Starting /dee2/code/volunteer_pipeline.sh SRR12682217 current disk space = 1547235622912 free memory = 1602156864 SRR12682217 SRAfilesize 44d43d22c1fbab82bfc54373cf318dbc SRR12682217.sra SRR12682217.sra file validated SRR12682217 is single end SRR12682217 is conventional basespace SRR12682217 read1 length is 35-150 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12682217_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 35-150 %GC 53 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 31.535 32.0 32.0 32.0 32.0 32.0 2 31.50925 32.0 32.0 32.0 32.0 32.0 3 31.6665 32.0 32.0 32.0 32.0 32.0 4 31.6355 32.0 32.0 32.0 32.0 32.0 5 31.65925 32.0 32.0 32.0 32.0 32.0 6 34.81425 36.0 36.0 36.0 36.0 36.0 7 35.1645 36.0 36.0 36.0 36.0 36.0 8 35.101 36.0 36.0 36.0 36.0 36.0 9 35.07475 36.0 36.0 36.0 36.0 36.0 10-14 35.0835 36.0 36.0 36.0 36.0 36.0 15-19 35.0512 36.0 36.0 36.0 36.0 36.0 20-24 34.97259999999999 36.0 36.0 36.0 36.0 36.0 25-29 34.842200000000005 36.0 36.0 36.0 32.8 36.0 30-34 34.7842 36.0 36.0 36.0 32.0 36.0 35-39 34.78139836209052 36.0 36.0 36.0 32.8 36.0 40-44 34.67581895473869 36.0 36.0 36.0 32.0 36.0 45-49 34.53468367091774 36.0 36.0 36.0 32.0 36.0 50-54 34.519282833811204 36.0 36.0 36.0 32.0 36.0 55-59 34.363119148670805 36.0 36.0 36.0 32.0 36.0 60-64 34.157758094217925 36.0 36.0 36.0 32.0 36.0 65-69 34.104546716601 36.0 36.0 36.0 32.0 36.0 70-74 34.118054562952665 36.0 36.0 36.0 32.0 36.0 75-79 33.985062389327744 36.0 36.0 36.0 31.0 36.0 80-84 33.91192604510708 36.0 36.0 36.0 30.0 36.0 85-89 33.813295126631786 36.0 36.0 36.0 28.0 36.0 90-94 33.832371859279085 36.0 36.0 36.0 28.0 36.0 95-99 33.79145801798059 36.0 36.0 36.0 27.0 36.0 100-104 33.70608570226276 36.0 36.0 36.0 27.0 36.0 105-109 33.3123276952585 36.0 32.8 36.0 27.0 36.0 110-114 33.205343993662254 36.0 32.8 36.0 27.0 36.0 115-119 32.827279663387955 36.0 32.0 36.0 27.0 36.0 120-124 32.147345361832734 34.4 32.0 36.0 24.6 36.0 125-129 32.02730457109591 33.6 32.0 36.0 23.4 36.0 130-134 31.56775371115271 32.0 32.0 36.0 21.0 36.0 135-139 31.458316685650185 32.8 32.0 36.0 21.0 36.0 140-144 31.72880316736226 34.4 32.0 36.0 19.6 36.0 145-149 31.589374864790056 32.0 32.0 36.0 21.0 36.0 150 26.17305151915456 27.0 14.0 32.0 14.0 36.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 1.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10 0.0 11 0.0 12 0.0 13 0.0 14 0.0 15 0.0 16 0.0 17 0.0 18 2.0 19 1.0 20 3.0 21 6.0 22 3.0 23 11.0 24 10.0 25 38.0 26 48.0 27 63.0 28 88.0 29 107.0 30 121.0 31 175.0 32 236.0 33 382.0 34 928.0 35 1777.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 32.25806451612903 8.32708177044261 8.527131782945736 50.88772193048262 2 22.255563890972745 11.902975743935984 30.582645661415352 35.25881470367592 3 22.655663915978995 14.20355088772193 19.35483870967742 43.785946486621654 4 28.707176794198553 21.330332583145786 17.554388597149288 32.40810202550637 5 26.756689172293076 26.756689172293076 21.680420105026258 24.8062015503876 6 23.20121181519818 29.967180005049233 24.21105781368341 22.620550366069175 7 19.654913728432106 20.830207551887973 37.30932733183296 22.20555138784696 8 20.255063765941486 18.72968242060515 30.48262065516379 30.532633158289574 9 20.43010752688172 19.02975743935984 32.68317079269817 27.85696424106027 10-14 23.320830207551886 24.046011502875718 24.651162790697676 27.981995498874717 15-19 23.640910227556887 22.72568142035509 25.55638909727432 28.077019254813703 20-24 24.246061515378845 23.845961490372595 24.431107776944234 27.47686921730433 25-29 23.43085771442861 22.810702675668917 24.82120530132533 28.937234308577143 30-34 24.221055263815956 22.20555138784696 24.151037759439863 29.422355588897226 35-39 24.036009002250562 22.67566891722931 24.76119029757439 28.527131782945737 40-44 24.58114528632158 22.815703925981495 24.66116529132283 27.941985496374095 45-49 24.151037759439863 22.535633908477116 25.346336584146034 27.966991747936987 50-54 22.747511131122117 23.28780829456201 25.378958427134922 28.58572214718095 55-59 23.456110499449505 23.03573215894305 24.767290561505355 28.740866780102092 60-64 23.671957142141892 21.19861813448155 25.904971711810944 29.224453011565615 65-69 22.883352548999948 22.83823750563938 25.62033184620783 28.65807809915284 70-74 23.930078360458108 22.126783202732568 25.2411091018686 28.702029334940725 75-79 24.88395560040363 22.270433905146316 23.773965691220987 29.071644803229063 80-84 24.58493622190727 22.06418303300263 24.38246608625228 28.968414658837823 85-89 24.084356375120983 22.281086037389844 24.405277367429065 29.22928022006011 90-94 25.147761730996553 22.038340956982065 24.36655188364085 28.447345428380533 95-99 22.888865721434527 22.289407839866556 25.72977481234362 29.091951626355296 100-104 24.050295700356973 22.707656241675103 24.78022270765624 28.46182535031169 105-109 24.45551056145343 23.12575243515377 24.98631936084054 27.43241764255226 110-114 25.09181309678513 23.035199728798236 24.26690773490028 27.606079439516357 115-119 24.84102684879887 22.479981158737637 24.422986340084783 28.256005652378708 120-124 24.55152789805765 22.70196709142645 24.2174935048868 28.5290115056291 125-129 24.900255085355486 23.029629145137026 21.89809667080908 30.17201909869841 130-134 25.19542155220547 21.670854271356784 23.743718592964825 29.390005583472924 135-139 25.0468832045608 22.833995949291126 23.614132473182806 28.50498837296527 140-144 24.57846952010376 23.111219195849547 22.754539559014265 29.555771725032425 145-149 25.93223377554679 21.943348870562925 23.09967730369308 29.024740050197202 150 27.476882430647294 0.0 31.43989431968296 41.08322324966975 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 1.0 1 0.5 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10 0.0 11 0.0 12 0.0 13 0.0 14 0.0 15 0.0 16 0.0 17 0.0 18 0.0 19 0.0 20 0.5 21 1.0 22 0.5 23 0.0 24 0.0 25 0.0 26 0.0 27 0.0 28 0.0 29 0.0 30 1.5 31 2.0 32 2.5 33 3.5 34 5.5 35 11.0 36 35.5 37 43.5 38 36.0 39 45.0 40 42.5 41 51.0 42 61.5 43 65.5 44 80.0 45 94.5 46 131.5 47 177.5 48 196.5 49 222.0 50 230.0 51 228.0 52 234.5 53 230.5 54 203.0 55 177.5 56 180.0 57 166.0 58 127.0 59 100.5 60 102.0 61 92.5 62 85.0 63 82.5 64 70.0 65 55.0 66 45.5 67 52.5 68 50.5 69 31.5 70 25.5 71 30.0 72 27.0 73 19.5 74 13.0 75 15.0 76 15.0 77 8.0 78 8.0 79 5.5 80 1.0 81 1.0 82 1.0 83 0.0 84 0.5 85 0.5 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 0.025 2 0.025 3 0.025 4 0.025 5 0.025 6 0.975 7 0.025 8 0.025 9 0.025 10-14 0.025 15-19 0.025 20-24 0.025 25-29 0.025 30-34 0.025 35-39 0.005001000200040008 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 0.0 >>END_MODULE >>Sequence Length Distribution warn #Length Count 35-39 1.0 40-44 0.0 45-49 1.0 50-54 1.0 55-59 1.0 60-64 2.0 65-69 9.0 70-74 13.0 75-79 15.0 80-84 18.0 85-89 27.0 90-94 47.0 95-99 79.0 100-104 80.0 105-109 114.0 110-114 139.0 115-119 155.0 120-124 169.0 125-129 189.0 130-134 192.0 135-139 197.0 140-144 206.0 145-149 831.0 150-151 1514.0 >>END_MODULE >>Sequence Duplication Levels warn #Total Deduplicated Percentage 69.55 #Duplication Level Percentage of deduplicated Percentage of total 1 81.48813803019411 56.675 2 8.806613946800864 12.25 3 4.24155283968368 8.85 4 2.372393961179008 6.6000000000000005 5 0.8986340762041696 3.125 6 0.8626887131560028 3.5999999999999996 7 0.28756290438533433 1.4000000000000001 8 0.2156721782890007 1.2 9 0.2516175413371675 1.575 >10 0.5751258087706687 4.725 >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 CCGACATCGAAGGATCAAAAAGCAACGTCGCTATGAACGCTTGGCTGCCA 16 0.4 No Hit CTCAGAGCCAATCCTTTTCCCGAAGTTACGGATCCGTTTTGCCGACTTCC 16 0.4 No Hit CTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATT 15 0.375 No Hit GTCGGGGCAGGCGGCGGGCGCAGGCGCCGCTTGCTAGCTTGGATTCTGAC 13 0.325 No Hit GTCCTTTTCATCTTTCCCTCGCGGTACTTGTTCGCTATCGGTCTCTCGCC 13 0.325 No Hit CCTCGCGGTACTTGTTCGCTATCGGTCTCTCGCCTGTATTTAGCCTTGGA 13 0.325 No Hit CCCGACTGTCCCTATTAATCATTACTCCGATCCCGAAGGCCAACACAATA 12 0.3 No Hit CCGGAACCCAAAGACTTTGATTTCTCATAAGGTGCCGGCGGAGTCCTATA 11 0.27499999999999997 No Hit CTTTTGTTCCACACGAGATTTCTGTTCTCGTTGAGCTCATCTTAGGACAC 10 0.25 No Hit CCCCGGAACCCAAAGACTTTGATTTCTCATAAGGTGCCGGCGGAGTCCTA 10 0.25 No Hit GTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACT 10 0.25 No Hit CTGTTATTGCCTCAAACTTCCGTCGCCTAAACGGCGATAGTCCCTCTAAG 10 0.25 No Hit CTAGAATTACTACGGTTATCCGAGTAGCACGTACCATCAAACAAACTATA 10 0.25 No Hit CCCAACTTTCGTTCTTGATTAATGAAAACATCCTTGGCAAATGCTTTCGC 10 0.25 No Hit GCCGCAGGCTCCACGCCTGGTGGTGCCCTTCCGTCAATTCCTTTAAGTTT 10 0.25 No Hit GCTCCAGCTATCCTGAGGGAAACTTCGGAGGGAACCAGCTACTAGATGGT 10 0.25 No Hit CCCGAAGTTACGGATCCGTTTTGCCGACTTCCCTTGCCTACATTGTTCCA 9 0.22499999999999998 No Hit CGGCAATTTCAAGCACTCTTTGACTCTCTTTTCAAAGTCCTTTTCATCTT 9 0.22499999999999998 No Hit GCCCAGTCCTCAGAGCCAATCCTTTTCCCGAAGTTACGGATCCGTTTTGC 9 0.22499999999999998 No Hit CTTGTTACGACTTCTCCTTCCTCTAAATGATAAGGTTCAATGGACTTCTC 9 0.22499999999999998 No Hit GGGAAACTTCGGAGGGAACCAGCTACTAGATGGTTCGATTAGTCTTTCGC 9 0.22499999999999998 No Hit CCTAATTCTCCGTCACCCGTCACCACCATGGTAGGCCCCTATCCTACCAT 9 0.22499999999999998 No Hit CCCATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCT 9 0.22499999999999998 No Hit CCGGAATCGAACCCTAATTCTCCGTCACCCGTCACCACCATGGTAGGCCC 8 0.2 No Hit ATCGCTTCGAGCCTCCACCAGAGTTTCCTCTGGCTTCGCCCCGCTCAGGC 8 0.2 No Hit GAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTG 8 0.2 No Hit GTGCGACGTGGGGCTGGATCTCAGTGGATCGTGGCAGCAAGGCCACTCTG 8 0.2 No Hit GCCACGCTTTCACGGTTCGTATTCGTACTGGAAATCAGAATCAAACGAGC 8 0.2 No Hit GTCCCGACAGGCGTGCTCCAACTCGAACCCTTCACAGAAGATCAGGGTCG 8 0.2 No Hit GCAGAAATTTGAATGATGCGTCGCCGGCACGAGGGCCGTGCGATCCGTCG 7 0.17500000000000002 No Hit CTGTATTTAGCCTTGGACGGAGTCTACCGCCCGATTTGGGCTGCATTCCC 7 0.17500000000000002 No Hit CAACAACTTAAATATACGCTATTGGAGCTGGAATTACCGCGGCTGCTGGC 7 0.17500000000000002 No Hit CCGGTATTGTTATTTATTGTCACTACCTCCCCGTGTCAGGATTGGGTAAT 7 0.17500000000000002 No Hit CGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACT 7 0.17500000000000002 No Hit ATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCTATA 7 0.17500000000000002 No Hit CCCAGTCCTCAGAGCCAATCCTTTTCCCGAAGTTACGGATCCGTTTTGCC 7 0.17500000000000002 No Hit CCCACTTATCCTACACCTCTCAAGTCATTTCACAAAGTCGGACTAGAGTC 7 0.17500000000000002 No Hit GCCCGGTATTGTTATTTATTGTCACTACCTCCCCGTGTCAGGATTGGGTA 6 0.15 No Hit GGTAAAACTAACCTGTCTCACGACGGTCTAAACCCAGCTCACGTTCCCTA 6 0.15 No Hit CTCTGACTATGAAATACGAATGCCCCCGACTGTCCCTATTAATCATTACT 6 0.15 No Hit CTCGCCTGTATTTAGCCTTGGACGGAGTCTACCGCCCGATTTGGGCTGCA 6 0.15 No Hit CCCAAGTCAGACGAACGATTTGCACGTCAGTATCGCTTCGAGCCTCCACC 6 0.15 No Hit CTTCCGTCAATTCCTTTAAGTTTCAGCCTTGCGACCATACTCCCCCCGGA 6 0.15 No Hit CCAACTACGAGCTTTTTAACTGCAACAACTTAAATATACGCTATTGGAGC 6 0.15 No Hit CCCCCATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGG 6 0.15 No Hit CCGCCGTTTACCCGCGCTTGGTTGAATTTCTTCACTTTGACATTCAGAGC 6 0.15 No Hit CTGACTATGAAATACGAATGCCCCCGACTGTCCCTATTAATCATTACTCC 6 0.15 No Hit GCTCATCTTAGGACACCTGCGTTATCTTTTAACAGATGTGCCGCCCCAGC 6 0.15 No Hit CCCGGAACCCAAAGACTTTGATTTCTCATAAGGTGCCGGCGGAGTCCTAT 6 0.15 No Hit GGCAGAAATTTGAATGATGCGTCGCCGGCACGAGGGCCGTGCGATCCGTC 6 0.15 No Hit CGCGTATTTAAGTCGTCTGCAAAGGATTCAGCCCGCCGCCCGTGGGGAAG 6 0.15 No Hit CCACGCTTTCACGGTTCGTATTCGTACTGGAAATCAGAATCAAACGAGCT 6 0.15 No Hit GGCAGAAATCACATTGCGTCAGCATCCGCGAGGACCATCGCAATGCTTTG 6 0.15 No Hit GGCTTTACCTGATAGAACTCGTAATGGGCTCCAGCTATCCTGAGGGAAAC 6 0.15 No Hit GTCGTCTGCAAAGGATTCAGCCCGCCGCCCGTGGGGAAGGGAGCTTCGAG 6 0.15 No Hit CCGACTCGTTGACGGCGCCTCGTGGGGCGACAGGGTCCGGGCCGGACGGG 6 0.15 No Hit GTTCAGTCATAATCCGGCACACGGTAGCTTCGCGCCACTGGCTTTTCAAC 6 0.15 No Hit CCTCAGAGCCAATCCTTTTCCCGAAGTTACGGATCCGTTTTGCCGACTTC 6 0.15 No Hit CATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACC 6 0.15 No Hit CGGTATTGTTATTTATTGTCACTACCTCCCCGTGTCAGGATTGGGTAATT 6 0.15 No Hit CCCCGACTGTCCCTATTAATCATTACTCCGATCCCGAAGGCCAACACAAT 6 0.15 No Hit GGCCACGCTTTCACGGTTCGTATTCGTACTGGAAATCAGAATCAAACGAG 5 0.125 No Hit CCGCATACGGCCAGGACGCATCGCCGGCCCCCATCCGCTTCCCTCCCGGC 5 0.125 No Hit CCCGCGTCAGCCTTTTATCTAATAAATGCGCCCCTCCCAGAAGTCGGGGT 5 0.125 No Hit GGCTACCTTAAGAGAGTCATAGTTACTCCCGCCGTTTACCCGCGCTTGGT 5 0.125 No Hit CCCCGCTCAGGCATAGTTCACCATCTTTCGGGTCCCGACAGGCGTGCTCC 5 0.125 No Hit TCTTGATTAATGAAAACATCCTTGGCAAATGCTTTCGCAGTTGTTCGTCT 5 0.125 No Hit GTCGGATGGGGAGCCCGCAGGCCGTTGCAGCGCAGTGCCCCGAGGGACAC 5 0.125 No Hit CCGCTGATTCCGCCAAGCCCGTTCCCTTGGCTGTGGTTTCGCTGGATAGT 5 0.125 No Hit CTCCCACTTATCCTACACCTCTCAAGTCATTTCACAAAGTCGGACTAGAG 5 0.125 No Hit GCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGC 5 0.125 No Hit CCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGG 5 0.125 No Hit CTTGTCCGTACCAGTTCTGAGTCGACTGTTCAGCGCTCGGGGAAAGCCCC 5 0.125 No Hit GGACGCATCGCCGGCCCCCATCCGCTTCCCTCCCGGCAATTTCAAGCACT 5 0.125 No Hit GTGGTTTCGCTGGATAGTAGACAGGGACAGTGGGAATCTCGTTAATCCAT 5 0.125 No Hit GGCCGACATCGAAGGATCAAAAAGCAACGTCGCTATGAACGCTTGGCTGC 5 0.125 No Hit GCTGTGGTTTCGCTGGATAGTAGACAGGGACAGTGGGAATCTCGTTAATC 5 0.125 No Hit CTAATTCTCCGTCACCCGTCACCACCATGGTAGGCCCCTATCCTACCATC 5 0.125 No Hit CACGCTTTCACGGTTCGTATTCGTACTGGAAATCAGAATCAAACGAGCTT 5 0.125 No Hit CCTCTAAGAAGCTAGCTGCGGAGGGATGGCTCCGCATAGCTAGTTAGCAG 5 0.125 No Hit CACGGTTCGTATTCGTACTGGAAATCAGAATCAAACGAGCTTTTACCCTT 5 0.125 No Hit GTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTA 5 0.125 No Hit GTCAGGATTGGGTAATTTGCGCGCCTGCTGCCTTCCTTGGATGTGGTAGC 5 0.125 No Hit CCCGGTATTGTTATTTATTGTCACTACCTCCCCGTGTCAGGATTGGGTAA 5 0.125 No Hit CTGGAAATCAGAATCAAACGAGCTTTTACCCTTTTGTTCCACACGAGATT 5 0.125 No Hit CCCTTTTGTTCCACACGAGATTTCTGTTCTCGTTGAGCTCATCTTAGGAC 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 0.0 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 0.0 0.0 0.0 0.0 0.0 70-71 0.0 0.0 0.0 0.0 0.0 72-73 0.0 0.0 0.0 0.0 0.0 74-75 0.0 0.0 0.0 0.0 0.0 76-77 0.0 0.0 0.0 0.0 0.0 78-79 0.0 0.0 0.0 0.0 0.0 80-81 0.0 0.0 0.0 0.0 0.0 82-83 0.0 0.0 0.0 0.0 0.0 84-85 0.0 0.0 0.0 0.0 0.0 86-87 0.0 0.0 0.0 0.0 0.0 88-89 0.0 0.0 0.0 0.0 0.0 90-91 0.0 0.0 0.0 0.0 0.0 92-93 0.0 0.0 0.0 0.0 0.0 94-95 0.0 0.0 0.0 0.0 0.0 96-97 0.0 0.0 0.0 0.0 0.0 98-99 0.0 0.0 0.0 0.0 0.0 100-101 0.0 0.0 0.0 0.0 0.0 102-103 0.0 0.0 0.0 0.0 0.0 104-105 0.0 0.0 0.0 0.0 0.0 106-107 0.0 0.0 0.0 0.0 0.0 108-109 0.0 0.0 0.0 0.0 0.0 110-111 0.0 0.0 0.0 0.0 0.0 112-113 0.0 0.0 0.0 0.0 0.0 114-115 0.0 0.0 0.0 0.0 0.0 116-117 0.0 0.0 0.0 0.0 0.0 118-119 0.0 0.0 0.0 0.0 0.0 120-121 0.0 0.0 0.0 0.0 0.0 122-123 0.0 0.0 0.0 0.0 0.0 124-125 0.0125 0.0 0.0 0.0 0.0 126-127 0.025 0.0 0.0 0.0 0.0 128-129 0.025 0.0 0.0 0.0 0.0 130-131 0.025 0.0 0.0 0.0 0.0 132-133 0.025 0.0 0.0 0.0 0.0 134-135 0.025 0.0 0.0 0.0 0.0 136-137 0.025 0.0 0.0 0.0 0.0 138 0.025 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TACTATC 10 0.009091687 131.775 4 >>END_MODULE Rejected 1587286 READS because READLEN < 1 Read 1587286 spots for SRR12682217.sra Written 1587286 spots for SRR12682217.sra Rejected 1587286 READS because READLEN < 1 Read 1587286 spots for SRR12682217.sra Written 1587286 spots for SRR12682217.sra Rejected 1587286 READS because READLEN < 1 Read 1587286 spots for SRR12682217.sra Written 1587286 spots for SRR12682217.sra Rejected 1587286 READS because READLEN < 1 Read 1587286 spots for SRR12682217.sra Written 1587286 spots for SRR12682217.sra Rejected 1587286 READS because READLEN < 1 Read 1587286 spots for SRR12682217.sra Written 1587286 spots for SRR12682217.sra Rejected 1587286 READS because READLEN < 1 Read 1587286 spots for SRR12682217.sra Written 1587286 spots for SRR12682217.sra Rejected 1587286 READS because READLEN < 1 Read 1587286 spots for SRR12682217.sra Written 1587286 spots for SRR12682217.sra Rejected 1587286 READS because READLEN < 1 Read 1587286 spots for SRR12682217.sra Written 1587286 spots for SRR12682217.sra Rejected 1587286 READS because READLEN < 1 Read 1587286 spots for SRR12682217.sra Written 1587286 spots for SRR12682217.sra Rejected 1587286 READS because READLEN < 1 Read 1587286 spots for SRR12682217.sra Written 1587286 spots for SRR12682217.sra Rejected 1587286 READS because READLEN < 1 Read 1587286 spots for SRR12682217.sra Written 1587286 spots for SRR12682217.sra Rejected 1587292 READS because READLEN < 1 Read 1587292 spots for SRR12682217.sra Written 1587292 spots for SRR12682217.sra Rejected 1587286 READS because READLEN < 1 Read 1587286 spots for SRR12682217.sra Written 1587286 spots for SRR12682217.sra Rejected 1587286 READS because READLEN < 1 Read 1587286 spots for SRR12682217.sra Written 1587286 spots for SRR12682217.sra Rejected 1587286 READS because READLEN < 1 Read 1587286 spots for SRR12682217.sra Written 1587286 spots for SRR12682217.sra Rejected 1587286 READS because READLEN < 1 Read 1587286 spots for SRR12682217.sra Written 1587286 spots for SRR12682217.sra Rejected 1587286 READS because READLEN < 1 Read 1587286 spots for SRR12682217.sra Written 1587286 spots for SRR12682217.sra Rejected 1587286 READS because READLEN < 1 Read 1587286 spots for SRR12682217.sra Written 1587286 spots for SRR12682217.sra Rejected 1587286 READS because READLEN < 1 Read 1587286 spots for SRR12682217.sra Written 1587286 spots for SRR12682217.sra Rejected 1587286 READS because READLEN < 1 Read 1587286 spots for SRR12682217.sra Written 1587286 spots for SRR12682217.sra SRR ids: ['SRR12682217.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_5dbw1yez SRR12682217.sra spots: 31745726 blocks: [[1, 1587286], [1587287, 3174572], [3174573, 4761858], [4761859, 6349144], [6349145, 7936430], [7936431, 9523716], [9523717, 11111002], [11111003, 12698288], [12698289, 14285574], [14285575, 15872860], [15872861, 17460146], [17460147, 19047432], [19047433, 20634718], [20634719, 22222004], [22222005, 23809290], [23809291, 25396576], [25396577, 26983862], [26983863, 28571148], [28571149, 30158434], [30158435, 31745726]] SRR12682217 file size 9905277 SRR12682217 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 SRR12682217 SRR12682217_1.fastq Input file: SRR12682217_1.fastq trimmed: SRR12682217-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -- 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 -- minimum overlap length for adapter detection (-k): inf -- number of concurrent threads (-t): 20 Sat Dec 7 02:52:07 2024 >> started Sat Dec 7 02:52:24 2024 >> done (17.314s) 31745726 reads processed; of these: 0 ( 0.00%) short reads filtered out after trimming by size control 2663 ( 0.01%) empty reads filtered out after trimming by size control 31743063 (99.99%) reads available; of these: 17043 ( 0.05%) trimmed reads available after processing 31726020 (99.95%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 22 11 0.00% 23 16 0.00% 24 24 0.00% 25 34 0.00% 26 60 0.00% 27 84 0.00% 28 97 0.00% 29 121 0.00% 30 138 0.00% 31 182 0.00% 32 176 0.00% 33 213 0.00% 34 294 0.00% 35 338 0.00% 36 388 0.00% 37 490 0.00% 38 588 0.00% 39 740 0.00% 40 817 0.00% 41 998 0.00% 42 1099 0.00% 43 1042 0.00% 44 1107 0.00% 45 1140 0.00% 46 1310 0.00% 47 1536 0.00% 48 2032 0.01% 49 2333 0.01% 50 2588 0.01% 51 2943 0.01% 52 3167 0.01% 53 3149 0.01% 54 3315 0.01% 55 3711 0.01% 56 3895 0.01% 57 4573 0.01% 58 5257 0.02% 59 5744 0.02% 60 6383 0.02% 61 7098 0.02% 62 7738 0.02% 63 7912 0.02% 64 8325 0.03% 65 8810 0.03% 66 9655 0.03% 67 10479 0.03% 68 11211 0.04% 69 12144 0.04% 70 12488 0.04% 71 15144 0.05% 72 16308 0.05% 73 18457 0.06% 74 19281 0.06% 75 20073 0.06% 76 21853 0.07% 77 23020 0.07% 78 25104 0.08% 79 27788 0.09% 80 29978 0.09% 81 32805 0.10% 82 36021 0.11% 83 37069 0.12% 84 40693 0.13% 85 46394 0.15% 86 51718 0.16% 87 54623 0.17% 88 58493 0.18% 89 60509 0.19% 90 64865 0.20% 91 68348 0.22% 92 77733 0.24% 93 83929 0.26% 94 88291 0.28% 95 98819 0.31% 96 106629 0.34% 97 111968 0.35% 98 129041 0.41% 99 128362 0.40% 100 130557 0.41% 101 134355 0.42% 102 143614 0.45% 103 153332 0.48% 104 162648 0.51% 105 161228 0.51% 106 170988 0.54% 107 183903 0.58% 108 174549 0.55% 109 192784 0.61% 110 195663 0.62% 111 207959 0.66% 112 226063 0.71% 113 219992 0.69% 114 236665 0.75% 115 253644 0.80% 116 259681 0.82% 117 250815 0.79% 118 248948 0.78% 119 261678 0.82% 120 279189 0.88% 121 263806 0.83% 122 294600 0.93% 123 302011 0.95% 124 286159 0.90% 125 286144 0.90% 126 299032 0.94% 127 291530 0.92% 128 295831 0.93% 129 320671 1.01% 130 298030 0.94% 131 297487 0.94% 132 300155 0.95% 133 305922 0.96% 134 293924 0.93% 135 299598 0.94% 136 306133 0.96% 137 309064 0.97% 138 297978 0.94% 139 305696 0.96% 140 297019 0.94% 141 292292 0.92% 142 290167 0.91% 143 285896 0.90% 144 297752 0.94% 145 281098 0.89% 146 346311 1.09% 147 532685 1.68% 148 1176851 3.71% 149 4115341 12.96% 150 12174316 38.35% 31743063 reads passed initial QC criterion=sequence-density sequence-density=1.02 sequence-density-rank=1 fanout-score=2.71 fanout-score-rank=32 prefix-density=2.74 prefix-fanout=1.0 sequence=CTTGGATGTGGCAGCCGTTTCTC criterion=fanout-score sequence-density=0.07 sequence-density-rank=29 fanout-score=42.09 fanout-score-rank=1 prefix-density=2.48 prefix-fanout=1.2 sequence=CCCCCGGAATAAGTA Started job on | Dec 07 02:52:57 Started mapping on | Dec 07 02:52:57 Finished on | Dec 07 02:54:42 Mapping speed, Million of reads per hour | 1088.33 Number of input reads | 31743063 Average input read length | 137 UNIQUE READS: Uniquely mapped reads number | 7617793 Uniquely mapped reads % | 24.00% Average mapped length | 137.00 Number of splices: Total | 2801723 Number of splices: Annotated (sjdb) | 2651393 Number of splices: GT/AG | 2762793 Number of splices: GC/AG | 33986 Number of splices: AT/AC | 2236 Number of splices: Non-canonical | 2708 Mismatch rate per base, % | 0.26% Deletion rate per base | 0.02% Deletion average length | 1.75 Insertion rate per base | 0.00% Insertion average length | 1.14 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 1486462 % of reads mapped to multiple loci | 4.68% Number of reads mapped to too many loci | 19427520 % of reads mapped to too many loci | 61.20% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.63% % of reads unmapped: other | 8.48% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 22638808 22638808 22638808 N_multimapping 1486462 1486462 1486462 N_noFeature 634327 7433339 697471 N_ambiguous 162030 659 41756 UnstrandedReadsAssigned:6821436 PositiveStrandReadsAssigned:183795 NegativeStrandReadsAssigned:6878566 Dataset is classified negative stranded MeadianReadLen=149 20thPercentileLength=122 echo kmer=117 SRR12682217 Starting Kallisto single end mapping to ensembl reference transcriptome. kmer=31 [quant] fragment length distribution is truncated gaussian with mean = 100, sd = 20 [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 single-end mode [quant] will process file 1: SRR12682217-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 31,743,063 reads, 7,115,113 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,240 rounds 52973 SRR12682217.ke.tsv 35125 SRR12682217.se.tsv 88098 total ==> SRR12682217.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 837 3.16248 0.746044 PNS24247 1044 945 9.47842 1.98046 PNS24249 1928 1829 73.6175 7.94748 PNS24246 1044 945 9.47842 1.98046 PNS24248 1044 945 9.47842 1.98046 PNS24244 1471 1372 68.7847 9.8992 PNS24243 293 194 1 1.0178 KQK14069 1603 1504 1714.76 225.122 KQK14071 474 375 99.6499 52.4696 ==> SRR12682217.se.tsv <== BRADI_1g14170v3 1943 BRADI_1g53295v3 27 BRADI_1g59795v3 95 BRADI_1g07683v3 0 BRADI_1g00485v3 1 BRADI_1g20270v3 564 BRADI_1g74790v3 81 BRADI_1g09890v3 0 BRADI_1g77505v3 65 BRADI_1g48960v3 0 SRR12682217 completed mapping pipeline successfully