Starting /dee2/code/volunteer_pipeline.sh SRR11389781 current disk space = 1545579708416 free memory = 1601955148 SRR11389781 SRAfilesize 150803d53be0eb4da51d293cb5dc4921 SRR11389781.sra SRR11389781.sra file validated SRR11389781 is paired end SRR11389781 is conventional basespace SRR11389781 read1 length is 35-76 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR11389781_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 48 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 31.1475 32.0 32.0 32.0 32.0 32.0 2 31.065 32.0 32.0 32.0 32.0 32.0 3 31.146 32.0 32.0 32.0 32.0 32.0 4 31.2795 32.0 32.0 32.0 32.0 32.0 5 31.098 32.0 32.0 32.0 32.0 32.0 6 34.15025 36.0 36.0 36.0 32.0 36.0 7 34.301 36.0 36.0 36.0 32.0 36.0 8 34.21325 36.0 36.0 36.0 32.0 36.0 9 34.2375 36.0 36.0 36.0 32.0 36.0 10-11 34.307625 36.0 36.0 36.0 32.0 36.0 12-13 34.306875000000005 36.0 36.0 36.0 32.0 36.0 14-15 34.267875000000004 36.0 36.0 36.0 32.0 36.0 16-17 34.220125 36.0 36.0 36.0 32.0 36.0 18-19 34.266375 36.0 36.0 36.0 32.0 36.0 20-21 34.09375 36.0 36.0 36.0 32.0 36.0 22-23 33.984750000000005 36.0 36.0 36.0 32.0 36.0 24-25 33.915125 36.0 36.0 36.0 32.0 36.0 26-27 33.767125 36.0 36.0 36.0 32.0 36.0 28-29 33.777 36.0 36.0 36.0 32.0 36.0 30-31 33.755875 36.0 36.0 36.0 32.0 36.0 32-33 33.60525 36.0 36.0 36.0 29.5 36.0 34-35 33.43575 36.0 36.0 36.0 27.0 36.0 36-37 33.570156984623296 36.0 36.0 36.0 27.0 36.0 38-39 33.4585445220801 36.0 36.0 36.0 27.0 36.0 40-41 33.49460612142499 36.0 36.0 36.0 24.0 36.0 42-43 33.289387857501254 36.0 36.0 36.0 21.0 36.0 44-45 33.12457890571832 36.0 36.0 36.0 14.0 36.0 46-47 33.04278544542033 36.0 36.0 36.0 17.5 36.0 48-49 32.88255959849435 36.0 36.0 36.0 14.0 36.0 50-51 32.8573400250941 36.0 36.0 36.0 14.0 36.0 52-53 32.778168130489334 36.0 36.0 36.0 14.0 36.0 54-55 32.61242158092848 36.0 36.0 36.0 14.0 36.0 56-57 32.51731493099122 36.0 36.0 36.0 14.0 36.0 58-59 32.28878012048193 36.0 32.0 36.0 14.0 36.0 60-61 32.10303714859438 36.0 32.0 36.0 14.0 36.0 62-63 32.00627510040161 36.0 32.0 36.0 14.0 36.0 64-65 31.984939759036145 36.0 32.0 36.0 14.0 36.0 66-67 31.622066788368638 36.0 32.0 36.0 14.0 36.0 68-69 31.819106201355762 36.0 32.0 36.0 14.0 36.0 70-71 31.58955645013034 36.0 32.0 36.0 14.0 36.0 72-73 31.527382613228163 36.0 32.0 36.0 14.0 36.0 74-75 31.44835482069893 36.0 32.0 36.0 14.0 36.0 76 30.937221396731054 36.0 32.0 36.0 14.0 36.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 12.0 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 5.0 23 6.0 24 19.0 25 14.0 26 41.0 27 91.0 28 110.0 29 153.0 30 228.0 31 335.0 32 473.0 33 708.0 34 1084.0 35 715.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 43.25476429287863 12.086258776328988 12.41223671013039 32.246740220661984 2 23.89669007021063 16.0481444332999 31.770310932798395 28.284854563691077 3 24.799398194583752 20.561685055165498 23.921765295887663 30.71715145436309 4 28.46038114343029 25.977933801404212 20.43630892678034 25.125376128385156 5 25.526579739217652 28.109327983951854 23.996990972918756 22.367101303911735 6 23.952846751943817 30.975670930524203 25.20692249811889 19.864559819413092 7 16.07321965897693 24.974924774322968 38.03911735205617 20.91273821464393 8 19.68405215646941 24.77432296890672 30.29087261785356 25.25075225677031 9 20.91273821464393 20.81243731193581 34.503510531594785 23.771313941825476 10-11 21.76529588766299 31.89568706118355 23.019057171514543 23.319959879638915 12-13 21.915747241725175 25.78986960882648 27.19408224674022 25.100300902708124 14-15 21.354231974921632 27.548589341692793 27.398119122257054 23.69905956112853 16-17 22.981444332998997 26.567201604814443 25.238214643931794 25.213139418254766 18-19 22.05366098294885 25.36359077231695 27.05616850551655 25.526579739217652 20-21 22.191574724172515 25.90270812437312 26.993480441323968 24.912236710130394 22-23 22.479939819458377 27.068706118355063 25.514042126379138 24.937311935807422 24-25 22.68054162487462 25.5641925777332 26.06569709127382 25.689568706118354 26-27 22.12888665997994 26.31644934804413 25.313440320962886 26.241223671013035 28-29 22.843530591775327 25.601805416248745 26.04062186559679 25.514042126379138 30-31 21.95336008024072 25.952858575727184 26.466900702106315 25.626880641925776 32-33 22.291875626880643 26.68004012036108 26.178535606820464 24.849548645937812 34-35 22.094043887147336 26.244514106583072 25.253918495297807 26.407523510971785 36-37 23.322884012539184 26.156739811912228 24.71473354231975 25.805642633228842 38-39 22.450771353317446 26.652452025586353 25.837200551862537 25.059576069233664 40-41 22.9833145151173 26.03186551248275 26.370593401078914 24.614226571321037 42-43 22.9177119919719 24.761665830406425 26.9568489713999 25.363773206221772 44-45 22.832768786852338 25.40459164471208 25.68059214653118 26.082047421904402 46-47 23.663739021329988 24.617314930991217 24.855708908406523 26.86323713927227 48-49 22.634880803011292 25.671267252195733 26.373902132998744 25.319949811794228 50-51 22.659974905897116 25.207026348808032 25.144291091593473 26.988707653701383 52-53 23.324968632371395 25.181932245922205 24.391468005018822 27.10163111668758 54-55 23.02383939774153 25.972396486825595 25.558343789209538 25.44542032622334 56-57 21.25470514429109 26.787954830614808 25.269761606022584 26.687578419071517 58-59 22.126004016064257 25.514558232931726 25.891064257028113 26.468373493975903 60-61 23.431224899598394 25.589859437751006 25.815763052208833 25.16315261044177 62-63 23.1425702811245 24.78664658634538 26.945281124497996 25.12550200803213 64-65 23.2429718875502 25.12550200803213 26.92018072289157 24.711345381526105 66-67 22.455127400527175 25.517760763147983 25.806451612903224 26.220660223421614 68-69 23.38689430077831 25.069043434597038 24.918403213658046 26.62565905096661 70-71 22.06177800100452 25.565042692114513 25.77850326469111 26.594676042189853 72-73 23.557571176618797 25.157470395565635 25.283446712018144 26.00151171579743 74-75 23.457609128300387 22.727875812657555 26.681703595595064 27.13281146344699 76 26.411589895988115 0.0 37.22139673105498 36.367013372956905 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 24.0 1 13.0 2 1.5 3 0.5 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 1.0 18 11.5 19 19.5 20 15.5 21 16.0 22 21.0 23 20.0 24 16.5 25 15.0 26 17.5 27 33.5 28 35.0 29 25.0 30 38.0 31 54.5 32 63.5 33 64.0 34 65.5 35 86.5 36 104.5 37 104.0 38 120.0 39 145.0 40 146.5 41 151.0 42 169.0 43 187.5 44 190.0 45 185.5 46 190.0 47 184.5 48 187.0 49 197.0 50 189.5 51 160.0 52 135.0 53 126.5 54 123.5 55 130.5 56 136.0 57 127.5 58 119.0 59 116.5 60 118.5 61 111.0 62 98.5 63 85.0 64 65.0 65 64.5 66 57.0 67 46.5 68 49.0 69 43.5 70 34.5 71 34.5 72 37.0 73 27.5 74 22.0 75 25.5 76 22.0 77 19.5 78 15.0 79 8.5 80 8.5 81 7.5 82 3.5 83 0.5 84 1.0 85 1.0 86 1.0 87 1.5 88 0.5 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 0.3 2 0.3 3 0.3 4 0.3 5 0.3 6 0.325 7 0.3 8 0.3 9 0.3 10-11 0.3 12-13 0.3 14-15 0.3125 16-17 0.3 18-19 0.3 20-21 0.3 22-23 0.3 24-25 0.3 26-27 0.3 28-29 0.3 30-31 0.3 32-33 0.3 34-35 0.3125 36-37 0.0 38-39 0.0 40-41 0.012543903662819869 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 12.0 36 1.0 37 0.0 38 1.0 39 0.0 40 0.0 41 0.0 42 0.0 43 0.0 44 1.0 45 0.0 46 0.0 47 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 1.0 58 0.0 59 0.0 60 0.0 61 0.0 62 0.0 63 0.0 64 0.0 65 0.0 66 1.0 67 0.0 68 0.0 69 0.0 70 2.0 71 2.0 72 20.0 73 62.0 74 257.0 75 948.0 76 2692.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 92.575 #Duplication Level Percentage of deduplicated Percentage of total 1 95.57115852011883 88.47500000000001 2 3.132595193086687 5.800000000000001 3 0.702133405347016 1.95 4 0.21604104779908181 0.8 5 0.13502565487442614 0.625 6 0.08101539292465569 0.44999999999999996 7 0.027005130974885227 0.17500000000000002 8 0.0 0.0 9 0.0 0.0 >10 0.13502565487442614 1.725 >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 GCCGAGTTTAATTGCAGTCAATTAGAAGAATAAAGAAGAATTACTGCATT 23 0.575 No Hit GCGGCTAGTTCAGGACTCCATTTGCAAGCTGCTCGGATAATTTCATTACC 13 0.325 No Hit NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN 12 0.3 No Hit AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 11 0.27499999999999997 No Hit GCGCGAACTCGAATTTGATCGCCTTCCATACTTCACAAGCTGCGGCTAGT 10 0.25 No Hit GTTTTATCTATTAATCGATAGTATCTACCGGCGCGAACTCGAATTTGATC 7 0.17500000000000002 No Hit CTAGTTCAGGACTCCATTTGCAAGCTGCTCGGATAATTTCATTACCTTCA 6 0.15 No Hit CAAAGATTTCGGTCAGAGCTGGCATATGCCAAACATGAATACCACCTGAAGCTACTGGTATAACACCTGGCATGG 6 0.15 No Hit GTCAATTAGAAGAATAAAGAAGAATTACTGCATTTCGTAACTTATTTTTT 6 0.15 No Hit GCTAGTTCAGGACTCCATTTGCAAGCTGCTCGGATAATTTCATTACCTTC 5 0.125 No Hit CTTCCATACTTCACAAGCTGCGGCTAGTTCAGGACTCCATTTGCAAGCTGCTCGGATAATTTCATTACCTTCACG 5 0.125 No Hit GTTCAGGACTCCATTTGCAAGCTGCTCGGATAATTTCATTACCTTCACGA 5 0.125 No Hit GCATTTCGTAACTTATTTTTTCTCTTTTTATTTTGTTTCTTTTTATTTAGACCTTCTTCATATTTAGTTTTATCT 5 0.125 No Hit GTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGCATTCCTCGTTGAAGACCAACA 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 SRR11389781 read2 length is 35-76 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR11389781_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 30.60425 32.0 32.0 32.0 32.0 32.0 2 30.18 32.0 32.0 32.0 21.0 32.0 3 30.084 32.0 32.0 32.0 21.0 32.0 4 29.974 32.0 32.0 32.0 21.0 32.0 5 29.97875 32.0 32.0 32.0 21.0 32.0 6 33.1365 36.0 36.0 36.0 21.0 36.0 7 33.096 36.0 36.0 36.0 21.0 36.0 8 33.07925 36.0 36.0 36.0 21.0 36.0 9 33.09825 36.0 36.0 36.0 21.0 36.0 10-11 32.94625 36.0 36.0 36.0 17.5 36.0 12-13 33.10425 36.0 36.0 36.0 21.0 36.0 14-15 32.950625 36.0 36.0 36.0 17.5 36.0 16-17 32.91825 36.0 36.0 36.0 17.5 36.0 18-19 32.918 36.0 36.0 36.0 14.0 36.0 20-21 32.7035 36.0 36.0 36.0 14.0 36.0 22-23 32.541 36.0 36.0 36.0 14.0 36.0 24-25 32.553 36.0 36.0 36.0 14.0 36.0 26-27 32.494625 36.0 36.0 36.0 14.0 36.0 28-29 32.381375000000006 36.0 36.0 36.0 14.0 36.0 30-31 32.395125 36.0 36.0 36.0 14.0 36.0 32-33 32.262375 36.0 36.0 36.0 14.0 36.0 34-35 32.341875 36.0 36.0 36.0 14.0 36.0 36-37 32.24629676123525 36.0 32.0 36.0 14.0 36.0 38-39 32.40449988795929 36.0 36.0 36.0 14.0 36.0 40-41 32.173782019085884 36.0 34.0 36.0 14.0 36.0 42-43 31.90745856353591 36.0 32.0 36.0 14.0 36.0 44-45 31.930939226519335 36.0 32.0 36.0 14.0 36.0 46-47 31.80399296835761 36.0 32.0 36.0 14.0 36.0 48-49 31.73392767453541 36.0 32.0 36.0 14.0 36.0 50-51 31.650552486187845 36.0 32.0 36.0 14.0 36.0 52-53 31.48066298342541 36.0 32.0 36.0 14.0 36.0 54-55 31.407709693621296 36.0 32.0 36.0 14.0 36.0 56-57 31.344299347061778 36.0 32.0 36.0 14.0 36.0 58-59 31.091811102738006 36.0 32.0 36.0 14.0 36.0 60-61 30.906430545089172 36.0 32.0 36.0 14.0 36.0 62-63 30.53516704345642 36.0 29.5 36.0 14.0 36.0 64-65 30.68324541572469 36.0 29.5 36.0 14.0 36.0 66-67 30.694925898015573 36.0 27.0 36.0 14.0 36.0 68-69 30.501130369253957 36.0 29.5 36.0 14.0 36.0 70-71 30.328802005605056 36.0 27.0 36.0 14.0 36.0 72-73 30.1027447289313 36.0 27.0 36.0 14.0 36.0 74-75 29.99261144666602 36.0 27.0 36.0 14.0 36.0 76 28.868003025718608 32.0 21.0 36.0 14.0 36.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 17.0 3 0.0 4 1.0 5 2.0 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 4.0 15 12.0 16 35.0 17 23.0 18 7.0 19 11.0 20 13.0 21 14.0 22 30.0 23 29.0 24 47.0 25 70.0 26 82.0 27 135.0 28 168.0 29 178.0 30 277.0 31 361.0 32 483.0 33 670.0 34 885.0 35 446.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 43.35927692693949 18.45342706502636 10.268641727341201 27.918654280692945 2 30.68039166457444 22.093899071051972 27.039919658548833 20.185789605824755 3 27.215666582977654 26.638212402711524 21.616871704745165 24.529249309565653 4 29.927190559879485 30.68039166457444 17.8508661812704 21.54155159427567 5 29.399949786593023 31.75997991463721 19.758975646497614 19.081094652272157 6 24.35350238513683 32.91488827516947 21.54155159427567 21.190057745418027 7 24.127542053728344 18.30278684408737 32.13658046698468 25.433090635199594 8 26.286718553853877 22.671353251318102 21.842832036153652 29.199096158674365 9 25.633944263118252 22.721566658297764 25.257343710770776 26.387145367813208 10-11 27.681487063551874 28.422506907812107 19.957297161517207 23.938708867118812 12-13 27.8643216080402 21.49497487437186 23.70603015075377 26.934673366834172 14-15 27.305855742648905 24.50364413169138 24.08896707715506 24.10153304850465 16-17 28.575018848957022 23.72455390801709 23.309876853480773 24.390550389545112 18-19 28.592964824120603 24.271356783919597 23.203517587939697 23.9321608040201 20-21 27.23730517848165 25.565610859728505 22.825540472599297 24.371543489190547 22-23 28.192559074912015 25.565610859728505 22.76269482151835 23.479135243841124 24-25 26.84091480271425 26.024126664991204 23.309876853480773 23.825081678813774 26-27 28.343388637506283 24.698340874811464 23.68024132730015 23.2780291603821 28-29 27.41206030150754 24.384422110552766 23.417085427135678 24.78643216080402 30-31 27.32412060301507 25.43969849246231 22.964824120603016 24.271356783919597 32-33 28.27889447236181 25.037688442211053 23.366834170854272 23.316582914572866 34-35 27.11161387631976 25.666163901458017 23.26546003016591 23.95676219205631 36-37 26.643207238909138 25.399019731054416 24.117129571446526 23.840643458589923 38-39 26.70940170940171 24.811463046757165 23.95676219205631 24.522373051784815 40-41 27.368685599396837 25.245036441316916 22.958029655692386 24.42824830359387 42-43 26.700188560653675 26.23507228158391 23.93463230672533 23.130106851037084 44-45 27.244153884837818 24.415388483781744 23.472466683429722 24.867990947950716 46-47 27.670268911786884 25.58431766775572 22.844935913546117 23.900477506911283 48-49 26.502388735227562 23.72391249685693 24.805129494593913 24.9685692733216 50-51 27.22473604826546 25.062845651080945 23.202614379084967 24.509803921568626 52-53 27.174459527400703 25.314228255404725 23.893916540975365 23.617395676219203 54-55 27.632570997738128 25.094244785121887 23.72455390801709 23.548630309122895 56-57 27.24644966695991 25.587532989820282 23.37564408696745 23.790373256252355 58-59 27.75961780236359 25.521750062861454 23.195876288659793 23.52275584611516 60-61 27.565392354124747 24.962273641851105 23.893360160965795 23.57897384305835 62-63 27.941176470588236 24.56008044243338 23.65510306686777 23.84364002011061 64-65 27.583605732964543 25.898918783002262 23.10787025396027 23.40960523007292 66-67 28.092006033182503 24.98743086978381 23.692810457516337 23.227752639517345 68-69 26.389238119185315 25.836057329645463 24.51596680915263 23.258737742016596 70-71 26.732050798440838 25.650697849867974 23.802338740098076 23.81491261159311 72-73 26.966860612193273 25.044270174550974 23.298760435112573 24.690108778143184 74-75 26.830579067580278 23.216444981862153 24.425634824667473 25.527341125890096 76 29.344945096554337 0.0 34.75956077243468 35.89549413101098 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 26.0 1 14.0 2 1.0 3 0.5 4 1.0 5 2.5 6 2.0 7 0.5 8 1.0 9 0.5 10 0.5 11 1.5 12 2.0 13 2.0 14 1.5 15 1.5 16 2.5 17 3.0 18 3.0 19 4.5 20 8.5 21 9.5 22 8.0 23 9.5 24 15.0 25 18.5 26 16.0 27 17.0 28 19.0 29 16.0 30 18.0 31 25.0 32 29.5 33 34.5 34 42.5 35 57.5 36 71.5 37 80.5 38 100.5 39 117.5 40 123.5 41 135.0 42 147.5 43 168.5 44 169.5 45 150.5 46 157.5 47 175.5 48 191.5 49 181.5 50 156.0 51 161.0 52 160.0 53 148.0 54 155.0 55 152.5 56 148.5 57 147.5 58 138.5 59 126.5 60 128.5 61 125.0 62 114.5 63 101.5 64 84.5 65 79.0 66 72.5 67 69.5 68 72.5 69 73.0 70 67.5 71 64.0 72 56.5 73 48.5 74 46.0 75 42.5 76 34.5 77 26.0 78 18.5 79 13.0 80 9.5 81 7.5 82 6.5 83 5.5 84 4.0 85 4.5 86 4.0 87 1.5 88 1.0 89 2.0 90 1.5 91 0.0 92 0.0 93 0.5 94 1.0 95 0.5 96 0.0 97 0.0 98 0.5 99 2.5 100 4.0 >>END_MODULE >>Per base N content pass #Base N-Count 1 0.42500000000000004 2 0.42500000000000004 3 0.42500000000000004 4 0.42500000000000004 5 0.42500000000000004 6 0.42500000000000004 7 0.42500000000000004 8 0.42500000000000004 9 0.42500000000000004 10-11 0.475 12-13 0.5 14-15 0.525 16-17 0.525 18-19 0.5 20-21 0.5499999999999999 22-23 0.5499999999999999 24-25 0.525 26-27 0.5499999999999999 28-29 0.5 30-31 0.5 32-33 0.5 34-35 0.5499999999999999 36-37 0.11298016570424303 38-39 0.11299435028248588 40-41 0.07533902561526871 42-43 0.11300853842290307 44-45 0.12556504269211452 46-47 0.07533902561526871 48-49 0.12556504269211452 50-51 0.10045203415369162 52-53 0.10045203415369162 54-55 0.07533902561526871 56-57 0.08789552988448016 58-59 0.10047726701833709 60-61 0.12559658377292138 62-63 0.07535795026375283 64-65 0.10047726701833709 66-67 0.07535795026375283 68-69 0.10047726701833709 70-71 0.07538635506973237 72-73 0.07583417593528817 74-75 0.08054772452678212 76 0.11346444780635401 >>END_MODULE >>Sequence Length Distribution warn #Length Count 35 17.0 36 0.0 37 0.0 38 1.0 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 1.0 58 0.0 59 0.0 60 0.0 61 0.0 62 0.0 63 0.0 64 0.0 65 0.0 66 0.0 67 0.0 68 0.0 69 0.0 70 3.0 71 11.0 72 22.0 73 76.0 74 289.0 75 936.0 76 2644.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 94.325 #Duplication Level Percentage of deduplicated Percentage of total 1 96.31592896899019 90.85 2 2.570898489265836 4.8500000000000005 3 0.6626027034190299 1.875 4 0.23853697323085077 0.8999999999999999 5 0.0795123244102836 0.375 6 0.026504108136761195 0.15 7 0.05300821627352239 0.35000000000000003 8 0.0 0.0 9 0.026504108136761195 0.22499999999999998 >10 0.026504108136761195 0.42500000000000004 >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 NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN 17 0.42500000000000004 No Hit CTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTG 9 0.22499999999999998 No Hit CTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGGGGAAATGCA 7 0.17500000000000002 No Hit AAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAAGGCGATCAAATTCG 7 0.17500000000000002 No Hit GGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACA 6 0.15 No Hit GAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGCACCCTAGATGGCTAAAGTCCAGTAGCCGA 5 0.125 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 5 0.125 No Hit GGGAACGCGAAATCACTTTAGGTTTTGTTGATTTATTGCGCGACGATTTT 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 487845 spots for SRR11389781.sra Written 487845 spots for SRR11389781.sra Read 487845 spots for SRR11389781.sra Written 487845 spots for SRR11389781.sra Read 487845 spots for SRR11389781.sra Written 487845 spots for SRR11389781.sra Read 487845 spots for SRR11389781.sra Written 487845 spots for SRR11389781.sra Read 487845 spots for SRR11389781.sra Written 487845 spots for SRR11389781.sra Read 487845 spots for SRR11389781.sra Written 487845 spots for SRR11389781.sra Read 487845 spots for SRR11389781.sra Written 487845 spots for SRR11389781.sra Read 487845 spots for SRR11389781.sra Written 487845 spots for SRR11389781.sra Read 487845 spots for SRR11389781.sra Written 487845 spots for SRR11389781.sra Read 487845 spots for SRR11389781.sra Written 487845 spots for SRR11389781.sra Read 487845 spots for SRR11389781.sra Written 487845 spots for SRR11389781.sra Read 487845 spots for SRR11389781.sra Written 487845 spots for SRR11389781.sra Read 487845 spots for SRR11389781.sra Written 487845 spots for SRR11389781.sra Read 487845 spots for SRR11389781.sra Written 487845 spots for SRR11389781.sra Read 487845 spots for SRR11389781.sra Written 487845 spots for SRR11389781.sra Read 487845 spots for SRR11389781.sra Written 487845 spots for SRR11389781.sra Read 487845 spots for SRR11389781.sra Written 487845 spots for SRR11389781.sra Read 487845 spots for SRR11389781.sra Written 487845 spots for SRR11389781.sra Read 487863 spots for SRR11389781.sra Written 487863 spots for SRR11389781.sra Read 487845 spots for SRR11389781.sra Written 487845 spots for SRR11389781.sra SRR ids: ['SRR11389781.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_utlwrl1v SRR11389781.sra spots: 9756918 blocks: [[1, 487845], [487846, 975690], [975691, 1463535], [1463536, 1951380], [1951381, 2439225], [2439226, 2927070], [2927071, 3414915], [3414916, 3902760], [3902761, 4390605], [4390606, 4878450], [4878451, 5366295], [5366296, 5854140], [5854141, 6341985], [6341986, 6829830], [6829831, 7317675], [7317676, 7805520], [7805521, 8293365], [8293366, 8781210], [8781211, 9269055], [9269056, 9756918]] SRR11389781 file size 1841135 SRR11389781 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 SRR11389781 SRR11389781_1.fastq SRR11389781_2.fastq Input file: SRR11389781_1.fastq Paired file: SRR11389781_2.fastq trimmed: SRR11389781-trimmed-pair1.fastq, SRR11389781-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 06:16:37 2024 >> started Sat Dec 7 06:16:45 2024 >> done (8.318s) 9756918 read pairs processed; of these: 529 ( 0.01%) short read pairs filtered out after trimming by size control 204346 ( 2.09%) empty read pairs filtered out after trimming by size control 9552043 (97.90%) read pairs available; of these: 24374 ( 0.26%) trimmed read pairs available after processing 9527669 (99.74%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 105 0.00% 19 77 0.00% 20 148 0.00% 21 95 0.00% 22 214 0.00% 23 87 0.00% 24 240 0.00% 25 64 0.00% 26 234 0.00% 27 49 0.00% 28 229 0.00% 29 44 0.00% 30 219 0.00% 31 31 0.00% 32 171 0.00% 33 18 0.00% 34 167 0.00% 35 110 0.00% 36 637 0.01% 37 64 0.00% 38 430 0.00% 39 79 0.00% 40 282 0.00% 41 73 0.00% 42 174 0.00% 43 127 0.00% 44 253 0.00% 45 110 0.00% 46 184 0.00% 47 172 0.00% 48 208 0.00% 49 184 0.00% 50 225 0.00% 51 205 0.00% 52 258 0.00% 53 289 0.00% 54 313 0.00% 55 590 0.01% 56 618 0.01% 57 596 0.01% 58 653 0.01% 59 590 0.01% 60 651 0.01% 61 539 0.01% 62 689 0.01% 63 747 0.01% 64 835 0.01% 65 916 0.01% 66 921 0.01% 67 1188 0.01% 68 970 0.01% 69 1321 0.01% 70 1578 0.02% 71 2663 0.03% 72 11170 0.12% 73 86608 0.91% 74 694409 7.27% 75 4329727 45.33% 76 4407495 46.14% 9552043 reads passed initial QC criterion=sequence-density sequence-density=1.47 sequence-density-rank=1 fanout-score=2.02 fanout-score-rank=23 prefix-density=1.39 prefix-fanout=2.0 sequence=TTCAAATGTACA criterion=fanout-score sequence-density=0.04 sequence-density-rank=27 fanout-score=12.58 fanout-score-rank=1 prefix-density=0.19 prefix-fanout=2.4 sequence=GATCCTTCCGCAGGTTCACCTACGGAAACCTTGTTACGACTTCTCCTTCCTCTAAATGATAAGGTTCAATGGACTTCTCGCGACGTCGGCGGCGGCGAACCGCCCCCGTCGCCGCGATCCGAACACTTCACCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGCATTCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCTATATACTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCGTCGCCTAAACGGCGATAGTCCCTCTAAGAAGCTAGCTGCGGAGGGATGGCTCCGCATAGCTAGTTAGCAGGCTGAGGTCTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCAC criterion=sequence-density sequence-density=0.52 sequence-density-rank=1 fanout-score=2.77 fanout-score-rank=16 prefix-density=0.57 prefix-fanout=2.6 sequence=CAGGTGCTCAAGGAGCTGGAGGAGGTCAAGAAGGAGTACCCGGACGCCTA criterion=fanout-score sequence-density=0.01 sequence-density-rank=31 fanout-score=23.86 fanout-score-rank=1 prefix-density=0.04 prefix-fanout=3.2 sequence=CCTCAAGCCAAAGCCTCTTGCTAAGCGTACCACACTATACAGACGTGCGCGCGCAGCCATGGCACCCACCGTGATGGCTTCCTCCGCCACCTCCGTGGC SRR11389781 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 07 06:17:28 Started mapping on | Dec 07 06:17:28 Finished on | Dec 07 06:18:52 Mapping speed, Million of reads per hour | 409.37 Number of input reads | 9552043 Average input read length | 151 UNIQUE READS: Uniquely mapped reads number | 6745023 Uniquely mapped reads % | 70.61% Average mapped length | 149.71 Number of splices: Total | 1950869 Number of splices: Annotated (sjdb) | 1840149 Number of splices: GT/AG | 1923977 Number of splices: GC/AG | 22722 Number of splices: AT/AC | 407 Number of splices: Non-canonical | 3763 Mismatch rate per base, % | 1.39% Deletion rate per base | 0.01% Deletion average length | 1.78 Insertion rate per base | 0.01% Insertion average length | 1.66 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 1383702 % of reads mapped to multiple loci | 14.49% Number of reads mapped to too many loci | 137618 % of reads mapped to too many loci | 1.44% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 7.34% % of reads unmapped: other | 6.12% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 1423319 1423319 1423319 N_multimapping 1383702 1383702 1383702 N_noFeature 324334 6521328 380497 N_ambiguous 251818 2113 95921 UnstrandedReadsAssigned:6168871 PositiveStrandReadsAssigned:221582 NegativeStrandReadsAssigned:6268605 Dataset is classified negative stranded MeadianReadLen=76 20thPercentileLength=75 echo kmer=71 SRR11389781 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: SRR11389781-trimmed-pair1.fastq SRR11389781-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 9,552,043 reads, 7,439,326 reads pseudoaligned [quant] estimated average fragment length: 205.046 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,069 rounds 52973 SRR11389781.ke.tsv 35125 SRR11389781.se.tsv 88098 total ==> SRR11389781.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 732.03 10.69 2.41382 PNS24247 1044 839.954 2.59428 0.510523 PNS24249 1928 1723.95 15.0893 1.44677 PNS24246 1044 839.954 2.59428 0.510523 PNS24248 1044 839.954 2.59428 0.510523 PNS24244 1471 1266.95 24.4378 3.18828 PNS24243 293 101.751 0 0 KQK14069 1603 1398.95 217.969 25.754 KQK14071 474 271.393 4.25438 2.59114 ==> SRR11389781.se.tsv <== BRADI_1g14170v3 243 BRADI_1g53295v3 1 BRADI_1g59795v3 60 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 31 BRADI_1g74790v3 107 BRADI_1g09890v3 0 BRADI_1g77505v3 94 BRADI_1g48960v3 0 SRR11389781 completed mapping pipeline successfully