Starting /dee2/code/volunteer_pipeline.sh SRR19784174 current disk space = 1551085801472 free memory = 1598275160 SRR19784174 SRAfilesize 5cfeba8ad092c17fa79a27aa44168fc3 SRR19784174.sra SRR19784174.sra file validated SRR19784174 is paired end SRR19784174 is conventional basespace SRR19784174 read1 length is 65-76 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR19784174_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 65-76 %GC 52 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 31.402 32.0 32.0 32.0 32.0 32.0 2 31.45275 32.0 32.0 32.0 32.0 32.0 3 31.488 32.0 32.0 32.0 32.0 32.0 4 31.53025 32.0 32.0 32.0 32.0 32.0 5 31.47275 32.0 32.0 32.0 32.0 32.0 6 34.631 36.0 36.0 36.0 32.0 36.0 7 34.94 36.0 36.0 36.0 32.0 36.0 8 34.88125 36.0 36.0 36.0 32.0 36.0 9 34.82025 36.0 36.0 36.0 32.0 36.0 10-11 34.816125 36.0 36.0 36.0 32.0 36.0 12-13 34.9615 36.0 36.0 36.0 32.0 36.0 14-15 34.94475 36.0 36.0 36.0 32.0 36.0 16-17 34.9155 36.0 36.0 36.0 32.0 36.0 18-19 34.8365 36.0 36.0 36.0 32.0 36.0 20-21 34.8465 36.0 36.0 36.0 32.0 36.0 22-23 34.832499999999996 36.0 36.0 36.0 32.0 36.0 24-25 34.740375 36.0 36.0 36.0 32.0 36.0 26-27 34.661625 36.0 36.0 36.0 32.0 36.0 28-29 34.6965 36.0 36.0 36.0 32.0 36.0 30-31 34.589749999999995 36.0 36.0 36.0 32.0 36.0 32-33 34.58725 36.0 36.0 36.0 32.0 36.0 34-35 34.474374999999995 36.0 36.0 36.0 32.0 36.0 36-37 34.678124999999994 36.0 36.0 36.0 32.0 36.0 38-39 34.55275 36.0 36.0 36.0 32.0 36.0 40-41 34.54775 36.0 36.0 36.0 32.0 36.0 42-43 34.530625 36.0 36.0 36.0 32.0 36.0 44-45 34.448125000000005 36.0 36.0 36.0 32.0 36.0 46-47 34.37225 36.0 36.0 36.0 32.0 36.0 48-49 34.52575 36.0 36.0 36.0 32.0 36.0 50-51 34.43675 36.0 36.0 36.0 32.0 36.0 52-53 34.500875 36.0 36.0 36.0 32.0 36.0 54-55 34.464875 36.0 36.0 36.0 32.0 36.0 56-57 34.34425 36.0 36.0 36.0 32.0 36.0 58-59 34.39425 36.0 36.0 36.0 32.0 36.0 60-61 34.358625 36.0 36.0 36.0 32.0 36.0 62-63 34.30575 36.0 36.0 36.0 32.0 36.0 64-65 34.2825 36.0 36.0 36.0 32.0 36.0 66-67 34.14391097774444 36.0 36.0 36.0 32.0 36.0 68-69 34.06104628496385 36.0 36.0 36.0 32.0 36.0 70-71 34.1046052306998 36.0 36.0 36.0 32.0 36.0 72-73 34.087239452898515 36.0 36.0 36.0 32.0 36.0 74-75 33.945778220371096 36.0 36.0 36.0 32.0 36.0 76 33.714910681735326 36.0 36.0 36.0 27.0 36.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 19 1.0 20 3.0 21 5.0 22 7.0 23 10.0 24 17.0 25 19.0 26 23.0 27 36.0 28 50.0 29 82.0 30 89.0 31 134.0 32 174.0 33 308.0 34 650.0 35 2392.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 33.025 9.15 11.025 46.800000000000004 2 20.349999999999998 15.7 31.25 32.7 3 24.15 18.6 19.075 38.175 4 31.374999999999996 22.900000000000002 17.125 28.599999999999998 5 27.950000000000003 27.6 21.075 23.375 6 23.89715149987396 33.47617847239728 21.804890345349133 20.82177968237963 7 19.75 21.6 37.35 21.3 8 22.1 22.675 27.400000000000002 27.825 9 22.375 21.425 30.95 25.25 10-11 24.7 29.099999999999998 21.0375 25.162499999999998 12-13 25.5375 21.5625 24.2875 28.6125 14-15 24.453056632079008 24.615576947118388 24.803100387548444 26.128266033254157 16-17 24.9 24.15 24.5 26.450000000000003 18-19 25.525 24.65 24.675 25.15 20-21 24.95 24.975 24.962500000000002 25.112499999999997 22-23 25.087500000000002 24.45 23.6375 26.825 24-25 25.45 24.1375 23.1875 27.224999999999998 26-27 24.3125 24.5375 24.212500000000002 26.937499999999996 28-29 26.16904226056514 24.131032758189548 23.005751437859466 26.694173543385848 30-31 25.525 24.637500000000003 23.0625 26.775 32-33 25.112499999999997 24.462500000000002 23.674999999999997 26.75 34-35 25.724999999999998 24.25 23.6375 26.387500000000003 36-37 25.76894223555889 24.168542135533883 23.1807951987997 26.881720430107524 38-39 24.95 24.5125 23.674999999999997 26.8625 40-41 25.887500000000003 23.8875 22.9625 27.2625 42-43 24.4375 24.4375 24.224999999999998 26.900000000000002 44-45 25.2375 24.4875 22.9875 27.287499999999998 46-47 25.974999999999998 24.5375 23.125 26.3625 48-49 24.96560350218887 24.11507191994997 22.664165103189493 28.25515947467167 50-51 25.5625 24.1625 22.625 27.650000000000002 52-53 25.7375 24.6125 22.2 27.450000000000003 54-55 25.662499999999998 24.4125 22.525000000000002 27.400000000000002 56-57 25.5125 24.95 22.975 26.5625 58-59 25.343835958989747 24.618654663665918 22.9057264316079 27.131782945736433 60-61 26.650000000000002 24.7875 22.25 26.3125 62-63 25.4375 24.525 23.3625 26.674999999999997 64-65 26.6125 23.9875 23.125 26.275 66-67 25.468867216804203 24.843710927731934 21.680420105026258 28.00700175043761 68-69 25.71607254534084 24.590368980612883 23.114446529080677 26.579111944965604 70-71 25.810083823345426 23.533091455023143 22.907544101088455 27.749280620542976 72-73 26.69432918395574 23.39997485225701 22.670690305545076 27.235005658242173 74-75 26.450331125827812 21.920529801324502 24.42384105960265 27.205298013245034 76 31.24316441851987 0.0 31.97229310973387 36.78454247174626 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 42.0 1 22.0 2 2.0 3 1.0 4 0.0 5 1.5 6 2.0 7 2.0 8 3.0 9 3.0 10 9.5 11 16.5 12 17.0 13 8.5 14 0.5 15 0.5 16 0.5 17 1.5 18 3.0 19 3.5 20 5.0 21 8.0 22 5.0 23 2.0 24 2.0 25 1.0 26 4.5 27 9.0 28 7.5 29 7.0 30 9.0 31 10.0 32 14.5 33 22.0 34 28.0 35 37.5 36 58.5 37 81.5 38 107.5 39 113.0 40 109.0 41 142.5 42 172.0 43 175.5 44 178.5 45 174.0 46 168.5 47 172.0 48 174.0 49 149.0 50 123.0 51 128.5 52 130.0 53 126.5 54 123.5 55 123.0 56 133.0 57 129.5 58 125.0 59 136.0 60 138.5 61 130.0 62 124.5 63 118.0 64 117.5 65 120.5 66 108.5 67 101.0 68 98.5 69 93.0 70 79.0 71 66.0 72 65.5 73 65.0 74 57.5 75 49.0 76 43.0 77 30.0 78 22.0 79 23.0 80 22.0 81 14.0 82 5.0 83 1.5 84 4.0 85 3.5 86 0.5 87 1.0 88 1.0 89 1.0 90 0.5 91 0.0 92 0.0 93 0.0 94 0.5 95 0.5 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 0.8250000000000001 7 0.0 8 0.0 9 0.0 10-11 0.0 12-13 0.0 14-15 0.0125 16-17 0.0 18-19 0.0 20-21 0.0 22-23 0.0 24-25 0.0 26-27 0.0 28-29 0.025 30-31 0.0 32-33 0.0 34-35 0.0 36-37 0.025 38-39 0.0 40-41 0.0 42-43 0.0 44-45 0.0 46-47 0.0 48-49 0.0625 50-51 0.0 52-53 0.0 54-55 0.0 56-57 0.0 58-59 0.025 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 0.052952078369075985 76 0.0 >>END_MODULE >>Sequence Length Distribution warn #Length Count 65 1.0 66 0.0 67 1.0 68 1.0 69 0.0 70 1.0 71 12.0 72 15.0 73 68.0 74 248.0 75 910.0 76 2743.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 93.425 #Duplication Level Percentage of deduplicated Percentage of total 1 95.63821246989563 89.35 2 3.2914102221032913 6.15 3 0.6422263848006422 1.7999999999999998 4 0.2675943270002676 1.0 5 0.08027829810008028 0.375 6 0.02675943270002676 0.15 7 0.0 0.0 8 0.02675943270002676 0.2 9 0.0 0.0 >10 0.02675943270002676 0.975 >50 0.0 0.0 >100 0.0 0.0 >500 0.0 0.0 >1k 0.0 0.0 >5k 0.0 0.0 >10k+ 0.0 0.0 >>END_MODULE >>Overrepresented sequences warn #Sequence Count Percentage Possible Source AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 39 0.975 No Hit CCAGGAACAGGCTCGATGTGATAGCATCGTCCTTTGTAACGATCAAGACT 8 0.2 No Hit GCCGAGTTTAATTGCAGTCAATTAGAAGAATAAAGAAGAATTACTGCATT 6 0.15 No Hit CTTCAAATAGATCTAATGGATAAGCTACATAACAGATCCATTGACTGTCTTCCCCAGGAACAGGCTCGATGTGAT 5 0.125 No Hit CTCGATTAGCTGCTGCACCAGGTGCATTTCCCCAAGGATGTCCTAAAGTT 5 0.125 No Hit CAAGGATGTCCTAAAGTTCCTCCACCAAATTGTAATACAGAATCATCCCC 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 SRR19784174 read2 length is 65-76 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR19784174_2.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 65-76 %GC 53 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 30.4515 32.0 32.0 32.0 32.0 32.0 2 30.425 32.0 32.0 32.0 21.0 32.0 3 30.54375 32.0 32.0 32.0 32.0 32.0 4 30.475 32.0 32.0 32.0 32.0 32.0 5 30.4545 32.0 32.0 32.0 32.0 32.0 6 33.8155 36.0 36.0 36.0 32.0 36.0 7 33.88325 36.0 36.0 36.0 32.0 36.0 8 33.391 36.0 36.0 36.0 21.0 36.0 9 33.815 36.0 36.0 36.0 32.0 36.0 10-11 33.626999999999995 36.0 36.0 36.0 27.0 36.0 12-13 33.49625 36.0 36.0 36.0 24.0 36.0 14-15 33.578875 36.0 36.0 36.0 26.5 36.0 16-17 33.458124999999995 36.0 36.0 36.0 24.0 36.0 18-19 33.436875 36.0 36.0 36.0 29.5 36.0 20-21 33.633875 36.0 36.0 36.0 27.0 36.0 22-23 33.83875 36.0 36.0 36.0 32.0 36.0 24-25 33.61825 36.0 36.0 36.0 32.0 36.0 26-27 33.426875 36.0 36.0 36.0 26.5 36.0 28-29 33.278875 36.0 36.0 36.0 24.0 36.0 30-31 33.342124999999996 36.0 36.0 36.0 24.0 36.0 32-33 33.438375 36.0 36.0 36.0 24.0 36.0 34-35 33.57575 36.0 36.0 36.0 27.0 36.0 36-37 33.458875 36.0 36.0 36.0 24.0 36.0 38-39 33.47925 36.0 36.0 36.0 24.0 36.0 40-41 33.476875 36.0 36.0 36.0 27.0 36.0 42-43 33.368125 36.0 36.0 36.0 21.0 36.0 44-45 33.350875 36.0 36.0 36.0 17.5 36.0 46-47 33.482375000000005 36.0 36.0 36.0 24.0 36.0 48-49 33.37075 36.0 36.0 36.0 21.0 36.0 50-51 33.409 36.0 36.0 36.0 21.0 36.0 52-53 33.429625 36.0 36.0 36.0 21.0 36.0 54-55 33.30675 36.0 36.0 36.0 17.5 36.0 56-57 33.418125 36.0 36.0 36.0 21.0 36.0 58-59 33.244625 36.0 36.0 36.0 21.0 36.0 60-61 33.129875 36.0 36.0 36.0 17.5 36.0 62-63 33.2425 36.0 36.0 36.0 21.0 36.0 64-65 33.113749999999996 36.0 36.0 36.0 17.5 36.0 66-67 33.17929482370592 36.0 36.0 36.0 21.0 36.0 68-69 33.231329183824805 36.0 36.0 36.0 21.0 36.0 70-71 32.971359883549965 36.0 36.0 36.0 17.5 36.0 72-73 32.944916384674855 36.0 36.0 36.0 14.0 36.0 74-75 33.12713227968751 36.0 36.0 36.0 14.0 36.0 76 32.86712527154236 36.0 36.0 36.0 21.0 36.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 14 15.0 15 10.0 16 13.0 17 17.0 18 19.0 19 16.0 20 23.0 21 19.0 22 30.0 23 21.0 24 35.0 25 44.0 26 59.0 27 65.0 28 91.0 29 89.0 30 131.0 31 179.0 32 190.0 33 353.0 34 674.0 35 1907.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 30.32209360845496 12.883744338198289 12.858580775037746 43.93558127830901 2 24.675 23.35 27.425 24.55 3 24.825 23.599999999999998 21.099999999999998 30.475 4 28.499999999999996 27.925 15.775 27.800000000000004 5 29.75 27.675 19.0 23.575 6 23.925 33.074999999999996 18.75 24.25 7 22.55 17.875 30.775000000000002 28.799999999999997 8 23.204005006257823 22.377972465581976 22.803504380475594 31.614518147684606 9 24.425 20.275000000000002 25.974999999999998 29.325000000000003 10-11 27.450000000000003 27.9375 18.3125 26.3 12-13 27.750000000000004 21.837500000000002 21.975 28.4375 14-15 25.324999999999996 25.05 23.3625 26.2625 16-17 27.952952952952952 22.347347347347345 22.30980980980981 27.38988988988989 18-19 26.56132430398796 23.501379483320793 23.68949084524705 26.247805367444194 20-21 26.613306653326664 23.43671835917959 23.374187093546773 26.575787893946973 22-23 26.9625 24.025 23.1375 25.874999999999996 24-25 26.484931849443544 24.99687382768538 21.820682756033513 26.697511566837562 26-27 26.633291614518146 24.49311639549437 23.291614518147686 25.5819774718398 28-29 27.474874371859297 23.605527638190953 22.286432160804022 26.633165829145728 30-31 27.188594297148573 24.312156078039017 21.52326163081541 26.975987993997 32-33 26.625 24.587500000000002 22.025 26.7625 34-35 26.525 24.0375 22.3125 27.125 36-37 26.500750375187593 24.712356178089045 23.274137068534266 25.512756378189096 38-39 26.677516274411616 25.225338007010517 21.932899349023536 26.164246369554334 40-41 28.157894736842103 23.784461152882205 21.528822055137844 26.528822055137844 42-43 27.458605117912693 25.23833416959358 21.625689914701454 25.67737079779227 44-45 26.72424583802729 24.633871573413444 22.64363499812242 25.99824759043685 46-47 26.738369184592298 24.074537268634316 22.36118059029515 26.825912956478238 48-49 25.84692597239649 24.79297365119197 22.30865746549561 27.051442910915934 50-51 26.978957915831664 25.288076152304612 21.8311623246493 25.90180360721443 52-53 26.231557889472366 24.36859214803701 21.705426356589147 27.694423605901473 54-55 26.637499999999996 24.587500000000002 22.7 26.075 56-57 27.051025512756375 24.92496248124062 22.123561780890444 25.900450225112557 58-59 26.23588456712673 24.680050188205772 22.88582183186951 26.198243412797993 60-61 26.424805423047953 24.315842329902086 22.483052975144364 26.7762992719056 62-63 27.521902377972467 24.367959949937422 22.052565707133915 26.057571964956196 64-65 27.656914228557138 24.243560890222557 21.517879469867466 26.581645411352838 66-67 26.569142285571395 24.193548387096776 22.893223305826456 26.344086021505376 68-69 27.36828932549118 25.003128519584532 21.736954073332498 25.89162808159179 70-71 26.25958034929011 24.28697072496545 22.301796708129164 27.15165221761528 72-73 26.51591712986357 23.90096008084891 23.26932794340576 26.31379484588176 74-75 27.51819986763733 21.455989410986103 23.295830575777632 27.729980145598944 76 29.65242577842143 0.0 30.919623461259953 39.42795076031861 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 16.0 1 14.0 2 10.5 3 6.0 4 3.0 5 4.5 6 6.5 7 8.0 8 9.0 9 9.5 10 9.5 11 10.0 12 11.0 13 8.0 14 5.0 15 2.5 16 0.5 17 1.0 18 2.0 19 2.5 20 2.0 21 2.0 22 2.0 23 1.5 24 1.5 25 1.5 26 3.5 27 6.5 28 7.0 29 7.0 30 10.5 31 16.5 32 18.5 33 19.0 34 23.5 35 46.5 36 70.0 37 76.0 38 90.5 39 100.0 40 103.0 41 120.0 42 131.5 43 149.0 44 177.0 45 163.5 46 143.5 47 164.5 48 167.5 49 135.5 50 120.5 51 125.0 52 129.5 53 122.0 54 114.0 55 120.5 56 126.5 57 121.0 58 116.5 59 138.5 60 159.5 61 149.5 62 137.0 63 131.0 64 130.5 65 126.5 66 115.0 67 115.5 68 111.5 69 101.0 70 88.0 71 82.5 72 86.0 73 85.5 74 69.0 75 54.5 76 47.0 77 32.5 78 26.0 79 27.0 80 27.0 81 18.0 82 8.5 83 5.0 84 4.5 85 5.0 86 4.5 87 3.5 88 2.0 89 1.0 90 0.5 91 0.0 92 0.0 93 0.0 94 0.0 95 0.5 96 1.0 97 1.0 98 0.5 99 0.0 100 0.0 >>END_MODULE >>Per base N content pass #Base N-Count 1 0.65 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.125 9 0.0 10-11 0.0 12-13 0.0 14-15 0.0 16-17 0.1 18-19 0.325 20-21 0.05 22-23 0.0 24-25 0.0375 26-27 0.125 28-29 0.5 30-31 0.05 32-33 0.0 34-35 0.0 36-37 0.05 38-39 0.15 40-41 0.25 42-43 0.35000000000000003 44-45 0.13749999999999998 46-47 0.05 48-49 0.375 50-51 0.2 52-53 0.025 54-55 0.0 56-57 0.05 58-59 0.375 60-61 0.42500000000000004 62-63 0.125 64-65 0.025 66-67 0.0 68-69 0.025021894157387717 70-71 0.3755163349605708 72-73 0.36500943989930773 74-75 0.026465528648934762 76 0.0 >>END_MODULE >>Sequence Length Distribution warn #Length Count 65 1.0 66 0.0 67 2.0 68 1.0 69 0.0 70 3.0 71 8.0 72 25.0 73 65.0 74 233.0 75 900.0 76 2762.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 95.8 #Duplication Level Percentage of deduplicated Percentage of total 1 96.58141962421712 92.525 2 2.7922755741127347 5.35 3 0.3914405010438413 1.125 4 0.15657620041753653 0.6 5 0.052192066805845504 0.25 6 0.026096033402922752 0.15 7 0.0 0.0 8 0.0 0.0 9 0.0 0.0 >10 0.0 0.0 >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 CTTGATTTTACCAAAGATGATGAAAACGTAAACTCACAACCATTTATGCG 6 0.15 No Hit CTTAACTGGGGGATTCACCGCAAATACTACTTTGGCTCATTATTGCCGCG 5 0.125 No Hit CAAAGCCTCTTGCTAAGCGTACCACACTATACAGACGTGCGCGCGCAGCC 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 1891009 spots for SRR19784174.sra Written 1891009 spots for SRR19784174.sra Read 1891009 spots for SRR19784174.sra Written 1891009 spots for SRR19784174.sra Read 1891009 spots for SRR19784174.sra Written 1891009 spots for SRR19784174.sra Read 1891009 spots for SRR19784174.sra Written 1891009 spots for SRR19784174.sra Read 1891024 spots for SRR19784174.sra Written 1891024 spots for SRR19784174.sra Read 1891009 spots for SRR19784174.sra Written 1891009 spots for SRR19784174.sra Read 1891009 spots for SRR19784174.sra Written 1891009 spots for SRR19784174.sra Read 1891009 spots for SRR19784174.sra Written 1891009 spots for SRR19784174.sra Read 1891009 spots for SRR19784174.sra Written 1891009 spots for SRR19784174.sra Read 1891009 spots for SRR19784174.sra Written 1891009 spots for SRR19784174.sra Read 1891009 spots for SRR19784174.sra Written 1891009 spots for SRR19784174.sra Read 1891009 spots for SRR19784174.sra Written 1891009 spots for SRR19784174.sra Read 1891009 spots for SRR19784174.sra Written 1891009 spots for SRR19784174.sra Read 1891009 spots for SRR19784174.sra Written 1891009 spots for SRR19784174.sra Read 1891009 spots for SRR19784174.sra Written 1891009 spots for SRR19784174.sra Read 1891009 spots for SRR19784174.sra Written 1891009 spots for SRR19784174.sra Read 1891009 spots for SRR19784174.sra Written 1891009 spots for SRR19784174.sra Read 1891009 spots for SRR19784174.sra Written 1891009 spots for SRR19784174.sra Read 1891009 spots for SRR19784174.sra Written 1891009 spots for SRR19784174.sra Read 1891009 spots for SRR19784174.sra Written 1891009 spots for SRR19784174.sra SRR ids: ['SRR19784174.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_3j7hdj1i SRR19784174.sra spots: 37820195 blocks: [[1, 1891009], [1891010, 3782018], [3782019, 5673027], [5673028, 7564036], [7564037, 9455045], [9455046, 11346054], [11346055, 13237063], [13237064, 15128072], [15128073, 17019081], [17019082, 18910090], [18910091, 20801099], [20801100, 22692108], [22692109, 24583117], [24583118, 26474126], [26474127, 28365135], [28365136, 30256144], [30256145, 32147153], [32147154, 34038162], [34038163, 35929171], [35929172, 37820195]] SRR19784174 file size 7217466 SRR19784174 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 SRR19784174 SRR19784174_1.fastq SRR19784174_2.fastq Input file: SRR19784174_1.fastq Paired file: SRR19784174_2.fastq trimmed: SRR19784174-trimmed-pair1.fastq, SRR19784174-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 Fri Dec 6 13:31:31 2024 >> started Fri Dec 6 13:32:05 2024 >> done (34.100s) 37820195 read pairs processed; of these: 6 ( 0.00%) short read pairs filtered out after trimming by size control 9687 ( 0.03%) empty read pairs filtered out after trimming by size control 37810502 (99.97%) read pairs available; of these: 71282 ( 0.19%) trimmed read pairs available after processing 37739220 (99.81%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 3 0.00% 19 2 0.00% 20 4 0.00% 21 5 0.00% 22 48 0.00% 23 67 0.00% 24 98 0.00% 25 128 0.00% 26 133 0.00% 27 165 0.00% 28 210 0.00% 29 264 0.00% 30 262 0.00% 31 651 0.00% 32 799 0.00% 33 315 0.00% 34 993 0.00% 35 630 0.00% 36 667 0.00% 37 737 0.00% 38 776 0.00% 39 861 0.00% 40 985 0.00% 41 1003 0.00% 42 1077 0.00% 43 1175 0.00% 44 1236 0.00% 45 1328 0.00% 46 1409 0.00% 47 1531 0.00% 48 1757 0.00% 49 1897 0.01% 50 2158 0.01% 51 2442 0.01% 52 2725 0.01% 53 2970 0.01% 54 3245 0.01% 55 3665 0.01% 56 3869 0.01% 57 4258 0.01% 58 4748 0.01% 59 5234 0.01% 60 5825 0.02% 61 6433 0.02% 62 7279 0.02% 63 8033 0.02% 64 8747 0.02% 65 9956 0.03% 66 10764 0.03% 67 12177 0.03% 68 13149 0.03% 69 15036 0.04% 70 20140 0.05% 71 24195 0.06% 72 51927 0.14% 73 297531 0.79% 74 2411019 6.38% 75 16698014 44.16% 76 18153747 48.01% 37810502 reads passed initial QC criterion=sequence-density sequence-density=0.55 sequence-density-rank=1 fanout-score=2.34 fanout-score-rank=22 prefix-density=0.63 prefix-fanout=2.0 sequence=GGCTTGAAGGCGATGAAGCTGATGCACTGCACCTGCCGGGTGTTGTCGAAGCCGATGATGCGGACATAGGCGTCCGGGTACTCCTTCTTGACCTCCTCCAGCTCCTTGAGCACCTGTGTGGCGTCGGT criterion=fanout-score sequence-density=0.09 sequence-density-rank=27 fanout-score=127.98 fanout-score-rank=1 prefix-density=0.88 prefix-fanout=13.4 sequence=GGCGGCGGCGAACCGCCCCCGTCGCCGCGATCCGAACACTTCACCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGCATTCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCTATATACTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCGTCGCCTAAACGGCGATAGTCCCTCTAAGAAGCTAGCTGCGGAGGGATGGCTCCGCATAGCTAGTTAGCAGGCTGAGGTCTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCATGCACCACCACCCATAGAATCAAGAAAGAGCTCTCAGTCTGTCAATCCTTGCTATGTCTGGACCTGGTAAG criterion=sequence-density sequence-density=0.49 sequence-density-rank=1 fanout-score=3.55 fanout-score-rank=15 prefix-density=0.54 prefix-fanout=3.2 sequence=GAGTTCAGCAAGGTCGGCTTCGTCTTCCGCGAGCACAACAG criterion=fanout-score sequence-density=0.01 sequence-density-rank=39 fanout-score=95.85 fanout-score-rank=1 prefix-density=0.51 prefix-fanout=1.9 sequence=CCGCTCCAACACTTCAGTTCTCACTCCACAGCTCAGAGTCAGAGCTACTAGCAATGGCAGCGGCGACCATGGCGCTCTCCTCCCCCGCGATGGCCGGCACCCCGGTGAAGGTCTCCAGGGCCACCCCCTTCGGCGAGGGCCGCATCACCATGCGCAAGAC SRR19784174 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 06 13:32:32 Started mapping on | Dec 06 13:32:34 Finished on | Dec 06 13:35:06 Mapping speed, Million of reads per hour | 895.51 Number of input reads | 37810502 Average input read length | 151 UNIQUE READS: Uniquely mapped reads number | 29093388 Uniquely mapped reads % | 76.95% Average mapped length | 150.53 Number of splices: Total | 10711502 Number of splices: Annotated (sjdb) | 10208919 Number of splices: GT/AG | 10572087 Number of splices: GC/AG | 123029 Number of splices: AT/AC | 2762 Number of splices: Non-canonical | 13624 Mismatch rate per base, % | 0.38% Deletion rate per base | 0.01% Deletion average length | 1.74 Insertion rate per base | 0.00% Insertion average length | 1.80 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 5074171 % of reads mapped to multiple loci | 13.42% Number of reads mapped to too many loci | 616302 % of reads mapped to too many loci | 1.63% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 4.20% % of reads unmapped: other | 3.80% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 3642946 3642946 3642946 N_multimapping 5074171 5074171 5074171 N_noFeature 1004829 28041056 1590385 N_ambiguous 612365 3588 149885 UnstrandedReadsAssigned:27476194 PositiveStrandReadsAssigned:1048744 NegativeStrandReadsAssigned:27353118 Dataset is classified negative stranded MeadianReadLen=76 20thPercentileLength=75 echo kmer=71 SRR19784174 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: SRR19784174-trimmed-pair1.fastq SRR19784174-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 37,810,502 reads, 31,891,045 reads pseudoaligned [quant] estimated average fragment length: 160.217 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,173 rounds 52973 SRR19784174.ke.tsv 35125 SRR19784174.se.tsv 88098 total ==> SRR19784174.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 776.864 0 0 PNS24247 1044 884.783 28.5764 1.33626 PNS24249 1928 1768.78 306.196 7.16214 PNS24246 1044 884.783 28.5764 1.33626 PNS24248 1044 884.783 28.5764 1.33626 PNS24244 1471 1311.78 23.0749 0.727772 PNS24243 293 140.077 0 0 KQK14069 1603 1443.78 17680.1 506.643 KQK14071 474 315.792 2339.26 306.476 ==> SRR19784174.se.tsv <== BRADI_1g14170v3 20619 BRADI_1g53295v3 36 BRADI_1g59795v3 797 BRADI_1g07683v3 0 BRADI_1g00485v3 2 BRADI_1g20270v3 483 BRADI_1g74790v3 394 BRADI_1g09890v3 0 BRADI_1g77505v3 337 BRADI_1g48960v3 1 SRR19784174 completed mapping pipeline successfully