Starting /dee2/code/volunteer_pipeline.sh SRR15142084 current disk space = 3085312643072 free memory = 1582504440 SRR15142084 SRAfilesize 732b962ca3c5103c097df668a7dcfcae SRR15142084.sra SRR15142084.sra file validated SRR15142084 is paired end SRR15142084 is conventional basespace SRR15142084 read1 length is 35-76 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR15142084_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 35-76 %GC 36 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 30.7085 32.0 32.0 32.0 32.0 32.0 2 31.135 32.0 32.0 32.0 32.0 32.0 3 31.222 32.0 32.0 32.0 32.0 32.0 4 31.33625 32.0 32.0 32.0 32.0 32.0 5 31.38 32.0 32.0 32.0 32.0 32.0 6 34.96525 36.0 36.0 36.0 36.0 36.0 7 34.97375 36.0 36.0 36.0 36.0 36.0 8 35.067 36.0 36.0 36.0 36.0 36.0 9 34.89625 36.0 36.0 36.0 36.0 36.0 10-11 34.873125 36.0 36.0 36.0 36.0 36.0 12-13 35.042500000000004 36.0 36.0 36.0 36.0 36.0 14-15 34.884 36.0 36.0 36.0 36.0 36.0 16-17 34.94325 36.0 36.0 36.0 36.0 36.0 18-19 34.948125000000005 36.0 36.0 36.0 36.0 36.0 20-21 34.870374999999996 36.0 36.0 36.0 36.0 36.0 22-23 34.859625 36.0 36.0 36.0 36.0 36.0 24-25 34.83262499999999 36.0 36.0 36.0 36.0 36.0 26-27 34.808499999999995 36.0 36.0 36.0 36.0 36.0 28-29 34.796625000000006 36.0 36.0 36.0 36.0 36.0 30-31 34.713125000000005 36.0 36.0 36.0 36.0 36.0 32-33 34.692 36.0 36.0 36.0 36.0 36.0 34-35 34.71 36.0 36.0 36.0 36.0 36.0 36-37 34.83517726929847 36.0 36.0 36.0 36.0 36.0 38-39 34.75446316318833 36.0 36.0 36.0 36.0 36.0 40-41 34.660422428966555 36.0 36.0 36.0 36.0 36.0 42-43 34.67852652753332 36.0 36.0 36.0 34.0 36.0 44-45 34.621016013101496 36.0 36.0 36.0 32.0 36.0 46-47 34.531941649899395 36.0 36.0 36.0 32.0 36.0 48-49 34.433584905660375 36.0 36.0 36.0 32.0 36.0 50-51 34.43232704402516 36.0 36.0 36.0 32.0 36.0 52-53 34.41482133870156 36.0 36.0 36.0 32.0 36.0 54-55 34.34973571608356 36.0 36.0 36.0 32.0 36.0 56-57 34.284766755604515 36.0 36.0 36.0 32.0 36.0 58-59 34.087761269201714 36.0 36.0 36.0 32.0 36.0 60-61 34.078947368421055 36.0 36.0 36.0 32.0 36.0 62-63 34.040923110859325 36.0 36.0 36.0 32.0 36.0 64-65 33.85783296883308 36.0 36.0 36.0 29.5 36.0 66-67 33.81886303723759 36.0 36.0 36.0 29.5 36.0 68-69 33.70404529193307 36.0 36.0 36.0 27.0 36.0 70-71 33.75673723825359 36.0 36.0 36.0 27.0 36.0 72-73 33.642186784287816 36.0 36.0 36.0 27.0 36.0 74-75 33.44587969998354 36.0 36.0 36.0 27.0 36.0 76 33.13859275053305 36.0 32.0 36.0 27.0 36.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 23.0 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 1.0 20 0.0 21 2.0 22 11.0 23 14.0 24 12.0 25 26.0 26 33.0 27 42.0 28 58.0 29 78.0 30 71.0 31 122.0 32 137.0 33 258.0 34 628.0 35 2484.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 37.22921914357683 12.468513853904282 15.894206549118389 34.4080604534005 2 30.802112144832787 17.500628614533568 30.299220517978377 21.39803872265527 3 29.24314810158411 25.823485038974102 20.090520492833793 24.842846366607997 4 27.860196127734472 32.486799094795074 19.00930349509681 20.643701282373648 5 25.42117173749057 37.515715363339204 20.995725421171738 16.06738747799849 6 19.738496354035707 41.53884837817451 24.339954739753583 14.382700528036207 7 16.746291174251947 30.349509680663818 40.53306512446568 12.371134020618557 8 18.481267286899673 30.827256726175513 32.964546140306766 17.726929846618052 9 21.674629117425194 28.06135277847624 33.06512446567765 17.19889363842092 10-11 18.21724918280111 44.103595675132006 23.52275584611516 14.156399295951722 12-13 19.235604727181293 33.65602212723158 31.028413376917275 16.079959768669852 14-15 18.996731204425448 33.819461905959265 30.223786773950213 16.960020115665074 16-17 18.669851646970077 37.40256474729696 27.219009303495096 16.70857430223787 18-19 18.30525521750063 35.416142821222024 28.652250440030176 17.626351521247173 20-21 19.499622831279858 35.50414885592155 27.2818707568519 17.714357555946695 22-23 19.021875785768167 36.74880563238622 27.420165954236865 16.80915262760875 24-25 18.61956248428464 35.64244405330651 28.9917022881569 16.746291174251947 26-27 18.833291425697762 35.76816696002012 28.023635906462157 17.374905707819966 28-29 19.90193613276339 36.560221272315815 27.75961780236359 15.778224792557205 30-31 19.47447824993714 36.107618808146846 27.935629871762636 16.482273070153383 32-33 21.586623082725673 35.24013075182298 27.244153884837818 15.929092280613528 34-35 20.530550666331408 36.20819713351773 27.470455116922306 15.790797083228563 36-37 18.896152879054565 36.032185064118686 27.935629871762636 17.136032185064117 38-39 18.053809404073423 35.290419914508426 29.733467437767164 16.922303243650994 40-41 19.047020367110886 35.629871762635155 28.639678149358815 16.683429720895145 42-43 19.813930098063867 34.46064873019864 29.368871008297713 16.356550163439778 44-45 19.01169370049038 34.77932855526217 29.37256381239784 16.836413931849616 46-47 18.91348088531187 34.41901408450704 29.71579476861167 16.951710261569417 48-49 18.842767295597483 34.80503144654088 30.062893081761004 16.28930817610063 50-51 17.635220125786162 34.0 32.0503144654088 16.31446540880503 52-53 17.627075993960744 33.920483140412685 32.05837946653246 16.394061399094113 54-55 17.41756858796879 34.33173923986912 32.368487289202115 15.88220488295998 56-57 17.424147047714968 34.29434722397079 32.75840362583407 15.523102102480172 58-59 17.01082850667338 34.99118609921934 31.629312515739112 16.36867287836817 60-61 16.59531604129942 35.60815915386553 31.893729539158898 15.902795265676154 62-63 17.512914199319642 35.05102683633615 31.069673680231823 16.366385284112386 64-65 17.10393541876892 34.73763874873865 31.849142280524724 16.30928355196771 66-67 17.558697298661954 34.89017924766473 31.242110578136835 16.30901287553648 68-69 17.519262346848556 35.21535935329039 31.42604521914867 15.839333080712393 70-71 17.161632756223934 35.85239479337798 30.696322507266522 16.289649943131558 72-73 16.806296014216805 35.326224930185326 31.32774815943133 16.539730896166542 74-75 17.118802619270348 33.06160630763063 32.393425096886276 17.426165976212747 76 21.535181236673772 0.0 51.08742004264393 27.377398720682304 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 40.0 1 21.0 2 3.5 3 4.5 4 4.0 5 6.0 6 12.5 7 15.0 8 13.0 9 10.0 10 13.5 11 17.5 12 14.5 13 12.5 14 13.0 15 21.0 16 27.0 17 24.0 18 24.0 19 31.5 20 46.0 21 55.5 22 63.0 23 93.5 24 104.0 25 94.0 26 101.5 27 129.5 28 164.5 29 176.5 30 201.0 31 212.5 32 202.0 33 214.5 34 223.5 35 217.0 36 216.0 37 212.5 38 200.5 39 194.0 40 189.0 41 161.5 42 136.0 43 127.0 44 112.0 45 117.5 46 128.5 47 113.0 48 96.5 49 80.0 50 61.5 51 63.5 52 70.5 53 65.5 54 62.0 55 55.0 56 44.5 57 43.5 58 43.0 59 29.0 60 19.0 61 16.5 62 9.5 63 10.0 64 11.0 65 8.5 66 3.0 67 0.0 68 0.5 69 1.5 70 1.0 71 0.0 72 0.5 73 0.5 74 0.0 75 0.0 76 0.5 77 0.5 78 0.0 79 0.0 80 0.0 81 0.0 82 0.0 83 0.0 84 0.0 85 0.5 86 0.5 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 0.75 2 0.575 3 0.575 4 0.575 5 0.575 6 0.575 7 0.575 8 0.575 9 0.575 10-11 0.575 12-13 0.575 14-15 0.575 16-17 0.575 18-19 0.575 20-21 0.575 22-23 0.575 24-25 0.575 26-27 0.575 28-29 0.575 30-31 0.575 32-33 0.575 34-35 0.575 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 0.0 >>END_MODULE >>Sequence Length Distribution warn #Length Count 35 23.0 36 0.0 37 0.0 38 0.0 39 0.0 40 0.0 41 0.0 42 0.0 43 0.0 44 1.0 45 0.0 46 0.0 47 1.0 48 0.0 49 0.0 50 0.0 51 1.0 52 0.0 53 1.0 54 0.0 55 1.0 56 1.0 57 0.0 58 0.0 59 0.0 60 0.0 61 0.0 62 5.0 63 1.0 64 2.0 65 1.0 66 2.0 67 1.0 68 1.0 69 1.0 70 1.0 71 5.0 72 24.0 73 73.0 74 225.0 75 1284.0 76 2345.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 94.25 #Duplication Level Percentage of deduplicated Percentage of total 1 98.85941644562334 93.175 2 0.610079575596817 1.15 3 0.05305039787798408 0.15 4 0.1326259946949602 0.5 5 0.10610079575596816 0.5 6 0.02652519893899204 0.15 7 0.0 0.0 8 0.0 0.0 9 0.0 0.0 >10 0.21220159151193632 4.375 >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 CGGCCAGTGAATTGTAATACGACTCACTATAGGGAGATCTGTATGCTGGT 49 1.225 No Hit GTGAATTGTAATACGACTCACTATAGGGAGATCTGTATGCTGGTTTTTTT 36 0.8999999999999999 No Hit NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN 23 0.575 No Hit GGCCAGTGAATTGTAATACGACTCACTATAGGGAGATCTGTATGCTGGTT 20 0.5 No Hit AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 15 0.375 No Hit CCAGTGAATTGTAATACGACTCACTATAGGGAGATCTGTATGCTGGTTTT 12 0.3 No Hit AGTGAATTGTAATACGACTCACTATAGGGAGATCTGTATGCTGGTTTTTT 10 0.25 No Hit GCCAGTGAATTGTAATACGACTCACTATAGGGAGATCTGTATGCTGGTTT 10 0.25 No Hit GACGGCCAGTGAATTGTAATACGACTCACTATAGGGAGATCTGTATGCTG 6 0.15 No Hit TGTAATACGACTCACTATAGGGAGATCTGTATGCTGGTTTTTTTTTTTTT 5 0.125 No Hit GTAATACGACTCACTATAGGGAGATCTGTATGCTGGTTTTTTTTTTTTTT 5 0.125 No Hit CTGGAATCTTAGGTAAATCCGGGATTCTAAGGCCGAGAGCTGATGACGAG 5 0.125 No Hit CAGTGAATTGTAATACGACTCACTATAGGGAGATCTGTATGCTGGTTTTT 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 0.0 0.0 0.0 0.0 0.0 11 0.0 0.0 0.0 0.0 0.0 12 0.0 0.0 0.0 0.0 0.0 13 0.0 0.0 0.0 0.0 0.0 14 0.0 0.0 0.0 0.0 0.0 15 0.0 0.0 0.0 0.0 0.0 16 0.0 0.0 0.0 0.0 0.0 17 0.0 0.0 0.0 0.0 0.0 18 0.0 0.0 0.0 0.0 0.0 19 0.0 0.0 0.0 0.0 0.0 20 0.0 0.0 0.0 0.0 0.0 21 0.0 0.0 0.0 0.0 0.0 22 0.0 0.0 0.0 0.0 0.0 23 0.0 0.0 0.0 0.0 0.0 24 0.0 0.0 0.0 0.0 0.0 25 0.0 0.0 0.0 0.0 0.0 26 0.0 0.0 0.0 0.0 0.0 27 0.0 0.0 0.0 0.0 0.0 28 0.0 0.0 0.0 0.0 0.0 29 0.0 0.0 0.0 0.0 0.0 30 0.0 0.0 0.0 0.0 0.0 31 0.0 0.0 0.0 0.0 0.0 32 0.0 0.0 0.0 0.0 0.0 33 0.0 0.0 0.0 0.0 0.0 34 0.0 0.0 0.0 0.0 0.0 35 0.0 0.0 0.0 0.0 0.0 36 0.0 0.0 0.0 0.0 0.0 37 0.0 0.0 0.0 0.0 0.0 38 0.0 0.0 0.0 0.0 0.0 39 0.0 0.0 0.0 0.0 0.0 40 0.0 0.0 0.0 0.0 0.0 41 0.0 0.0 0.0 0.0 0.0 42 0.0 0.0 0.0 0.0 0.0 43 0.0 0.0 0.0 0.0 0.0 44 0.0 0.0 0.0 0.0 0.0 45 0.0 0.0 0.0 0.0 0.0 46 0.0 0.0 0.0 0.0 0.0 47 0.0 0.0 0.0 0.0 0.0 48 0.0 0.0 0.0 0.0 0.0 49 0.0 0.0 0.0 0.0 0.0 50 0.0 0.0 0.0 0.0 0.0 51 0.0 0.0 0.0 0.0 0.0 52 0.0 0.0 0.0 0.0 0.0 53 0.0 0.0 0.0 0.0 0.0 54 0.0 0.0 0.0 0.0 0.0 55 0.0 0.0 0.0 0.0 0.0 56 0.0 0.0 0.0 0.0 0.0 57 0.0 0.0 0.0 0.0 0.0 58 0.0 0.0 0.0 0.0 0.0 59 0.0 0.0 0.0 0.0 0.0 60 0.0 0.0 0.0 0.0 0.0 61 0.0 0.0 0.0 0.0 0.0 62 0.0 0.0 0.0 0.0 0.0 63 0.0 0.0 0.0 0.0 0.0 64 0.0 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE SRR15142084 read2 length is 44-76 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR15142084_2.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 44-76 %GC 35 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 30.288 32.0 32.0 32.0 21.0 32.0 2 30.832 32.0 32.0 32.0 32.0 32.0 3 31.083 32.0 32.0 32.0 32.0 32.0 4 31.11475 32.0 32.0 32.0 32.0 32.0 5 31.21125 32.0 32.0 32.0 32.0 32.0 6 34.915 36.0 36.0 36.0 36.0 36.0 7 35.0045 36.0 36.0 36.0 36.0 36.0 8 34.99325 36.0 36.0 36.0 36.0 36.0 9 34.90025 36.0 36.0 36.0 36.0 36.0 10-11 34.913250000000005 36.0 36.0 36.0 36.0 36.0 12-13 34.95625 36.0 36.0 36.0 36.0 36.0 14-15 34.890875 36.0 36.0 36.0 36.0 36.0 16-17 34.966750000000005 36.0 36.0 36.0 36.0 36.0 18-19 34.880250000000004 36.0 36.0 36.0 36.0 36.0 20-21 34.555875 36.0 36.0 36.0 34.0 36.0 22-23 34.288624999999996 36.0 36.0 36.0 32.0 36.0 24-25 33.83725 36.0 36.0 36.0 32.0 36.0 26-27 33.402625 36.0 36.0 36.0 21.0 36.0 28-29 33.1045 36.0 36.0 36.0 14.0 36.0 30-31 32.674 36.0 36.0 36.0 14.0 36.0 32-33 32.51175 36.0 36.0 36.0 14.0 36.0 34-35 32.33775 36.0 36.0 36.0 14.0 36.0 36-37 32.2315 36.0 36.0 36.0 14.0 36.0 38-39 32.16425 36.0 36.0 36.0 14.0 36.0 40-41 32.161125 36.0 36.0 36.0 14.0 36.0 42-43 32.13825 36.0 36.0 36.0 14.0 36.0 44-45 32.22377716304076 36.0 36.0 36.0 14.0 36.0 46-47 32.19804951237809 36.0 36.0 36.0 14.0 36.0 48-49 31.904827413706855 36.0 34.0 36.0 14.0 36.0 50-51 31.6615807903952 36.0 32.0 36.0 14.0 36.0 52-53 31.654702351175587 36.0 32.0 36.0 14.0 36.0 54-55 31.78583937953465 36.0 32.0 36.0 14.0 36.0 56-57 31.546867612293145 36.0 32.0 36.0 14.0 36.0 58-59 31.37371714643304 36.0 32.0 36.0 14.0 36.0 60-61 31.381476846057573 36.0 32.0 36.0 14.0 36.0 62-63 31.2175584899461 36.0 32.0 36.0 14.0 36.0 64-65 30.891107806553215 36.0 32.0 36.0 14.0 36.0 66-67 31.007026221665498 36.0 32.0 36.0 14.0 36.0 68-69 30.836219879518072 36.0 32.0 36.0 14.0 36.0 70-71 30.662641975507913 36.0 32.0 36.0 14.0 36.0 72-73 30.71351561449403 36.0 32.0 36.0 14.0 36.0 74-75 30.680026003357995 36.0 29.5 36.0 14.0 36.0 76 29.959429000751314 36.0 27.0 36.0 14.0 36.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 15 1.0 16 0.0 17 5.0 18 3.0 19 6.0 20 10.0 21 28.0 22 40.0 23 82.0 24 92.0 25 133.0 26 144.0 27 133.0 28 119.0 29 132.0 30 128.0 31 143.0 32 189.0 33 336.0 34 895.0 35 1381.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 30.67469275144219 15.274642588412341 24.805618259342864 29.24504640080261 2 19.25 20.925 44.824999999999996 15.0 3 19.3 22.975 42.325 15.4 4 24.6 27.6 33.074999999999996 14.725 5 21.7 29.225 36.65 12.425 6 14.799999999999999 31.724999999999998 39.425 14.05 7 13.325000000000001 15.85 56.89999999999999 13.925 8 18.4 21.3 43.8 16.5 9 18.5 20.674999999999997 42.775 18.05 10-11 17.275 29.062500000000004 39.574999999999996 14.0875 12-13 15.562500000000002 22.075 48.112500000000004 14.249999999999998 14-15 13.4375 24.7875 49.425000000000004 12.35 16-17 12.962499999999999 25.424999999999997 48.0 13.612499999999999 18-19 12.7625 26.7625 46.5 13.975000000000001 20-21 14.662500000000001 25.4875 44.3125 15.537500000000001 22-23 15.275 27.187499999999996 42.262499999999996 15.275 24-25 15.375 28.237499999999997 41.575 14.8125 26-27 16.98962370296287 28.91611451431429 38.89236154519315 15.201900237529692 28-29 17.6375 29.775000000000002 37.525 15.0625 30-31 17.875 30.049999999999997 36.725 15.35 32-33 19.82747843480435 30.078759844980624 35.041880235029375 15.051881485185648 34-35 18.814851856482058 30.97887235904488 34.25428178522315 15.951993999249906 36-37 18.627328416052006 31.328916114514314 34.70433804225529 15.339417427178399 38-39 17.325 30.7875 35.462500000000006 16.425 40-41 18.3625 29.862499999999997 35.85 15.925 42-43 18.242060515128784 30.770192548137032 35.183795948987246 15.803950987746937 44-45 17.606602475928472 30.62398399399775 35.500812804801804 16.268600725271977 46-47 18.384192096048025 28.901950975487743 35.44272136068034 17.27113556778389 48-49 21.388367729831145 27.67979987492183 34.73420888055034 16.197623514696684 50-51 22.11105552776388 27.326163081540773 35.71785892946473 14.844922461230613 52-53 22.773886943471737 26.21310655327664 35.74287143571786 15.270135067533767 54-55 21.584084084084086 27.152152152152155 35.86086086086086 15.402902902902904 56-57 23.357116034547502 26.824383527350104 34.57253723870322 15.245963199399174 58-59 22.058087130696045 28.04206309464196 33.28743114672008 16.612418627941913 60-61 22.959439158738107 27.103154732098144 34.52679018527792 15.410615923885828 62-63 23.130870381966186 26.67501565435191 34.27676894176581 15.917345021916093 64-65 23.87816495362246 25.933817999498622 34.36951616946603 15.818500877412886 66-67 23.30364981813621 26.175843471717048 34.14022325348049 16.38028345666625 68-69 24.767762992719057 26.16118503640472 33.492342455435605 15.578709515440622 70-71 23.42082129850559 26.434760768554565 34.30867763405752 15.835740298882332 72-73 23.69316034765084 25.98564050888021 34.26124197002141 16.059957173447536 74-75 23.68352108986115 24.35158501440922 34.34634529735394 17.61854859837569 76 27.08489857250188 0.0 50.45078888054094 22.464312546957174 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 29.0 1 20.0 2 17.0 3 17.0 4 11.0 5 19.5 6 26.5 7 24.0 8 23.5 9 20.5 10 16.0 11 17.0 12 18.5 13 16.5 14 20.0 15 26.5 16 29.5 17 32.5 18 35.0 19 36.5 20 45.0 21 58.5 22 68.0 23 92.5 24 108.5 25 104.0 26 109.5 27 127.0 28 161.0 29 189.5 30 214.0 31 219.0 32 210.0 33 219.0 34 217.0 35 204.0 36 203.5 37 208.0 38 190.5 39 170.5 40 160.5 41 143.0 42 122.0 43 117.5 44 109.5 45 107.0 46 116.0 47 99.5 48 76.5 49 66.0 50 62.0 51 63.0 52 55.5 53 53.5 54 59.5 55 53.0 56 48.0 57 43.0 58 35.5 59 32.5 60 23.0 61 12.5 62 11.0 63 10.0 64 10.5 65 9.0 66 4.5 67 1.5 68 2.5 69 2.5 70 1.5 71 1.5 72 1.0 73 0.5 74 0.5 75 1.0 76 0.5 77 0.0 78 0.0 79 0.0 80 0.5 81 0.5 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 1.0 92 2.0 93 1.5 94 1.5 95 1.5 96 1.0 97 1.5 98 2.5 99 5.5 100 8.0 >>END_MODULE >>Per base N content pass #Base N-Count 1 0.325 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 0.0125 28-29 0.0 30-31 0.0 32-33 0.0125 34-35 0.0125 36-37 0.0125 38-39 0.0 40-41 0.0 42-43 0.025 44-45 0.025003125390673835 46-47 0.025006251562890724 48-49 0.01250625312656328 50-51 0.0 52-53 0.0 54-55 0.02501876407305479 56-57 0.02502815667626079 58-59 0.025031289111389236 60-61 0.025031289111389236 62-63 0.025040691123075 64-65 0.02506265664160401 66-67 0.012540757461750688 68-69 0.0251004016064257 70-71 0.025109855618330193 72-73 0.02518574486840448 74-75 0.026191723415400735 76 0.0 >>END_MODULE >>Sequence Length Distribution warn #Length Count 44 1.0 45 0.0 46 0.0 47 1.0 48 0.0 49 0.0 50 0.0 51 0.0 52 0.0 53 1.0 54 0.0 55 1.0 56 1.0 57 0.0 58 0.0 59 0.0 60 0.0 61 0.0 62 3.0 63 1.0 64 2.0 65 1.0 66 2.0 67 2.0 68 0.0 69 1.0 70 1.0 71 6.0 72 11.0 73 70.0 74 154.0 75 1079.0 76 2662.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 96.175 #Duplication Level Percentage of deduplicated Percentage of total 1 98.8822459059007 95.1 2 0.5718741876787107 1.0999999999999999 3 0.1819599688068625 0.525 4 0.12997140629061607 0.5 5 0.02599428125812321 0.125 6 0.10397712503249285 0.6 7 0.0 0.0 8 0.02599428125812321 0.2 9 0.0 0.0 >10 0.07798284377436965 1.8499999999999999 >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 CGGCCAGTGAATTGTAATACGACTCACTATAGGGAGATCTGTATGCTGGT 33 0.8250000000000001 No Hit AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 27 0.675 No Hit GTGAATTGTAATACGACTCACTATAGGGAGATCTGTATGCTGGTTTTTTT 14 0.35000000000000003 No Hit GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 8 0.2 No Hit GACGGCCAGTGAATTGTAATACGACTCACTATAGGGAGATCTGTATGCTG 6 0.15 No Hit GTCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 6 0.15 No Hit CCAGTGAATTGTAATACGACTCACTATAGGGAGATCTGTATGCTGGTTTT 6 0.15 No Hit GGCCAGTGAATTGTAATACGACTCACTATAGGGAGATCTGTATGCTGGTT 6 0.15 No Hit GCTGGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 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 0.0 0.0 0.0 0.0 0.0 11 0.0 0.0 0.0 0.0 0.0 12 0.0 0.0 0.0 0.0 0.0 13 0.0 0.0 0.0 0.0 0.0 14 0.0 0.0 0.0 0.0 0.0 15 0.0 0.0 0.0 0.0 0.0 16 0.0 0.0 0.0 0.0 0.0 17 0.0 0.0 0.0 0.0 0.0 18 0.0 0.0 0.0 0.0 0.0 19 0.0 0.0 0.0 0.0 0.0 20 0.0 0.0 0.0 0.0 0.0 21 0.0 0.0 0.0 0.0 0.0 22 0.0 0.0 0.0 0.0 0.0 23 0.0 0.0 0.0 0.0 0.0 24 0.0 0.0 0.0 0.0 0.0 25 0.0 0.0 0.0 0.0 0.0 26 0.0 0.0 0.0 0.0 0.0 27 0.0 0.0 0.0 0.0 0.0 28 0.0 0.0 0.0 0.0 0.0 29 0.0 0.0 0.0 0.0 0.0 30 0.0 0.0 0.0 0.0 0.0 31 0.0 0.0 0.0 0.0 0.0 32 0.0 0.0 0.0 0.0 0.0 33 0.0 0.0 0.0 0.0 0.0 34 0.0 0.0 0.0 0.0 0.0 35 0.0 0.0 0.0 0.0 0.0 36 0.0 0.0 0.0 0.0 0.0 37 0.0 0.0 0.0 0.0 0.0 38 0.0 0.0 0.0 0.0 0.0 39 0.0 0.0 0.0 0.0 0.0 40 0.0 0.0 0.0 0.0 0.0 41 0.0 0.0 0.0 0.0 0.0 42 0.0 0.0 0.0 0.0 0.0 43 0.0 0.0 0.0 0.0 0.0 44 0.0 0.0 0.0 0.0 0.0 45 0.0 0.0 0.0 0.0 0.0 46 0.0 0.0 0.0 0.0 0.0 47 0.0 0.0 0.0 0.0 0.0 48 0.0 0.0 0.0 0.0 0.0 49 0.0 0.0 0.0 0.0 0.0 50 0.0 0.0 0.0 0.0 0.0 51 0.0 0.0 0.0 0.0 0.0 52 0.0 0.0 0.0 0.0 0.0 53 0.0 0.0 0.0 0.0 0.0 54 0.0 0.0 0.0 0.0 0.0 55 0.0 0.0 0.0 0.0 0.0 56 0.0 0.0 0.0 0.0 0.0 57 0.0 0.0 0.0 0.0 0.0 58 0.0 0.0 0.0 0.0 0.0 59 0.0 0.0 0.0 0.0 0.0 60 0.0 0.0 0.0 0.0 0.0 61 0.0 0.0 0.0 0.0 0.0 62 0.0 0.0 0.0 0.0 0.0 63 0.0 0.0 0.0 0.0 0.0 64 0.0 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TCTGTAT 30 5.3931895E-4 46.325 1 CTGTATG 35 0.0011526627 39.70714 2 TGTATGC 40 0.0022222116 34.74375 3 GTATGCT 50 0.0066310917 27.794998 4 TATGCTG 50 0.0066310917 27.794998 5 >>END_MODULE Read 291986 spots for SRR15142084.sra Written 291986 spots for SRR15142084.sra Read 291986 spots for SRR15142084.sra Written 291986 spots for SRR15142084.sra Read 291986 spots for SRR15142084.sra Written 291986 spots for SRR15142084.sra Read 291986 spots for SRR15142084.sra Written 291986 spots for SRR15142084.sra Read 291986 spots for SRR15142084.sra Written 291986 spots for SRR15142084.sra Read 291986 spots for SRR15142084.sra Written 291986 spots for SRR15142084.sra Read 291986 spots for SRR15142084.sra Written 291986 spots for SRR15142084.sra Read 291986 spots for SRR15142084.sra Written 291986 spots for SRR15142084.sra Read 291986 spots for SRR15142084.sra Written 291986 spots for SRR15142084.sra Read 291986 spots for SRR15142084.sra Written 291986 spots for SRR15142084.sra Read 291986 spots for SRR15142084.sra Written 291986 spots for SRR15142084.sra Read 291986 spots for SRR15142084.sra Written 291986 spots for SRR15142084.sra Read 291986 spots for SRR15142084.sra Written 291986 spots for SRR15142084.sra Read 292003 spots for SRR15142084.sra Written 292003 spots for SRR15142084.sra Read 291986 spots for SRR15142084.sra Written 291986 spots for SRR15142084.sra Read 291986 spots for SRR15142084.sra Written 291986 spots for SRR15142084.sra Read 291986 spots for SRR15142084.sra Written 291986 spots for SRR15142084.sra Read 291986 spots for SRR15142084.sra Written 291986 spots for SRR15142084.sra Read 291986 spots for SRR15142084.sra Written 291986 spots for SRR15142084.sra Read 291986 spots for SRR15142084.sra Written 291986 spots for SRR15142084.sra SRR ids: ['SRR15142084.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_degy5qiy SRR15142084.sra spots: 5839737 blocks: [[1, 291986], [291987, 583972], [583973, 875958], [875959, 1167944], [1167945, 1459930], [1459931, 1751916], [1751917, 2043902], [2043903, 2335888], [2335889, 2627874], [2627875, 2919860], [2919861, 3211846], [3211847, 3503832], [3503833, 3795818], [3795819, 4087804], [4087805, 4379790], [4379791, 4671776], [4671777, 4963762], [4963763, 5255748], [5255749, 5547734], [5547735, 5839737]] SRR15142084 file size 1095715 SRR15142084 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 SRR15142084 SRR15142084_1.fastq SRR15142084_2.fastq Input file: SRR15142084_1.fastq Paired file: SRR15142084_2.fastq trimmed: SRR15142084-trimmed-pair1.fastq, SRR15142084-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 Fri Feb 14 06:19:15 2025 >> started Fri Feb 14 06:19:20 2025 >> done (4.723s) 5839737 read pairs processed; of these: 1063 ( 0.02%) short read pairs filtered out after trimming by size control 89048 ( 1.52%) empty read pairs filtered out after trimming by size control 5749626 (98.46%) read pairs available; of these: 18361 ( 0.32%) trimmed read pairs available after processing 5731265 (99.68%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 4 0.00% 19 1 0.00% 20 2 0.00% 21 0 0.00% 22 32 0.00% 23 24 0.00% 24 29 0.00% 25 40 0.00% 26 37 0.00% 27 26 0.00% 28 35 0.00% 29 39 0.00% 30 60 0.00% 31 170 0.00% 32 84 0.00% 33 31 0.00% 34 114 0.00% 35 89 0.00% 36 83 0.00% 37 82 0.00% 38 102 0.00% 39 123 0.00% 40 158 0.00% 41 154 0.00% 42 191 0.00% 43 258 0.00% 44 263 0.00% 45 250 0.00% 46 297 0.01% 47 511 0.01% 48 460 0.01% 49 578 0.01% 50 759 0.01% 51 911 0.02% 52 602 0.01% 53 857 0.01% 54 894 0.02% 55 818 0.01% 56 954 0.02% 57 1029 0.02% 58 1123 0.02% 59 1016 0.02% 60 1032 0.02% 61 1060 0.02% 62 1202 0.02% 63 1290 0.02% 64 1480 0.03% 65 1472 0.03% 66 1591 0.03% 67 1870 0.03% 68 2027 0.04% 69 2634 0.05% 70 2793 0.05% 71 3616 0.06% 72 5393 0.09% 73 36360 0.63% 74 399668 6.95% 75 3238955 56.33% 76 2033893 35.37% 5749626 reads passed initial QC criterion=sequence-density sequence-density=0.26 sequence-density-rank=1 fanout-score=3.68 fanout-score-rank=20 prefix-density=0.28 prefix-fanout=3.4 sequence=GGGAGGCTGAGGCAGGAGAAT criterion=fanout-score sequence-density=0.06 sequence-density-rank=28 fanout-score=65.52 fanout-score-rank=1 prefix-density=0.18 prefix-fanout=23.1 sequence=AAAAAAAAAACCAGCATACAGATCTCCC criterion=sequence-density sequence-density=0.40 sequence-density-rank=1 fanout-score=3.37 fanout-score-rank=30 prefix-density=0.43 prefix-fanout=3.1 sequence=TTTTTTTTTTATTT criterion=fanout-score sequence-density=0.10 sequence-density-rank=30 fanout-score=96.63 fanout-score-rank=1 prefix-density=0.92 prefix-fanout=10.8 sequence=TTTTATTTTTTT SRR15142084 testing PE reads STAR mapping to Ensembl genome Unpaired reads removal Started job on | Feb 14 06:21:59 Started mapping on | Feb 14 06:21:59 Finished on | Feb 14 06:24:48 Mapping speed, Million of reads per hour | 122.45 Number of input reads | 5748303 Average input read length | 130 UNIQUE READS: Uniquely mapped reads number | 392751 Uniquely mapped reads % | 6.83% Average mapped length | 127.52 Number of splices: Total | 19316 Number of splices: Annotated (sjdb) | 15689 Number of splices: GT/AG | 17340 Number of splices: GC/AG | 256 Number of splices: AT/AC | 13 Number of splices: Non-canonical | 1707 Mismatch rate per base, % | 0.76% Deletion rate per base | 0.08% Deletion average length | 1.57 Insertion rate per base | 0.08% Insertion average length | 1.26 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 88133 % of reads mapped to multiple loci | 1.53% Number of reads mapped to too many loci | 61937 % of reads mapped to too many loci | 1.08% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 90.49% % of reads unmapped: other | 0.06% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 5267441 5267441 5267441 N_multimapping 88133 88133 88133 N_noFeature 108717 134758 362148 N_ambiguous 6661 1977 124 UnstrandedReadsAssigned:277373 PositiveStrandReadsAssigned:256016 NegativeStrandReadsAssigned:30479 Dataset is classified positive stranded MeadianReadLen=56 20thPercentileLength=55 echo kmer=51 SRR15142084 Starting Kallisto paired end mapping to ensembl reference transcriptome [quant] fragment length distribution will be estimated from the data [index] k-mer length: 31 [index] number of targets: 52,400 [index] number of k-mers: 62,057,036 [index] number of equivalence classes: 130,681 [quant] running in paired-end mode [quant] will process pair 1: SRR15142084-trimmed-pair1.fastq SRR15142084-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 5,748,303 reads, 593,329 reads pseudoaligned [quant] estimated average fragment length: 137.763 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 890 rounds 52401 SRR15142084.ke.tsv 34699 SRR15142084.se.tsv 87100 total ==> SRR15142084.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1881.24 1 0.720107 Potri.005G024800.1.v4.1 1035 898.237 0 0 Potri.004G059700.1.v4.1 961 824.237 0 0 Potri.007G009000.2.v4.1 1416 1279.24 0 0 Potri.003G141000.2.v4.1 2943 2806.24 16 7.72389 Potri.016G087400.1.v4.1 270 136.157 17 169.141 Potri.015G069301.1.v4.1 564 427.318 0 0 Potri.010G195200.1.v4.1 1773 1636.24 0 0 Potri.012G127500.1.v4.1 977 840.237 148 238.617 ==> SRR15142084.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 1 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 6 Potri.001G212900.v4.1 0 Potri.001G182400.v4.1 0 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 0 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 0 SRR15142084 completed mapping pipeline successfully