0.31% 98 44078 0.32% 99 44652 0.32% 100 52644 0.38% 101 12854101 92.65% 13874426 reads passed initial QC criterion=sequence-density sequence-density=0.35 sequence-density-rank=1 fanout-score=1.97 fanout-score-rank=33 prefix-density=0.35 prefix-fanout=2.0 sequence=GTATTTAGCCTTG criterion=fanout-score sequence-density=0.07 sequence-density-rank=17 fanout-score=247.19 fanout-score-rank=1 prefix-density=0.65 prefix-fanout=24.9 sequence=GCCGCCGCCGCC criterion=sequence-density sequence-density=0.19 sequence-density-rank=1 fanout-score=1.99 fanout-score-rank=34 prefix-density=0.19 prefix-fanout=2.0 sequence=CAAGTGTTGGATT criterion=fanout-score sequence-density=0.08 sequence-density-rank=22 fanout-score=306.25 fanout-score-rank=1 prefix-density=0.84 prefix-fanout=27.7 sequence=GGCGGCGGCGGTGG ERR3450058 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 07 14:11:54 Started mapping on | Dec 07 14:11:54 Finished on | Dec 07 14:13:08 Mapping speed, Million of reads per hour | 674.97 Number of input reads | 13874426 Average input read length | 199 UNIQUE READS: Uniquely mapped reads number | 10329936 Uniquely mapped reads % | 74.45% Average mapped length | 198.92 Number of splices: Total | 6239089 Number of splices: Annotated (sjdb) | 5901258 Number of splices: GT/AG | 6159940 Number of splices: GC/AG | 67809 Number of splices: AT/AC | 3943 Number of splices: Non-canonical | 7397 Mismatch rate per base, % | 0.25% Deletion rate per base | 0.01% Deletion average length | 2.15 Insertion rate per base | 0.01% Insertion average length | 1.97 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 557877 % of reads mapped to multiple loci | 4.02% Number of reads mapped to too many loci | 471382 % of reads mapped to too many loci | 3.40% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 3.32% % of reads unmapped: other | 14.81% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 2986613 2986613 2986613 N_multimapping 557877 557877 557877 N_noFeature 336909 9954249 560419 N_ambiguous 181563 1477 30581 UnstrandedReadsAssigned:9811464 PositiveStrandReadsAssigned:374210 NegativeStrandReadsAssigned:9738936 Dataset is classified negative stranded MeadianReadLen=101 20thPercentileLength=101 echo kmer=97 ERR3450058 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: ERR3450058-trimmed-pair1.fastq ERR3450058-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 13,874,426 reads, 10,193,285 reads pseudoaligned [quant] estimated average fragment length: 190.438 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,222 rounds 52973 ERR3450058.ke.tsv 35125 ERR3450058.se.tsv 88098 total ==> ERR3450058.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 746.706 0 0 PNS24247 1044 854.562 20.0028 3.47333 PNS24249 1928 1738.56 137.576 11.7422 PNS24246 1044 854.562 20.0028 3.47333 PNS24248 1044 854.562 20.0028 3.47333 PNS24244 1471 1281.56 20.4158 2.36389 PNS24243 293 125.047 0 0 KQK14069 1603 1413.56 2299.72 241.412 KQK14071 474 288.343 108.558 55.8667 ==> ERR3450058.se.tsv <== BRADI_1g14170v3 2482 BRADI_1g53295v3 25 BRADI_1g59795v3 100 BRADI_1g07683v3 0 BRADI_1g00485v3 20 BRADI_1g20270v3 1430 BRADI_1g74790v3 168 BRADI_1g09890v3 31 BRADI_1g77505v3 125 BRADI_1g48960v3 0 ERR3450058 completed mapping pipeline successfully