Starting /dee2/code/volunteer_pipeline.sh SRR19784176 current disk space = 1551069945856 free memory = 1597700492 SRR19784176 SRAfilesize 60dfa85cdffcb34d0f50ea8bef840a01 SRR19784176.sra SRR19784176.sra file validated SRR19784176 is paired end SRR19784176 is conventional basespace SRR19784176 read1 length is 35-76 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR19784176_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 53 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 31.321 32.0 32.0 32.0 32.0 32.0 2 31.30125 32.0 32.0 32.0 32.0 32.0 3 31.49175 32.0 32.0 32.0 32.0 32.0 4 31.46525 32.0 32.0 32.0 32.0 32.0 5 31.52425 32.0 32.0 32.0 32.0 32.0 6 34.66925 36.0 36.0 36.0 36.0 36.0 7 34.90575 36.0 36.0 36.0 32.0 36.0 8 34.85325 36.0 36.0 36.0 32.0 36.0 9 34.80725 36.0 36.0 36.0 32.0 36.0 10-11 34.7555 36.0 36.0 36.0 32.0 36.0 12-13 34.937875 36.0 36.0 36.0 32.0 36.0 14-15 34.762375 36.0 36.0 36.0 32.0 36.0 16-17 34.916 36.0 36.0 36.0 32.0 36.0 18-19 34.79175 36.0 36.0 36.0 32.0 36.0 20-21 34.812625 36.0 36.0 36.0 32.0 36.0 22-23 34.782125 36.0 36.0 36.0 32.0 36.0 24-25 34.708124999999995 36.0 36.0 36.0 32.0 36.0 26-27 34.669375 36.0 36.0 36.0 32.0 36.0 28-29 34.67375 36.0 36.0 36.0 32.0 36.0 30-31 34.51025 36.0 36.0 36.0 32.0 36.0 32-33 34.51049999999999 36.0 36.0 36.0 32.0 36.0 34-35 34.489125 36.0 36.0 36.0 32.0 36.0 36-37 34.55440220110055 36.0 36.0 36.0 32.0 36.0 38-39 34.48824412206103 36.0 36.0 36.0 32.0 36.0 40-41 34.405952976488244 36.0 36.0 36.0 32.0 36.0 42-43 34.32991495747874 36.0 36.0 36.0 32.0 36.0 44-45 34.44547273636818 36.0 36.0 36.0 32.0 36.0 46-47 34.32691345672836 36.0 36.0 36.0 32.0 36.0 48-49 34.41745872936468 36.0 36.0 36.0 32.0 36.0 50-51 34.52245540458495 36.0 36.0 36.0 32.0 36.0 52-53 34.315900182143615 36.0 36.0 36.0 32.0 36.0 54-55 34.39126626626627 36.0 36.0 36.0 32.0 36.0 56-57 34.33633633633634 36.0 36.0 36.0 32.0 36.0 58-59 34.28895140447081 36.0 36.0 36.0 32.0 36.0 60-61 34.30375469336671 36.0 36.0 36.0 32.0 36.0 62-63 34.27403605408112 36.0 36.0 36.0 32.0 36.0 64-65 34.26755685744996 36.0 36.0 36.0 32.0 36.0 66-67 34.247813877943905 36.0 36.0 36.0 32.0 36.0 68-69 34.12688064192578 36.0 36.0 36.0 32.0 36.0 70-71 34.16990905623819 36.0 36.0 36.0 32.0 36.0 72-73 34.00918030972347 36.0 36.0 36.0 29.5 36.0 74-75 34.015170068387434 36.0 36.0 36.0 32.0 36.0 76 33.895886421550784 36.0 36.0 36.0 27.0 36.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 2.0 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 1.0 21 4.0 22 14.0 23 11.0 24 26.0 25 18.0 26 26.0 27 28.0 28 56.0 29 75.0 30 100.0 31 149.0 32 175.0 33 272.0 34 637.0 35 2406.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 39.1695847923962 8.129064532266133 11.205602801400701 41.49574787393696 2 22.828535669586984 12.290362953692116 29.887359198998748 34.993742177722154 3 22.26113056528264 14.457228614307155 19.634817408704354 43.64682341170585 4 30.81540770385193 21.1855927963982 16.30815407703852 31.690845422711355 5 28.639319659829916 24.88744372186093 21.585792896448226 24.88744372186093 6 26.191076380136124 28.711872951852786 22.53592135114696 22.56112931686413 7 21.410705352676338 21.785892946473236 34.092046023011505 22.71135567783892 8 23.28664332166083 21.83591795897949 27.43871935967984 27.43871935967984 9 24.81240620310155 21.11055527763882 29.63981990995498 24.437218609304654 10-11 26.063031515757878 28.68934467233617 22.448724362181093 22.798899449724864 12-13 26.000500250125064 21.810905452726363 24.899949974987493 27.288644322161083 14-15 25.01876407305479 23.079809857393045 26.169627220415308 25.73179884913685 16-17 24.58729364682341 23.82441220610305 24.92496248124062 26.663331665832917 18-19 25.950475237618807 23.861930965482742 24.674837418709355 25.512756378189096 20-21 25.30015007503752 23.961980990495245 25.22511255627814 25.512756378189096 22-23 25.912956478239117 22.98649324662331 25.050025012506254 26.050525262631314 24-25 26.21310655327664 23.12406203101551 23.336668334167083 27.326163081540773 26-27 25.243932949712285 23.692769577182887 23.8804103077308 27.18288716537403 28-29 25.494120590442833 23.817863397548162 23.792844633475106 26.8951713785339 30-31 26.3631815907954 23.1615807903952 22.923961980990494 27.55127563781891 32-33 25.350175087543768 22.973986993496748 25.012506253126567 26.663331665832917 34-35 26.563281640820406 22.798899449724864 24.037018509254626 26.600800400200097 36-37 25.94445834375782 23.642732049036777 23.517638228671505 26.8951713785339 38-39 24.64982491245623 24.012006003001503 24.77488744372186 26.563281640820406 40-41 25.625312656328163 23.774387193596798 23.499249624812407 27.101050525262632 42-43 26.025512756378188 23.36168084042021 23.799399699849925 26.813406703351678 44-45 25.975487743871934 23.6368184092046 23.19909954977489 27.188594297148573 46-47 25.54096310193871 24.265165728580364 23.239524702939338 26.95434646654159 48-49 26.752628943415125 24.14872308462694 22.1206810215323 26.977966950425635 50-51 25.215759849906195 24.56535334584115 23.101938711694807 27.11694809255785 52-53 26.99862379582134 24.271237332666082 21.906668334792943 26.82347053671963 54-55 24.974974974974977 24.637137137137138 23.073073073073072 27.314814814814813 56-57 26.33883883883884 23.54854854854855 23.323323323323322 26.789289289289293 58-59 24.97183627487796 24.859181374389784 22.568531731130303 27.60045061960195 60-61 25.68531731130304 23.60746025785455 22.70622105394918 28.00100137689323 62-63 26.3335837716003 23.628850488354622 22.827448034059607 27.210117705985475 64-65 27.043946412920995 23.72605483911356 22.561662701890572 26.66833604607487 66-67 26.738503946873827 23.70630246836236 21.964666081944618 27.590527502819196 68-69 26.303911735205617 23.73370110330993 23.03159478435306 26.930792377131397 70-71 26.39498432601881 24.413793103448274 22.382445141065833 26.808777429467085 72-73 26.907125801181348 23.802940806836748 21.81726781450295 27.47266557747895 74-75 26.356077603273064 21.261713079055035 24.112445558928336 28.269763758743565 76 31.634510374954495 0.0 29.99635966508919 38.36912995995632 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 18.0 1 10.0 2 1.5 3 0.5 4 0.0 5 0.0 6 0.5 7 1.5 8 2.0 9 3.5 10 12.0 11 17.0 12 15.0 13 9.0 14 2.5 15 2.0 16 1.5 17 1.5 18 3.0 19 3.5 20 6.5 21 11.5 22 8.0 23 2.0 24 1.5 25 3.0 26 4.5 27 4.5 28 3.5 29 5.5 30 7.5 31 8.5 32 11.5 33 15.0 34 18.0 35 26.0 36 44.0 37 65.0 38 79.5 39 103.0 40 118.0 41 123.5 42 132.0 43 165.0 44 189.5 45 182.5 46 185.0 47 184.5 48 168.5 49 168.5 50 178.0 51 147.5 52 114.0 53 116.0 54 121.5 55 132.5 56 147.0 57 140.5 58 136.0 59 145.0 60 154.0 61 134.0 62 112.0 63 103.0 64 107.0 65 115.0 66 111.5 67 109.5 68 95.0 69 78.0 70 78.5 71 85.0 72 84.0 73 72.0 74 54.5 75 48.5 76 47.0 77 34.0 78 24.5 79 24.5 80 20.5 81 11.0 82 4.5 83 4.0 84 6.0 85 5.0 86 2.5 87 2.0 88 1.0 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 1.5 100 3.0 >>END_MODULE >>Per base N content pass #Base N-Count 1 0.05 2 0.125 3 0.05 4 0.05 5 0.05 6 0.8250000000000001 7 0.05 8 0.05 9 0.05 10-11 0.05 12-13 0.05 14-15 0.075 16-17 0.05 18-19 0.05 20-21 0.05 22-23 0.05 24-25 0.05 26-27 0.075 28-29 0.075 30-31 0.05 32-33 0.05 34-35 0.05 36-37 0.02501250625312656 38-39 0.0 40-41 0.0 42-43 0.0 44-45 0.0 46-47 0.01250625312656328 48-49 0.10005002501250625 50-51 0.0 52-53 0.0 54-55 0.0 56-57 0.0 58-59 0.02502815667626079 60-61 0.012515644555694618 62-63 0.025037556334501748 64-65 0.0 66-67 0.0 68-69 0.0 70-71 0.0 72-73 0.0 74-75 0.052763487666534756 76 0.0 >>END_MODULE >>Sequence Length Distribution warn #Length Count 35 2.0 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 0.0 45 0.0 46 0.0 47 0.0 48 0.0 49 0.0 50 1.0 51 0.0 52 1.0 53 0.0 54 0.0 55 0.0 56 0.0 57 0.0 58 1.0 59 0.0 60 0.0 61 1.0 62 0.0 63 0.0 64 1.0 65 1.0 66 3.0 67 1.0 68 0.0 69 0.0 70 1.0 71 4.0 72 9.0 73 60.0 74 247.0 75 920.0 76 2747.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 93.4 #Duplication Level Percentage of deduplicated Percentage of total 1 95.42291220556746 89.125 2 3.3725910064239826 6.3 3 0.6156316916488223 1.725 4 0.32119914346895073 1.2 5 0.13383297644539613 0.625 6 0.05353319057815846 0.3 7 0.02676659528907923 0.17500000000000002 8 0.02676659528907923 0.2 9 0.0 0.0 >10 0.02676659528907923 0.35000000000000003 >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 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 14 0.35000000000000003 No Hit GTCCAAACAGTTGTCCATGTACCAGTAGAAGATTCGGCAGCTACTGCAGCCCCTGCTTCTTCGGGCGGAACCCC 8 0.2 No Hit CCCAAGGATGTCCTAAAGTTCCTCCACCAAATTGTAATACAGAATCATCC 7 0.17500000000000002 No Hit CTTCAAATAGATCTAATGGATAAGCTACATAACAGATCCATTGACTGTCTTCCCCAGGAACAGGCTCGATGTGAT 6 0.15 No Hit GCTTAATAGTACATCCCAATAAAGGACGACCATACTTGTTCAACTTATCT 6 0.15 No Hit CCAGGAACAGGCTCGATGTGATAGCATCGTCCTTTGTAACGATCAAGACT 5 0.125 No Hit TGCATTTCGTAACTTATTTTTTCTCTTTTTATTTTGTTTCTTTTTATTTA 5 0.125 No Hit CCCGCAGTTGCATTCAAGTAATGCCCCTTGATTTCACCGGTTTCCGCCTGTGATTTATAAATAGCTTCGGCACAA 5 0.125 No Hit CCCCAGTTAAGTAGTCATGCATTACAATAGGAACACCTAATTCTCTCGCA 5 0.125 No Hit CTTCTTCATATTTAGTTTTATCTATTAATCGATAGTATCTACCGGCGCGA 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 SRR19784176 read2 length is 50-76 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR19784176_2.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 50-76 %GC 53 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 30.62 32.0 32.0 32.0 32.0 32.0 2 30.3215 32.0 32.0 32.0 21.0 32.0 3 30.458 32.0 32.0 32.0 32.0 32.0 4 30.458 32.0 32.0 32.0 32.0 32.0 5 30.35125 32.0 32.0 32.0 21.0 32.0 6 33.607 36.0 36.0 36.0 21.0 36.0 7 33.76925 36.0 36.0 36.0 32.0 36.0 8 33.657 36.0 36.0 36.0 27.0 36.0 9 33.9055 36.0 36.0 36.0 32.0 36.0 10-11 33.677375 36.0 36.0 36.0 29.5 36.0 12-13 33.523250000000004 36.0 36.0 36.0 24.0 36.0 14-15 33.62325 36.0 36.0 36.0 29.5 36.0 16-17 33.5095 36.0 36.0 36.0 29.5 36.0 18-19 33.548249999999996 36.0 36.0 36.0 29.5 36.0 20-21 33.639875 36.0 36.0 36.0 27.0 36.0 22-23 33.850875 36.0 36.0 36.0 32.0 36.0 24-25 33.61825 36.0 36.0 36.0 26.5 36.0 26-27 33.616625 36.0 36.0 36.0 29.5 36.0 28-29 33.372375 36.0 36.0 36.0 24.0 36.0 30-31 33.5085 36.0 36.0 36.0 27.0 36.0 32-33 33.4405 36.0 36.0 36.0 27.0 36.0 34-35 33.631125 36.0 36.0 36.0 27.0 36.0 36-37 33.551249999999996 36.0 36.0 36.0 24.0 36.0 38-39 33.452749999999995 36.0 36.0 36.0 24.0 36.0 40-41 33.50725 36.0 36.0 36.0 27.0 36.0 42-43 33.4105 36.0 36.0 36.0 21.0 36.0 44-45 33.422 36.0 36.0 36.0 21.0 36.0 46-47 33.4655 36.0 36.0 36.0 24.0 36.0 48-49 33.41025 36.0 36.0 36.0 21.0 36.0 50-51 33.53557692548137 36.0 36.0 36.0 24.0 36.0 52-53 33.394646654409975 36.0 36.0 36.0 21.0 36.0 54-55 33.36693346673337 36.0 36.0 36.0 21.0 36.0 56-57 33.43734367183592 36.0 36.0 36.0 21.0 36.0 58-59 33.22575748719994 36.0 36.0 36.0 21.0 36.0 60-61 33.226419814861146 36.0 36.0 36.0 17.5 36.0 62-63 33.19306806806807 36.0 36.0 36.0 21.0 36.0 64-65 33.21473983370103 36.0 36.0 36.0 21.0 36.0 66-67 33.252607174354615 36.0 36.0 36.0 21.0 36.0 68-69 33.13911247786048 36.0 36.0 36.0 17.5 36.0 70-71 32.97793678602107 36.0 36.0 36.0 17.5 36.0 72-73 33.04087284422707 36.0 36.0 36.0 14.0 36.0 74-75 33.223809890754424 36.0 36.0 36.0 21.0 36.0 76 32.82414414414414 36.0 36.0 36.0 14.0 36.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 14 3.0 15 6.0 16 17.0 17 27.0 18 13.0 19 19.0 20 19.0 21 28.0 22 31.0 23 33.0 24 30.0 25 42.0 26 43.0 27 69.0 28 89.0 29 107.0 30 104.0 31 164.0 32 240.0 33 307.0 34 656.0 35 1953.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 34.2713567839196 15.92964824120603 12.462311557788945 37.336683417085425 2 24.85 23.875 25.174999999999997 26.1 3 26.0 23.575 21.675 28.749999999999996 4 28.925 27.425 16.25 27.400000000000002 5 28.725 28.549999999999997 19.025 23.7 6 25.525 33.725 17.724999999999998 23.025000000000002 7 24.4 19.15 29.375 27.075 8 25.95095095095095 21.72172172172172 21.62162162162162 30.705705705705704 9 25.456364091022753 21.255313828457115 24.406101525381345 28.882220555138783 10-11 26.675837918959477 26.788394197098548 19.609804902451224 26.92596298149075 12-13 27.775 23.2625 21.637500000000003 27.325 14-15 26.924999999999997 24.175 22.6375 26.2625 16-17 27.306873669713283 23.650932765744333 21.62263678477526 27.419556779767124 18-19 27.063243581715717 24.470882905447713 21.891045710707576 26.574827802128993 20-21 26.87593796898449 23.3991995997999 22.14857428714357 27.576288144072038 22-23 26.8625 23.8625 22.175 27.1 24-25 26.406601650412604 24.468617154288573 22.66816704176044 26.456614153538382 26-27 27.852852852852855 24.637137137137138 21.834334334334336 25.675675675675674 28-29 27.149491653068907 24.651688213882263 20.371532571858918 27.827287561189905 30-31 26.68500687757909 24.20907840440165 22.020757784169064 27.085156933850197 32-33 26.35329416177022 24.56557069633704 23.29041130141268 25.790723840480062 34-35 26.7625 24.45 22.037499999999998 26.75 36-37 26.47242716018507 24.771789421032885 21.908215580842814 26.84756783793923 38-39 26.777666499749625 25.28793189784677 21.519779669504256 26.41462193289935 40-41 26.136505948653728 23.731997495303695 22.705072010018785 27.426424546023792 42-43 26.881585549422983 24.498243853487207 22.190165579528347 26.430005017561463 44-45 26.01402103154732 23.97346019028543 22.058087130696045 27.954431647471207 46-47 26.572464674252842 24.496686257346507 21.670626484931848 27.260222583468803 48-49 26.527028721936535 23.817885363100462 22.939922237551738 26.71516367741126 50-51 26.355327407036434 24.164266933767372 22.849630649805935 26.630775009390263 52-53 27.17377705492306 24.4463905917678 21.268610033779556 27.11122231952959 54-55 26.263131565782892 24.84992496248124 21.898449224612307 26.988494247123562 56-57 26.360565494807958 24.721631427499062 22.106843488052043 26.810959589640937 58-59 27.22710163111669 24.62986198243413 21.25470514429109 26.888331242158092 60-61 26.98392767453541 24.49773982923154 22.011551983927674 26.506780512305372 62-63 27.139456208495176 24.95927828592908 21.300588898634256 26.600676606941487 64-65 27.73813994242083 24.72149205157091 20.95381149079985 26.58655651520841 66-67 26.900438321853475 24.733876017532875 22.204132748904197 26.161552911709457 68-69 27.07784881534411 24.833897455183653 22.088504450294597 25.999749279177635 70-71 27.015469752232423 24.927682052572003 21.758269400075463 26.298578795120108 72-73 27.21871049304678 23.666245259165613 22.604298356510746 26.510745891276866 74-75 26.920516575688993 21.62162162162162 23.6852616162961 27.77260018639329 76 30.270270270270274 0.0 31.135135135135133 38.5945945945946 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 21.0 1 17.5 2 10.5 3 6.0 4 5.0 5 2.5 6 1.5 7 5.0 8 7.0 9 8.0 10 6.5 11 3.0 12 2.0 13 4.5 14 4.0 15 2.0 16 3.5 17 4.0 18 3.0 19 1.5 20 1.0 21 1.5 22 3.0 23 2.5 24 3.0 25 5.5 26 4.0 27 4.5 28 8.5 29 9.0 30 9.5 31 14.0 32 17.5 33 18.0 34 20.5 35 39.5 36 57.5 37 68.5 38 85.5 39 90.5 40 92.0 41 105.0 42 120.5 43 144.5 44 165.5 45 176.0 46 177.0 47 154.0 48 147.0 49 152.5 50 147.0 51 149.0 52 143.5 53 131.0 54 121.5 55 125.5 56 134.5 57 131.5 58 122.5 59 140.5 60 161.0 61 149.5 62 135.0 63 127.0 64 122.5 65 118.0 66 114.5 67 111.5 68 106.5 69 94.0 70 87.5 71 87.5 72 78.0 73 72.0 74 67.5 75 58.5 76 49.0 77 38.5 78 26.0 79 16.5 80 18.5 81 17.0 82 11.0 83 8.5 84 8.5 85 7.0 86 3.0 87 1.5 88 2.5 89 2.0 90 0.5 91 1.0 92 2.0 93 2.0 94 1.0 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 0.5 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.1 9 0.025 10-11 0.05 12-13 0.0 14-15 0.0 16-17 0.1625 18-19 0.1875 20-21 0.05 22-23 0.0 24-25 0.025 26-27 0.1 28-29 0.41250000000000003 30-31 0.0375 32-33 0.0125 34-35 0.0 36-37 0.0375 38-39 0.15 40-41 0.1875 42-43 0.35000000000000003 44-45 0.15 46-47 0.0375 48-49 0.3375 50-51 0.15001875234404302 52-53 0.05001875703388771 54-55 0.0 56-57 0.03751875937968985 58-59 0.31269543464665417 60-61 0.3752814610958219 62-63 0.13763763763763764 64-65 0.02502815667626079 66-67 0.0 68-69 0.025065797719012406 70-71 0.3009404388714733 72-73 0.3024955886059995 74-75 0.02662052442433116 76 0.0 >>END_MODULE >>Sequence Length Distribution warn #Length Count 50 1.0 51 0.0 52 1.0 53 0.0 54 0.0 55 0.0 56 0.0 57 0.0 58 1.0 59 0.0 60 0.0 61 1.0 62 0.0 63 0.0 64 1.0 65 1.0 66 3.0 67 1.0 68 1.0 69 0.0 70 3.0 71 9.0 72 20.0 73 66.0 74 269.0 75 847.0 76 2775.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 94.89999999999999 #Duplication Level Percentage of deduplicated Percentage of total 1 95.94309799789252 91.05 2 3.2402528977871445 6.15 3 0.553213909378293 1.575 4 0.10537407797681769 0.4 5 0.13171759747102213 0.625 6 0.0 0.0 7 0.0 0.0 8 0.026343519494204423 0.2 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 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 8 0.2 No Hit CTTGATTTTACCAAAGATGATGAAAACGTAAACTCACAACCATTTATGCG 5 0.125 No Hit TGGGTATCCATGCCAGGTGTTATACCAGTAGCTTCAGGTGGTATTCATGTTTGGCATATGCCAGCTCTGACCGAA 5 0.125 No Hit GTAGTAGGTAAGTTAGAAGGGGAACGCGAAATCACTTTAGGTTTTGTTGATTTATTGCGCGACGATTTTATTGAA 5 0.125 No Hit CTGATATCTTGGCAGCATTCCGAGTATCTCCTCAACCTGGGGTTCCGCCC 5 0.125 No Hit TGAAAACGTAAACTCACAACCATTTATGCGCTGGAGAGATCGTTTTGTCTTTTGTGCCGAAGCTATTTATAAATC 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 Read 2125223 spots for SRR19784176.sra Written 2125223 spots for SRR19784176.sra Read 2125223 spots for SRR19784176.sra Written 2125223 spots for SRR19784176.sra Read 2125223 spots for SRR19784176.sra Written 2125223 spots for SRR19784176.sra Read 2125223 spots for SRR19784176.sra Written 2125223 spots for SRR19784176.sra Read 2125223 spots for SRR19784176.sra Written 2125223 spots for SRR19784176.sra Read 2125223 spots for SRR19784176.sra Written 2125223 spots for SRR19784176.sra Read 2125223 spots for SRR19784176.sra Written 2125223 spots for SRR19784176.sra Read 2125229 spots for SRR19784176.sra Written 2125229 spots for SRR19784176.sra Read 2125223 spots for SRR19784176.sra Written 2125223 spots for SRR19784176.sra Read 2125223 spots for SRR19784176.sra Written 2125223 spots for SRR19784176.sra Read 2125223 spots for SRR19784176.sra Written 2125223 spots for SRR19784176.sra Read 2125223 spots for SRR19784176.sra Written 2125223 spots for SRR19784176.sra Read 2125223 spots for SRR19784176.sra Written 2125223 spots for SRR19784176.sra Read 2125223 spots for SRR19784176.sra Written 2125223 spots for SRR19784176.sra Read 2125223 spots for SRR19784176.sra Written 2125223 spots for SRR19784176.sra Read 2125223 spots for SRR19784176.sra Written 2125223 spots for SRR19784176.sra Read 2125223 spots for SRR19784176.sra Written 2125223 spots for SRR19784176.sra Read 2125223 spots for SRR19784176.sra Written 2125223 spots for SRR19784176.sra Read 2125223 spots for SRR19784176.sra Written 2125223 spots for SRR19784176.sra Read 2125223 spots for SRR19784176.sra Written 2125223 spots for SRR19784176.sra SRR ids: ['SRR19784176.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_kamby97k SRR19784176.sra spots: 42504466 blocks: [[1, 2125223], [2125224, 4250446], [4250447, 6375669], [6375670, 8500892], [8500893, 10626115], [10626116, 12751338], [12751339, 14876561], [14876562, 17001784], [17001785, 19127007], [19127008, 21252230], [21252231, 23377453], [23377454, 25502676], [25502677, 27627899], [27627900, 29753122], [29753123, 31878345], [31878346, 34003568], [34003569, 36128791], [36128792, 38254014], [38254015, 40379237], [40379238, 42504466]] SRR19784176 file size 8112738 SRR19784176 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 SRR19784176 SRR19784176_1.fastq SRR19784176_2.fastq Input file: SRR19784176_1.fastq Paired file: SRR19784176_2.fastq trimmed: SRR19784176-trimmed-pair1.fastq, SRR19784176-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 Dec 6 13:34:42 2024 >> started Fri Dec 6 13:35:37 2024 >> done (54.554s) 42504466 read pairs processed; of these: 7 ( 0.00%) short read pairs filtered out after trimming by size control 30026 ( 0.07%) empty read pairs filtered out after trimming by size control 42474433 (99.93%) read pairs available; of these: 49263 ( 0.12%) trimmed read pairs available after processing 42425170 (99.88%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 1 0.00% 19 0 0.00% 20 5 0.00% 21 4 0.00% 22 27 0.00% 23 61 0.00% 24 92 0.00% 25 140 0.00% 26 169 0.00% 27 182 0.00% 28 235 0.00% 29 304 0.00% 30 388 0.00% 31 989 0.00% 32 1204 0.00% 33 507 0.00% 34 1529 0.00% 35 830 0.00% 36 1018 0.00% 37 1027 0.00% 38 1160 0.00% 39 1289 0.00% 40 1414 0.00% 41 1594 0.00% 42 1665 0.00% 43 1787 0.00% 44 1958 0.00% 45 2033 0.00% 46 2090 0.00% 47 2255 0.01% 48 2498 0.01% 49 2868 0.01% 50 3029 0.01% 51 3448 0.01% 52 3751 0.01% 53 4080 0.01% 54 4227 0.01% 55 4856 0.01% 56 5051 0.01% 57 5393 0.01% 58 5819 0.01% 59 6414 0.02% 60 6966 0.02% 61 7799 0.02% 62 8253 0.02% 63 9397 0.02% 64 10349 0.02% 65 11214 0.03% 66 11941 0.03% 67 13452 0.03% 68 14018 0.03% 69 15870 0.04% 70 21629 0.05% 71 25025 0.06% 72 52065 0.12% 73 323107 0.76% 74 2624204 6.18% 75 18494886 43.54% 76 20746867 48.85% 42474433 reads passed initial QC criterion=sequence-density sequence-density=0.48 sequence-density-rank=1 fanout-score=2.02 fanout-score-rank=30 prefix-density=0.46 prefix-fanout=2.0 sequence=TTCAAATGTACA criterion=fanout-score sequence-density=0.14 sequence-density-rank=27 fanout-score=67.79 fanout-score-rank=1 prefix-density=0.95 prefix-fanout=10.0 sequence=GGCGGCGGCGAACCGCCCCCGTCGCCGCGATCCGAACACTTCACCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGCATTCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCTATATACTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCGTCGCCTAAACGGCGATAGTCCCTCTAAGAAGCTAGCTGCGGAGGGATGGCTCCGCATAGCTAGTTAGCAGGCTGAGGTCTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCATGCACCACCACCCATAGAATCAAGAAAGAGCTCTCAGTCTGTCAATCCTTGCTATGTCTGGACCTGGTAAG criterion=sequence-density sequence-density=0.45 sequence-density-rank=1 fanout-score=3.93 fanout-score-rank=17 prefix-density=0.53 prefix-fanout=3.4 sequence=GAGTTCAGCAAGGTCGGCTTCGTCTTCCGCGAGCACAACAG criterion=fanout-score sequence-density=0.17 sequence-density-rank=24 fanout-score=123.45 fanout-score-rank=1 prefix-density=1.21 prefix-fanout=17.4 sequence=GCCGCCGCCACCCT SRR19784176 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 06 13:36:17 Started mapping on | Dec 06 13:36:18 Finished on | Dec 06 13:38:43 Mapping speed, Million of reads per hour | 1054.54 Number of input reads | 42474433 Average input read length | 151 UNIQUE READS: Uniquely mapped reads number | 31176718 Uniquely mapped reads % | 73.40% Average mapped length | 150.53 Number of splices: Total | 11406522 Number of splices: Annotated (sjdb) | 10920689 Number of splices: GT/AG | 11257289 Number of splices: GC/AG | 132846 Number of splices: AT/AC | 2716 Number of splices: Non-canonical | 13671 Mismatch rate per base, % | 0.37% Deletion rate per base | 0.01% Deletion average length | 1.82 Insertion rate per base | 0.00% Insertion average length | 1.85 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 6103324 % of reads mapped to multiple loci | 14.37% Number of reads mapped to too many loci | 1178973 % of reads mapped to too many loci | 2.78% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 3.16% % of reads unmapped: other | 6.30% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 5194393 5194393 5194393 N_multimapping 6103324 6103324 6103324 N_noFeature 886116 29888565 1704567 N_ambiguous 635194 4289 170894 UnstrandedReadsAssigned:29655408 PositiveStrandReadsAssigned:1283864 NegativeStrandReadsAssigned:29301257 Dataset is classified negative stranded MeadianReadLen=76 20thPercentileLength=75 echo kmer=71 SRR19784176 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: SRR19784176-trimmed-pair1.fastq SRR19784176-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 42,474,433 reads, 34,721,109 reads pseudoaligned [quant] estimated average fragment length: 160.873 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,187 rounds 52973 SRR19784176.ke.tsv 35125 SRR19784176.se.tsv 88098 total ==> SRR19784176.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 776.195 0 0 PNS24247 1044 884.127 26.802 1.15062 PNS24249 1928 1768.13 212.039 4.55181 PNS24246 1044 884.127 26.802 1.15062 PNS24248 1044 884.127 26.802 1.15062 PNS24244 1471 1311.13 20.5551 0.595054 PNS24243 293 138.206 0 0 KQK14069 1603 1443.13 1417.82 37.2904 KQK14071 474 314.967 325.055 39.1718 ==> SRR19784176.se.tsv <== BRADI_1g14170v3 2054 BRADI_1g53295v3 26 BRADI_1g59795v3 317 BRADI_1g07683v3 0 BRADI_1g00485v3 3 BRADI_1g20270v3 221 BRADI_1g74790v3 151 BRADI_1g09890v3 0 BRADI_1g77505v3 192 BRADI_1g48960v3 0 SRR19784176 completed mapping pipeline successfully