Starting /dee2/code/volunteer_pipeline.sh ERR1942995 current disk space = 1523547058176 free memory = 1563608640 ERR1942995 SRAfilesize 06e8acf0775c06bbd7bbf1fed8f7199d ERR1942995.sra ERR1942995.sra file validated ERR1942995 is single end ERR1942995 is conventional basespace ERR1942995 read1 length is 25-280 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR1942995_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 25-280 %GC 62 >>END_MODULE >>Per base sequence quality fail #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 24.9255 26.0 23.0 27.0 20.0 29.0 2 23.501 24.0 21.0 27.0 17.0 29.0 3 23.59075 24.0 22.0 27.0 15.0 29.0 4 24.27575 26.0 22.0 27.0 14.0 29.0 5 23.28275 24.0 20.0 27.0 14.0 28.0 6 24.16025 25.0 22.0 27.0 15.0 29.0 7 23.82475 25.0 22.0 27.0 17.0 28.0 8 24.78925 26.0 23.0 28.0 20.0 29.0 9 23.59725 24.0 21.0 27.0 18.0 28.0 10-14 24.4491 25.4 22.4 27.4 19.2 28.8 15-19 24.25785 25.6 22.2 27.6 18.4 28.8 20-24 24.059 25.2 22.2 27.2 18.0 28.2 25-29 23.822624468411192 25.0 21.6 27.2 17.2 28.2 30-34 23.97618904828756 24.8 22.0 27.4 18.2 28.0 35-39 23.988464432981875 25.0 22.2 27.0 18.6 28.0 40-44 24.077259442899066 25.0 22.2 27.0 18.6 28.0 45-49 24.085631988028457 25.2 22.4 27.0 18.6 28.0 50-54 23.65522601765004 25.2 21.6 27.0 15.6 28.0 55-59 23.575225841482585 24.6 21.2 27.0 16.2 28.0 60-64 23.731359978612684 24.6 21.6 27.0 16.6 28.0 65-69 23.09257779690622 24.0 20.8 26.8 14.0 28.0 70-74 23.34859486999004 24.4 21.2 27.0 14.8 28.0 75-79 22.77827796185746 24.0 20.0 26.8 14.6 28.2 80-84 22.335968594631684 23.6 19.8 26.8 13.2 28.0 85-89 21.89912247071046 23.0 19.0 26.6 13.0 28.0 90-94 21.24123167145811 22.4 18.0 25.6 12.8 27.8 95-99 21.6857136919538 23.2 18.8 26.4 12.2 27.8 100-104 22.407015928580126 23.6 19.8 26.4 13.8 27.8 105-109 21.75253066234151 22.8 19.0 26.2 13.2 27.8 110-114 22.12112322109001 23.0 19.6 26.2 13.2 28.0 115-119 21.299905961848193 22.2 18.2 25.4 13.0 27.2 120-124 19.73212344401221 20.6 14.8 24.4 10.8 26.8 125-129 19.540721507972904 20.2 14.0 24.2 10.2 26.8 130-134 19.48542976743539 20.0 14.0 24.2 9.8 27.0 135-139 20.677599791519665 21.6 17.2 25.0 12.6 27.0 140-144 20.221210222338378 21.4 16.2 24.2 13.0 26.2 145-149 20.80038561154427 22.0 18.4 24.6 13.0 26.0 150-154 21.009796190784925 22.0 18.4 25.0 13.4 26.8 155-159 20.60507178649376 21.8 18.0 24.2 13.6 26.2 160-164 20.292236694622193 21.8 16.4 24.2 12.8 26.0 165-169 20.228166146769023 21.2 16.6 24.2 13.0 26.0 170-174 20.321191049099287 21.4 17.4 24.2 13.0 26.0 175-179 20.528920807928138 21.4 17.6 24.2 13.6 26.0 180-184 20.149831826579476 21.0 16.8 24.0 12.8 26.0 185-189 20.568185524636117 21.6 18.2 24.0 13.8 26.0 190-194 20.413083490698828 21.4 17.6 24.0 13.4 26.0 195-199 20.51009611706094 21.6 17.6 24.4 13.2 26.0 200-204 20.470858027179716 21.4 17.4 24.6 12.8 26.4 205-209 20.28658062628847 21.4 17.0 24.4 12.0 26.2 210-214 19.273433920951696 20.0 14.2 23.8 11.4 25.4 215-219 19.580448211291692 20.4 15.8 23.6 12.0 25.4 220-224 19.3637688299171 20.4 14.6 23.6 12.0 25.0 225-229 18.747774087321865 19.0 14.0 23.0 11.0 24.0 230-234 19.41953823953824 NaN NaN NaN NaN NaN 235-239 18.852015809997635 NaN NaN NaN NaN NaN 240-244 19.693813314677477 NaN NaN NaN NaN NaN 245-249 19.4178216374269 NaN NaN NaN NaN NaN 250-254 17.221818181818183 NaN NaN NaN NaN NaN 255-259 16.59 NaN NaN NaN NaN NaN 260-264 14.116666666666665 NaN NaN NaN NaN NaN 265-269 11.933333333333334 NaN NaN NaN NaN NaN 270-274 15.8 NaN NaN NaN NaN NaN 275-279 23.0 NaN NaN NaN NaN NaN 280 20.0 NaN NaN NaN NaN NaN >>END_MODULE >>Per sequence quality scores warn #Quality Count 15 2.0 16 16.0 17 47.0 18 150.0 19 301.0 20 427.0 21 529.0 22 532.0 23 501.0 24 534.0 25 463.0 26 372.0 27 125.0 28 1.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 15.1 63.125 4.475 17.299999999999997 2 17.075000000000003 52.25 0.15 30.525000000000002 3 12.825000000000001 21.675 5.8500000000000005 59.650000000000006 4 55.95 19.55 3.5749999999999997 20.925 5 18.4 47.3 15.975 18.325 6 11.55 16.925 14.7 56.825 7 6.6000000000000005 38.975 35.4 19.025 8 27.450000000000003 16.075 5.800000000000001 50.675000000000004 9 11.0 26.025 7.025 55.95 10-14 31.064999999999998 22.935 9.135 36.864999999999995 15-19 31.669999999999998 25.3 6.4350000000000005 36.595 20-24 22.175 28.24 12.015 37.57 25-29 35.17248285184999 25.66965403294448 5.872928453412107 33.28493466179342 30-34 30.10021654832049 28.62466636450622 10.540363599738127 30.734753487435164 35-39 33.81155881155881 28.627391127391128 8.608058608058608 28.952991452991455 40-44 25.074138459965233 33.45945393189488 11.744554657940483 29.721852950199406 45-49 24.475847893114082 31.01233299075026 13.273381294964029 31.238437821171633 50-54 25.178849144634523 32.17729393468118 11.1767755313634 31.46708138932089 55-59 23.125370081283307 27.743984496958607 14.604080314367229 34.52656510739086 60-64 16.122819567490232 30.79293457326803 26.368788862598358 26.715456996643372 65-69 37.568108528855774 15.684421216501724 15.367508061825866 31.379962192816635 70-74 34.00878081729146 13.418890014634696 22.7344365642238 29.83789260385005 75-79 28.96870717222476 24.73161260849703 14.607126541799909 31.6925536774783 80-84 36.462658722994526 16.663657699945837 11.951615815129085 34.922067761930556 85-89 30.073668426885714 19.336332225047265 23.22837212334572 27.361627224721296 90-94 16.086143618862963 25.282182674330034 12.097500173118206 46.53417353368881 95-99 27.06415420023015 19.174338319907942 23.43210586881473 30.32940161104718 100-104 18.40981012658228 20.205696202531644 14.612341772151899 46.77215189873418 105-109 32.34207443453185 17.067675948454536 10.570424439037577 40.01982517797603 110-114 32.67493796526055 18.838709677419356 13.77667493796526 34.70967741935484 115-119 20.62409588758008 20.262450919611492 16.13969828476958 42.973754908038856 120-124 31.783121597096187 16.31125226860254 11.161524500907442 40.74410163339383 125-129 35.645933014354064 14.077058675396625 11.798035759254596 38.47897255099471 130-134 25.59119325903778 12.883935852133732 8.630062516988312 52.89480837184017 135-139 23.379145503435915 28.27905587092919 12.05557215416791 36.28622647146699 140-144 32.46618106139438 21.22788761706556 12.261533125216788 34.04439819632327 145-149 25.65995938711464 15.008307181096548 15.414436034705556 43.91729739708325 150-154 29.17624521072797 21.47509578544061 11.839080459770116 37.5095785440613 155-159 29.509525739764896 14.997973246858532 16.436967977300366 39.055533036076206 160-164 28.07780320366133 14.874141876430205 14.508009153318078 42.54004576659039 165-169 33.11950582086006 22.071751009741032 8.077928248990258 36.73081492040865 170-174 28.057199211045365 18.91025641025641 13.732741617357004 39.299802761341226 175-179 27.50132345156167 10.455267337215458 25.33086289041821 36.712546320804655 180-184 29.681779780343565 10.898338496198253 22.866798085046465 36.553083638411714 185-189 29.232283464566926 14.173228346456693 14.63254593175853 41.96194225721785 190-194 20.21513353115727 23.92433234421365 18.212166172106826 37.64836795252226 195-199 23.277539898793304 12.300506033476061 26.274815103152978 38.14713896457766 200-204 30.427422767668215 17.139229792636478 18.239526026237833 34.19382141345747 205-209 28.324808184143222 17.647058823529413 17.007672634271103 37.02046035805627 210-214 24.442379182156134 10.87360594795539 29.36802973977695 35.31598513011153 215-219 31.30034522439586 14.614499424626008 21.173762945914845 32.91139240506329 220-224 28.468208092485547 21.242774566473987 10.404624277456648 39.884393063583815 225-229 20.454545454545457 25.681818181818183 14.09090909090909 39.77272727272727 230-234 16.463414634146343 17.682926829268293 25.609756097560975 40.243902439024396 235-239 26.71232876712329 9.931506849315069 35.273972602739725 28.08219178082192 240-244 32.18390804597701 21.455938697318008 16.85823754789272 29.50191570881226 245-249 31.84713375796178 21.019108280254777 7.643312101910828 39.490445859872615 250-254 25.0 25.0 18.181818181818183 31.818181818181817 255-259 56.52173913043478 13.043478260869565 17.391304347826086 13.043478260869565 260-264 25.0 12.5 25.0 37.5 265-269 36.36363636363637 36.36363636363637 9.090909090909092 18.181818181818183 270-274 20.0 20.0 20.0 40.0 275-279 40.0 0.0 40.0 20.0 280 0.0 100.0 0.0 0.0 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 0.0 1 0.0 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 0.0 16 0.0 17 0.0 18 0.5 19 0.5 20 0.5 21 1.0 22 1.0 23 0.5 24 0.0 25 0.0 26 0.0 27 1.0 28 1.5 29 0.5 30 0.0 31 0.0 32 0.0 33 0.0 34 0.0 35 0.0 36 0.0 37 0.5 38 1.0 39 1.0 40 1.0 41 26.5 42 51.5 43 28.5 44 6.0 45 7.5 46 47.5 47 104.0 48 71.0 49 41.0 50 40.5 51 32.5 52 31.0 53 64.0 54 75.0 55 67.0 56 90.5 57 62.0 58 49.5 59 154.5 60 266.8333333333333 61 259.66666666666663 62 345.16666666666663 63 716.833333333342 64 713.166666666675 65 360.99999999999795 66 200.66666666666734 67 101.66666666666659 68 39.666666666666664 69 22.0 70 22.0 71 29.5 72 32.0 73 29.0 74 29.5 75 29.0 76 23.0 77 17.5 78 15.0 79 13.5 80 8.0 81 2.0 82 1.0 83 1.0 84 0.5 85 0.0 86 0.0 87 0.0 88 0.0 89 0.0 90 0.0 91 0.0 92 0.0 93 0.0 94 0.0 95 0.0 96 0.0 97 0.0 98 0.0 99 0.0 100 0.0 >>END_MODULE >>Per base N content pass #Base N-Count 1 0.0 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10-14 0.0 15-19 0.0 20-24 0.0 25-29 0.0 30-34 0.0 35-39 0.0 40-44 0.0 45-49 0.0 50-54 0.0 55-59 0.0 60-64 0.0 65-69 0.0 70-74 0.0 75-79 0.0 80-84 0.0 85-89 0.0 90-94 0.0 95-99 0.0 100-104 0.0 105-109 0.0 110-114 0.0 115-119 0.0 120-124 0.0 125-129 0.0 130-134 0.0 135-139 0.0 140-144 0.0 145-149 0.0 150-154 0.0 155-159 0.0 160-164 0.0 165-169 0.0 170-174 0.0 175-179 0.0 180-184 0.0 185-189 0.0 190-194 0.0 195-199 0.0 200-204 0.0 205-209 0.0 210-214 0.0 215-219 0.0 220-224 0.0 225-229 0.0 230-234 0.0 235-239 0.0 240-244 0.0 245-249 0.0 250-254 0.0 255-259 0.0 260-264 0.0 265-269 0.0 270-274 0.0 275-279 0.0 280 0.0 >>END_MODULE >>Sequence Length Distribution warn #Length Count 20-29 18.0 30-39 60.0 40-49 43.0 50-59 231.0 60-69 75.0 70-79 186.0 80-89 451.0 90-99 365.0 100-109 536.0 110-119 166.0 120-129 352.0 130-139 327.0 140-149 135.0 150-159 157.0 160-169 74.0 170-179 101.0 180-189 172.0 190-199 58.0 200-209 264.0 210-219 68.0 220-229 91.0 230-239 13.0 240-249 42.0 250-259 11.0 260-269 3.0 270-279 0.0 280-281 1.0 >>END_MODULE >>Sequence Duplication Levels fail #Total Deduplicated Percentage 20.925 #Duplication Level Percentage of deduplicated Percentage of total 1 82.67622461170848 17.299999999999997 2 6.5710872162485074 2.75 3 3.464755077658303 2.175 4 1.1947431302270013 1.0 5 0.35842293906810035 0.375 6 0.8363201911589008 1.05 7 0.11947431302270012 0.17500000000000002 8 0.11947431302270012 0.2 9 0.23894862604540024 0.44999999999999996 >10 2.5089605734767026 14.499999999999998 >50 1.0752688172043012 16.25 >100 0.7168458781362007 26.150000000000002 >500 0.11947431302270012 17.625 >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 AACGACTCCAGCCCCAGCGGCTCCGGCACCGGCAGCCGGAACGACCAAGA 705 17.625 No Hit ACCGGCAGCCGGAACGACCAAGACGACCAACATAACAGGCGTGCTAGCGA 318 7.95 No Hit AACATAACAGGCGTGCTAGCGAAAGCCGGGCAGTTCAACACGTTCATCCG 209 5.225 No Hit GAAGTTTATGGTGTCCGAGCCCGAGGTTGAAGACGTACACATTGCATATA 190 4.75 No Hit ACGACTCCAGCCCCAGCGGCTCCGGCACCGGCAGCCGGAACGACCAAGAC 119 2.9749999999999996 No Hit GCTGATAGCTAGAGTTTCACGATTACACCACCAGAATGGAAGCCATGCAG 107 2.675 No Hit AACGACCAAGACGACCAACATAACAGGCGTGCTAGCGAAAGCCGGGCAGT 103 2.5749999999999997 No Hit AGCCCCAGCGGCTCCGGCACCGGCAGCCGGAACGACCAAGACGACCAACA 97 2.4250000000000003 No Hit CGACCAACATAACAGGCGTGCTAGCGAAAGCCGGGCAGTTCAACACGTTC 91 2.275 No Hit TAACAGGCGTGCTAGCGAAAGCCGGGCAGTTCAACACGTTCATCCGGCTG 85 2.125 No Hit CCGGAACGACCAAGACGACCAACATAACAGGCGTGCTAGCGAAAGCCGGG 75 1.875 No Hit CATTTGTCCTCGCTGATAGCTAGAGTTTCACGATTACACCACCAGAATGG 70 1.7500000000000002 No Hit CGGCACCGGCAGCCGGAACGACCAAGACGACCAACATAACAGGCGTGCTA 61 1.525 No Hit ACCAACATAACAGGCGTGCTAGCGAAAGCCGGGCAGTTCAACACGTTCATCCGGC 61 1.525 No Hit ACGACCAAGACGACCAACATAACAGGCGTGCTAGCGAAAGCCGGGCAGTT 59 1.4749999999999999 No Hit GGAACGACCAAGACGACCAACATAACAGGCGTGCTAGCGAAAGCCGGGCA 51 1.275 No Hit TGACACTTCTTTCAGAGAACAGAGAACTAACTTCAGGAGAAATTCAAGAGACGGTGG 48 1.2 No Hit CGACCAAGACGACCAACATAACAGGCGTGCTAGCGAAAGCCGGGCAGTTC 48 1.2 No Hit CACCGGCAGCCGGAACGACCAAGACGACCAACATAACAGGCGTGCTAGCG 45 1.125 No Hit GAACGACCAAGACGACCAACATAACAGGCGTGCTAGCGAAAGCCGGGCAG 44 1.0999999999999999 No Hit CCAGCGGCTCCGGCACCGGCAGCCGGAACGACCAAGACGACCAACATAAC 43 1.075 No Hit AACGACTCCAGCCCCAGCGGCTTCCGGCACGCTCAACTCGCTTTCGGACAGCC 42 1.05 No Hit AGCAGCAGCAGTGGAGGATACAGAAAAAGTGCCGCAGAGGCGAAGCTAAA 39 0.975 No Hit ACCAACATAACAGGCGTGCTAGCGAAAGCCGGGCAGTTCAACACGTTCAT 32 0.8 No Hit AACGACTCCAGCCCCCAGCGGCTCCGGCACCGGCAGCCGGAACGACCAAG 30 0.75 No Hit ACCGGCAGCCGGAACGACCAAGACGCCAACATAACAGGCGTGCTAGCGAA 25 0.625 No Hit GCATTTGTCCTCGCTGATAGCTAGAGTTTCACGATTACACCACCAGAAAT 25 0.625 No Hit GCCCAGCGGCTCCGGCACCGGCAGCCGGAACGACCAAGACGACCAACATA 22 0.5499999999999999 No Hit CGGAACGACCAAGACGACCAACATAACAGGCGTGCTAGCGAAAGCCGGGC 21 0.525 No Hit ACCGGCAGCCGGAACGACCAAGACGACCACATAACAGGCGTGCTAGCGAA 20 0.5 No Hit CAACATAACAGGCGTGCTAGCGAAAGCCGGGCAGTTCAACACGTTCATCC 20 0.5 No Hit GACGACCAACATAACAGGCGTGCTAGCGAAAGCCGGGCAGTTCAACACGT 19 0.475 No Hit GCTGATAGCTAGAGTTTCACGATTACACCACCAGAATGGAGCCATGCAGA 14 0.35000000000000003 No Hit CGACTGAGAGTGAGAGGCCACTTGGATCACCATGACCGCCGCCTCGCGCC 12 0.3 No Hit AGCCCCCAGCGGCTCCGGCACCGGCAGCCGGAACGACCAAGACGACCAAC 11 0.27499999999999997 No Hit GGCGCCAACGACTCCAGCCCCAGCGGCTCCGGC 10 0.25 No Hit AACGACTCCAGCCCCAGCGGCTCCGGCACCGGCAGCCGGAACGACCAGAC 10 0.25 No Hit AGCGGCTCCGGCACCGGCAGCCGGAACGACCAAGACGACCAACATAACAG 9 0.22499999999999998 No Hit AACGACTCCAGCCCCAGCGGCTCCGGCACGGCAGCCGGAACGACCAAGAC 9 0.22499999999999998 No Hit CGATTACACCACCAGAATGGAAGCCATGCAGAGATCATTTCTAGTGCTGC 8 0.2 No Hit AACGACTCCAGCCCCAGCGGCTCCGGCACCGGCAGCCGGACGACCAAGAC 7 0.17500000000000002 No Hit AGTGCTGCTCGTGATCTCAGCGGCGACAACATCC 6 0.15 No Hit AACGACTCCAGCCCCAGCGGCTCCGGCACCGGCAGCCGGAACGCCAAGAC 6 0.15 No Hit CGGCACCGGCAGCCGGAACGACCAAGACGCCAACATAACAGGCGTGCTAG 6 0.15 No Hit AACGACTCCAGCCCAGCGGCTCCGGCACCGGCAGCCGGAACGACCAAGAC 6 0.15 No Hit AACGACTCCAGTCCCAGCGGCTCCGGCACCGGCAGCCGGAACGACCAAGA 6 0.15 No Hit AAACGACTCCAGCCCCAGCGGCTCCGGCACCGGCAGCCGGAACGACCAAG 6 0.15 No Hit GAACGACCAAGACGACCGACATAACAGGCGTGCTAGCGAAAGCCGGGCAG 6 0.15 No Hit ACGACTCCAGCCCCCAGCGGCTCCGGCACCGGCAGCCGGAACGACCAAGA 5 0.125 No Hit GCCCCAGCGGCTCCGGCACCGGCAGCCGGAACGACCAAGACGACCAACAT 5 0.125 No Hit ACCGGCAGCCGGAACGACCAAGACGACCAACATAAACAGGCGTGCTAGCG 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 10-14 0.0 0.0 0.0 0.0 0.0 15-19 0.0 0.0 0.0 0.0 0.0 20-24 0.0 0.0 0.0 0.0 0.0 25-29 0.0 0.0 0.0 0.0 0.0 30-34 0.0 0.0 0.0 0.0 0.0 35-39 0.0 0.0 0.0 0.0 0.0 40-44 0.0 0.0 0.0 0.0 0.0 45-49 0.0 0.0 0.0 0.0 0.0 50-54 0.0 0.0 0.0 0.0 0.0 55-59 0.0 0.0 0.0 0.0 0.0 60-64 0.0 0.0 0.0 0.0 0.0 65-69 0.0 0.0 0.0 0.0 0.0 70-74 0.0 0.0 0.0 0.0 0.0 75-79 0.0 0.0 0.0 0.0 0.0 80-84 0.0 0.0 0.0 0.0 0.0 85-89 0.0 0.0 0.0 0.0 0.0 90-94 0.0 0.0 0.0 0.0 0.0 95-99 0.0 0.0 0.0 0.0 0.0 100-104 0.0 0.0 0.0 0.0 0.0 105-109 0.0 0.0 0.0 0.0 0.0 110-114 0.0 0.0 0.0 0.0 0.0 115-119 0.0 0.0 0.0 0.0 0.0 120-124 0.0 0.0 0.0 0.0 0.0 125-129 0.0 0.0 0.0 0.0 0.0 130-134 0.0 0.0 0.0 0.0 0.0 135-139 0.0 0.0 0.0 0.0 0.0 140-144 0.0 0.0 0.0 0.0 0.0 145-149 0.0 0.0 0.0 0.0 0.0 150-154 0.0 0.0 0.0 0.0 0.0 155-159 0.0 0.0 0.0 0.0 0.0 160-164 0.0 0.0 0.0 0.0 0.0 165-169 0.0 0.0 0.0 0.0 0.0 170-174 0.0 0.0 0.0 0.0 0.0 175-179 0.0 0.0 0.0 0.0 0.0 180-184 0.0 0.0 0.0 0.0 0.0 185-189 0.0 0.0 0.0 0.0 0.0 190-194 0.0 0.0 0.0 0.0 0.0 195-199 0.0 0.0 0.0 0.0 0.0 200-204 0.0 0.0 0.0 0.0 0.0 205-209 0.0 0.0 0.0 0.0 0.0 210-214 0.0 0.0 0.0 0.0 0.0 215-219 0.0 0.0 0.0 0.0 0.0 220-224 0.0 0.0 0.0 0.0 0.0 225-229 0.0 0.0 0.0 0.0 0.0 230-234 0.0 0.0 0.0 0.0 0.0 235-239 0.0 0.0 0.0 0.0 0.0 240-244 0.0 0.0 0.0 0.0 0.0 245-249 0.0 0.0 0.0 0.0 0.0 250-254 0.0 0.0 0.0 0.0 0.0 255-259 0.0 0.0 0.0 0.0 0.0 260-264 0.0 0.0 0.0 0.0 0.0 265-268 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 GGTTGCA 5 1.9737304E-4 4555.5 205-209 TCGCTGG 10 0.007891457 911.1 200-204 CGGACAG 55 0.0 828.27277 215-216 GCTTTCG 70 0.0 650.7857 210-214 CTTTCGG 70 7.736786E-5 325.39285 210-214 TTCGGAC 55 0.0027681473 207.06819 210-214 ACTCGCT 75 2.2919229E-4 202.46666 205-209 CTCGCTT 65 0.0053669037 175.21153 205-209 TCGGACA 55 0.0027681473 165.65456 210-214 TCGCTTT 70 0.0071966187 130.15714 205-209 TTATGGT 20 6.250433E-6 113.8875 6 ATGGTGT 20 6.250433E-6 113.8875 8 GTTTATG 20 6.250433E-6 113.8875 4 TGGTGTC 20 6.250433E-6 113.8875 9 TTTATGG 20 6.250433E-6 113.8875 5 TATGGTG 20 6.250433E-6 113.8875 7 CGCTTTC 70 0.0071966187 108.46428 205-209 AACGACT 125 0.0 91.11 1 GAAGTTT 25 1.8944465E-5 91.11 1 AGTTTAT 25 1.8944465E-5 91.11 3 >>END_MODULE Read 1373135 spots for ERR1942995.sra Written 1373135 spots for ERR1942995.sra Read 1373135 spots for ERR1942995.sra Written 1373135 spots for ERR1942995.sra Read 1373135 spots for ERR1942995.sra Written 1373135 spots for ERR1942995.sra Read 1373135 spots for ERR1942995.sra Written 1373135 spots for ERR1942995.sra Read 1373135 spots for ERR1942995.sra Written 1373135 spots for ERR1942995.sra Read 1373145 spots for ERR1942995.sra Written 1373145 spots for ERR1942995.sra Read 1373135 spots for ERR1942995.sra Written 1373135 spots for ERR1942995.sra Read 1373135 spots for ERR1942995.sra Written 1373135 spots for ERR1942995.sra Read 1373135 spots for ERR1942995.sra Written 1373135 spots for ERR1942995.sra Read 1373135 spots for ERR1942995.sra Written 1373135 spots for ERR1942995.sra Read 1373135 spots for ERR1942995.sra Written 1373135 spots for ERR1942995.sra Read 1373135 spots for ERR1942995.sra Written 1373135 spots for ERR1942995.sra Read 1373135 spots for ERR1942995.sra Written 1373135 spots for ERR1942995.sra Read 1373135 spots for ERR1942995.sra Written 1373135 spots for ERR1942995.sra Read 1373135 spots for ERR1942995.sra Written 1373135 spots for ERR1942995.sra Read 1373135 spots for ERR1942995.sra Written 1373135 spots for ERR1942995.sra Read 1373135 spots for ERR1942995.sra Written 1373135 spots for ERR1942995.sra Read 1373135 spots for ERR1942995.sra Written 1373135 spots for ERR1942995.sra Read 1373135 spots for ERR1942995.sra Written 1373135 spots for ERR1942995.sra Read 1373135 spots for ERR1942995.sra Written 1373135 spots for ERR1942995.sra SRR ids: ['ERR1942995.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_wqzi9zr2 ERR1942995.sra spots: 27462710 blocks: [[1, 1373135], [1373136, 2746270], [2746271, 4119405], [4119406, 5492540], [5492541, 6865675], [6865676, 8238810], [8238811, 9611945], [9611946, 10985080], [10985081, 12358215], [12358216, 13731350], [13731351, 15104485], [15104486, 16477620], [16477621, 17850755], [17850756, 19223890], [19223891, 20597025], [20597026, 21970160], [21970161, 23343295], [23343296, 24716430], [24716431, 26089565], [26089566, 27462710]] ERR1942995 file size 7628286 ERR1942995 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 ERR1942995 ERR1942995_1.fastq Input file: ERR1942995_1.fastq trimmed: ERR1942995-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -- maximum error ratio allowed (-r): 0.100 -- maximum indel error ratio allowed (-d): 0.030 -- end quality threshold (-q): 10 -- minimum read length allowed after trimming (-l): 18 -- file format (-f): Sanger/Illumina 1.8+ FASTQ -- minimum overlap length for adapter detection (-k): inf -- number of concurrent threads (-t): 20 Tue Dec 10 00:47:30 2024 >> started Tue Dec 10 00:47:46 2024 >> done (16.258s) 27462710 reads processed; of these: 418 ( 0.00%) short reads filtered out after trimming by size control 105 ( 0.00%) empty reads filtered out after trimming by size control 27462187 (100.00%) reads available; of these: 1811996 ( 6.60%) trimmed reads available after processing 25650191 (93.40%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 478 0.00% 19 680 0.00% 20 1061 0.00% 21 1809 0.01% 22 3213 0.01% 23 3718 0.01% 24 8768 0.03% 25 45927 0.17% 26 47575 0.17% 27 50174 0.18% 28 50976 0.19% 29 52618 0.19% 30 53263 0.19% 31 54360 0.20% 32 56484 0.21% 33 58156 0.21% 34 59202 0.22% 35 60890 0.22% 36 63990 0.23% 37 64847 0.24% 38 65774 0.24% 39 67936 0.25% 40 70139 0.26% 41 74067 0.27% 42 75659 0.28% 43 78734 0.29% 44 80285 0.29% 45 82380 0.30% 46 86826 0.32% 47 88344 0.32% 48 91015 0.33% 49 92171 0.34% 50 96606 0.35% 51 99372 0.36% 52 99119 0.36% 53 104108 0.38% 54 106864 0.39% 55 107644 0.39% 56 113275 0.41% 57 116387 0.42% 58 117621 0.43% 59 118722 0.43% 60 125711 0.46% 61 126495 0.46% 62 129025 0.47% 63 135177 0.49% 64 129663 0.47% 65 131807 0.48% 66 134385 0.49% 67 134936 0.49% 68 137309 0.50% 69 149948 0.55% 70 144868 0.53% 71 147764 0.54% 72 150052 0.55% 73 148076 0.54% 74 154289 0.56% 75 156983 0.57% 76 160385 0.58% 77 163919 0.60% 78 165020 0.60% 79 163084 0.59% 80 167759 0.61% 81 169468 0.62% 82 176656 0.64% 83 177645 0.65% 84 174173 0.63% 85 179620 0.65% 86 189390 0.69% 87 183761 0.67% 88 188904 0.69% 89 187101 0.68% 90 194359 0.71% 91 199210 0.73% 92 193218 0.70% 93 200204 0.73% 94 194285 0.71% 95 206139 0.75% 96 208168 0.76% 97 209410 0.76% 98 228191 0.83% 99 206291 0.75% 100 206528 0.75% 101 211639 0.77% 102 212772 0.77% 103 211251 0.77% 104 209224 0.76% 105 213762 0.78% 106 208872 0.76% 107 217934 0.79% 108 223398 0.81% 109 231945 0.84% 110 224409 0.82% 111 226220 0.82% 112 229762 0.84% 113 219415 0.80% 114 223555 0.81% 115 223831 0.82% 116 223034 0.81% 117 222679 0.81% 118 226325 0.82% 119 220874 0.80% 120 231180 0.84% 121 219291 0.80% 122 220178 0.80% 123 215565 0.78% 124 218660 0.80% 125 212593 0.77% 126 222158 0.81% 127 223278 0.81% 128 221307 0.81% 129 221640 0.81% 130 216958 0.79% 131 213994 0.78% 132 209002 0.76% 133 206205 0.75% 134 205753 0.75% 135 210408 0.77% 136 202656 0.74% 137 202144 0.74% 138 212324 0.77% 139 202129 0.74% 140 203957 0.74% 141 211952 0.77% 142 194234 0.71% 143 192614 0.70% 144 192602 0.70% 145 190099 0.69% 146 190321 0.69% 147 190363 0.69% 148 184532 0.67% 149 180199 0.66% 150 181830 0.66% 151 174619 0.64% 152 176684 0.64% 153 181708 0.66% 154 176381 0.64% 155 172155 0.63% 156 162934 0.59% 157 158148 0.58% 158 153326 0.56% 159 159747 0.58% 160 158573 0.58% 161 156559 0.57% 162 166555 0.61% 163 162494 0.59% 164 158266 0.58% 165 153126 0.56% 166 143692 0.52% 167 142623 0.52% 168 137349 0.50% 169 132118 0.48% 170 127619 0.46% 171 127362 0.46% 172 123653 0.45% 173 120944 0.44% 174 119257 0.43% 175 117486 0.43% 176 115563 0.42% 177 117215 0.43% 178 114928 0.42% 179 108382 0.39% 180 103301 0.38% 181 100023 0.36% 182 96846 0.35% 183 97359 0.35% 184 95015 0.35% 185 88769 0.32% 186 88713 0.32% 187 86362 0.31% 188 80679 0.29% 189 80142 0.29% 190 77577 0.28% 191 74640 0.27% 192 73998 0.27% 193 74126 0.27% 194 71668 0.26% 195 69758 0.25% 196 68317 0.25% 197 64132 0.23% 198 62911 0.23% 199 59993 0.22% 200 57299 0.21% 201 55687 0.20% 202 55570 0.20% 203 53754 0.20% 204 52150 0.19% 205 50920 0.19% 206 48580 0.18% 207 47402 0.17% 208 44976 0.16% 209 42584 0.16% 210 41514 0.15% 211 40829 0.15% 212 41392 0.15% 213 42152 0.15% 214 40619 0.15% 215 37601 0.14% 216 34266 0.12% 217 32277 0.12% 218 31459 0.11% 219 29660 0.11% 220 27647 0.10% 221 25670 0.09% 222 24329 0.09% 223 23291 0.08% 224 22341 0.08% 225 20888 0.08% 226 20261 0.07% 227 19409 0.07% 228 18407 0.07% 229 17120 0.06% 230 16545 0.06% 231 15972 0.06% 232 15342 0.06% 233 14657 0.05% 234 13442 0.05% 235 12684 0.05% 236 11772 0.04% 237 11055 0.04% 238 10033 0.04% 239 9596 0.03% 240 9006 0.03% 241 8334 0.03% 242 7734 0.03% 243 7208 0.03% 244 6782 0.02% 245 6311 0.02% 246 6133 0.02% 247 5623 0.02% 248 5269 0.02% 249 4702 0.02% 250 4392 0.02% 251 3915 0.01% 252 3637 0.01% 253 3421 0.01% 254 3135 0.01% 255 2802 0.01% 256 2552 0.01% 257 2383 0.01% 258 2261 0.01% 259 2005 0.01% 260 1854 0.01% 261 1666 0.01% 262 1550 0.01% 263 1280 0.00% 264 1238 0.00% 265 1113 0.00% 266 975 0.00% 267 921 0.00% 268 792 0.00% 269 762 0.00% 270 717 0.00% 271 599 0.00% 272 563 0.00% 273 500 0.00% 274 419 0.00% 275 359 0.00% 276 337 0.00% 277 282 0.00% 278 263 0.00% 279 236 0.00% 280 178 0.00% 281 182 0.00% 282 151 0.00% 283 119 0.00% 284 113 0.00% 285 84 0.00% 286 88 0.00% 287 69 0.00% 288 60 0.00% 289 53 0.00% 290 46 0.00% 291 45 0.00% 292 36 0.00% 293 33 0.00% 294 23 0.00% 295 23 0.00% 296 14 0.00% 297 20 0.00% 298 16 0.00% 299 10 0.00% 300 9 0.00% 301 8 0.00% 302 5 0.00% 303 6 0.00% 304 5 0.00% 305 8 0.00% 306 8 0.00% 307 5 0.00% 308 12 0.00% 309 5 0.00% 310 6 0.00% 311 5 0.00% 312 6 0.00% 313 7 0.00% 314 5 0.00% 315 3 0.00% 316 3 0.00% 317 4 0.00% 318 5 0.00% 319 4 0.00% 320 4 0.00% 321 3 0.00% 322 1 0.00% 323 2 0.00% 324 3 0.00% 325 7 0.00% 326 2 0.00% 327 3 0.00% 328 4 0.00% 329 2 0.00% 330 2 0.00% 331 2 0.00% 332 2 0.00% 333 3 0.00% 334 1 0.00% 335 2 0.00% 336 0 0.00% 337 1 0.00% 338 3 0.00% 339 3 0.00% 340 1 0.00% 341 3 0.00% 342 4 0.00% 343 0 0.00% 344 2 0.00% 345 0 0.00% 346 1 0.00% 347 2 0.00% 348 0 0.00% 349 2 0.00% 350 1 0.00% 351 1 0.00% 352 2 0.00% 353 0 0.00% 354 0 0.00% 355 2 0.00% 356 3 0.00% 357 1 0.00% 358 0 0.00% 359 2 0.00% 360 0 0.00% 361 0 0.00% 362 1 0.00% 363 2 0.00% 364 0 0.00% 365 1 0.00% 366 1 0.00% 367 4 0.00% 368 1 0.00% 27462187 reads passed initial QC criterion=sequence-density sequence-density=2.54 sequence-density-rank=1 fanout-score=2.94 fanout-score-rank=32 prefix-density=0.03 prefix-fanout=2.9 sequence=ACAGCTATCACACACAGGCAAAACACAGCTGATTCGTGTACTCGATCTCCCCAGCAAGTTAAGGCCACCATGTCGAGCGGCTGCGGCAACTGCGACTGCGCTGACAAGACCCAGTGTGTGAAGAAGGGAAACGGCTACGGCATCGTCATGGTTGACACCGAGAAGAGCCACTTCGAGGTGCAGGAGTCCGCGGCGGAGAACGACGGCAAGTGCAAGTGCGGCACCAGCTGC criterion=fanout-score sequence-density=0.02 sequence-density-rank=34 fanout-score=70.22 fanout-score-rank=1 prefix-density=0.23 prefix-fanout=5.9 sequence=CATCTCCTCCAGAGATTAAGGGTTTGATAAAGGATAAGAAGACAGCCAAGATCAAGAAGAACTCTGTTGCAGTCACCAAGTTCCTTGATGATT Potential 3prime adapter identified. Now checking if in reference sequence Warning: gzbuffer added in zlib v1.2.3.5. Unable to change buffer size from default of 8192. 1 reads; of these: 1 (100.00%) were unpaired; of these: 0 (0.00%) aligned 0 times 1 (100.00%) aligned exactly 1 time 0 (0.00%) aligned >1 times 100.00% overall alignment rate Potential adapter found in reference sequence. Continuing without clipping. Started job on | Dec 10 00:48:05 Started mapping on | Dec 10 00:48:05 Finished on | Dec 10 00:48:57 Mapping speed, Million of reads per hour | 1901.23 Number of input reads | 27462187 Average input read length | 120 UNIQUE READS: Uniquely mapped reads number | 23842627 Uniquely mapped reads % | 86.82% Average mapped length | 118.16 Number of splices: Total | 7831583 Number of splices: Annotated (sjdb) | 7138332 Number of splices: GT/AG | 7438872 Number of splices: GC/AG | 99391 Number of splices: AT/AC | 5886 Number of splices: Non-canonical | 287434 Mismatch rate per base, % | 0.40% Deletion rate per base | 0.26% Deletion average length | 1.17 Insertion rate per base | 0.22% Insertion average length | 1.16 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 881365 % of reads mapped to multiple loci | 3.21% Number of reads mapped to too many loci | 311495 % of reads mapped to too many loci | 1.13% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 8.22% % of reads unmapped: other | 0.62% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 2738195 2738195 2738195 N_multimapping 881365 881365 881365 N_noFeature 763069 926550 23195335 N_ambiguous 552066 75815 3289 UnstrandedReadsAssigned:22527492 PositiveStrandReadsAssigned:22840262 NegativeStrandReadsAssigned:644003 Dataset is classified positive stranded MeadianReadLen=120 20thPercentileLength=80 echo kmer=75 ERR1942995 Starting Kallisto single end mapping to ensembl reference transcriptome. kmer=31 [quant] fragment length distribution is truncated gaussian with mean = 100, sd = 20 [index] k-mer length: 31 [index] number of targets: 52,972 [index] number of k-mers: 66,720,672 [index] number of equivalence classes: 111,837 [quant] running in single-end mode [quant] will process file 1: ERR1942995-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 27,462,187 reads, 23,224,674 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,217 rounds 52973 ERR1942995.ke.tsv 35125 ERR1942995.se.tsv 88098 total ==> ERR1942995.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 837 0 0 PNS24247 1044 945 34.3932 2.18503 PNS24249 1928 1829 0 0 PNS24246 1044 945 34.3932 2.18503 PNS24248 1044 945 34.3932 2.18503 PNS24244 1471 1372 658.82 28.829 PNS24243 293 194 0 0 KQK14069 1603 1504 7155.45 285.631 KQK14071 474 375 1.34132 0.214742 ==> ERR1942995.se.tsv <== BRADI_1g14170v3 7093 BRADI_1g53295v3 0 BRADI_1g59795v3 618 BRADI_1g07683v3 0 BRADI_1g00485v3 85 BRADI_1g20270v3 1454 BRADI_1g74790v3 97 BRADI_1g09890v3 29 BRADI_1g77505v3 390 BRADI_1g48960v3 0 ERR1942995 completed mapping pipeline successfully