Starting /dee2/code/volunteer_pipeline.sh SRR11389788 current disk space = 1545396772864 free memory = 1603716432 SRR11389788 SRAfilesize 292bbea693fe938e4382fda7317d0f40 SRR11389788.sra SRR11389788.sra file validated SRR11389788 is paired end SRR11389788 is conventional basespace SRR11389788 read1 length is 35-76 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR11389788_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 30.31425 32.0 32.0 32.0 32.0 32.0 2 30.27475 32.0 32.0 32.0 32.0 32.0 3 30.33325 32.0 32.0 32.0 32.0 32.0 4 30.37825 32.0 32.0 32.0 32.0 32.0 5 30.28975 32.0 32.0 32.0 32.0 32.0 6 33.081 36.0 36.0 36.0 21.0 36.0 7 33.25325 36.0 36.0 36.0 32.0 36.0 8 33.219 36.0 36.0 36.0 32.0 36.0 9 33.146 36.0 36.0 36.0 21.0 36.0 10-11 33.265875 36.0 36.0 36.0 26.5 36.0 12-13 33.45125 36.0 36.0 36.0 32.0 36.0 14-15 33.285250000000005 36.0 36.0 36.0 26.5 36.0 16-17 33.372375000000005 36.0 36.0 36.0 32.0 36.0 18-19 33.20125 36.0 36.0 36.0 21.0 36.0 20-21 33.18825 36.0 36.0 36.0 21.0 36.0 22-23 33.116375 36.0 36.0 36.0 21.0 36.0 24-25 33.058499999999995 36.0 36.0 36.0 24.0 36.0 26-27 32.89975 36.0 36.0 36.0 21.0 36.0 28-29 32.857875 36.0 36.0 36.0 17.5 36.0 30-31 32.84725 36.0 36.0 36.0 17.5 36.0 32-33 32.649625 36.0 36.0 36.0 14.0 36.0 34-35 32.629875 36.0 36.0 36.0 14.0 36.0 36-37 33.62561321972631 36.0 36.0 36.0 27.0 36.0 38-39 33.50942421895172 36.0 36.0 36.0 27.0 36.0 40-41 33.381358120320165 36.0 36.0 36.0 24.0 36.0 42-43 33.465272398657376 36.0 36.0 36.0 24.0 36.0 44-45 33.31345210431191 36.0 36.0 36.0 21.0 36.0 46-47 33.24903175832688 36.0 36.0 36.0 21.0 36.0 48-49 33.045959204750844 36.0 36.0 36.0 17.5 36.0 50-51 32.87567776917118 36.0 36.0 36.0 14.0 36.0 52-53 32.90562871159308 36.0 36.0 36.0 14.0 36.0 54-55 32.74554608830364 36.0 36.0 36.0 14.0 36.0 56-57 32.66782855667441 36.0 36.0 36.0 14.0 36.0 58-59 32.438483778884546 36.0 32.0 36.0 14.0 36.0 60-61 32.37487086776859 36.0 32.0 36.0 14.0 36.0 62-63 32.1823347107438 36.0 32.0 36.0 14.0 36.0 64-65 32.24253978647113 36.0 32.0 36.0 14.0 36.0 66-67 31.99715835701369 36.0 32.0 36.0 14.0 36.0 68-69 31.78119349005425 36.0 32.0 36.0 14.0 36.0 70-71 31.64952083107533 36.0 32.0 36.0 14.0 36.0 72-73 31.548224798224798 36.0 32.0 36.0 14.0 36.0 74-75 31.442399251968126 36.0 32.0 36.0 14.0 36.0 76 30.709495101733232 36.0 32.0 36.0 14.0 36.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 127.0 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 0.0 21 1.0 22 3.0 23 6.0 24 9.0 25 24.0 26 29.0 27 60.0 28 114.0 29 164.0 30 189.0 31 343.0 32 490.0 33 690.0 34 1080.0 35 671.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 39.96901626646011 12.419313193906532 11.438161631809967 36.17350890782339 2 25.79395817195972 13.503743867802736 34.88252001032791 25.81977794990963 3 23.599277046217402 19.44229279628195 23.28943971081849 33.66899044668216 4 29.150529305447975 25.89723728375936 19.158275238832946 25.79395817195972 5 26.207074619158277 29.4861864187968 22.5148463723212 21.791892589723727 6 22.919896640826874 30.775193798449614 25.1937984496124 21.11111111111111 7 17.60908856183837 25.432481280660983 37.2579395817196 19.70049057578105 8 18.95171701523367 24.141492383165506 31.50012909888975 25.406661502711074 9 20.604182804027886 21.998450813323007 32.40382132713659 24.993545055512524 10-11 22.643945262070748 31.52594887683966 22.97960237541957 22.850503485670025 12-13 23.018332042344436 24.761167053963337 25.884327394784407 26.336173508907823 14-15 23.534727601342627 25.613219726310355 26.516911954557195 24.335140717789827 16-17 22.83759359669507 25.76813839400981 25.316292279886394 26.077975729408724 18-19 23.173250710043895 25.406661502711074 26.052155951458815 25.367931835786212 20-21 22.476116705396336 26.930028401755745 25.54867028143558 25.045184611412342 22-23 23.521817712367675 26.69765040020656 25.781048282984763 23.999483604441004 24-25 23.121611154144077 25.2001032791118 26.000516395558996 25.677769171185126 26-27 22.992512264394527 25.083914278337204 26.478182287632322 25.44539116963594 28-29 23.883294603666407 27.252775626129615 24.115672605215597 24.74825716498838 30-31 23.018332042344436 25.755228505034854 25.39375161373612 25.83268783888459 32-33 22.38574748257165 26.568551510457013 25.781048282984763 25.264652723986575 34-35 23.767105602891817 25.54867028143558 25.535760392460627 25.14846372321198 36-37 23.599277046217402 26.361993286857732 24.438419829589467 25.6003098373354 38-39 23.857474825716498 25.058094500387295 25.71649883810999 25.367931835786212 40-41 23.044151820294346 25.49703072553576 26.491092176607285 24.967725277562614 42-43 23.366899044668216 25.613219726310355 25.316292279886394 25.703588949135035 44-45 22.68267492899561 25.09682416731216 25.7423186160599 26.478182287632322 46-47 23.870384714691454 24.7998967208882 25.303382390911437 26.026336173508906 48-49 22.721404595920475 26.026336173508906 25.651949393235217 25.6003098373354 50-51 24.051123160340822 25.213013168086757 25.87141750580945 24.864446165762974 52-53 23.61218693519236 25.303382390911437 24.464239607539376 26.62019106635683 54-55 23.250710043893623 25.703588949135035 25.07100438936225 25.974696617609087 56-57 23.599277046217402 25.84559772785954 24.45132971856442 26.103795507358633 58-59 22.724338282763075 25.810200129115557 24.958037443511945 26.507424144609427 60-61 23.424586776859506 25.400309917355372 25.09039256198347 26.084710743801654 62-63 23.256714876033058 25.3099173553719 25.74896694214876 25.68440082644628 64-65 23.66008007232339 24.292909724912825 26.37220715484954 25.674803047914246 66-67 23.32730560578662 24.77396021699819 25.200206664944456 26.69852751227073 68-69 23.430638078016017 23.92146732110566 25.949367088607595 26.69852751227073 70-71 23.9886260824609 24.660721209771232 24.81582008530438 26.53483262246349 72-73 23.375275651835516 24.23141782332339 25.39888442080685 26.994422104034243 74-75 23.98412915583527 22.602271172527022 26.036393487481185 27.37720618415652 76 27.24189902034665 0.0 35.19216277317257 37.56593820648078 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 128.0 1 64.0 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10 0.0 11 0.0 12 0.0 13 0.0 14 0.0 15 0.5 16 2.0 17 2.0 18 5.5 19 13.0 20 16.5 21 19.0 22 22.0 23 16.0 24 10.0 25 11.0 26 13.5 27 31.0 28 36.0 29 20.5 30 27.5 31 43.0 32 50.0 33 57.5 34 67.5 35 87.0 36 100.0 37 100.5 38 122.5 39 153.5 40 154.0 41 151.5 42 167.5 43 176.5 44 191.5 45 195.5 46 187.5 47 188.5 48 172.5 49 157.5 50 151.0 51 142.5 52 132.0 53 123.5 54 116.0 55 112.0 56 104.5 57 104.0 58 111.5 59 106.5 60 104.0 61 98.0 62 90.0 63 86.0 64 83.5 65 79.5 66 65.0 67 57.0 68 57.5 69 58.0 70 49.0 71 39.5 72 40.0 73 37.5 74 32.0 75 28.0 76 23.5 77 16.0 78 11.5 79 10.5 80 10.0 81 8.0 82 5.5 83 3.5 84 2.5 85 1.0 86 0.0 87 0.0 88 0.0 89 0.5 90 0.5 91 0.0 92 0.0 93 0.0 94 0.0 95 0.0 96 0.0 97 0.5 98 0.5 99 0.0 100 0.0 >>END_MODULE >>Per base N content pass #Base N-Count 1 3.175 2 3.175 3 3.175 4 3.175 5 3.175 6 3.25 7 3.175 8 3.175 9 3.175 10-11 3.175 12-13 3.175 14-15 3.175 16-17 3.175 18-19 3.175 20-21 3.175 22-23 3.175 24-25 3.175 26-27 3.175 28-29 3.175 30-31 3.175 32-33 3.175 34-35 3.175 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 35 127.0 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 0.0 51 0.0 52 0.0 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 0.0 62 0.0 63 0.0 64 1.0 65 0.0 66 0.0 67 0.0 68 0.0 69 0.0 70 5.0 71 5.0 72 13.0 73 72.0 74 243.0 75 879.0 76 2654.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 93.125 #Duplication Level Percentage of deduplicated Percentage of total 1 97.66442953020135 90.95 2 1.6107382550335572 3.0 3 0.37583892617449666 1.05 4 0.1342281879194631 0.5 5 0.1342281879194631 0.625 6 0.0 0.0 7 0.0 0.0 8 0.0 0.0 9 0.026845637583892613 0.22499999999999998 >10 0.026845637583892613 0.475 >50 0.0 0.0 >100 0.026845637583892613 3.175 >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 NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN 127 3.175 No Hit GCCGAGTTTAATTGCAGTCAATTAGAAGAATAAAGAAGAATTACTGCATT 19 0.475 No Hit GTCAATTAGAAGAATAAAGAAGAATTACTGCATTTCGTAACTTATTTTTT 9 0.22499999999999998 No Hit GCTAGTTCAGGACTCCATTTGCAAGCTGCTCGGATAATTTCATTACCTTC 5 0.125 No Hit TATTAATCGATAGTATCTACCGGCGCGAACTCGAATTTGATCGCCTTCCATACTTCACAAGCTGCGGCTAGTTC 5 0.125 No Hit GCGGCTAGTTCAGGACTCCATTTGCAAGCTGCTCGGATAATTTCATTACC 5 0.125 No Hit GATCGGAAGAGCACACGTCTGAACTCCAGTCACTCCGCGAAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAA 5 0.125 TruSeq Adapter, Index 6 (97% over 36bp) GTCAGGGTTCAAATGTACATATGCTCCTCGAGCCCATGTCGGTACATTCA 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 0.025 0.0 0.0 0.0 0.0 12 0.025 0.0 0.0 0.0 0.0 13 0.025 0.0 0.0 0.0 0.0 14 0.025 0.0 0.0 0.0 0.0 15 0.025 0.0 0.0 0.0 0.0 16 0.025 0.0 0.0 0.0 0.0 17 0.025 0.0 0.0 0.0 0.0 18 0.025 0.0 0.0 0.0 0.0 19 0.025 0.0 0.0 0.0 0.0 20 0.025 0.0 0.0 0.0 0.0 21 0.025 0.0 0.0 0.0 0.0 22 0.025 0.0 0.0 0.0 0.0 23 0.025 0.0 0.0 0.0 0.0 24 0.025 0.0 0.0 0.0 0.0 25 0.025 0.0 0.0 0.0 0.0 26 0.025 0.0 0.0 0.0 0.0 27 0.025 0.0 0.0 0.0 0.0 28 0.025 0.0 0.0 0.0 0.0 29 0.025 0.0 0.0 0.0 0.0 30 0.025 0.0 0.0 0.0 0.0 31 0.025 0.0 0.0 0.0 0.0 32 0.025 0.0 0.0 0.0 0.0 33 0.025 0.0 0.0 0.0 0.0 34 0.025 0.0 0.0 0.0 0.0 35 0.025 0.0 0.0 0.0 0.0 36 0.025 0.0 0.0 0.0 0.0 37 0.025 0.0 0.0 0.0 0.0 38 0.025 0.0 0.0 0.0 0.0 39 0.025 0.0 0.0 0.0 0.0 40 0.025 0.0 0.0 0.0 0.0 41 0.05 0.0 0.0 0.0 0.0 42 0.05 0.0 0.0 0.0 0.0 43 0.05 0.0 0.0 0.0 0.0 44 0.05 0.0 0.0 0.0 0.0 45 0.05 0.0 0.0 0.0 0.0 46 0.05 0.0 0.0 0.0 0.0 47 0.05 0.0 0.0 0.0 0.0 48 0.05 0.0 0.0 0.0 0.0 49 0.05 0.0 0.0 0.0 0.0 50 0.05 0.0 0.0 0.0 0.0 51 0.05 0.0 0.0 0.0 0.0 52 0.05 0.0 0.0 0.0 0.0 53 0.05 0.0 0.0 0.0 0.0 54 0.05 0.0 0.0 0.0 0.0 55 0.05 0.0 0.0 0.0 0.0 56 0.05 0.0 0.0 0.0 0.0 57 0.05 0.0 0.0 0.0 0.0 58 0.05 0.0 0.0 0.0 0.0 59 0.05 0.0 0.0 0.0 0.0 60 0.05 0.0 0.0 0.0 0.0 61 0.05 0.0 0.0 0.0 0.0 62 0.05 0.0 0.0 0.0 0.0 63 0.05 0.0 0.0 0.0 0.0 64 0.05 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE SRR11389788 read2 length is 35-76 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR11389788_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 51 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 29.958 32.0 32.0 32.0 21.0 32.0 2 29.622 32.0 32.0 32.0 14.0 32.0 3 29.48825 32.0 32.0 32.0 14.0 32.0 4 29.33275 32.0 32.0 32.0 14.0 32.0 5 29.56875 32.0 32.0 32.0 21.0 32.0 6 32.5515 36.0 36.0 36.0 14.0 36.0 7 32.6455 36.0 36.0 36.0 21.0 36.0 8 32.567 36.0 36.0 36.0 14.0 36.0 9 32.57875 36.0 36.0 36.0 14.0 36.0 10-11 32.507375 36.0 36.0 36.0 14.0 36.0 12-13 32.6555 36.0 36.0 36.0 17.5 36.0 14-15 32.41075 36.0 36.0 36.0 14.0 36.0 16-17 32.446625 36.0 36.0 36.0 14.0 36.0 18-19 32.39375 36.0 36.0 36.0 14.0 36.0 20-21 32.25075 36.0 36.0 36.0 14.0 36.0 22-23 32.304375 36.0 36.0 36.0 14.0 36.0 24-25 32.179 36.0 36.0 36.0 14.0 36.0 26-27 32.014125 36.0 36.0 36.0 14.0 36.0 28-29 32.099374999999995 36.0 36.0 36.0 14.0 36.0 30-31 32.023125 36.0 36.0 36.0 14.0 36.0 32-33 31.8845 36.0 36.0 36.0 14.0 36.0 34-35 32.007625000000004 36.0 36.0 36.0 14.0 36.0 36-37 32.74367905056759 36.0 36.0 36.0 14.0 36.0 38-39 32.80711158826858 36.0 36.0 36.0 14.0 36.0 40-41 32.75209565840092 36.0 36.0 36.0 14.0 36.0 42-43 32.55562725864739 36.0 36.0 36.0 14.0 36.0 44-45 32.391972121837895 36.0 36.0 36.0 14.0 36.0 46-47 32.238642230252964 36.0 34.0 36.0 14.0 36.0 48-49 32.32679401135777 36.0 34.0 36.0 14.0 36.0 50-51 32.117320598864225 36.0 32.0 36.0 14.0 36.0 52-53 32.092152813629326 36.0 34.0 36.0 14.0 36.0 54-55 31.745740836344865 36.0 32.0 36.0 14.0 36.0 56-57 31.597702632937533 36.0 32.0 36.0 14.0 36.0 58-59 31.48883441231213 36.0 32.0 36.0 14.0 36.0 60-61 31.392847921507876 36.0 32.0 36.0 14.0 36.0 62-63 31.30893364317067 36.0 32.0 36.0 14.0 36.0 64-65 31.10228773101766 36.0 32.0 36.0 14.0 36.0 66-67 30.985408057851238 36.0 32.0 36.0 14.0 36.0 68-69 30.896952479338843 36.0 32.0 36.0 14.0 36.0 70-71 30.664115512003455 36.0 29.5 36.0 14.0 36.0 72-73 30.739704497930244 36.0 29.5 36.0 14.0 36.0 74-75 30.544159304952576 36.0 27.0 36.0 14.0 36.0 76 29.420852359208524 32.0 27.0 36.0 14.0 36.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 124.0 3 0.0 4 2.0 5 1.0 6 1.0 7 1.0 8 0.0 9 1.0 10 0.0 11 0.0 12 0.0 13 3.0 14 3.0 15 5.0 16 4.0 17 6.0 18 8.0 19 8.0 20 11.0 21 17.0 22 16.0 23 25.0 24 42.0 25 67.0 26 71.0 27 106.0 28 123.0 29 203.0 30 231.0 31 356.0 32 482.0 33 645.0 34 874.0 35 564.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 38.080495356037154 20.20123839009288 10.113519091847266 31.604747162022704 2 30.779153766769866 23.03921568627451 27.24458204334365 18.937048503611972 3 25.412796697626415 27.76057791537668 22.987616099071207 23.8390092879257 4 29.489164086687307 32.68833849329205 17.647058823529413 20.175438596491226 5 29.927760577915375 31.811145510835914 19.16924664602683 19.09184726522188 6 23.219814241486066 34.82972136222911 20.588235294117645 21.36222910216718 7 23.9422084623323 17.569659442724458 33.69453044375645 24.79360165118679 8 24.109447599380484 22.818791946308725 24.62570986060919 28.4460505937016 9 23.464119772844604 23.412493546721734 25.348477026329373 27.774909654104285 10-11 26.53667355371901 28.719008264462808 19.653925619834713 25.09039256198347 12-13 28.041849651252903 21.738568845259625 23.391888400929993 26.827693102557475 14-15 26.5158371040724 25.106658047834518 24.292178409825468 24.085326438267614 16-17 27.712401396611924 23.75533428165007 22.694943747575326 25.837320574162682 18-19 26.545125420222394 24.65735712438583 24.21773985001293 24.579777605378847 20-21 27.16336825766395 24.77040486353641 23.55452076057431 24.511706118225327 22-23 27.0434557682359 24.96120020693223 23.422141748577342 24.573202276254527 24-25 27.0434557682359 25.064666321779615 23.318675633729953 24.573202276254527 26-27 26.05433376455369 25.420439844760672 23.842173350582147 24.68305304010349 28-29 27.685149282667698 24.143724957994053 23.122657360734134 25.04846839860411 30-31 25.94364012409514 25.34901758014478 23.552223371251294 25.15511892450879 32-33 26.67097608274079 25.28765352294764 23.59405300581771 24.447317388493857 34-35 26.558861578266495 25.536869340232858 23.583441138421733 24.320827943078914 36-37 27.34799482535576 25.39456662354463 22.470892626131953 24.78654592496766 38-39 26.94347432414953 25.274867416893027 22.29983184581555 25.481826413141896 40-41 27.836650297234428 24.631687774618765 22.82243473765831 24.709227190488498 42-43 26.868373416084818 25.381432635117662 23.803982415309026 23.946211533488494 44-45 26.112260734609414 24.314536989136055 23.887739265390586 25.68546301086394 46-47 27.869700103412615 24.638055842812822 22.453464322647363 25.038779731127196 48-49 26.956409261415082 24.317682059242014 23.683870133229853 25.042038546113048 50-51 26.907163175588312 24.463408326868375 23.519524178950093 25.109904318593223 52-53 27.965334368128314 24.809209675333076 22.79135946190661 24.434096494632 54-55 25.90197853355748 25.8631837579206 23.664813138497347 24.57002457002457 56-57 26.321913380736913 25.145442792501616 23.19327731092437 25.339366515837103 58-59 28.017074117190532 24.03311343939982 24.058983313930927 23.89082912947872 60-61 26.607165955245115 25.236062605096365 22.81722933643772 25.339542103220797 62-63 27.760537884665116 25.57538143263512 22.239462115334884 24.424618567364885 64-65 26.88227684346701 24.954721862871928 23.053040103492886 25.10996119016818 66-67 26.949437475753264 25.785594206646838 22.772533298849087 24.492435018750808 68-69 26.749450265166214 25.417151726814126 24.00724356486871 23.82615444315095 70-71 26.633881195806914 24.35615374660282 23.281998188171347 25.72796686941892 72-73 26.110170595129574 24.32608412553718 24.430264357338196 25.133480921995048 74-75 26.1553317698993 22.66519519933784 25.396606428472897 25.78286660228997 76 28.250095310712926 0.0 34.7693480747236 36.980556614563476 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 125.0 1 62.5 2 1.0 3 1.5 4 1.0 5 0.5 6 0.0 7 0.0 8 0.0 9 0.5 10 1.5 11 2.0 12 2.0 13 3.0 14 4.0 15 3.5 16 4.0 17 4.0 18 4.0 19 4.5 20 5.0 21 7.0 22 10.0 23 13.0 24 15.0 25 15.5 26 15.0 27 14.0 28 14.5 29 20.0 30 25.0 31 32.5 32 39.0 33 40.0 34 39.5 35 55.0 36 74.0 37 79.5 38 90.5 39 114.0 40 133.0 41 136.0 42 142.5 43 142.5 44 151.0 45 178.0 46 196.0 47 194.0 48 177.5 49 160.5 50 152.5 51 148.0 52 133.5 53 131.5 54 138.5 55 126.0 56 119.0 57 123.5 58 122.0 59 121.0 60 121.0 61 121.5 62 118.5 63 108.0 64 98.0 65 82.0 66 80.0 67 88.0 68 83.0 69 73.5 70 65.5 71 61.0 72 54.0 73 52.5 74 52.0 75 47.0 76 33.5 77 22.0 78 17.5 79 12.0 80 9.5 81 7.5 82 4.0 83 2.0 84 2.5 85 3.0 86 3.0 87 3.0 88 1.5 89 0.0 90 0.5 91 0.5 92 0.0 93 1.0 94 2.0 95 1.0 96 0.0 97 0.0 98 0.5 99 1.0 100 1.0 >>END_MODULE >>Per base N content pass #Base N-Count 1 3.1 2 3.1 3 3.1 4 3.1 5 3.1 6 3.1 7 3.1 8 3.15 9 3.15 10-11 3.2 12-13 3.225 14-15 3.3125 16-17 3.3375000000000004 18-19 3.325 20-21 3.3625000000000003 22-23 3.35 24-25 3.35 26-27 3.375 28-29 3.2875 30-31 3.3000000000000003 32-33 3.3125 34-35 3.375 36-37 0.2837977296181631 38-39 0.2580312217778351 40-41 0.14195380049038586 42-43 0.18069179143004646 44-45 0.20650490449148168 46-47 0.15487867836861124 48-49 0.21941146102219927 50-51 0.18069179143004646 52-53 0.21941146102219927 54-55 0.19359834796076408 56-57 0.16778523489932887 58-59 0.2065315606041048 60-61 0.19364833462432224 62-63 0.1549186676994578 64-65 0.19367333763718528 66-67 0.14204545454545456 68-69 0.1678719008264463 70-71 0.15505879312572685 72-73 0.13005592404734034 74-75 0.15151515151515152 76 0.1902587519025875 >>END_MODULE >>Sequence Length Distribution warn #Length Count 35 124.0 36 0.0 37 0.0 38 1.0 39 0.0 40 1.0 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 0.0 51 0.0 52 0.0 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 0.0 62 0.0 63 0.0 64 1.0 65 0.0 66 0.0 67 0.0 68 0.0 69 0.0 70 5.0 71 9.0 72 27.0 73 74.0 74 254.0 75 875.0 76 2628.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 93.15 #Duplication Level Percentage of deduplicated Percentage of total 1 97.42351046698873 90.75 2 1.6371443907675791 3.05 3 0.5904455179817499 1.6500000000000001 4 0.13419216317767044 0.5 5 0.13419216317767044 0.625 6 0.026838432635534086 0.15 7 0.026838432635534086 0.17500000000000002 8 0.0 0.0 9 0.0 0.0 >10 0.0 0.0 >50 0.0 0.0 >100 0.026838432635534086 3.1 >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 NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN 124 3.1 No Hit CCTGAACTAGCCGCAGCTTGTGAAGTATGGAAGGCGATCAAATTCGAGTT 7 0.17500000000000002 No Hit GGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACA 6 0.15 No Hit GAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGA 5 0.125 No Hit CTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCC 5 0.125 No Hit GTTTGGCATATGCCAGCTCTGACCGAAATCTTTGGGGATGATTCTGTATT 5 0.125 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 5 0.125 No Hit GGCAGGTACTGGACAATGTGGAAGCTGCCCATGTTCGGGTGCACCGACGC 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 0.025 0.0 0.0 0.0 0.0 14 0.025 0.0 0.0 0.0 0.0 15 0.075 0.0 0.0 0.0 0.0 16 0.075 0.0 0.0 0.0 0.0 17 0.075 0.0 0.0 0.0 0.0 18 0.075 0.0 0.0 0.0 0.0 19 0.075 0.0 0.0 0.0 0.0 20 0.075 0.0 0.0 0.0 0.0 21 0.075 0.0 0.0 0.0 0.0 22 0.075 0.0 0.0 0.0 0.0 23 0.075 0.0 0.0 0.0 0.0 24 0.075 0.0 0.0 0.0 0.0 25 0.075 0.0 0.0 0.0 0.0 26 0.075 0.0 0.0 0.0 0.0 27 0.075 0.0 0.0 0.0 0.0 28 0.075 0.0 0.0 0.0 0.0 29 0.075 0.0 0.0 0.0 0.0 30 0.075 0.0 0.0 0.0 0.0 31 0.075 0.0 0.0 0.0 0.0 32 0.075 0.0 0.0 0.0 0.0 33 0.075 0.0 0.0 0.0 0.0 34 0.075 0.0 0.0 0.0 0.0 35 0.075 0.0 0.0 0.0 0.0 36 0.075 0.0 0.0 0.0 0.0 37 0.075 0.0 0.0 0.0 0.0 38 0.075 0.0 0.0 0.0 0.0 39 0.075 0.0 0.0 0.0 0.0 40 0.075 0.0 0.0 0.0 0.0 41 0.075 0.0 0.0 0.0 0.0 42 0.075 0.0 0.0 0.0 0.0 43 0.075 0.0 0.0 0.0 0.0 44 0.075 0.0 0.0 0.0 0.0 45 0.075 0.0 0.0 0.0 0.0 46 0.075 0.0 0.0 0.0 0.0 47 0.075 0.0 0.0 0.0 0.0 48 0.075 0.0 0.0 0.0 0.0 49 0.075 0.0 0.0 0.0 0.0 50 0.075 0.0 0.0 0.0 0.0 51 0.075 0.0 0.0 0.0 0.0 52 0.075 0.0 0.0 0.0 0.0 53 0.075 0.0 0.0 0.0 0.0 54 0.075 0.0 0.0 0.0 0.0 55 0.075 0.0 0.0 0.0 0.0 56 0.075 0.0 0.0 0.0 0.0 57 0.075 0.0 0.0 0.0 0.0 58 0.075 0.0 0.0 0.0 0.0 59 0.075 0.0 0.0 0.0 0.0 60 0.075 0.0 0.0 0.0 0.0 61 0.075 0.0 0.0 0.0 0.0 62 0.075 0.0 0.0 0.0 0.0 63 0.075 0.0 0.0 0.0 0.0 64 0.075 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Read 475018 spots for SRR11389788.sra Written 475018 spots for SRR11389788.sra Read 475018 spots for SRR11389788.sra Written 475018 spots for SRR11389788.sra Read 475018 spots for SRR11389788.sra Written 475018 spots for SRR11389788.sra Read 475018 spots for SRR11389788.sra Written 475018 spots for SRR11389788.sra Read 475018 spots for SRR11389788.sra Written 475018 spots for SRR11389788.sra Read 475018 spots for SRR11389788.sra Written 475018 spots for SRR11389788.sra Read 475018 spots for SRR11389788.sra Written 475018 spots for SRR11389788.sra Read 475018 spots for SRR11389788.sra Written 475018 spots for SRR11389788.sra Read 475018 spots for SRR11389788.sra Written 475018 spots for SRR11389788.sra Read 475018 spots for SRR11389788.sra Written 475018 spots for SRR11389788.sra Read 475018 spots for SRR11389788.sra Written 475018 spots for SRR11389788.sra Read 475018 spots for SRR11389788.sra Written 475018 spots for SRR11389788.sra Read 475018 spots for SRR11389788.sra Written 475018 spots for SRR11389788.sra Read 475018 spots for SRR11389788.sra Written 475018 spots for SRR11389788.sra Read 475018 spots for SRR11389788.sra Written 475018 spots for SRR11389788.sra Read 475018 spots for SRR11389788.sra Written 475018 spots for SRR11389788.sra Read 475018 spots for SRR11389788.sra Written 475018 spots for SRR11389788.sra Read 475018 spots for SRR11389788.sra Written 475018 spots for SRR11389788.sra Read 475018 spots for SRR11389788.sra Written 475018 spots for SRR11389788.sra Read 475019 spots for SRR11389788.sra Written 475019 spots for SRR11389788.sra SRR ids: ['SRR11389788.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_ck0e_qsz SRR11389788.sra spots: 9500361 blocks: [[1, 475018], [475019, 950036], [950037, 1425054], [1425055, 1900072], [1900073, 2375090], [2375091, 2850108], [2850109, 3325126], [3325127, 3800144], [3800145, 4275162], [4275163, 4750180], [4750181, 5225198], [5225199, 5700216], [5700217, 6175234], [6175235, 6650252], [6650253, 7125270], [7125271, 7600288], [7600289, 8075306], [8075307, 8550324], [8550325, 9025342], [9025343, 9500361]] SRR11389788 file size 1772616 SRR11389788 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 SRR11389788 SRR11389788_1.fastq SRR11389788_2.fastq Input file: SRR11389788_1.fastq Paired file: SRR11389788_2.fastq trimmed: SRR11389788-trimmed-pair1.fastq, SRR11389788-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 06:30:33 2024 >> started Sat Dec 7 06:30:40 2024 >> done (7.142s) 9500361 read pairs processed; of these: 809 ( 0.01%) short read pairs filtered out after trimming by size control 380316 ( 4.00%) empty read pairs filtered out after trimming by size control 9119236 (95.99%) read pairs available; of these: 22348 ( 0.25%) trimmed read pairs available after processing 9096888 (99.75%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 1331 0.01% 19 32 0.00% 20 1895 0.02% 21 33 0.00% 22 2096 0.02% 23 37 0.00% 24 2345 0.03% 25 38 0.00% 26 2271 0.02% 27 34 0.00% 28 2127 0.02% 29 30 0.00% 30 1732 0.02% 31 25 0.00% 32 1402 0.02% 33 17 0.00% 34 1148 0.01% 35 77 0.00% 36 2220 0.02% 37 88 0.00% 38 1202 0.01% 39 65 0.00% 40 572 0.01% 41 66 0.00% 42 302 0.00% 43 78 0.00% 44 225 0.00% 45 75 0.00% 46 118 0.00% 47 97 0.00% 48 128 0.00% 49 113 0.00% 50 155 0.00% 51 135 0.00% 52 167 0.00% 53 153 0.00% 54 204 0.00% 55 336 0.00% 56 1133 0.01% 57 726 0.01% 58 468 0.01% 59 449 0.00% 60 503 0.01% 61 404 0.00% 62 474 0.01% 63 555 0.01% 64 591 0.01% 65 709 0.01% 66 776 0.01% 67 901 0.01% 68 887 0.01% 69 1064 0.01% 70 1502 0.02% 71 2228 0.02% 72 10794 0.12% 73 85071 0.93% 74 638062 7.00% 75 4114093 45.11% 76 4234677 46.44% 9119236 reads passed initial QC criterion=sequence-density sequence-density=0.91 sequence-density-rank=1 fanout-score=2.00 fanout-score-rank=25 prefix-density=0.87 prefix-fanout=2.0 sequence=TTCAAATGTACA criterion=fanout-score sequence-density=0.03 sequence-density-rank=28 fanout-score=12.46 fanout-score-rank=1 prefix-density=0.20 prefix-fanout=1.6 sequence=TTTAGGAATTCTACCAAGGGCTATAGTCATAGTGATCCTCCTATTCAATTACTTCAACCATTTCCGAGCACCTCGTATCACTTCCAAGGCATATGATAGTTTGATTATCTGTGGACGATTTCTTTCTCGTGCAATGCCGTTTTTCAATGGTCTCGAAGATATAAATTTTTTCATTTTTATCTATGGAGTCACAACCGAGGTCGTGGTAAATCCATAAATTGGATTCGATTTTTTTCTTAT criterion=sequence-density sequence-density=0.56 sequence-density-rank=1 fanout-score=2.43 fanout-score-rank=22 prefix-density=0.59 prefix-fanout=2.3 sequence=CAGGTGCTCAAGGAGCTGGAGGAGGTCAAGAAGGAGTACCCGGACGCCTA criterion=fanout-score sequence-density=0.07 sequence-density-rank=33 fanout-score=13.89 fanout-score-rank=1 prefix-density=0.33 prefix-fanout=3.2 sequence=CGTCGTCGCCAGCCTCGGCACCCCGGCCCCGTCCTCTTCCGGCAGCTTCCGGCCCAGGCTCATCAGGAACGCCCCCGTCCAGGCCGCGCCCGTCGCGCCCGCATTGATGGACGCCGCCGTGGAGCGCCTCAAGACCGGGTTCGAGAAGTTCAAGACCGAGGTCTACGACAAGAAGCCGGATGTCTTCGAGCCGCTCAAGGCCGGCCAGGCCCCCAAGTACATGGTGTTCGCCTGCGCCGACTCACGTGTGTGCCCGTCGGTGACCCTGGGCCTGGAGCCCGGTGAGGCCTTCACCGTCCGCAACATCGCCAACATGGTCCCGTCCTACTGCAAGAACAAGTACGCCGGTGTTGGGTCGGCCATCGAGTACGCCGTGTGTGCCCTCAAGGTTGAGGTCATCGTGGTGATTGGCCACAGCCGCTGCGGTGGAATCAAGGCACTCCTCTCGCTCAAGGATGGTGCAGATGACAGCTTCCACTTCGTCGAGGACTGGGTCAGGATCGGGTTCCCG SRR11389788 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 07 06:31:29 Started mapping on | Dec 07 06:31:29 Finished on | Dec 07 06:32:34 Mapping speed, Million of reads per hour | 505.07 Number of input reads | 9119236 Average input read length | 150 UNIQUE READS: Uniquely mapped reads number | 7425736 Uniquely mapped reads % | 81.43% Average mapped length | 149.80 Number of splices: Total | 2511026 Number of splices: Annotated (sjdb) | 2379592 Number of splices: GT/AG | 2476794 Number of splices: GC/AG | 29150 Number of splices: AT/AC | 730 Number of splices: Non-canonical | 4352 Mismatch rate per base, % | 1.34% Deletion rate per base | 0.01% Deletion average length | 1.71 Insertion rate per base | 0.01% Insertion average length | 1.74 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 1132626 % of reads mapped to multiple loci | 12.42% Number of reads mapped to too many loci | 23941 % of reads mapped to too many loci | 0.26% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 4.63% % of reads unmapped: other | 1.25% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 560877 560877 560877 N_multimapping 1132626 1132626 1132626 N_noFeature 283846 7178094 362931 N_ambiguous 243151 1243 83860 UnstrandedReadsAssigned:6898739 PositiveStrandReadsAssigned:246399 NegativeStrandReadsAssigned:6978945 Dataset is classified negative stranded MeadianReadLen=76 20thPercentileLength=75 echo kmer=71 SRR11389788 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: SRR11389788-trimmed-pair1.fastq SRR11389788-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 9,119,236 reads, 8,019,886 reads pseudoaligned [quant] estimated average fragment length: 194.482 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,038 rounds 52973 SRR11389788.ke.tsv 35125 SRR11389788.se.tsv 88098 total ==> SRR11389788.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 742.761 0 0 PNS24247 1044 850.518 4.69528 0.877393 PNS24249 1928 1734.52 37.3036 3.41812 PNS24246 1044 850.518 4.69528 0.877393 PNS24248 1044 850.518 4.69528 0.877393 PNS24244 1471 1277.52 50.6106 6.29637 PNS24243 293 111.712 0 0 KQK14069 1603 1409.52 1503.07 169.483 KQK14071 474 282.285 57.574 32.4156 ==> SRR11389788.se.tsv <== BRADI_1g14170v3 1655 BRADI_1g53295v3 0 BRADI_1g59795v3 132 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 59 BRADI_1g74790v3 69 BRADI_1g09890v3 0 BRADI_1g77505v3 110 BRADI_1g48960v3 0 SRR11389788 completed mapping pipeline successfully