Starting /dee2/code/volunteer_pipeline.sh SRR11389775 current disk space = 1545960456192 free memory = 1601913228 SRR11389775 SRAfilesize 9d199d816e1749f24a858d3617adab41 SRR11389775.sra SRR11389775.sra file validated SRR11389775 is paired end SRR11389775 is conventional basespace SRR11389775 read1 length is 35-76 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR11389775_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 31.20525 32.0 32.0 32.0 32.0 32.0 2 31.14125 32.0 32.0 32.0 32.0 32.0 3 31.02575 32.0 32.0 32.0 32.0 32.0 4 31.0695 32.0 32.0 32.0 32.0 32.0 5 31.092 32.0 32.0 32.0 32.0 32.0 6 34.114 36.0 36.0 36.0 32.0 36.0 7 34.23925 36.0 36.0 36.0 32.0 36.0 8 34.0555 36.0 36.0 36.0 32.0 36.0 9 34.09825 36.0 36.0 36.0 32.0 36.0 10-11 34.14975 36.0 36.0 36.0 32.0 36.0 12-13 34.268249999999995 36.0 36.0 36.0 32.0 36.0 14-15 34.14575 36.0 36.0 36.0 32.0 36.0 16-17 34.178749999999994 36.0 36.0 36.0 32.0 36.0 18-19 34.107625 36.0 36.0 36.0 32.0 36.0 20-21 33.978750000000005 36.0 36.0 36.0 32.0 36.0 22-23 34.102374999999995 36.0 36.0 36.0 32.0 36.0 24-25 34.000875 36.0 36.0 36.0 32.0 36.0 26-27 33.821 36.0 36.0 36.0 32.0 36.0 28-29 33.783500000000004 36.0 36.0 36.0 32.0 36.0 30-31 33.568625 36.0 36.0 36.0 32.0 36.0 32-33 33.557500000000005 36.0 36.0 36.0 27.0 36.0 34-35 33.577875000000006 36.0 36.0 36.0 29.5 36.0 36-37 33.68282270215972 36.0 36.0 36.0 29.5 36.0 38-39 33.73493219487695 36.0 36.0 36.0 29.5 36.0 40-41 33.51770467101959 36.0 36.0 36.0 27.0 36.0 42-43 33.43721747865394 36.0 36.0 36.0 24.0 36.0 44-45 33.38929481208518 36.0 36.0 36.0 24.0 36.0 46-47 33.42137653855815 36.0 36.0 36.0 24.0 36.0 48-49 33.0435820145692 36.0 36.0 36.0 17.5 36.0 50-51 33.062919249601435 36.0 36.0 36.0 14.0 36.0 52-53 32.902638190954775 36.0 36.0 36.0 14.0 36.0 54-55 32.755904522613065 36.0 36.0 36.0 14.0 36.0 56-57 32.53920583061071 36.0 34.0 36.0 14.0 36.0 58-59 32.36089469716009 36.0 34.0 36.0 14.0 36.0 60-61 32.45727569741141 36.0 36.0 36.0 14.0 36.0 62-63 32.10105580693816 36.0 32.0 36.0 14.0 36.0 64-65 32.14901696449757 36.0 32.0 36.0 14.0 36.0 66-67 31.848824551080064 36.0 32.0 36.0 14.0 36.0 68-69 31.68931901431796 36.0 32.0 36.0 14.0 36.0 70-71 31.769023632017614 36.0 32.0 36.0 14.0 36.0 72-73 31.55648096809816 36.0 32.0 36.0 14.0 36.0 74-75 31.38590823826855 36.0 32.0 36.0 14.0 36.0 76 30.647403072421362 36.0 32.0 36.0 14.0 36.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 18.0 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 1.0 19 0.0 20 0.0 21 1.0 22 6.0 23 3.0 24 9.0 25 19.0 26 31.0 27 76.0 28 101.0 29 180.0 30 246.0 31 333.0 32 454.0 33 662.0 34 1115.0 35 745.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 41.296156744536546 12.459181110273802 13.890982165285104 32.35367997990455 2 23.907584128578605 14.866901054746359 34.58061275740833 26.644902059266702 3 21.99899547965846 21.948769462581616 24.585635359116022 31.4665996986439 4 27.800100452034155 28.02611752887996 19.588146659969865 24.585635359116022 5 25.288799598191865 31.64239075841286 22.626820693119036 20.441988950276244 6 22.350577599196384 31.215469613259668 26.519337016574585 19.914615770969363 7 16.675037669512808 23.27975891511803 39.97990959316926 20.0652938221999 8 18.031140130587644 23.505775991963837 32.446007031642395 26.017076845806127 9 19.763937719738824 22.425916624811652 34.229030637870416 23.58111501757911 10-11 21.572074334505274 30.97689603214465 23.191863385233553 24.25916624811652 12-13 21.433952787543948 24.183827222501257 28.327473631341032 26.054746358613762 14-15 21.911099949773984 25.665494726268207 28.013561024610752 24.40984429934706 16-17 22.76494224008036 25.64038171772978 26.381215469613263 25.213460572576597 18-19 22.325464590657962 25.35158211953792 27.51130085384229 24.81165243596183 20-21 22.388247112004017 26.795580110497237 26.695128076343543 24.1210447011552 22-23 22.275238573581117 25.991963837267708 27.36062280261175 24.37217478653943 24-25 22.664490205926672 25.464590657960823 26.670015067805124 25.200904068307384 26-27 22.275238573581117 26.582119537920647 26.406328478151682 24.736313410346558 28-29 22.363134103465594 26.004520341536917 26.13008538422903 25.50226017076846 30-31 21.911099949773984 26.04218985434455 26.933701657458563 25.113008538422903 32-33 22.50125565042692 26.833249623304873 26.067302862882975 24.59819186338523 34-35 23.204419889502763 25.69060773480663 26.481667503766953 24.623304871923658 36-37 23.07885484681065 26.406328478151682 25.816172777498746 24.698643897538926 38-39 22.833458929917107 25.898015573976384 26.136649083144935 25.131876412961567 40-41 22.682743029389602 25.596583772921377 26.68927405174579 25.03139914594323 42-43 22.50125565042692 24.949773982923155 27.611752887995983 24.937217478653942 44-45 21.750596508853448 25.568253170915483 27.087780987065173 25.593369333165896 46-47 22.92713567839196 25.037688442211053 25.339195979899497 26.695979899497484 48-49 21.969601808817988 24.758196206506717 27.220198467529205 26.052003517146087 50-51 22.91457286432161 24.77386934673367 26.507537688442213 25.804020100502512 52-53 23.44515642668677 24.17389119236085 26.20932277924362 26.17162960170876 54-55 22.78210605679819 25.270168384016085 26.551897461673786 25.395828097511934 56-57 23.237401030539147 25.248209124041725 25.49956013572955 26.01482970968958 58-59 22.131456579112733 25.51212768631394 26.56780193540279 25.78861379917054 60-61 22.473604826546005 24.773755656108598 26.82252388134741 25.930115635997993 62-63 23.40960523007292 24.893135529293435 26.967563490067892 24.729695750565753 64-65 22.89989939637827 24.949698189134807 26.672535211267608 25.47786720321932 66-67 22.6946785759215 25.210718329349604 25.852308466473772 26.242294628255124 68-69 22.58998238107224 23.87364711804682 27.05763906367984 26.47873143720111 70-71 22.672880715455346 25.066129235420075 26.741403199395393 25.519586849729187 72-73 23.289057558507274 24.60468058191018 25.85705249841872 26.24920936116382 74-75 23.62717723706954 23.294774631033107 26.153437042946415 26.92461108895094 76 25.969275786393563 0.0 38.47841989758595 35.55230431602048 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 18.0 1 9.0 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 1.0 16 2.5 17 3.5 18 9.5 19 19.5 20 26.5 21 30.5 22 28.5 23 23.0 24 17.5 25 14.5 26 26.0 27 44.5 28 46.5 29 41.5 30 47.5 31 57.0 32 59.0 33 63.5 34 77.5 35 92.0 36 107.0 37 120.0 38 139.5 39 150.5 40 143.0 41 161.0 42 181.5 43 177.5 44 182.0 45 193.5 46 193.5 47 179.0 48 176.5 49 181.5 50 163.0 51 146.0 52 130.5 53 113.0 54 110.5 55 119.0 56 124.5 57 112.5 58 106.0 59 108.5 60 101.5 61 91.5 62 85.0 63 72.0 64 58.0 65 60.5 66 56.0 67 43.0 68 46.0 69 48.0 70 47.0 71 49.0 72 45.5 73 38.0 74 25.5 75 17.0 76 18.0 77 20.5 78 15.5 79 7.0 80 7.0 81 8.0 82 5.0 83 3.0 84 2.5 85 2.0 86 2.0 87 2.0 88 1.0 89 0.0 90 0.0 91 0.0 92 0.0 93 0.0 94 0.0 95 0.0 96 0.0 97 0.0 98 0.0 99 0.0 100 0.0 >>END_MODULE >>Per base N content pass #Base N-Count 1 0.475 2 0.44999999999999996 3 0.44999999999999996 4 0.44999999999999996 5 0.44999999999999996 6 0.44999999999999996 7 0.44999999999999996 8 0.44999999999999996 9 0.44999999999999996 10-11 0.44999999999999996 12-13 0.44999999999999996 14-15 0.44999999999999996 16-17 0.44999999999999996 18-19 0.44999999999999996 20-21 0.44999999999999996 22-23 0.44999999999999996 24-25 0.44999999999999996 26-27 0.44999999999999996 28-29 0.44999999999999996 30-31 0.44999999999999996 32-33 0.44999999999999996 34-35 0.44999999999999996 36-37 0.0 38-39 0.025113008538422906 40-41 0.025113008538422906 42-43 0.0 44-45 0.0 46-47 0.025119316754584273 48-49 0.012559658377292136 50-51 0.012561236025624922 52-53 0.01256281407035176 54-55 0.02512562814070352 56-57 0.012565971349585321 58-59 0.012565971349585321 60-61 0.025131942699170642 62-63 0.025138260432378077 64-65 0.01257387149503332 66-67 0.025154068670607474 68-69 0.012583364791745311 70-71 0.0 72-73 0.012648621300278268 74-75 0.0 76 0.0 >>END_MODULE >>Sequence Length Distribution warn #Length Count 35 18.0 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 1.0 45 0.0 46 0.0 47 0.0 48 0.0 49 0.0 50 1.0 51 0.0 52 0.0 53 0.0 54 0.0 55 1.0 56 0.0 57 0.0 58 0.0 59 0.0 60 0.0 61 1.0 62 0.0 63 1.0 64 1.0 65 0.0 66 1.0 67 1.0 68 1.0 69 2.0 70 3.0 71 10.0 72 10.0 73 60.0 74 255.0 75 899.0 76 2734.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 94.35 #Duplication Level Percentage of deduplicated Percentage of total 1 97.08532061473238 91.60000000000001 2 2.0402755696873345 3.85 3 0.39745627980922094 1.125 4 0.1589825119236884 0.6 5 0.10598834128245893 0.5 6 0.026497085320614733 0.15 7 0.052994170641229466 0.35000000000000003 8 0.0 0.0 9 0.052994170641229466 0.44999999999999996 >10 0.0794912559618442 1.375 >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 27 0.675 No Hit NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN 18 0.44999999999999996 No Hit GTCAATTAGAAGAATAAAGAAGAATTACTGCATTTCGTAACTTATTTTTT 10 0.25 No Hit CCGAGTTTAATTGCAGTCAATTAGAAGAATAAAGAAGAATTACTGCATTT 9 0.22499999999999998 No Hit CTTTCTTTTCCTCTGGCTACTAAGATGTTTCAGTTCGCCAGGTTGTCTCTTGCCTGCTCATGGATTCAGCAGGC 9 0.22499999999999998 No Hit GTTCAGGACTCCATTTGCAAGCTGCTCGGATAATTTCATTACCTTCACGA 7 0.17500000000000002 No Hit GTCAGGGTTCAAATGTACATATGCTCCTCGAGCCCATGTCGGTACATTCA 7 0.17500000000000002 No Hit GTTCTTTTCACCTTTCCCTCACGGTACTACTTCGCTATCGGTCACCCAGG 6 0.15 No Hit AGAAGAATTACTGCATTTCGTAACTTATTTTTTCTCTTTTTATTTTGTTT 5 0.125 No Hit GTAACTTATTTTTTCTCTTTTTATTTTGTTTCTTTTTATTTAGACCTTCT 5 0.125 No Hit GCATTTCGTAACTTATTTTTTCTCTTTTTATTTTGTTTCTTTTTATTTAGACCTTCTTCATATTTAGTTTTATCT 5 0.125 No Hit CTTCTTCATATTTAGTTTTATCTATTAATCGATAGTATCTACCGGCGCGA 5 0.125 No Hit >>END_MODULE >>Adapter Content pass #Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence SOLID Small RNA Adapter 1 0.0 0.0 0.0 0.0 0.0 2 0.0 0.0 0.0 0.0 0.0 3 0.0 0.0 0.0 0.0 0.0 4 0.0 0.0 0.0 0.0 0.0 5 0.0 0.0 0.0 0.0 0.0 6 0.0 0.0 0.0 0.0 0.0 7 0.0 0.0 0.0 0.0 0.0 8 0.0 0.0 0.0 0.0 0.0 9 0.0 0.0 0.0 0.0 0.0 10 0.0 0.0 0.0 0.0 0.0 11 0.0 0.0 0.0 0.0 0.0 12 0.0 0.0 0.0 0.0 0.0 13 0.0 0.0 0.0 0.0 0.0 14 0.0 0.0 0.0 0.0 0.0 15 0.0 0.0 0.0 0.0 0.0 16 0.0 0.0 0.0 0.0 0.0 17 0.0 0.0 0.0 0.0 0.0 18 0.0 0.0 0.0 0.0 0.0 19 0.0 0.0 0.0 0.0 0.0 20 0.0 0.0 0.0 0.0 0.0 21 0.0 0.0 0.0 0.0 0.0 22 0.0 0.0 0.0 0.0 0.0 23 0.0 0.0 0.0 0.0 0.0 24 0.0 0.0 0.0 0.0 0.0 25 0.0 0.0 0.0 0.0 0.0 26 0.0 0.0 0.0 0.0 0.0 27 0.0 0.0 0.0 0.0 0.0 28 0.0 0.0 0.0 0.0 0.0 29 0.0 0.0 0.0 0.0 0.0 30 0.0 0.0 0.0 0.0 0.0 31 0.0 0.0 0.0 0.0 0.0 32 0.0 0.0 0.0 0.0 0.0 33 0.0 0.0 0.0 0.0 0.0 34 0.0 0.0 0.0 0.0 0.0 35 0.0 0.0 0.0 0.0 0.0 36 0.0 0.0 0.0 0.0 0.0 37 0.0 0.0 0.0 0.0 0.0 38 0.0 0.0 0.0 0.0 0.0 39 0.0 0.0 0.0 0.0 0.0 40 0.0 0.0 0.0 0.0 0.0 41 0.0 0.0 0.0 0.0 0.0 42 0.0 0.0 0.0 0.0 0.0 43 0.0 0.0 0.0 0.0 0.0 44 0.0 0.0 0.0 0.0 0.0 45 0.0 0.0 0.0 0.0 0.0 46 0.0 0.0 0.0 0.0 0.0 47 0.0 0.0 0.0 0.0 0.0 48 0.0 0.0 0.0 0.0 0.0 49 0.0 0.0 0.0 0.0 0.0 50 0.0 0.0 0.0 0.0 0.0 51 0.0 0.0 0.0 0.0 0.0 52 0.0 0.0 0.0 0.0 0.0 53 0.0 0.0 0.0 0.0 0.0 54 0.0 0.0 0.0 0.0 0.0 55 0.0 0.0 0.0 0.0 0.0 56 0.025 0.0 0.0 0.0 0.0 57 0.025 0.0 0.0 0.0 0.0 58 0.025 0.0 0.0 0.0 0.0 59 0.025 0.0 0.0 0.0 0.0 60 0.025 0.0 0.0 0.0 0.0 61 0.025 0.0 0.0 0.0 0.0 62 0.025 0.0 0.0 0.0 0.0 63 0.025 0.0 0.0 0.0 0.0 64 0.025 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE SRR11389775 read2 length is 35-76 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR11389775_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 30.6825 32.0 32.0 32.0 32.0 32.0 2 30.29425 32.0 32.0 32.0 32.0 32.0 3 30.15725 32.0 32.0 32.0 21.0 32.0 4 30.05075 32.0 32.0 32.0 21.0 32.0 5 30.145 32.0 32.0 32.0 21.0 32.0 6 33.14 36.0 36.0 36.0 21.0 36.0 7 33.2975 36.0 36.0 36.0 21.0 36.0 8 33.34775 36.0 36.0 36.0 21.0 36.0 9 33.30775 36.0 36.0 36.0 21.0 36.0 10-11 33.17 36.0 36.0 36.0 17.5 36.0 12-13 33.24575 36.0 36.0 36.0 21.0 36.0 14-15 33.006249999999994 36.0 36.0 36.0 14.0 36.0 16-17 33.037375 36.0 36.0 36.0 17.5 36.0 18-19 33.032250000000005 36.0 36.0 36.0 17.5 36.0 20-21 33.09925 36.0 36.0 36.0 21.0 36.0 22-23 32.857749999999996 36.0 36.0 36.0 14.0 36.0 24-25 32.883250000000004 36.0 36.0 36.0 14.0 36.0 26-27 32.91775 36.0 36.0 36.0 14.0 36.0 28-29 32.764875 36.0 36.0 36.0 14.0 36.0 30-31 32.702375 36.0 36.0 36.0 14.0 36.0 32-33 32.719 36.0 36.0 36.0 14.0 36.0 34-35 32.460750000000004 36.0 36.0 36.0 14.0 36.0 36-37 32.6467555331992 36.0 36.0 36.0 14.0 36.0 38-39 32.71415995975855 36.0 36.0 36.0 14.0 36.0 40-41 32.4297032193159 36.0 36.0 36.0 14.0 36.0 42-43 32.40845070422535 36.0 34.0 36.0 14.0 36.0 44-45 32.09936993027347 36.0 32.0 36.0 14.0 36.0 46-47 32.219245283018864 36.0 32.0 36.0 14.0 36.0 48-49 32.035471698113206 36.0 32.0 36.0 14.0 36.0 50-51 31.851141349589945 36.0 32.0 36.0 14.0 36.0 52-53 31.80221439355813 36.0 32.0 36.0 14.0 36.0 54-55 31.653749370910923 36.0 32.0 36.0 14.0 36.0 56-57 31.456948640483382 36.0 32.0 36.0 14.0 36.0 58-59 30.93277945619335 36.0 32.0 36.0 14.0 36.0 60-61 31.2345166163142 36.0 32.0 36.0 14.0 36.0 62-63 31.106873111782477 36.0 32.0 36.0 14.0 36.0 64-65 31.01761685951105 36.0 32.0 36.0 14.0 36.0 66-67 30.816599039164704 36.0 29.5 36.0 14.0 36.0 68-69 30.83123266952357 36.0 29.5 36.0 14.0 36.0 70-71 30.61100797678092 36.0 29.5 36.0 14.0 36.0 72-73 30.630567055062308 36.0 27.0 36.0 14.0 36.0 74-75 30.19358964912604 36.0 27.0 36.0 14.0 36.0 76 29.163117870722434 32.0 27.0 36.0 14.0 36.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 24.0 3 0.0 4 0.0 5 0.0 6 1.0 7 0.0 8 0.0 9 0.0 10 1.0 11 0.0 12 0.0 13 0.0 14 3.0 15 3.0 16 11.0 17 12.0 18 14.0 19 11.0 20 17.0 21 13.0 22 18.0 23 38.0 24 36.0 25 52.0 26 107.0 27 100.0 28 161.0 29 189.0 30 274.0 31 345.0 32 487.0 33 651.0 34 913.0 35 519.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 41.93710691823899 19.622641509433965 11.270440251572326 27.169811320754718 2 29.20754716981132 22.69182389937107 28.67924528301887 19.42138364779874 3 24.924547283702214 27.96780684104628 22.082494969818914 25.025150905432596 4 28.3953722334004 33.727364185110666 17.228370221327967 20.648893360160965 5 29.77867203219316 31.48893360160966 20.070422535211268 18.661971830985916 6 23.46579476861167 34.73340040241449 21.705231388329977 20.095573440643864 7 24.673038229376257 17.077464788732392 35.26156941649899 22.987927565392354 8 24.069416498993963 23.893360160965795 24.471830985915492 27.565392354124747 9 26.634808853118713 23.163983903420522 23.843058350100605 26.358148893360163 10-11 27.292164507609108 29.027795245881023 19.55728839139731 24.122751855112565 12-13 27.81481947414769 22.858221159894327 23.512391495785636 25.81456787017235 14-15 25.730478589420652 25.4911838790932 24.16876574307305 24.6095717884131 16-17 26.445760362857502 25.8032002015875 23.232959556507495 24.518079879047498 18-19 27.1045677614194 25.305146596199823 23.480558701396752 24.109726940984018 20-21 27.098804279421017 25.89049716803021 24.040276903713025 22.970421648835746 22-23 26.90080563947633 26.472809667673715 22.922960725075527 23.70342396777442 24-25 26.220432813286358 26.421741318570707 23.57825868142929 23.77956718671364 26-27 27.253272910372605 25.037764350453173 23.778952668680766 23.930010070493456 28-29 26.6742195367573 26.007049345417926 23.388721047331316 23.930010070493456 30-31 25.91240875912409 25.962748552730936 23.936571860055373 24.188270828089607 32-33 26.177285318559555 25.598086124401913 23.923444976076556 24.301183580961975 34-35 26.586102719033235 25.579053373615306 23.527190332326285 24.307653575025174 36-37 26.42245720040282 25.71752265861027 24.06847935548842 23.791540785498487 38-39 26.643162931251574 26.706119365399143 23.319063208259884 23.3316544950894 40-41 26.711983887210472 25.90634441087613 22.734138972809667 24.647532729103727 42-43 26.346928499496475 26.611278952668684 24.13141993957704 22.910372608257802 44-45 25.739458779106357 27.123977344241663 23.599748269351796 23.536815607300188 46-47 25.764631843927 26.381371932032728 23.322844556324732 24.531151667715545 48-49 26.769075799546716 25.925459581969278 23.986401410224126 23.319063208259884 50-51 26.057401812688823 25.90634441087613 23.66565961732125 24.370594159113796 52-53 26.230333543108873 27.589679043423537 22.32850849590938 23.851478917558214 54-55 26.68344870988043 27.061044682190055 23.398363750786658 22.857142857142858 56-57 25.135373378667676 26.633925198337742 24.59387986399698 23.636821558997607 58-59 26.61290322580645 25.642641129032256 23.538306451612904 24.206149193548388 60-61 25.734089477000634 26.74228103339635 24.221802142407057 23.301827347195967 62-63 25.98564050888021 25.935256329512534 24.62526766595289 23.453835495654367 64-65 26.77671370967742 25.60483870967742 23.046875 24.571572580645164 66-67 26.35825034665322 26.421278204966598 23.761502584142193 23.458968864237995 68-69 26.70196671709531 25.542107917297024 24.256177508825015 23.49974785678265 70-71 25.5966662457381 25.96287410026519 25.230458391211013 23.210001262785706 72-73 26.312452447375094 26.09688054780624 23.64950545270099 23.941161552117677 74-75 25.908906609001214 22.922016488714693 25.476415731855656 25.692661170428437 76 28.22365918600228 0.0 35.45074172689235 36.32559908710537 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 24.0 1 12.0 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.5 8 0.5 9 0.0 10 1.5 11 3.0 12 2.5 13 1.5 14 1.0 15 2.5 16 4.0 17 4.0 18 10.5 19 15.5 20 11.5 21 12.5 22 18.0 23 14.5 24 16.0 25 24.5 26 25.5 27 31.0 28 32.5 29 24.5 30 34.0 31 52.5 32 57.5 33 55.5 34 51.0 35 63.5 36 86.0 37 96.5 38 104.0 39 116.0 40 124.5 41 131.0 42 136.0 43 153.0 44 171.5 45 175.5 46 177.5 47 185.0 48 184.5 49 170.5 50 167.0 51 160.0 52 143.5 53 133.5 54 126.5 55 148.5 56 160.5 57 129.5 58 117.0 59 116.0 60 107.0 61 102.0 62 100.0 63 99.0 64 88.0 65 79.5 66 77.0 67 70.5 68 70.5 69 64.0 70 55.0 71 53.0 72 49.5 73 46.5 74 41.0 75 35.0 76 28.5 77 19.5 78 17.5 79 17.0 80 13.0 81 11.5 82 10.0 83 6.5 84 4.0 85 1.5 86 2.0 87 2.5 88 1.5 89 1.0 90 1.0 91 1.5 92 2.0 93 1.0 94 0.0 95 0.0 96 0.0 97 0.5 98 0.5 99 0.5 100 1.0 >>END_MODULE >>Per base N content pass #Base N-Count 1 0.625 2 0.625 3 0.6 4 0.6 5 0.6 6 0.6 7 0.6 8 0.6 9 0.6 10-11 0.6125 12-13 0.6375 14-15 0.75 16-17 0.7875 18-19 0.6625 20-21 0.6875 22-23 0.7000000000000001 24-25 0.65 26-27 0.7000000000000001 28-29 0.7000000000000001 30-31 0.675 32-33 0.7250000000000001 34-35 0.7000000000000001 36-37 0.1006036217303823 38-39 0.12575452716297786 40-41 0.1006036217303823 42-43 0.1006036217303823 44-45 0.07546220601182241 46-47 0.06289308176100629 48-49 0.10062893081761005 50-51 0.0629009938357026 52-53 0.0377453447408153 54-55 0.0377453447408153 56-57 0.0377643504531722 58-59 0.10070493454179255 60-61 0.11329305135951663 62-63 0.06294058408862034 64-65 0.0629643621710112 66-67 0.06298815822625346 68-69 0.025207965717166627 70-71 0.06309944472488642 72-73 0.02535496957403651 74-75 0.0675310642895732 76 0.03802281368821293 >>END_MODULE >>Sequence Length Distribution warn #Length Count 35 24.0 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 1.0 45 0.0 46 0.0 47 0.0 48 0.0 49 0.0 50 1.0 51 0.0 52 0.0 53 0.0 54 0.0 55 2.0 56 0.0 57 0.0 58 0.0 59 0.0 60 0.0 61 0.0 62 0.0 63 1.0 64 1.0 65 0.0 66 2.0 67 1.0 68 0.0 69 2.0 70 6.0 71 4.0 72 22.0 73 75.0 74 312.0 75 916.0 76 2630.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 95.3 #Duplication Level Percentage of deduplicated Percentage of total 1 96.98321091290661 92.425 2 2.2560335781741867 4.3 3 0.5246589716684155 1.5 4 0.07869884575026233 0.3 5 0.0 0.0 6 0.07869884575026233 0.44999999999999996 7 0.026232948583420776 0.17500000000000002 8 0.0 0.0 9 0.0 0.0 >10 0.05246589716684155 0.8500000000000001 >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 24 0.6 No Hit TGCAAATGGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAAGGCGATCAAATTCGAGTTCGCGCCGGTAGAT 10 0.25 No Hit GGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACA 7 0.17500000000000002 No Hit AAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAAGGCGATCAAATTCG 6 0.15 No Hit ATCGATTAATAGATAAAACTAAATATGAAGAAGGTCTAAATAAAAAGAAA 6 0.15 No Hit GCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGC 6 0.15 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 0.025 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 0.025 0.0 0.0 0.0 0.0 42 0.025 0.0 0.0 0.0 0.0 43 0.025 0.0 0.0 0.0 0.0 44 0.025 0.0 0.0 0.0 0.0 45 0.025 0.0 0.0 0.0 0.0 46 0.025 0.0 0.0 0.0 0.0 47 0.025 0.0 0.0 0.0 0.0 48 0.025 0.0 0.0 0.0 0.0 49 0.025 0.0 0.0 0.0 0.0 50 0.025 0.0 0.0 0.0 0.0 51 0.025 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 Read 916524 spots for SRR11389775.sra Written 916524 spots for SRR11389775.sra Read 916524 spots for SRR11389775.sra Written 916524 spots for SRR11389775.sra Read 916524 spots for SRR11389775.sra Written 916524 spots for SRR11389775.sra Read 916524 spots for SRR11389775.sra Written 916524 spots for SRR11389775.sra Read 916524 spots for SRR11389775.sra Written 916524 spots for SRR11389775.sra Read 916524 spots for SRR11389775.sra Written 916524 spots for SRR11389775.sra Read 916524 spots for SRR11389775.sra Written 916524 spots for SRR11389775.sra Read 916524 spots for SRR11389775.sra Written 916524 spots for SRR11389775.sra Read 916542 spots for SRR11389775.sra Written 916542 spots for SRR11389775.sra Read 916524 spots for SRR11389775.sra Written 916524 spots for SRR11389775.sra Read 916524 spots for SRR11389775.sra Written 916524 spots for SRR11389775.sra Read 916524 spots for SRR11389775.sra Written 916524 spots for SRR11389775.sra Read 916524 spots for SRR11389775.sra Written 916524 spots for SRR11389775.sra Read 916524 spots for SRR11389775.sra Written 916524 spots for SRR11389775.sra Read 916524 spots for SRR11389775.sra Written 916524 spots for SRR11389775.sra Read 916524 spots for SRR11389775.sra Written 916524 spots for SRR11389775.sra Read 916524 spots for SRR11389775.sra Written 916524 spots for SRR11389775.sra Read 916524 spots for SRR11389775.sra Written 916524 spots for SRR11389775.sra Read 916524 spots for SRR11389775.sra Written 916524 spots for SRR11389775.sra Read 916524 spots for SRR11389775.sra Written 916524 spots for SRR11389775.sra SRR ids: ['SRR11389775.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_cq6eiokj SRR11389775.sra spots: 18330498 blocks: [[1, 916524], [916525, 1833048], [1833049, 2749572], [2749573, 3666096], [3666097, 4582620], [4582621, 5499144], [5499145, 6415668], [6415669, 7332192], [7332193, 8248716], [8248717, 9165240], [9165241, 10081764], [10081765, 10998288], [10998289, 11914812], [11914813, 12831336], [12831337, 13747860], [13747861, 14664384], [14664385, 15580908], [15580909, 16497432], [16497433, 17413956], [17413957, 18330498]] SRR11389775 file size 3477748 SRR11389775 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 SRR11389775 SRR11389775_1.fastq SRR11389775_2.fastq Input file: SRR11389775_1.fastq Paired file: SRR11389775_2.fastq trimmed: SRR11389775-trimmed-pair1.fastq, SRR11389775-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 05:52:18 2024 >> started Sat Dec 7 05:52:37 2024 >> done (19.045s) 18330498 read pairs processed; of these: 406 ( 0.00%) short read pairs filtered out after trimming by size control 161098 ( 0.88%) empty read pairs filtered out after trimming by size control 18168994 (99.12%) read pairs available; of these: 13365 ( 0.07%) trimmed read pairs available after processing 18155629 (99.93%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 92 0.00% 19 22 0.00% 20 111 0.00% 21 20 0.00% 22 148 0.00% 23 18 0.00% 24 162 0.00% 25 13 0.00% 26 142 0.00% 27 20 0.00% 28 122 0.00% 29 18 0.00% 30 109 0.00% 31 16 0.00% 32 85 0.00% 33 7 0.00% 34 65 0.00% 35 169 0.00% 36 399 0.00% 37 212 0.00% 38 321 0.00% 39 232 0.00% 40 321 0.00% 41 346 0.00% 42 358 0.00% 43 427 0.00% 44 476 0.00% 45 510 0.00% 46 587 0.00% 47 668 0.00% 48 672 0.00% 49 738 0.00% 50 866 0.00% 51 938 0.01% 52 1083 0.01% 53 1238 0.01% 54 1402 0.01% 55 1501 0.01% 56 1836 0.01% 57 1970 0.01% 58 2272 0.01% 59 2314 0.01% 60 2632 0.01% 61 2775 0.02% 62 3156 0.02% 63 3734 0.02% 64 4133 0.02% 65 4440 0.02% 66 4611 0.03% 67 5353 0.03% 68 5234 0.03% 69 5942 0.03% 70 7118 0.04% 71 10439 0.06% 72 26481 0.15% 73 168003 0.92% 74 1307144 7.19% 75 8351053 45.96% 76 8233720 45.32% 18168994 reads passed initial QC criterion=sequence-density sequence-density=0.90 sequence-density-rank=1 fanout-score=2.03 fanout-score-rank=27 prefix-density=0.86 prefix-fanout=2.0 sequence=TTCAAATGTACA criterion=fanout-score sequence-density=0.03 sequence-density-rank=30 fanout-score=61.46 fanout-score-rank=1 prefix-density=0.10 prefix-fanout=15.3 sequence=AAAAAAAAAAGTATGTTTGCATCAATGATAATCCCAAAGTAGGAAGTGTGTACGTAGTAGCAAGTGTTATACATACATAAAATTAAGCGATGCGTTTCGATCAAGTACTTGGCATCATCGATCACATACGTACATTTCACAGCAGGTAGCTACGTACATTACAGGCATACGTACATGCAGAGAGATACCCGGCCCTGTGTTGTGTTTGCAATTGCATAGATGAGAATGAGATGACTTGATTCTTAATTAGCCGGCGAGAGCGCTGGTGTTGTAGACGAGGAGGGCGCCGCCGCCGAGGAGGCCGGCCAGGGTGACGGCCCAGATCAGGAGCCCCGTCGTCCCACCGGCGTAGCGGTCGCCAGATTCGGACCATACCTCCGGCGTGTAGATCGGGCTGTAGCCGTCGACGTTGGCGCCGTACTTGTCAACAAACTGGTACACACCCTTTCCCGTGCCCTTCCTGCCGTTGGCGTCGATGTCCACCGTCAAGCCACCTCCGATCCCGAGGGGC criterion=sequence-density sequence-density=0.50 sequence-density-rank=1 fanout-score=2.19 fanout-score-rank=26 prefix-density=0.50 prefix-fanout=2.2 sequence=CAGGTGCTCAAGGAGCTGGAGGAGGTCAAGAAGGAGTACCCGGACGCCTA criterion=fanout-score sequence-density=0.02 sequence-density-rank=36 fanout-score=180.10 fanout-score-rank=1 prefix-density=0.31 prefix-fanout=10.6 sequence=AAAAAAAGAAATTTTCTTCCTTCCAATTTTGTTTGCACAAAAGACAACTTTATTTTCTCTCCATTTTGTCGAGTCATTACACGGATTCCATAAATGATTATCAAGTGGTTCTTATTCGAAGAACCCTTGCCTTTTGTTTAGCTTGAGACTCAATCATCGTGGCTCTAGTATGAATCTAAGGTTTAAATTGAACTGATTCATAGGATCGCAACAAGATAATTTCTATCAGAAAACTACTAGAATTTTGGCTTTCTTTATTTACTAGTAAATAAAGAGTAAATCCGCATTACACACAAAAAAATAAAT SRR11389775 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 07 05:53:18 Started mapping on | Dec 07 05:53:19 Finished on | Dec 07 05:54:50 Mapping speed, Million of reads per hour | 718.77 Number of input reads | 18168994 Average input read length | 150 UNIQUE READS: Uniquely mapped reads number | 13601014 Uniquely mapped reads % | 74.86% Average mapped length | 149.94 Number of splices: Total | 4024496 Number of splices: Annotated (sjdb) | 3774001 Number of splices: GT/AG | 3966923 Number of splices: GC/AG | 46959 Number of splices: AT/AC | 1076 Number of splices: Non-canonical | 9538 Mismatch rate per base, % | 0.98% Deletion rate per base | 0.01% Deletion average length | 1.69 Insertion rate per base | 0.01% Insertion average length | 1.69 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 3071573 % of reads mapped to multiple loci | 16.91% Number of reads mapped to too many loci | 128756 % of reads mapped to too many loci | 0.71% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 3.85% % of reads unmapped: other | 3.67% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 1496434 1496434 1496434 N_multimapping 3071573 3071573 3071573 N_noFeature 837821 13112212 986958 N_ambiguous 505856 3228 191660 UnstrandedReadsAssigned:12257337 PositiveStrandReadsAssigned:485574 NegativeStrandReadsAssigned:12422396 Dataset is classified negative stranded MeadianReadLen=76 20thPercentileLength=75 echo kmer=71 SRR11389775 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: SRR11389775-trimmed-pair1.fastq SRR11389775-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 18,168,994 reads, 14,797,710 reads pseudoaligned [quant] estimated average fragment length: 180.08 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,297 rounds 52973 SRR11389775.ke.tsv 35125 SRR11389775.se.tsv 88098 total ==> SRR11389775.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 756.97 0 0 PNS24247 1044 864.92 3.48698 0.331474 PNS24249 1928 1748.92 13.5646 0.637695 PNS24246 1044 864.92 3.48698 0.331474 PNS24248 1044 864.92 3.48698 0.331474 PNS24244 1471 1291.92 219.974 13.9995 PNS24243 293 123.422 0 0 KQK14069 1603 1423.92 3810.9 220.048 KQK14071 474 296.131 169.052 46.9367 ==> SRR11389775.se.tsv <== BRADI_1g14170v3 4188 BRADI_1g53295v3 23 BRADI_1g59795v3 280 BRADI_1g07683v3 0 BRADI_1g00485v3 1 BRADI_1g20270v3 68 BRADI_1g74790v3 137 BRADI_1g09890v3 0 BRADI_1g77505v3 230 BRADI_1g48960v3 0 SRR11389775 completed mapping pipeline successfully