Starting /dee2/code/volunteer_pipeline.sh SRR11389841 current disk space = 1544429535232 free memory = 1600693144 SRR11389841 SRAfilesize 77ffc3520b64cee0c700e8ff1ca93ff5 SRR11389841.sra SRR11389841.sra file validated SRR11389841 is paired end SRR11389841 is conventional basespace SRR11389841 read1 length is 35-76 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR11389841_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 49 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 31.00125 32.0 32.0 32.0 32.0 32.0 2 30.972 32.0 32.0 32.0 32.0 32.0 3 31.2205 32.0 32.0 32.0 32.0 32.0 4 31.12575 32.0 32.0 32.0 32.0 32.0 5 31.126 32.0 32.0 32.0 32.0 32.0 6 34.1145 36.0 36.0 36.0 32.0 36.0 7 33.875 36.0 36.0 36.0 32.0 36.0 8 33.91175 36.0 36.0 36.0 32.0 36.0 9 34.228 36.0 36.0 36.0 32.0 36.0 10-11 33.825625 36.0 36.0 36.0 32.0 36.0 12-13 34.119625 36.0 36.0 36.0 32.0 36.0 14-15 34.0555 36.0 36.0 36.0 32.0 36.0 16-17 34.005375 36.0 36.0 36.0 32.0 36.0 18-19 34.015875 36.0 36.0 36.0 32.0 36.0 20-21 33.78475 36.0 36.0 36.0 32.0 36.0 22-23 33.738375000000005 36.0 36.0 36.0 32.0 36.0 24-25 33.769125 36.0 36.0 36.0 32.0 36.0 26-27 33.673874999999995 36.0 36.0 36.0 32.0 36.0 28-29 33.445375 36.0 36.0 36.0 24.0 36.0 30-31 33.36525 36.0 36.0 36.0 21.0 36.0 32-33 33.459374999999994 36.0 36.0 36.0 24.0 36.0 34-35 33.353375 36.0 36.0 36.0 24.0 36.0 36-37 33.29857464366091 36.0 36.0 36.0 21.0 36.0 38-39 33.31032758189547 36.0 36.0 36.0 21.0 36.0 40-41 33.205676419104776 36.0 36.0 36.0 17.5 36.0 42-43 33.08014503625907 36.0 36.0 36.0 14.0 36.0 44-45 32.7379939969985 36.0 36.0 36.0 14.0 36.0 46-47 33.04628217911808 36.0 36.0 36.0 17.5 36.0 48-49 32.80600750938673 36.0 36.0 36.0 14.0 36.0 50-51 32.6127188842367 36.0 34.0 36.0 14.0 36.0 52-53 32.647582292057194 36.0 34.0 36.0 14.0 36.0 54-55 32.36450770496141 36.0 32.0 36.0 14.0 36.0 56-57 32.18112308849335 36.0 32.0 36.0 14.0 36.0 58-59 32.03513517512045 36.0 32.0 36.0 14.0 36.0 60-61 31.981426463121366 36.0 32.0 36.0 14.0 36.0 62-63 31.99897848163507 36.0 32.0 36.0 14.0 36.0 64-65 32.02002587564385 36.0 32.0 36.0 14.0 36.0 66-67 31.85325236148299 36.0 32.0 36.0 14.0 36.0 68-69 31.777967626334565 36.0 32.0 36.0 14.0 36.0 70-71 31.899624487786706 36.0 32.0 36.0 14.0 36.0 72-73 31.670339687290813 36.0 32.0 36.0 14.0 36.0 74-75 31.584913826550203 36.0 32.0 36.0 14.0 36.0 76 30.103549213318697 36.0 27.0 36.0 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 0.0 19 0.0 20 2.0 21 4.0 22 2.0 23 11.0 24 30.0 25 33.0 26 70.0 27 100.0 28 143.0 29 201.0 30 272.0 31 306.0 32 474.0 33 543.0 34 899.0 35 909.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 34.808702175543885 9.577394348587147 16.704176044011003 38.90972743185797 2 23.78094523630908 15.003750937734434 28.857214303575894 32.358089522380595 3 24.60615153788447 16.954238559639908 25.28132033008252 33.158289572393095 4 28.707176794198553 24.48112028007002 19.80495123780945 27.00675168792198 5 27.60690172543136 28.08202050512628 23.10577644411103 21.205301325331334 6 21.780445111277817 33.23330832708177 25.78144536134033 19.204801200300075 7 18.02950737684421 25.581395348837212 35.90897724431108 20.4801200300075 8 20.68017004251063 25.406351587896975 29.83245811452863 24.081020255063766 9 19.70492623155789 21.680420105026258 34.808702175543885 23.80595148787197 10-11 24.056014003500874 29.132283070767688 24.131032758189548 22.680670167541887 12-13 22.893223305826456 25.468867216804203 26.319079769942487 25.318829707426854 14-15 22.58064516129032 25.681420355088775 26.76919229807452 24.968742185546386 16-17 23.018254563640912 26.219054763690924 25.481370342585645 25.28132033008252 18-19 22.680670167541887 25.568892223055762 26.881720430107524 24.868717179294826 20-21 23.705926481620406 25.618904726181547 25.968992248062015 24.706176544136035 22-23 23.53088272068017 26.59414853713428 25.10627656914228 24.76869217304326 24-25 22.868217054263564 25.36884221055264 25.881470367591895 25.881470367591895 26-27 23.43085771442861 26.294073518379594 25.23130782695674 25.04376094023506 28-29 23.330832708177045 25.568892223055762 26.069017254313575 25.03125781445361 30-31 23.305826456614152 25.506376594148538 26.04401100275069 25.143785946486624 32-33 22.58064516129032 26.206551637909474 25.893973493373345 25.318829707426854 34-35 23.718429607401852 25.943985996499126 24.781195298824706 25.55638909727432 36-37 22.88072018004501 26.356589147286826 25.731432858214554 25.03125781445361 38-39 23.13078269567392 25.393848462115532 26.294073518379594 25.18129532383096 40-41 23.15578894723681 25.30632658164541 25.468867216804203 26.069017254313575 42-43 22.843210802700675 24.918729682420604 27.24431107776944 24.99374843710928 44-45 22.36118059029515 25.63781890945473 26.300650325162582 25.700350175087543 46-47 24.377736085053158 24.92808005003127 25.01563477173233 25.67854909318324 48-49 21.6270337922403 26.25782227784731 26.057571964956196 26.057571964956196 50-51 22.899712032052086 25.704269437836487 25.91711531238262 25.47890321772881 52-53 23.9073262366938 25.097056981840954 25.572949279899817 25.42266750156543 54-55 23.09908555680822 25.090817988224977 26.092947513466115 25.71714894150069 56-57 22.92554524943595 25.119077463023316 26.936575582852846 25.018801704687892 58-59 23.108769288671436 25.918956216284027 25.806046920085308 25.166227574959226 60-61 23.34254143646409 25.376695128076342 26.092415871421398 25.18834756403817 62-63 23.755656108597282 24.421820010055303 25.94268476621418 25.879839115133237 64-65 23.67228794361943 24.36446010571357 26.894034734457588 25.069217216209417 66-67 23.358124290936594 24.593470313878736 25.42543804361528 26.622967351569393 68-69 23.608832807570977 25.160883280757098 25.488958990536275 25.741324921135643 70-71 24.02630247850278 24.75973697521497 25.442589782498736 25.77137076378351 72-73 24.73336719146775 24.822244794311835 25.63484002031488 24.809547993905536 74-75 23.595355665287602 22.75457093287068 26.651541438676098 26.99853196316562 76 26.527625320160997 0.0 36.077570435418956 37.39480424442005 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 43.0 1 28.5 2 8.5 3 3.0 4 3.0 5 2.5 6 1.5 7 1.0 8 1.0 9 1.5 10 2.0 11 1.0 12 0.0 13 0.0 14 1.0 15 1.5 16 1.5 17 1.5 18 5.0 19 11.0 20 12.5 21 13.5 22 13.0 23 9.5 24 5.5 25 2.5 26 4.5 27 11.5 28 16.0 29 17.5 30 21.0 31 29.5 32 45.0 33 56.0 34 50.5 35 63.0 36 88.5 37 100.0 38 132.0 39 159.5 40 164.0 41 172.5 42 195.0 43 221.5 44 225.5 45 201.0 46 188.0 47 187.5 48 176.5 49 169.5 50 171.0 51 169.5 52 148.5 53 132.5 54 130.5 55 128.0 56 122.5 57 131.0 58 142.5 59 136.0 60 118.5 61 100.0 62 94.5 63 87.0 64 76.0 65 71.0 66 61.0 67 54.5 68 60.0 69 52.0 70 40.5 71 40.5 72 33.0 73 33.0 74 30.5 75 19.5 76 19.0 77 17.0 78 9.0 79 5.0 80 8.0 81 9.5 82 6.0 83 3.0 84 2.5 85 2.0 86 2.5 87 3.0 88 1.5 89 0.5 90 1.0 91 0.5 92 0.0 93 0.5 94 0.5 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 0.025 7 0.025 8 0.025 9 0.025 10-11 0.025 12-13 0.025 14-15 0.025 16-17 0.025 18-19 0.025 20-21 0.025 22-23 0.025 24-25 0.025 26-27 0.025 28-29 0.025 30-31 0.025 32-33 0.025 34-35 0.025 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 1.0 36 0.0 37 0.0 38 0.0 39 0.0 40 0.0 41 0.0 42 0.0 43 1.0 44 0.0 45 0.0 46 1.0 47 2.0 48 0.0 49 1.0 50 1.0 51 0.0 52 1.0 53 0.0 54 1.0 55 2.0 56 0.0 57 3.0 58 1.0 59 2.0 60 2.0 61 2.0 62 2.0 63 3.0 64 2.0 65 5.0 66 1.0 67 2.0 68 3.0 69 5.0 70 4.0 71 5.0 72 18.0 73 60.0 74 245.0 75 891.0 76 2733.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 96.475 #Duplication Level Percentage of deduplicated Percentage of total 1 98.03057786991448 94.575 2 1.528893495724281 2.9499999999999997 3 0.233221041720653 0.675 4 0.07774034724021767 0.3 5 0.051826898160145116 0.25 6 0.025913449080072558 0.15 7 0.025913449080072558 0.17500000000000002 8 0.0 0.0 9 0.0 0.0 >10 0.025913449080072558 0.9249999999999999 >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 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 37 0.9249999999999999 No Hit GCGGCTAGTTCAGGACTCCATTTGCAAGCTGCTCGGATAATTTCATTACC 7 0.17500000000000002 No Hit GTCAATTAGAAGAATAAAGAAGAATTACTGCATTTCGTAACTTATTTTTT 6 0.15 No Hit GCTTATTACAAATTCACATCGAGCCATCCGGCATGCAGTACTGGAAAATA 5 0.125 No Hit AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 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 SRR11389841 read2 length is 35-76 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR11389841_2.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 50 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 30.42625 32.0 32.0 32.0 27.0 32.0 2 30.14675 32.0 32.0 32.0 21.0 32.0 3 30.08175 32.0 32.0 32.0 21.0 32.0 4 30.18925 32.0 32.0 32.0 21.0 32.0 5 30.2905 32.0 32.0 32.0 21.0 32.0 6 33.4445 36.0 36.0 36.0 21.0 36.0 7 33.28875 36.0 36.0 36.0 21.0 36.0 8 33.18025 36.0 36.0 36.0 21.0 36.0 9 32.95575 36.0 36.0 36.0 14.0 36.0 10-11 33.173249999999996 36.0 36.0 36.0 17.5 36.0 12-13 33.035125 36.0 36.0 36.0 21.0 36.0 14-15 33.08875 36.0 36.0 36.0 21.0 36.0 16-17 33.186625 36.0 36.0 36.0 21.0 36.0 18-19 33.08225 36.0 36.0 36.0 14.0 36.0 20-21 32.989999999999995 36.0 36.0 36.0 14.0 36.0 22-23 32.872 36.0 36.0 36.0 14.0 36.0 24-25 32.69125 36.0 36.0 36.0 14.0 36.0 26-27 32.70875 36.0 36.0 36.0 14.0 36.0 28-29 32.685 36.0 36.0 36.0 14.0 36.0 30-31 32.67825 36.0 36.0 36.0 14.0 36.0 32-33 32.6235 36.0 36.0 36.0 14.0 36.0 34-35 32.472625 36.0 36.0 36.0 14.0 36.0 36-37 32.38034508627157 36.0 36.0 36.0 14.0 36.0 38-39 32.42123030757689 36.0 36.0 36.0 14.0 36.0 40-41 32.229432358089525 36.0 34.0 36.0 14.0 36.0 42-43 32.266441610402595 36.0 34.0 36.0 14.0 36.0 44-45 32.232991495747875 36.0 34.0 36.0 14.0 36.0 46-47 32.07890460116223 36.0 34.0 36.0 14.0 36.0 48-49 32.033917396745935 36.0 32.0 36.0 14.0 36.0 50-51 32.01226344901775 36.0 32.0 36.0 14.0 36.0 52-53 31.908094613971244 36.0 32.0 36.0 14.0 36.0 54-55 31.79417137331541 36.0 32.0 36.0 14.0 36.0 56-57 31.57476779800419 36.0 32.0 36.0 14.0 36.0 58-59 31.52477850645389 36.0 32.0 36.0 14.0 36.0 60-61 31.606587006331797 36.0 32.0 36.0 14.0 36.0 62-63 31.61266589848276 36.0 32.0 36.0 14.0 36.0 64-65 31.46178192575934 36.0 32.0 36.0 14.0 36.0 66-67 31.352249565127764 36.0 32.0 36.0 14.0 36.0 68-69 31.30537542878615 36.0 32.0 36.0 14.0 36.0 70-71 31.379699293590477 36.0 32.0 36.0 14.0 36.0 72-73 31.19864252622181 36.0 32.0 36.0 14.0 36.0 74-75 30.989860811187732 36.0 32.0 36.0 14.0 36.0 76 29.227756653992394 32.0 27.0 36.0 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 14.0 15 20.0 16 25.0 17 30.0 18 15.0 19 13.0 20 15.0 21 18.0 22 21.0 23 19.0 24 30.0 25 59.0 26 68.0 27 102.0 28 160.0 29 201.0 30 249.0 31 300.0 32 389.0 33 598.0 34 862.0 35 791.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 35.00875218804701 15.853963490872719 14.753688422105526 34.38359589897475 2 30.882720680170046 24.431107776944234 23.78094523630908 20.905226306576644 3 28.457114278569644 28.582145536384097 19.579894973743436 23.380845211302827 4 30.957739434858716 30.75768942235559 17.75443860965241 20.530132533133283 5 29.15728932233058 33.9584896224056 19.554888722180543 17.329332333083272 6 23.58089522380595 34.55863965991498 22.330582645661416 19.529882470617654 7 23.53088272068017 18.27956989247312 32.70817704426106 25.481370342585645 8 26.456614153538382 22.80570142535634 25.156289072268066 25.581395348837212 9 24.956239059764943 23.1807951987997 27.38184546136534 24.48112028007002 10-11 28.582145536384097 26.819204801200303 20.80520130032508 23.793448362090523 12-13 26.79419854963741 23.58089522380595 23.918479619904975 25.70642660665166 14-15 25.968992248062015 25.406351587896975 25.056264066016503 23.568392098024507 16-17 27.84446111527882 24.706176544136035 23.718429607401852 23.730932733183295 18-19 26.356589147286826 25.10627656914228 24.543635908977244 23.99349837459365 20-21 26.944236059014752 25.168792198049513 24.468617154288573 23.418354588647162 22-23 26.60665166291573 25.63140785196299 24.50612653163291 23.25581395348837 24-25 26.79419854963741 24.81870467616904 23.88097024256064 24.50612653163291 26-27 27.00675168792198 26.60665166291573 23.25581395348837 23.13078269567392 28-29 27.04426106526632 25.93148287071768 22.74318579644911 24.281070267566893 30-31 26.78169542385596 25.481370342585645 24.218554638659665 23.518379594898725 32-33 25.806451612903224 26.081520380095025 24.318579644911228 23.793448362090523 34-35 27.619404851212803 24.81870467616904 23.680920230057513 23.88097024256064 36-37 26.51912978244561 25.03125781445361 24.006001500375092 24.44361090272568 38-39 26.30657664416104 25.10627656914228 24.543635908977244 24.043510877719427 40-41 26.069017254313575 25.70642660665166 23.843460865216304 24.381095273818453 42-43 26.294073518379594 26.006501625406354 24.056014003500874 23.643410852713178 44-45 26.20060030015007 25.850425212606304 24.137068534267133 23.81190595297649 46-47 26.40400250156348 24.652908067542214 24.577861163227016 24.36522826766729 48-49 26.33291614518148 26.0450563204005 24.25531914893617 23.366708385481854 50-51 25.441342181044195 25.779391511205706 24.22686866157506 24.552397646175034 52-53 26.261740763932373 25.898559799624294 23.443957420162807 24.395742016280526 54-55 26.205687085055747 26.14305398972817 23.85068270073907 23.800576224477012 56-57 25.824244703522623 26.288078224896577 23.968910618026825 23.918766453553967 58-59 26.659139380253414 25.730774055952825 23.648224814954208 23.961861748839546 60-61 26.481667503766953 26.04218985434455 23.643897538925163 23.832245102963334 62-63 25.911491073673627 27.04299723409605 24.013075182298216 23.03243650993211 64-65 27.218934911242602 25.330479667631877 23.668639053254438 23.781946367871083 66-67 26.106696935300793 25.841846386681798 24.65632488333964 23.395131794677766 68-69 25.325085216513067 25.703825274586546 24.769599798005302 24.20148971089509 70-71 26.068808499873512 25.689349860865168 23.88059701492537 24.36124462433595 72-73 24.87928843710292 25.362134688691235 25.044472681067344 24.7141041931385 74-75 26.182112942447986 23.318022156174006 25.965955147257496 24.533909754120508 76 28.44106463878327 0.0 34.752851711026615 36.80608365019011 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 40.0 1 22.5 2 2.5 3 0.5 4 1.0 5 0.5 6 0.0 7 1.0 8 2.0 9 1.0 10 1.0 11 2.0 12 2.5 13 1.5 14 3.0 15 4.0 16 2.0 17 3.5 18 4.5 19 4.5 20 5.0 21 4.5 22 5.0 23 11.0 24 14.0 25 9.5 26 9.0 27 13.5 28 16.5 29 14.0 30 18.5 31 34.5 32 41.5 33 40.5 34 46.5 35 60.0 36 78.5 37 98.0 38 120.5 39 137.5 40 149.0 41 168.5 42 183.5 43 187.5 44 185.5 45 186.5 46 190.5 47 186.5 48 168.5 49 157.5 50 158.0 51 146.0 52 134.0 53 133.5 54 127.5 55 125.5 56 132.5 57 124.5 58 122.0 59 133.5 60 134.5 61 120.5 62 108.5 63 100.0 64 85.0 65 75.5 66 77.0 67 77.0 68 73.0 69 68.5 70 55.0 71 46.0 72 47.5 73 41.0 74 37.0 75 38.5 76 31.0 77 24.0 78 16.0 79 8.0 80 9.5 81 9.0 82 5.0 83 3.5 84 3.0 85 3.0 86 3.5 87 4.0 88 2.5 89 1.0 90 2.5 91 2.5 92 1.0 93 0.5 94 2.0 95 2.0 96 0.0 97 1.0 98 3.0 99 6.0 100 8.0 >>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 0.025 7 0.025 8 0.025 9 0.025 10-11 0.025 12-13 0.025 14-15 0.025 16-17 0.025 18-19 0.025 20-21 0.025 22-23 0.025 24-25 0.025 26-27 0.025 28-29 0.025 30-31 0.025 32-33 0.025 34-35 0.025 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 1.0 36 0.0 37 0.0 38 0.0 39 0.0 40 0.0 41 0.0 42 0.0 43 1.0 44 0.0 45 0.0 46 1.0 47 2.0 48 0.0 49 1.0 50 1.0 51 0.0 52 1.0 53 0.0 54 1.0 55 2.0 56 1.0 57 2.0 58 1.0 59 2.0 60 2.0 61 2.0 62 4.0 63 3.0 64 1.0 65 6.0 66 1.0 67 2.0 68 3.0 69 4.0 70 4.0 71 3.0 72 26.0 73 94.0 74 254.0 75 944.0 76 2630.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 96.975 #Duplication Level Percentage of deduplicated Percentage of total 1 98.04073214746069 95.075 2 1.5725702500644496 3.05 3 0.23201856148491878 0.675 4 0.051559680329981955 0.2 5 0.025779840164990978 0.125 6 0.0 0.0 7 0.0 0.0 8 0.0 0.0 9 0.025779840164990978 0.22499999999999998 >10 0.051559680329981955 0.65 >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 16 0.4 No Hit TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 10 0.25 No Hit GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 9 0.22499999999999998 No Hit CTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTG 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 668707 spots for SRR11389841.sra Written 668707 spots for SRR11389841.sra Read 668707 spots for SRR11389841.sra Written 668707 spots for SRR11389841.sra Read 668707 spots for SRR11389841.sra Written 668707 spots for SRR11389841.sra Read 668707 spots for SRR11389841.sra Written 668707 spots for SRR11389841.sra Read 668707 spots for SRR11389841.sra Written 668707 spots for SRR11389841.sra Read 668716 spots for SRR11389841.sra Written 668716 spots for SRR11389841.sra Read 668707 spots for SRR11389841.sra Written 668707 spots for SRR11389841.sra Read 668707 spots for SRR11389841.sra Written 668707 spots for SRR11389841.sra Read 668707 spots for SRR11389841.sra Written 668707 spots for SRR11389841.sra Read 668707 spots for SRR11389841.sra Written 668707 spots for SRR11389841.sra Read 668707 spots for SRR11389841.sra Written 668707 spots for SRR11389841.sra Read 668707 spots for SRR11389841.sra Written 668707 spots for SRR11389841.sra Read 668707 spots for SRR11389841.sra Written 668707 spots for SRR11389841.sra Read 668707 spots for SRR11389841.sra Written 668707 spots for SRR11389841.sra Read 668707 spots for SRR11389841.sra Written 668707 spots for SRR11389841.sra Read 668707 spots for SRR11389841.sra Written 668707 spots for SRR11389841.sra Read 668707 spots for SRR11389841.sra Written 668707 spots for SRR11389841.sra Read 668707 spots for SRR11389841.sra Written 668707 spots for SRR11389841.sra Read 668707 spots for SRR11389841.sra Written 668707 spots for SRR11389841.sra Read 668707 spots for SRR11389841.sra Written 668707 spots for SRR11389841.sra SRR ids: ['SRR11389841.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_v_vmklc0 SRR11389841.sra spots: 13374149 blocks: [[1, 668707], [668708, 1337414], [1337415, 2006121], [2006122, 2674828], [2674829, 3343535], [3343536, 4012242], [4012243, 4680949], [4680950, 5349656], [5349657, 6018363], [6018364, 6687070], [6687071, 7355777], [7355778, 8024484], [8024485, 8693191], [8693192, 9361898], [9361899, 10030605], [10030606, 10699312], [10699313, 11368019], [11368020, 12036726], [12036727, 12705433], [12705434, 13374149]] SRR11389841 file size 2534521 SRR11389841 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 SRR11389841 SRR11389841_1.fastq SRR11389841_2.fastq Input file: SRR11389841_1.fastq Paired file: SRR11389841_2.fastq trimmed: SRR11389841-trimmed-pair1.fastq, SRR11389841-trimmed-pair2.fastq Parameters used: -- 3' end adapter sequence (-x): AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -- paired 3' end adapter sequence (-y): AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA -- maximum error ratio allowed (-r): 0.100 -- maximum indel error ratio allowed (-d): 0.030 -- end quality threshold (-q): 10 -- minimum read length allowed after trimming (-l): 18 -- file format (-f): Sanger/Illumina 1.8+ FASTQ -- number of concurrent threads (-t): 20 Sat Dec 7 07:57:25 2024 >> started Sat Dec 7 07:57:36 2024 >> done (10.802s) 13374149 read pairs processed; of these: 1 ( 0.00%) short read pairs filtered out after trimming by size control 101641 ( 0.76%) empty read pairs filtered out after trimming by size control 13272507 (99.24%) read pairs available; of these: 138943 ( 1.05%) trimmed read pairs available after processing 13133564 (98.95%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 22 1 0.00% 23 1 0.00% 24 0 0.00% 25 0 0.00% 26 1 0.00% 27 4 0.00% 28 2 0.00% 29 5 0.00% 30 3 0.00% 31 2 0.00% 32 6 0.00% 33 9 0.00% 34 6 0.00% 35 347 0.00% 36 366 0.00% 37 444 0.00% 38 555 0.00% 39 688 0.01% 40 858 0.01% 41 972 0.01% 42 1088 0.01% 43 1279 0.01% 44 1430 0.01% 45 1553 0.01% 46 1679 0.01% 47 1870 0.01% 48 2087 0.02% 49 2297 0.02% 50 2565 0.02% 51 2849 0.02% 52 3303 0.02% 53 3748 0.03% 54 3948 0.03% 55 4430 0.03% 56 4983 0.04% 57 5375 0.04% 58 5918 0.04% 59 6615 0.05% 60 7078 0.05% 61 7466 0.06% 62 8482 0.06% 63 9046 0.07% 64 10086 0.08% 65 11089 0.08% 66 11922 0.09% 67 13141 0.10% 68 13590 0.10% 69 14712 0.11% 70 15867 0.12% 71 19272 0.15% 72 29314 0.22% 73 124414 0.94% 74 1037962 7.82% 75 5864127 44.18% 76 6013652 45.31% 13272507 reads passed initial QC criterion=sequence-density sequence-density=0.79 sequence-density-rank=1 fanout-score=2.01 fanout-score-rank=21 prefix-density=0.77 prefix-fanout=2.0 sequence=TTCAAATGTACA criterion=fanout-score sequence-density=0.01 sequence-density-rank=26 fanout-score=36.49 fanout-score-rank=1 prefix-density=0.04 prefix-fanout=8.0 sequence=AAAAAAAAAAGTATGTTTGCATCAATGATAATCCCAAAGTAGGAAGTGTGTACGTAGTAGCAAGTGTTATACATACATAAAATTAAGCGATGCGTTTCGATCAAGTACTTGGCATCATCGATCACATACGTACATTTCACAGCAGGTAGCTACGTACATTACAGGCATACGTACATGCAGAGAGATACCCGGCCCTGTGTTGTGTTTGCAATTGCATAGATGAGAATGAGATGACTTGATTCTTAATTAGCCGGCGAGAGCGCTGGTGTTGTAGACGAGGAGGGCGCCGCCGCCGAGGAGGCCGGCCAGGGTGACGGCCCAGATCAGGAGCCCCGTCGTCCCACCGGCGTAGCGGTCGCCAGATTCGGACCATACCTCCGGCGTGTAGATCGGGCTGTAGCCGTCGACGTTGGCGCCGTACTTGTCAACAAACTGGTACACACCCTTTCCCGTGCCCTTCCTGCCGTTGGCGTCGATGTCCACCGTCAAGCCACCTCCGATCCCGAGGGGC criterion=sequence-density sequence-density=0.70 sequence-density-rank=1 fanout-score=2.84 fanout-score-rank=11 prefix-density=0.79 prefix-fanout=2.5 sequence=AAGAAGGAGTACCC criterion=fanout-score sequence-density=0.02 sequence-density-rank=32 fanout-score=7.73 fanout-score-rank=1 prefix-density=0.05 prefix-fanout=2.3 sequence=CCTCAAGCCAAAGCCTCTTGCTAAGCGTACCACACTATACAGACGTGCGCGCGCAGCCATGGCACCCACCGTGATGGCTTCCTCCGCCACCTCCGTGGCTCCTTTCCA SRR11389841 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 07 07:58:07 Started mapping on | Dec 07 07:58:07 Finished on | Dec 07 07:59:09 Mapping speed, Million of reads per hour | 770.66 Number of input reads | 13272507 Average input read length | 150 UNIQUE READS: Uniquely mapped reads number | 10901892 Uniquely mapped reads % | 82.14% Average mapped length | 149.81 Number of splices: Total | 4775733 Number of splices: Annotated (sjdb) | 4549838 Number of splices: GT/AG | 4708562 Number of splices: GC/AG | 59464 Number of splices: AT/AC | 1557 Number of splices: Non-canonical | 6150 Mismatch rate per base, % | 0.74% Deletion rate per base | 0.01% Deletion average length | 1.68 Insertion rate per base | 0.01% Insertion average length | 1.68 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 1285677 % of reads mapped to multiple loci | 9.69% Number of reads mapped to too many loci | 37191 % of reads mapped to too many loci | 0.28% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 6.30% % of reads unmapped: other | 1.59% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 1084938 1084938 1084938 N_multimapping 1285677 1285677 1285677 N_noFeature 402156 10549056 549592 N_ambiguous 271595 1661 71306 UnstrandedReadsAssigned:10228141 PositiveStrandReadsAssigned:351175 NegativeStrandReadsAssigned:10280994 Dataset is classified negative stranded MeadianReadLen=76 20thPercentileLength=75 echo kmer=71 SRR11389841 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: SRR11389841-trimmed-pair1.fastq SRR11389841-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 13,272,507 reads, 11,686,986 reads pseudoaligned [quant] estimated average fragment length: 196.849 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,083 rounds 52973 SRR11389841.ke.tsv 35125 SRR11389841.se.tsv 88098 total ==> SRR11389841.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 740.241 0 0 PNS24247 1044 848.151 18.0769 2.48489 PNS24249 1928 1732.15 40.5978 2.73258 PNS24246 1044 848.151 18.0769 2.48489 PNS24248 1044 848.151 18.0769 2.48489 PNS24244 1471 1275.15 39.1714 3.58148 PNS24243 293 124.889 0 0 KQK14069 1603 1407.15 208.168 17.2476 KQK14071 474 281.954 8.83855 3.65475 ==> SRR11389841.se.tsv <== BRADI_1g14170v3 219 BRADI_1g53295v3 17 BRADI_1g59795v3 156 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 65 BRADI_1g74790v3 157 BRADI_1g09890v3 0 BRADI_1g77505v3 147 BRADI_1g48960v3 0 SRR11389841 completed mapping pipeline successfully