Starting /dee2/code/volunteer_pipeline.sh SRR5578449 current disk space = 1523407167488 free memory = 1567514768 SRR5578449 SRAfilesize ec29a13c68157a8554956590d7f2ddea SRR5578449.sra SRR5578449.sra file validated SRR5578449 is paired end SRR5578449 is conventional basespace SRR5578449 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR5578449_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 46 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 33.10525 34.0 34.0 34.0 33.0 34.0 2 33.57275 34.0 34.0 34.0 33.0 34.0 3 33.62125 34.0 34.0 34.0 33.0 34.0 4 33.65525 34.0 34.0 34.0 33.0 34.0 5 33.63775 34.0 34.0 34.0 33.0 34.0 6 37.3845 38.0 38.0 38.0 36.0 38.0 7 37.46125 38.0 38.0 38.0 37.0 38.0 8 37.633 38.0 38.0 38.0 38.0 38.0 9 37.701 38.0 38.0 38.0 38.0 38.0 10-14 37.709649999999996 38.0 38.0 38.0 38.0 38.0 15-19 37.68235 38.0 38.0 38.0 38.0 38.0 20-24 37.66735 38.0 38.0 38.0 38.0 38.0 25-29 37.58855 38.0 38.0 38.0 38.0 38.0 30-34 37.5165 38.0 38.0 38.0 38.0 38.0 35-39 37.44099999999999 38.0 38.0 38.0 38.0 38.0 40-44 37.3247 38.0 38.0 38.0 38.0 38.0 45-49 37.329150000000006 38.0 38.0 38.0 37.8 38.0 50-54 37.34695 38.0 38.0 38.0 38.0 38.0 55-59 37.306250000000006 38.0 38.0 38.0 37.6 38.0 60-64 37.2684 38.0 38.0 38.0 37.4 38.0 65-69 37.183949999999996 38.0 38.0 38.0 37.0 38.0 70-74 37.12365 38.0 38.0 38.0 37.0 38.0 75-79 36.7757 38.0 38.0 38.0 36.0 38.0 80-84 36.716750000000005 38.0 38.0 38.0 36.2 38.0 85-89 36.5897 38.0 38.0 38.0 36.0 38.0 90-94 36.50214999999999 38.0 38.0 38.0 35.6 38.0 95-99 36.4083 38.0 38.0 38.0 35.0 38.0 100-104 36.2924 38.0 38.0 38.0 34.8 38.0 105-109 36.2093 38.0 38.0 38.0 34.4 38.0 110-114 36.09114999999999 38.0 38.0 38.0 34.0 38.0 115-119 35.9441 38.0 38.0 38.0 33.8 38.0 120-124 35.8769 38.0 38.0 38.0 33.6 38.0 125-129 35.62624999999999 38.0 37.6 38.0 32.8 38.0 130-134 35.4454 38.0 36.6 38.0 31.8 38.0 135-139 35.1976 38.0 36.0 38.0 31.0 38.0 140-144 34.75335 38.0 35.6 38.0 28.6 38.0 145-149 34.244550000000004 38.0 35.0 38.0 26.6 38.0 150-151 30.725125000000002 36.5 29.5 38.0 8.5 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 4 1.0 5 0.0 6 2.0 7 4.0 8 6.0 9 5.0 10 1.0 11 1.0 12 2.0 13 2.0 14 2.0 15 1.0 16 3.0 17 9.0 18 15.0 19 26.0 20 4.0 21 4.0 22 4.0 23 6.0 24 6.0 25 6.0 26 10.0 27 11.0 28 20.0 29 8.0 30 14.0 31 22.0 32 39.0 33 56.0 34 95.0 35 190.0 36 492.0 37 2933.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 42.92980671414038 11.571719226856562 9.84231943031536 35.656154628687695 2 27.725 13.450000000000001 30.975 27.85 3 24.012006003001503 16.53326663331666 23.536768384192097 35.91795897948975 4 26.825 24.125 23.3 25.75 5 27.325 26.55 25.775 20.349999999999998 6 23.5 29.4 26.125 20.974999999999998 7 16.05 25.074999999999996 41.475 17.4 8 18.675 25.924999999999997 32.475 22.925 9 19.575 22.55 35.05 22.825 10-14 22.99 27.139999999999997 27.305 22.564999999999998 15-19 22.325 26.424999999999997 27.405 23.845 20-24 22.97 25.695 27.565 23.77 25-29 21.740000000000002 26.669999999999998 28.599999999999998 22.99 30-34 21.914382876575313 27.38047609521904 27.245449089817964 23.459691938387678 35-39 21.959391878375676 26.840368073614723 27.285457091418287 23.914782956591317 40-44 24.013404691642073 25.62396838893613 26.69434302005702 23.668283899364777 45-49 23.742374237423743 26.982698269826983 27.262726272627262 22.012201220122012 50-54 24.275 26.255 26.015 23.455000000000002 55-59 22.689999999999998 26.52 27.265 23.525 60-64 22.0 27.255000000000003 26.450000000000003 24.295 65-69 21.759999999999998 28.54 26.200000000000003 23.5 70-74 23.035 28.285 25.66 23.02 75-79 22.62 25.985000000000003 26.755000000000003 24.64 80-84 22.925 26.974999999999998 26.240000000000002 23.86 85-89 23.565 26.200000000000003 26.685 23.549999999999997 90-94 23.951197559877993 25.706285314265713 27.03635181759088 23.306165308265413 95-99 21.775 26.05 28.084999999999997 24.09 100-104 23.22 26.6 26.179999999999996 24.0 105-109 23.599999999999998 27.134999999999998 26.0 23.265 110-114 22.08 26.534999999999997 25.865 25.52 115-119 21.95 27.35 25.77 24.93 120-124 23.69329265242835 26.944430550692744 24.7136497774221 24.64862701945681 125-129 22.953772263358015 27.606563938363017 24.349609765859515 25.090054032419452 130-134 23.609165499299582 26.23574144486692 25.600360216129676 24.55473283970382 135-139 22.586776032809844 28.16845053516055 25.982794838451532 23.26197859357807 140-144 23.541177058852945 27.431371568578427 25.216260813040652 23.811190559527976 145-149 23.221161058052903 29.066453322666135 23.311165558277914 24.401220061003052 150-151 23.30497873405054 26.7575681761321 24.893670252689517 25.04378283712785 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 1.0 1 1.0 2 0.5 3 1.0 4 2.0 5 1.5 6 0.5 7 1.5 8 1.5 9 1.0 10 1.0 11 1.0 12 1.5 13 0.5 14 0.0 15 0.5 16 0.5 17 1.0 18 1.5 19 1.0 20 2.0 21 3.0 22 3.0 23 2.0 24 1.0 25 1.0 26 1.0 27 2.5 28 5.5 29 18.5 30 30.5 31 48.5 32 63.0 33 63.0 34 73.5 35 89.5 36 124.5 37 159.5 38 156.0 39 133.0 40 130.0 41 125.0 42 104.5 43 100.5 44 113.0 45 128.5 46 136.0 47 147.5 48 152.0 49 156.0 50 158.5 51 149.0 52 161.5 53 163.0 54 146.0 55 141.5 56 127.5 57 113.0 58 101.0 59 86.5 60 60.0 61 41.5 62 43.0 63 39.0 64 33.0 65 21.5 66 15.0 67 16.5 68 14.5 69 10.5 70 11.5 71 10.0 72 8.0 73 10.0 74 7.0 75 3.5 76 6.0 77 6.0 78 2.0 79 0.5 80 0.5 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 1.7000000000000002 2 0.0 3 0.05 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 0.02 35-39 0.02 40-44 0.034999999999999996 45-49 0.01 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 0.005 95-99 0.0 100-104 0.0 105-109 0.0 110-114 0.0 115-119 0.0 120-124 0.034999999999999996 125-129 0.06 130-134 0.06 135-139 0.03 140-144 0.005 145-149 0.005 150-151 0.075 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 75.375 #Duplication Level Percentage of deduplicated Percentage of total 1 86.53399668325041 65.225 2 7.429519071310116 11.200000000000001 3 2.8855721393034823 6.525 4 0.9618573797678276 2.9000000000000004 5 0.5970149253731344 2.25 6 0.4975124378109453 2.25 7 0.16583747927031509 0.8750000000000001 8 0.26533996683250416 1.6 9 0.16583747927031509 1.125 >10 0.4975124378109453 6.05 >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 GATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGACTATCTCGTATGC 39 0.975 TruSeq Adapter, Index 7 (97% over 37bp) GCCTTATGTGATAGATGCCTCTTTAAAATATCTAAGTGCTGGGGTTATGA 30 0.75 No Hit GCCTCACTTAGTTACAGTTTTATGGATAATTGGGATATTCTTTGGTATAG 22 0.5499999999999999 No Hit GGAAGCTATACTATATAGGTGGCTATCTATCCCTACCAAGGCTTATATTG 19 0.475 No Hit CCCATTTTTAGTTATAATGATGCCTTATGTGATAGATGCCTCTTTAAAAT 17 0.42500000000000004 No Hit CTTATGTGATAGATGCCTCTTTAAAATATCTAAGTGCTGGGGTTATGAGT 16 0.4 No Hit GGGGTTATGAGTAGGGATGAGCATAAACCAACAACTCTCAAAGAAGATGG 16 0.4 No Hit GATGCCTTATGTGATAGATGCCTCTTTAAAATATCTAAGTGCTGGGGTTA 12 0.3 No Hit GGGAAGCTATACTATATAGGTGGCTATCTATCCCTACCAAGGCTTATATT 11 0.27499999999999997 No Hit GCCCGTTTCAGGTGGTCCTCAGCGTACGGCGGGACCTCTGAGAATTGGGA 10 0.25 No Hit CTCACTTAGTTACAGTTTTATGGATAATTGGGATATTCTTTGGTATAGTT 10 0.25 No Hit GTGGCTATCTATCCCTACCAAGGCTTATATTGAAGTATAAACCAATGAGA 10 0.25 No Hit CCTCACTTAGTTACAGTTTTATGGATAATTGGGATATTCTTTGGTATAGT 10 0.25 No Hit GGATAATTGGGATATTCTTTGGTATAGTTGGGATTTTAATATCATTAATA 10 0.25 No Hit GGGATATTCTTTGGTATAGTTGGGATTTTAATATCATTAATAGCATGATG 10 0.25 No Hit GCTGGGGTTATGAGTAGGGATGAGCATAAACCAACAACTCTCAAAGAAGA 9 0.22499999999999998 No Hit GCCCATAACAATAGGAAATATCAGAAATCCAATAAGAATCAGCAATTCAG 9 0.22499999999999998 No Hit CTCAGACGCTGCCCTAACTGCGCAGTTAATAATTCTGGCAATTCGTCTCC 9 0.22499999999999998 No Hit CGGCTGTCGAGTTGTACGGCCGTTCAGCCACGAGTCACGGGGTCTAACGC 9 0.22499999999999998 No Hit GCCTCTTTAAAATATCTAAGTGCTGGGGTTATGAGTAGGGATGAGCATAA 9 0.22499999999999998 No Hit GGCTATCTATCCCTACCAAGGCTTATATTGAAGTATAAACCAATGAGAGA 8 0.2 No Hit GGGGATAATTGCGCGGTTTTGACTGCGGAAGGAAGCCAAGGCCCACCTAA 8 0.2 No Hit CCAGGAGATGTTGGAACTCTACCAATTGGAGCTTTCTTAGCTGTCTTAGC 8 0.2 No Hit GTGATAGATGCCTCTTTAAAATATCTAAGTGCTGGGGTTATGAGTAGGGA 8 0.2 No Hit GTAGTTTATAAGGAATATATCCCATTTTTAGTTATAATGATGCCTTATGT 8 0.2 No Hit TGGCTATCTATCCCTACCAAGGCTTATATTGAAGTATAAACCAATGAGAG 8 0.2 No Hit GGCAGTTTCCAGAAACGTGTATCACATCTAGGCATGGAATCTTATGCCAG 8 0.2 No Hit GCTATCTATCCCTACCAAGGCTTATATTGAAGTATAAACCAATGAGAGAG 8 0.2 No Hit CTATATTTCGTTTTTCTGAGACCTATCCGAGTTCAGTGCGACCGTACAGC 7 0.17500000000000002 No Hit GTGTACACCGCCCTTAGACGTCTTGGTATACGGACAACTGATGGACCCAC 7 0.17500000000000002 No Hit GGTGGCTATCTATCCCTACCAAGGCTTATATTGAAGTATAAACCAATGAG 7 0.17500000000000002 No Hit GGATATTCTTTGGTATAGTTGGGATTTTAATATCATTAATAGCATGATGG 7 0.17500000000000002 No Hit GGGATAATTGCGCGGTTTTGACTGCGGAAGGAAGCCAAGGCCCACCTAAA 7 0.17500000000000002 No Hit GGGCTATTGATATTTAACAAATATCCAGCAAAGGTTTTTCCAGGAGATGT 6 0.15 No Hit GGCTATTGATATTTAACAAATATCCAGCAAAGGTTTTTCCAGGAGATGTT 6 0.15 No Hit CAGCAATTCAGGAAGAAATATGACAAGGAGTAGTAGTGTGGATGTTGTTG 6 0.15 No Hit GGAGTAGTAGTGTGGATGTTGTTGTTAGACACTTCTTTTTGTCTTTAAAT 6 0.15 No Hit GTTATGAGTAGGGATGAGCATAAACCAACAACTCTCAAAGAAGATGGGAA 6 0.15 No Hit GCCAGCTAACGGAACAAGCTTTGTGCCATTCGGACCTACCGTAAGCCTAT 6 0.15 No Hit ATTTTTAGTTATAATGATGCCTTATGTGATAGATGCCTCTTTAAAATATC 6 0.15 No Hit ATGCCTTATGTGATAGATGCCTCTTTAAAATATCTAAGTGCTGGGGTTAT 6 0.15 No Hit GTGTGCTAGCCCGTCGAGACTGAAAAGCTATAACCCGCAGACCCGAGCGA 6 0.15 No Hit CACTTAGTTACAGTTTTATGGATAATTGGGATATTCTTTGGTATAGTTGG 6 0.15 No Hit CGACGAACAACGAAGAGCGACGATGCCCGTTTCAGGTGGTCCTCAGCGTA 6 0.15 No Hit CCGGGGAACAGTCGCATGACGAGGCAGTTTCCAGAAACGTGTATCACATC 6 0.15 No Hit TCTGCATCCTATTTAGGGCTATTGATATTTAACAAATATCCAGCAAAGGT 6 0.15 No Hit GCCTTCTCTCGTTCTCGCCCGCTTTGCAAAAATATCTAATATCAATTGCG 6 0.15 No Hit AGGAGATGTTGGAACTCTACCAATTGGAGCTTTCTTAGCTGTCTTAGCAG 6 0.15 No Hit CTTGGTATACGGACAACTGATGGACCCACGTTGCGAGTCCAGTAAATCAG 5 0.125 No Hit ATCACATCTAGGCATGGAATCTTATGCCAGCTAACGGAACAAGCTTTGTG 5 0.125 No Hit TGGGGTTATGAGTAGGGATGAGCATAAACCAACAACTCTCAAAGAAGATG 5 0.125 No Hit CTGAGACAGAGTCGCTATCGTTATGTCTCCTTCCCGCGGTCAAGGCGAAA 5 0.125 No Hit GCAGTTTCCAGAAACGTGTATCACATCTAGGCATGGAATCTTATGCCAGC 5 0.125 No Hit GCGGTTTTGACTGCGGAAGGAAGCCAAGGCCCACCTAAAGTATGCTGCAA 5 0.125 No Hit CCGCTTTGATATTCTCTGCATCCTATTTAGGGCTATTGATATTTAACAAA 5 0.125 No Hit CCTATCTTTAATCCTCTCACTCCACAAATTCATAAGCTTCACCATTTTAC 5 0.125 No Hit GTCCTTACAAGTCCGCTCCTCGGGGAGCTTGATTGATAATTCTGTATAAG 5 0.125 No Hit CTTTGGTATAGTTGGGATTTTAATATCATTAATAGCATGATGGTGATTGT 5 0.125 No Hit CATAACAATAGGAAATATCAGAAATCCAATAAGAATCAGCAATTCAGGAA 5 0.125 No Hit ATGTGATAGATGCCTCTTTAAAATATCTAAGTGCTGGGGTTATGAGTAGG 5 0.125 No Hit GTTGGAACTCTACCAATTGGAGCTTTCTTAGCTGTCTTAGCAGTAGTTTA 5 0.125 No Hit GCCATTCGGACCTACCGTAAGCCTATATTTCGTTTTTCTGAGACCTATCC 5 0.125 No Hit CCCCTCTTTACAGCAAATACCAGCGGCCCTGACCCCGGGGAACAGTCGCA 5 0.125 No Hit GTCGAGACTGAAAAGCTATAACCCGCAGACCCGAGCGAAAGCGGCGGTCC 5 0.125 No Hit CGGCAATAGGATTGTAGCCCAGGATGAGTCCCTCAGCGTGACGCAGTAAA 5 0.125 No Hit GTGCCTTATGTGATAGATGCCTCTTTAAAATATCTAAGTGCTGGGGTTAT 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 0.0125 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 0.025 0.0 0.0 0.0 0.0 38-39 0.025 0.0 0.0 0.0 0.0 40-41 0.025 0.0 0.0 0.0 0.0 42-43 0.025 0.0 0.0 0.0 0.0 44-45 0.025 0.0 0.0 0.0 0.0 46-47 0.025 0.0 0.0 0.0 0.0 48-49 0.025 0.0 0.0 0.0 0.0 50-51 0.025 0.0 0.0 0.0 0.0 52-53 0.025 0.0 0.0 0.0 0.0 54-55 0.025 0.0 0.0 0.0 0.0 56-57 0.025 0.0 0.0 0.0 0.0 58-59 0.025 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 0.05 0.0 0.0 0.0 0.0 70-71 0.05 0.0 0.0 0.0 0.0 72-73 0.15 0.0 0.0 0.0 0.0 74-75 0.15 0.0 0.0 0.0 0.0 76-77 0.175 0.0 0.0 0.0 0.0 78-79 0.30000000000000004 0.0 0.0 0.0 0.0 80-81 0.35 0.0 0.0 0.0 0.0 82-83 0.375 0.0 0.0 0.0 0.0 84-85 0.4125 0.0 0.0 0.0 0.0 86-87 0.5125 0.0 0.0 0.0 0.0 88-89 0.6125 0.0 0.0 0.0 0.0 90-91 0.7 0.0 0.0 0.0 0.0 92-93 0.9125 0.0 0.0 0.0 0.0 94-95 1.1375 0.0 0.0 0.0 0.0 96-97 1.325 0.0 0.0 0.0 0.0 98-99 1.55 0.0 0.0 0.0 0.0 100-101 1.8624999999999998 0.0 0.0 0.0 0.0 102-103 2.1875 0.0 0.0 0.0 0.0 104-105 2.45 0.0 0.0 0.0 0.0 106-107 2.8 0.0 0.0 0.0 0.0 108-109 3.2750000000000004 0.0 0.0 0.0 0.0 110-111 3.7125 0.0 0.0 0.0 0.0 112-113 4.075 0.0 0.0 0.0 0.0 114-115 4.75 0.0 0.0 0.0 0.0 116-117 5.112500000000001 0.0 0.0 0.0 0.0 118-119 5.5125 0.0 0.0 0.0 0.0 120-121 6.112500000000001 0.0 0.0 0.0 0.0 122-123 6.75 0.0 0.0 0.0 0.0 124-125 7.525 0.0 0.0 0.0 0.0 126-127 8.1875 0.0 0.0 0.0 0.0 128-129 9.0 0.0 0.0 0.0 0.0 130-131 9.8375 0.0 0.0 0.0 0.0 132-133 10.587499999999999 0.0 0.0 0.0 0.0 134-135 11.2375 0.0 0.0 0.0 0.0 136-137 11.9625 0.0 0.0 0.0 0.0 138-139 12.850000000000001 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position CCCATAC 10 0.0063298983 148.6923 1 ACTGCCA 10 0.0068343505 144.975 6 TGCCACC 10 0.0068343505 144.975 8 TACTGCC 10 0.0068343505 144.975 5 GCCACCG 10 0.0068343505 144.975 9 CCATACT 10 0.0068343505 144.975 2 CTGCCAC 10 0.0068343505 144.975 7 ATACTGC 10 0.0068343505 144.975 4 CATACTG 10 0.0068343505 144.975 3 TTATATT 40 0.0076626483 18.121876 130-134 >>END_MODULE SRR5578449 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR5578449_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 47 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 33.0925 33.0 33.0 34.0 33.0 34.0 2 33.1505 34.0 33.0 34.0 33.0 34.0 3 33.12625 34.0 33.0 34.0 33.0 34.0 4 33.091 34.0 33.0 34.0 33.0 34.0 5 33.12075 34.0 33.0 34.0 33.0 34.0 6 37.28525 38.0 38.0 38.0 37.0 38.0 7 37.2805 38.0 38.0 38.0 38.0 38.0 8 37.319 38.0 38.0 38.0 37.0 38.0 9 37.23925 38.0 38.0 38.0 38.0 38.0 10-14 37.3017 38.0 38.0 38.0 38.0 38.0 15-19 37.293099999999995 38.0 38.0 38.0 38.0 38.0 20-24 37.29690000000001 38.0 38.0 38.0 37.8 38.0 25-29 37.31115 38.0 38.0 38.0 38.0 38.0 30-34 37.3005 38.0 38.0 38.0 37.8 38.0 35-39 37.266099999999994 38.0 38.0 38.0 37.8 38.0 40-44 37.2216 38.0 38.0 38.0 37.2 38.0 45-49 37.161300000000004 38.0 38.0 38.0 37.0 38.0 50-54 37.1601 38.0 38.0 38.0 37.0 38.0 55-59 37.1468 38.0 38.0 38.0 37.0 38.0 60-64 37.05675 38.0 38.0 38.0 37.0 38.0 65-69 36.9255 38.0 38.0 38.0 37.0 38.0 70-74 36.6185 38.0 38.0 38.0 36.0 38.0 75-79 36.568 38.0 38.0 38.0 36.0 38.0 80-84 36.4879 38.0 38.0 38.0 35.6 38.0 85-89 36.40995 38.0 38.0 38.0 35.0 38.0 90-94 36.398 38.0 38.0 38.0 35.0 38.0 95-99 36.212300000000006 38.0 38.0 38.0 34.2 38.0 100-104 35.9913 38.0 38.0 38.0 33.8 38.0 105-109 35.8063 38.0 38.0 38.0 33.4 38.0 110-114 35.6417 38.0 38.0 38.0 33.0 38.0 115-119 35.43005 38.0 37.8 38.0 31.8 38.0 120-124 35.168099999999995 38.0 36.6 38.0 30.2 38.0 125-129 34.84385 38.0 36.0 38.0 28.6 38.0 130-134 34.53439999999999 38.0 35.8 38.0 27.2 38.0 135-139 34.0322 38.0 34.6 38.0 25.0 38.0 140-144 33.20479999999999 38.0 33.0 38.0 17.8 38.0 145-149 31.869 38.0 33.0 38.0 8.0 38.0 150-151 26.505499999999998 33.5 16.5 37.0 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 8.0 3 2.0 4 1.0 5 0.0 6 2.0 7 2.0 8 2.0 9 2.0 10 0.0 11 4.0 12 1.0 13 2.0 14 6.0 15 10.0 16 5.0 17 36.0 18 4.0 19 6.0 20 5.0 21 11.0 22 16.0 23 9.0 24 8.0 25 13.0 26 10.0 27 19.0 28 28.0 29 26.0 30 31.0 31 51.0 32 60.0 33 83.0 34 136.0 35 232.0 36 594.0 37 2575.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 35.85 19.2 14.524999999999999 30.425 2 28.125 24.075 26.700000000000003 21.099999999999998 3 22.900000000000002 24.55 27.900000000000002 24.65 4 25.15 31.574999999999996 22.125 21.15 5 27.725 32.2 21.625 18.45 6 24.099999999999998 35.175 21.025 19.7 7 21.725 21.725 34.449999999999996 22.1 8 22.625 26.05 24.75 26.575 9 22.775000000000002 25.374999999999996 29.25 22.6 10-14 26.16 27.245 22.43 24.165 15-19 26.095000000000002 25.995 24.94 22.97 20-24 25.7 26.534999999999997 23.98 23.785 25-29 26.674999999999997 26.240000000000002 24.255 22.830000000000002 30-34 27.485 25.669999999999998 24.645 22.2 35-39 25.81 25.19 24.945 24.055 40-44 26.655 25.045 24.715 23.585 45-49 25.564999999999998 24.959999999999997 26.395000000000003 23.080000000000002 50-54 24.884999999999998 24.18 27.05 23.885 55-59 23.525 25.635 27.775 23.064999999999998 60-64 23.595 26.279999999999998 27.0 23.125 65-69 23.044999999999998 27.395000000000003 26.375 23.185 70-74 23.29 26.540000000000003 26.72 23.45 75-79 22.275 27.935 25.919999999999998 23.87 80-84 23.169999999999998 27.85 25.56 23.419999999999998 85-89 23.150000000000002 27.834999999999997 25.865 23.150000000000002 90-94 23.14 28.065 26.71 22.085 95-99 23.205000000000002 28.849999999999998 25.77 22.175 100-104 23.369999999999997 28.449999999999996 24.975 23.205000000000002 105-109 24.099999999999998 28.98 24.845 22.075 110-114 22.98 28.389999999999997 24.965 23.665 115-119 24.09 29.755 23.815 22.34 120-124 24.11 28.895 24.85 22.145 125-129 24.935 29.38 24.08 21.605 130-134 24.545 27.735 25.330000000000002 22.39 135-139 24.785 28.535 25.119999999999997 21.560000000000002 140-144 26.255 27.389999999999997 25.795 20.560000000000002 145-149 26.14 27.425 25.11 21.325 150-151 26.5 26.85 25.45 21.2 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 0.0 1 0.0 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10 0.0 11 0.0 12 0.0 13 0.0 14 0.0 15 1.0 16 2.0 17 1.0 18 0.0 19 1.0 20 1.0 21 0.0 22 1.5 23 2.0 24 1.0 25 0.5 26 0.5 27 2.5 28 5.0 29 9.5 30 17.0 31 26.5 32 29.0 33 28.0 34 49.5 35 70.5 36 91.5 37 128.5 38 162.5 39 157.5 40 214.0 41 186.0 42 91.5 43 107.0 44 110.5 45 111.5 46 115.5 47 131.0 48 160.5 49 157.0 50 130.5 51 121.5 52 142.0 53 168.0 54 183.0 55 183.0 56 155.5 57 123.5 58 105.0 59 89.0 60 70.5 61 51.0 62 38.5 63 34.0 64 28.5 65 28.5 66 24.0 67 24.5 68 23.0 69 19.5 70 18.5 71 14.0 72 10.0 73 8.5 74 8.0 75 6.0 76 5.5 77 5.0 78 3.0 79 1.5 80 1.0 81 1.0 82 1.0 83 0.5 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 0.0 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 71.675 #Duplication Level Percentage of deduplicated Percentage of total 1 86.15277293337984 61.75000000000001 2 7.638646668991978 10.95 3 2.720613882106732 5.8500000000000005 4 1.2905476107429368 3.6999999999999997 5 0.6627136379490757 2.375 6 0.24415765608650158 1.05 7 0.17439832577607256 0.8750000000000001 8 0.20927799093128704 1.2 9 0.03487966515521451 0.22499999999999998 >10 0.8719916288803629 12.025 >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 fail #Sequence Count Percentage Possible Source GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCG 41 1.0250000000000001 Illumina Single End PCR Primer 1 (100% over 50bp) CATTAATTAGGGCTGAAAGCCCTAACTTAATGGACGGGAGGTATCCCAAT 38 0.95 No Hit ATTAGGGCTGAAAGCCCTAACTTAATGGACGGGAGGTATCCCAATAGGAG 31 0.775 No Hit GGCTGAAAGCCCTAACTTAATGGACGGGAGGTATCCCAATAGGAGGTTTC 28 0.7000000000000001 No Hit AATTAGGGCTGAAAGCCCTAACTTAATGGACGGGAGGTATCCCAATAGGA 28 0.7000000000000001 No Hit CCCTAACTTAATGGACGGGAGGTATCCCAATAGGAGGTTTCCTCCTATGG 28 0.7000000000000001 No Hit CTTCAATATAAGCCTTGGTAGGGATAGATAGCCACCTATATAGTATAGCT 23 0.575 No Hit GGGCTGAAAGCCCTAACTTAATGGACGGGAGGTATCCCAATAGGAGGTTT 22 0.5499999999999999 No Hit GGGAGGTATCCCAATAGGAGGTTTCCTCCTATGGTTTTCAAAACAATCAC 20 0.5 No Hit GCTGAAAGCCCTAACTTAATGGACGGGAGGTATCCCAATAGGAGGTTTCC 19 0.475 No Hit ATTAATTAGGGCTGAAAGCCCTAACTTAATGGACGGGAGGTATCCCAATA 17 0.42500000000000004 No Hit GCCACAGGCGTCATACTTCCCAAGAAGCGGCCATAGCCCAGATGCGAGGT 16 0.4 No Hit AGGGCTGAAAGCCCTAACTTAATGGACGGGAGGTATCCCAATAGGAGGTT 15 0.375 No Hit GAAAGCCCTAACTTAATGGACGGGAGGTATCCCAATAGGAGGTTTCCTCC 15 0.375 No Hit GGACATTAATTAGGGCTGAAAGCCCTAACTTAATGGACGGGAGGTATCCC 15 0.375 No Hit CCTAACTTAATGGACGGGAGGTATCCCAATAGGAGGTTTCCTCCTATGGT 15 0.375 No Hit TAGGGCTGAAAGCCCTAACTTAATGGACGGGAGGTATCCCAATAGGAGGT 15 0.375 No Hit CTAACTTAATGGACGGGAGGTATCCCAATAGGAGGTTTCCTCCTATGGTT 13 0.325 No Hit AAAGCCCTAACTTAATGGACGGGAGGTATCCCAATAGGAGGTTTCCTCCT 12 0.3 No Hit CTGAAAGCCCTAACTTAATGGACGGGAGGTATCCCAATAGGAGGTTTCCT 12 0.3 No Hit GGTAGGAATGGGAGTATTTGCACTTGTGGTAACGGTATTTGCATTATTGA 12 0.3 No Hit CCCAATTATCCATAAAACTGTAACTAAGTGAGGCTCTCTCATTGGTTTAT 12 0.3 No Hit GTAGGAATGGGAGTATTTGCACTTGTGGTAACGGTATTTGCATTATTGAT 12 0.3 No Hit TAATTAGGGCTGAAAGCCCTAACTTAATGGACGGGAGGTATCCCAATAGG 12 0.3 No Hit TCCATTTCCGCCCAAGCTGCTCACAGTATACGGGCGTCGGCATCCAGACC 10 0.25 No Hit GCCCTAACTTAATGGACGGGAGGTATCCCAATAGGAGGTTTCCTCCTATG 9 0.22499999999999998 No Hit CCCAATAGGAGGTTTCCTCCTATGGTTTTCAAAACAATCACCATCATGCT 8 0.2 No Hit GTTAGGGCAGCGTCTGAGGAAGTTTGCTGCGGTTTCGCCTTGACCGCGGG 8 0.2 No Hit AAAGAATATCCCAATTATCCATAAAACTGTAACTAAGTGAGGCTCTCTCA 8 0.2 No Hit CTCGTAACCAAACATGCACAGCGGTCAAACAGTATGTCCCAAGGGGACTT 8 0.2 No Hit CGGGCGTCGGCATCCAGACCGTCGGCTGATCGTGGTTTTACTAGGCTAGA 8 0.2 No Hit GGAGTATTTGCACTTGTGGTAACGGTATTTGCATTATTGATGGTTTTTAC 8 0.2 No Hit CTTCCATTTCCGCCCAAGCTGCTCACAGTATACGGGCGTCGGCATCCAGA 7 0.17500000000000002 No Hit AAGCTGCTCACAGTATACGGGCGTCGGCATCCAGACCGTCGGCTGATCGT 7 0.17500000000000002 No Hit CAAAGAATATCCCAATTATCCATAAAACTGTAACTAAGTGAGGCTCTCTC 7 0.17500000000000002 No Hit GGTATCCCAATAGGAGGTTTCCTCCTATGGTTTTCAAAACAATCACCATC 7 0.17500000000000002 No Hit CTGGACATTAATTAGGGCTGAAAGCCCTAACTTAATGGACGGGAGGTATC 7 0.17500000000000002 No Hit TGGACATTAATTAGGGCTGAAAGCCCTAACTTAATGGACGGGAGGTATCC 6 0.15 No Hit GCTGCTCACAGTATACGGGCGTCGGCATCCAGACCGTCGGCTGATCGTGG 6 0.15 No Hit CAATTATCCATAAAACTGTAACTAAGTGAGGCTCTCTCATTGGTTTATAC 6 0.15 No Hit CTCTCTCATTGGTTTATACTTCAATATAAGCCTTGGTAGGGATAGATAGC 6 0.15 No Hit GGACGGGAGGTATCCCAATAGGAGGTTTCCTCCTATGGTTTTCAAAACAA 6 0.15 No Hit TAGGAATGGGAGTATTTGCACTTGTGGTAACGGTATTTGCATTATTGATG 6 0.15 No Hit TTAATTAGGGCTGAAAGCCCTAACTTAATGGACGGGAGGTATCCCAATAG 6 0.15 No Hit GGGAGTATTTGCACTTGTGGTAACGGTATTTGCATTATTGATGGTTTTTA 5 0.125 No Hit GGAATGGGAGTATTTGCACTTGTGGTAACGGTATTTGCATTATTGATGGT 5 0.125 No Hit CAAGCTGCTCACAGTATACGGGCGTCGGCATCCAGACCGTCGGCTGATCG 5 0.125 No Hit CTTAATGGACGGGAGGTATCCCAATAGGAGGTTTCCTCCTATGGTTTTCA 5 0.125 No Hit GCTCACAGTATACGGGCGTCGGCATCCAGACCGTCGGCTGATCGTGGTTT 5 0.125 No Hit CTTTGGAGAGGTAGGAATGGGAGTATTTGCACTTGTGGTAACGGTATTTG 5 0.125 No Hit GTCGCACTGAACTCGGATAGGTCTCAGAAAAACGAAATATAGGCTTACGG 5 0.125 No Hit AGCTGCTCACAGTATACGGGCGTCGGCATCCAGACCGTCGGCTGATCGTG 5 0.125 No Hit GATTACTTCCATTTCCGCCCAAGCTGCTCACAGTATACGGGCGTCGGCAT 5 0.125 No Hit CAGATTACTTCCATTTCCGCCCAAGCTGCTCACAGTATACGGGCGTCGGC 5 0.125 No Hit GGGATAGATAGCCACCTATATAGTATAGCTTCCCATCTTCTTTGAGAGTT 5 0.125 No Hit CGCCACAGGCGTCATACTTCCCAAGAAGCGGCCATAGCCCAGATGCGAGG 5 0.125 No Hit TGGGAGTATTTGCACTTGTGGTAACGGTATTTGCATTATTGATGGTTTTT 5 0.125 No Hit GACGAATTGCCAGAATTATTAACTGCGCAGTTAGGGCAGCGTCTGAGGAA 5 0.125 No Hit GCTGATCGTGGTTTTACTAGGCTAGACTAGCGTACGAGCACTATGGTCAG 5 0.125 No Hit CGGGAAGGAGACATAACGATAGCGACTCTGTCTCAGGGGATCTGCATATG 5 0.125 No Hit GCCGTACGCTGAGGACCACCTGAAACGGGCATCGTCGCTCTTCGTTGTTC 5 0.125 No Hit TTAGGGCTGAAAGCCCTAACTTAATGGACGGGAGGTATCCCAATAGGAGG 5 0.125 No Hit CGAATAGCTCGTAACCAAACATGCACAGCGGTCAAACAGTATGTCCCAAG 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 0.0 0.0 0.0 0.0 0.0 62-63 0.0 0.0 0.0 0.0 0.0 64-65 0.0 0.0 0.0 0.0 0.0 66-67 0.0 0.0 0.0 0.0 0.0 68-69 0.025 0.0 0.0 0.0 0.0 70-71 0.025 0.0 0.0 0.0 0.0 72-73 0.125 0.0 0.0 0.0 0.0 74-75 0.125 0.0 0.0 0.0 0.0 76-77 0.15 0.0 0.0 0.0 0.0 78-79 0.275 0.0 0.0 0.0 0.0 80-81 0.325 0.0 0.0 0.0 0.0 82-83 0.3375 0.0 0.0 0.0 0.0 84-85 0.3625 0.0 0.0 0.0 0.0 86-87 0.4375 0.0 0.0 0.0 0.0 88-89 0.5375 0.0 0.0 0.0 0.0 90-91 0.625 0.0 0.0 0.0 0.0 92-93 0.8375 0.0 0.0 0.0 0.0 94-95 1.0625 0.0 0.0 0.0 0.0 96-97 1.25 0.0 0.0 0.0 0.0 98-99 1.4375 0.0 0.0 0.0 0.0 100-101 1.7125 0.0 0.0 0.0 0.0 102-103 2.0375 0.0 0.0 0.0 0.0 104-105 2.2874999999999996 0.0 0.0 0.0 0.0 106-107 2.625 0.0 0.0 0.0 0.0 108-109 3.0999999999999996 0.0 0.0 0.0 0.0 110-111 3.5375 0.0 0.0 0.0 0.0 112-113 3.9000000000000004 0.0 0.0 0.0 0.0 114-115 4.525 0.0 0.0 0.0 0.0 116-117 4.875 0.0 0.0 0.0 0.0 118-119 5.2375 0.0 0.0 0.0 0.0 120-121 5.862500000000001 0.0 0.0 0.0 0.0 122-123 6.4625 0.0 0.0 0.0 0.0 124-125 7.225 0.0 0.0 0.0 0.0 126-127 7.8375 0.0 0.0 0.0 0.0 128-129 8.712499999999999 0.0 0.0 0.0 0.0 130-131 9.55 0.0 0.0 0.0 0.0 132-133 10.337499999999999 0.0 0.0 0.0 0.0 134-135 11.0375 0.0 0.0 0.0 0.0 136-137 11.7625 0.0 0.0 0.0 0.0 138-139 12.600000000000001 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TATGCCT 10 0.006830828 145.0 3 AGGGCTG 25 8.7132835E-4 87.0 4 CTGAAAG 40 0.005621335 54.375 8 >>END_MODULE Read 660573 spots for SRR5578449.sra Written 660573 spots for SRR5578449.sra Read 660573 spots for SRR5578449.sra Written 660573 spots for SRR5578449.sra Read 660573 spots for SRR5578449.sra Written 660573 spots for SRR5578449.sra Read 660573 spots for SRR5578449.sra Written 660573 spots for SRR5578449.sra Read 660573 spots for SRR5578449.sra Written 660573 spots for SRR5578449.sra Read 660573 spots for SRR5578449.sra Written 660573 spots for SRR5578449.sra Read 660573 spots for SRR5578449.sra Written 660573 spots for SRR5578449.sra Read 660573 spots for SRR5578449.sra Written 660573 spots for SRR5578449.sra Read 660573 spots for SRR5578449.sra Written 660573 spots for SRR5578449.sra Read 660585 spots for SRR5578449.sra Written 660585 spots for SRR5578449.sra Read 660573 spots for SRR5578449.sra Written 660573 spots for SRR5578449.sra Read 660573 spots for SRR5578449.sra Written 660573 spots for SRR5578449.sra Read 660573 spots for SRR5578449.sra Written 660573 spots for SRR5578449.sra Read 660573 spots for SRR5578449.sra Written 660573 spots for SRR5578449.sra Read 660573 spots for SRR5578449.sra Written 660573 spots for SRR5578449.sra Read 660573 spots for SRR5578449.sra Written 660573 spots for SRR5578449.sra Read 660573 spots for SRR5578449.sra Written 660573 spots for SRR5578449.sra Read 660573 spots for SRR5578449.sra Written 660573 spots for SRR5578449.sra Read 660573 spots for SRR5578449.sra Written 660573 spots for SRR5578449.sra Read 660573 spots for SRR5578449.sra Written 660573 spots for SRR5578449.sra SRR ids: ['SRR5578449.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_fh0f2ngi SRR5578449.sra spots: 13211472 blocks: [[1, 660573], [660574, 1321146], [1321147, 1981719], [1981720, 2642292], [2642293, 3302865], [3302866, 3963438], [3963439, 4624011], [4624012, 5284584], [5284585, 5945157], [5945158, 6605730], [6605731, 7266303], [7266304, 7926876], [7926877, 8587449], [8587450, 9248022], [9248023, 9908595], [9908596, 10569168], [10569169, 11229741], [11229742, 11890314], [11890315, 12550887], [12550888, 13211472]] SRR5578449 file size 4455233 SRR5578449 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 SRR5578449 SRR5578449_1.fastq SRR5578449_2.fastq Input file: SRR5578449_1.fastq Paired file: SRR5578449_2.fastq trimmed: SRR5578449-trimmed-pair1.fastq, SRR5578449-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 Dec 9 18:02:39 2024 >> started Mon Dec 9 18:02:53 2024 >> done (14.616s) 13211472 read pairs processed; of these: 17438 ( 0.13%) short read pairs filtered out after trimming by size control 143004 ( 1.08%) empty read pairs filtered out after trimming by size control 13051030 (98.79%) read pairs available; of these: 6545289 (50.15%) trimmed read pairs available after processing 6505741 (49.85%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 4 0.00% 19 9 0.00% 20 16 0.00% 21 9 0.00% 22 16 0.00% 23 18 0.00% 24 32 0.00% 25 22 0.00% 26 37 0.00% 27 28 0.00% 28 38 0.00% 29 49 0.00% 30 31 0.00% 31 42 0.00% 32 44 0.00% 33 61 0.00% 34 59 0.00% 35 1489 0.01% 36 549 0.00% 37 62 0.00% 38 532 0.00% 39 42 0.00% 40 50 0.00% 41 64 0.00% 42 34 0.00% 43 67 0.00% 44 76 0.00% 45 118 0.00% 46 151 0.00% 47 150 0.00% 48 193 0.00% 49 190 0.00% 50 204 0.00% 51 196 0.00% 52 239 0.00% 53 211 0.00% 54 254 0.00% 55 239 0.00% 56 303 0.00% 57 346 0.00% 58 379 0.00% 59 377 0.00% 60 441 0.00% 61 482 0.00% 62 504 0.00% 63 566 0.00% 64 669 0.01% 65 1023 0.01% 66 1147 0.01% 67 1323 0.01% 68 1986 0.02% 69 8237 0.06% 70 9920 0.08% 71 4639 0.04% 72 2648 0.02% 73 2247 0.02% 74 2190 0.02% 75 2472 0.02% 76 2506 0.02% 77 2914 0.02% 78 3029 0.02% 79 3638 0.03% 80 3614 0.03% 81 4113 0.03% 82 4754 0.04% 83 5507 0.04% 84 6815 0.05% 85 8192 0.06% 86 9440 0.07% 87 11734 0.09% 88 13185 0.10% 89 13317 0.10% 90 13887 0.11% 91 13435 0.10% 92 14346 0.11% 93 14959 0.11% 94 14941 0.11% 95 15710 0.12% 96 16322 0.13% 97 16891 0.13% 98 17805 0.14% 99 19202 0.15% 100 20549 0.16% 101 21281 0.16% 102 22314 0.17% 103 23659 0.18% 104 25065 0.19% 105 26650 0.20% 106 28669 0.22% 107 30356 0.23% 108 31527 0.24% 109 31190 0.24% 110 32065 0.25% 111 34182 0.26% 112 35358 0.27% 113 39792 0.30% 114 44097 0.34% 115 46991 0.36% 116 47021 0.36% 117 45293 0.35% 118 45515 0.35% 119 45239 0.35% 120 49074 0.38% 121 48595 0.37% 122 51133 0.39% 123 52842 0.40% 124 54628 0.42% 125 55989 0.43% 126 58201 0.45% 127 60337 0.46% 128 58429 0.45% 129 62627 0.48% 130 62814 0.48% 131 63291 0.48% 132 66010 0.51% 133 67799 0.52% 134 70322 0.54% 135 70278 0.54% 136 71585 0.55% 137 72613 0.56% 138 76934 0.59% 139 81216 0.62% 140 84331 0.65% 141 84761 0.65% 142 96214 0.74% 143 99159 0.76% 144 104597 0.80% 145 119279 0.91% 146 137853 1.06% 147 170164 1.30% 148 237962 1.82% 149 477542 3.66% 150 2704117 20.72% 151 6505741 49.85% 13051030 reads passed initial QC criterion=sequence-density sequence-density=0.66 sequence-density-rank=1 fanout-score=21.21 fanout-score-rank=1 prefix-density=7.13 prefix-fanout=2.0 sequence=TTCGTTTTTTTTCTTG criterion=fanout-score sequence-density=0.66 sequence-density-rank=1 fanout-score=21.21 fanout-score-rank=1 prefix-density=7.13 prefix-fanout=2.0 sequence=TTCGTTTTTTTTCTTG criterion=sequence-density sequence-density=1.13 sequence-density-rank=1 fanout-score=4.67 fanout-score-rank=7 prefix-density=5.23 prefix-fanout=1.0 sequence=CAAGAAAAAAAACGAA criterion=fanout-score sequence-density=0.01 sequence-density-rank=33 fanout-score=43.47 fanout-score-rank=1 prefix-density=0.30 prefix-fanout=1.0 sequence=AATTCATCTCCTCTAACTTTGGAGAGGTAGGAATGGGAGTATTTGCACTTGTGGTAACGGTATTTGCATTATTGATGGTTTTTACTATGTTGGGTATGCTGTTCGATTTCTTAAAGGACTGAATATTCGGTGGCAGTATGGGATTTCTAAAAATAATGTTAAGAATTTTTGCTGGTTTTTTGCGACGTTGGTGTTGTATTCTATAGCTCCATTATGGCCGTTATATGGAATCATTGGAGTGCCAGTAATTCTACCACGCCTTATATTTAAAGACAAAAAGAAGTGTCTAACAACAACATCCACACTACTACTCCTTGTCATATTTCTTCCTGAATTGCTGATTCTTATTGGATTTCTGATATTTCCTATTGTTATGGGCTATTACATCTCTAAGGAATTGGTGAAGTAAAATGGTGAAGCTTATGAATTTGTGGAGTGAGAGGATTAAAGATAGGGAAGTTGTTGAAGTTATTGGCTGTGAGAGAGTGCCATTGATGAAACGT SRR5578449 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 09 18:04:54 Started mapping on | Dec 09 18:04:54 Finished on | Dec 09 18:56:02 Mapping speed, Million of reads per hour | 15.31 Number of input reads | 13051030 Average input read length | 289 UNIQUE READS: Uniquely mapped reads number | 3784429 Uniquely mapped reads % | 29.00% Average mapped length | 288.16 Number of splices: Total | 2752010 Number of splices: Annotated (sjdb) | 2579559 Number of splices: GT/AG | 2714864 Number of splices: GC/AG | 32971 Number of splices: AT/AC | 1454 Number of splices: Non-canonical | 2721 Mismatch rate per base, % | 0.10% Deletion rate per base | 0.01% Deletion average length | 1.43 Insertion rate per base | 0.00% Insertion average length | 1.11 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 443305 % of reads mapped to multiple loci | 3.40% Number of reads mapped to too many loci | 92708 % of reads mapped to too many loci | 0.71% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 62.73% % of reads unmapped: other | 4.17% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 8827041 8827041 8827041 N_multimapping 443305 443305 443305 N_noFeature 383660 3675824 408619 N_ambiguous 96001 465 12909 UnstrandedReadsAssigned:3304768 PositiveStrandReadsAssigned:108140 NegativeStrandReadsAssigned:3362901 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=145 echo kmer=141 SRR5578449 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: SRR5578449-trimmed-pair1.fastq SRR5578449-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 13,051,030 reads, 3,480,818 reads pseudoaligned [quant] estimated average fragment length: 202.153 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,058 rounds 52973 SRR5578449.ke.tsv 35125 SRR5578449.se.tsv 88098 total ==> SRR5578449.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 735.014 0 0 PNS24247 1044 842.847 8.46234 3.21342 PNS24249 1928 1726.85 7.55732 1.40068 PNS24246 1044 842.847 8.46234 3.21342 PNS24248 1044 842.847 8.46234 3.21342 PNS24244 1471 1269.85 39.0557 9.84372 PNS24243 293 115.469 0 0 KQK14069 1603 1401.85 559.832 127.815 KQK14071 474 278.53 3.94715 4.53563 ==> SRR5578449.se.tsv <== BRADI_1g14170v3 572 BRADI_1g53295v3 4 BRADI_1g59795v3 70 BRADI_1g07683v3 0 BRADI_1g00485v3 3 BRADI_1g20270v3 311 BRADI_1g74790v3 8 BRADI_1g09890v3 0 BRADI_1g77505v3 78 BRADI_1g48960v3 0 SRR5578449 completed mapping pipeline successfully