Starting /dee2/code/volunteer_pipeline.sh SRR19784175 current disk space = 1551078731776 free memory = 1595716856 SRR19784175 SRAfilesize 8c11638136416963c7813513db1cd3a1 SRR19784175.sra SRR19784175.sra file validated SRR19784175 is paired end SRR19784175 is conventional basespace SRR19784175 read1 length is 35-76 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR19784175_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 53 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 31.36775 32.0 32.0 32.0 32.0 32.0 2 31.40275 32.0 32.0 32.0 32.0 32.0 3 31.43225 32.0 32.0 32.0 32.0 32.0 4 31.49025 32.0 32.0 32.0 32.0 32.0 5 31.52125 32.0 32.0 32.0 32.0 32.0 6 34.744 36.0 36.0 36.0 36.0 36.0 7 34.9305 36.0 36.0 36.0 32.0 36.0 8 35.0125 36.0 36.0 36.0 36.0 36.0 9 34.93925 36.0 36.0 36.0 32.0 36.0 10-11 34.809124999999995 36.0 36.0 36.0 34.0 36.0 12-13 34.935 36.0 36.0 36.0 34.0 36.0 14-15 34.898375 36.0 36.0 36.0 32.0 36.0 16-17 34.89975 36.0 36.0 36.0 32.0 36.0 18-19 34.9025 36.0 36.0 36.0 32.0 36.0 20-21 34.83975 36.0 36.0 36.0 32.0 36.0 22-23 34.764624999999995 36.0 36.0 36.0 32.0 36.0 24-25 34.753125 36.0 36.0 36.0 32.0 36.0 26-27 34.691500000000005 36.0 36.0 36.0 32.0 36.0 28-29 34.668499999999995 36.0 36.0 36.0 32.0 36.0 30-31 34.57575 36.0 36.0 36.0 32.0 36.0 32-33 34.407875000000004 36.0 36.0 36.0 32.0 36.0 34-35 34.576499999999996 36.0 36.0 36.0 32.0 36.0 36-37 34.587712712712715 36.0 36.0 36.0 32.0 36.0 38-39 34.54792292292292 36.0 36.0 36.0 32.0 36.0 40-41 34.46921921921921 36.0 36.0 36.0 32.0 36.0 42-43 34.4964956195244 36.0 36.0 36.0 32.0 36.0 44-45 34.50926157697121 36.0 36.0 36.0 32.0 36.0 46-47 34.47997496871089 36.0 36.0 36.0 32.0 36.0 48-49 34.3514392991239 36.0 36.0 36.0 32.0 36.0 50-51 34.51764705882353 36.0 36.0 36.0 32.0 36.0 52-53 34.45894868585732 36.0 36.0 36.0 32.0 36.0 54-55 34.51764705882353 36.0 36.0 36.0 32.0 36.0 56-57 34.37108461339643 36.0 36.0 36.0 32.0 36.0 58-59 34.264153306613224 36.0 36.0 36.0 32.0 36.0 60-61 34.34581663326654 36.0 36.0 36.0 32.0 36.0 62-63 34.26970082736257 36.0 36.0 36.0 32.0 36.0 64-65 34.377709306158636 36.0 36.0 36.0 32.0 36.0 66-67 34.187938816449346 36.0 36.0 36.0 32.0 36.0 68-69 34.203177228904124 36.0 36.0 36.0 32.0 36.0 70-71 34.078696347809434 36.0 36.0 36.0 32.0 36.0 72-73 34.08672197161971 36.0 36.0 36.0 32.0 36.0 74-75 33.964507186268506 36.0 36.0 36.0 32.0 36.0 76 33.8094709581946 36.0 36.0 36.0 27.0 36.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 4.0 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 1.0 20 3.0 21 11.0 22 11.0 23 8.0 24 18.0 25 25.0 26 17.0 27 25.0 28 44.0 29 59.0 30 92.0 31 150.0 32 204.0 33 274.0 34 629.0 35 2425.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 36.46146146146146 8.183183183183184 11.16116116116116 44.19419419419419 2 22.22222222222222 11.861861861861863 31.256256256256254 34.65965965965966 3 22.07207207207207 15.665665665665665 19.344344344344343 42.91791791791792 4 30.605605605605607 20.395395395395397 17.56756756756757 31.431431431431434 5 29.37937937937938 24.44944944944945 22.147147147147148 24.024024024024023 6 24.584382871536523 30.075566750629722 22.16624685138539 23.173803526448363 7 22.097097097097095 21.82182182182182 34.209209209209206 21.871871871871875 8 22.872872872872875 22.67267267267267 29.22922922922923 25.225225225225223 9 22.922922922922922 22.24724724724725 31.656656656656658 23.173173173173172 10-11 26.08858858858859 27.7027027027027 22.735235235235233 23.473473473473476 12-13 25.275275275275277 22.07207207207207 26.176176176176174 26.476476476476474 14-15 24.44944944944945 23.94894894894895 24.96246246246246 26.63913913913914 16-17 25.375375375375377 23.96146146146146 24.386886886886888 26.276276276276278 18-19 25.913413413413412 23.185685685685687 25.25025025025025 25.650650650650654 20-21 25.212712712712715 23.623623623623622 24.324324324324326 26.83933933933934 22-23 25.663163163163162 23.135635635635634 24.624624624624623 26.576576576576578 24-25 25.475475475475474 23.1981981981982 24.261761761761765 27.064564564564563 26-27 25.707133917396746 23.454317897371716 24.242803504380475 26.595744680851062 28-29 26.279564510073833 23.413840570641973 24.014516330872233 26.292078588411965 30-31 24.96246246246246 23.84884884884885 24.261761761761765 26.926926926926924 32-33 25.225225225225223 24.186686686686688 24.16166166166166 26.426426426426424 34-35 25.325325325325327 23.71121121121121 23.773773773773772 27.18968968968969 36-37 25.428607183080963 24.014516330872233 24.23976974095858 26.317106745088225 38-39 25.237737737737735 24.31181181181181 24.136636636636634 26.313813813813812 40-41 25.863363363363362 24.136636636636634 23.01051051051051 26.989489489489486 42-43 25.043804755944933 24.480600750938674 23.016270337922403 27.459324155193993 44-45 25.344180225281605 23.642052565707132 23.178973717146434 27.83479349186483 46-47 26.18272841051314 23.992490613266586 23.504380475594495 26.320400500625784 48-49 25.435409096604435 23.994486906402706 22.85427891241699 27.71582508457587 50-51 24.97183627487796 23.832770058830892 23.67004631368131 27.525347352609835 52-53 26.207759699624532 24.367959949937422 22.51564455569462 26.90863579474343 54-55 25.632040050062578 24.956195244055067 21.802252816020026 27.609511889862326 56-57 26.3428070614749 23.337924126705897 23.638412420182796 26.68085639163641 58-59 25.839178356713425 24.28607214428858 23.43436873747495 26.44038076152305 60-61 25.388276553106216 24.336172344689377 23.79759519038076 26.47795591182365 62-63 26.43447757454272 24.204460035078927 23.026810323227263 26.33425206715109 64-65 26.588943211733735 24.05666290585433 23.10392378087 26.250470101541936 66-67 25.90270812437312 23.59578736208626 23.05667001003009 27.444834503510528 68-69 26.188385802082024 23.62975040762574 22.91483757682177 27.267026213470462 70-71 26.229919678714857 23.908132530120483 22.740963855421686 27.12098393574297 72-73 26.43649193548387 23.500504032258064 22.895665322580644 27.16733870967742 74-75 26.76037660787694 21.084736772311363 23.85625248640764 28.29863413340406 76 33.148353681095074 0.0 29.1527931927488 37.69885312615612 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 19.0 1 11.5 2 3.5 3 2.0 4 1.0 5 1.0 6 1.0 7 3.0 8 5.0 9 6.5 10 11.5 11 15.0 12 15.0 13 9.0 14 1.5 15 0.5 16 1.0 17 1.0 18 3.5 19 7.0 20 7.5 21 6.5 22 6.0 23 5.0 24 3.5 25 3.0 26 4.5 27 8.5 28 13.5 29 14.0 30 11.5 31 12.0 32 19.5 33 29.0 34 32.5 35 38.0 36 46.5 37 63.5 38 91.0 39 100.5 40 106.5 41 138.0 42 161.5 43 169.5 44 167.5 45 152.0 46 154.5 47 162.5 48 164.5 49 165.0 50 156.5 51 145.5 52 129.0 53 123.0 54 123.0 55 138.0 56 141.0 57 133.5 58 139.5 59 143.0 60 135.0 61 128.5 62 131.5 63 122.0 64 123.0 65 127.5 66 104.0 67 86.5 68 94.5 69 91.5 70 83.5 71 84.0 72 81.0 73 71.5 74 59.5 75 50.0 76 44.0 77 35.5 78 24.0 79 15.5 80 14.0 81 12.0 82 7.5 83 4.5 84 4.0 85 2.5 86 1.0 87 1.0 88 1.0 89 1.5 90 1.0 91 0.0 92 0.0 93 0.0 94 0.0 95 0.0 96 0.0 97 0.5 98 0.5 99 0.0 100 0.0 >>END_MODULE >>Per base N content pass #Base N-Count 1 0.1 2 0.1 3 0.1 4 0.1 5 0.1 6 0.75 7 0.1 8 0.1 9 0.1 10-11 0.1 12-13 0.1 14-15 0.1 16-17 0.1 18-19 0.1 20-21 0.1 22-23 0.1 24-25 0.1 26-27 0.125 28-29 0.11249999999999999 30-31 0.1 32-33 0.1 34-35 0.1 36-37 0.012512512512512512 38-39 0.0 40-41 0.0 42-43 0.0 44-45 0.0 46-47 0.0 48-49 0.11264080100125157 50-51 0.012515644555694618 52-53 0.0 54-55 0.0 56-57 0.0 58-59 0.0 60-61 0.0 62-63 0.012526619065514218 64-65 0.0 66-67 0.0 68-69 0.0 70-71 0.0 72-73 0.0 74-75 0.013259082471492973 76 0.0 >>END_MODULE >>Sequence Length Distribution warn #Length Count 35 4.0 36 0.0 37 0.0 38 0.0 39 0.0 40 0.0 41 1.0 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 1.0 56 1.0 57 1.0 58 0.0 59 0.0 60 0.0 61 0.0 62 1.0 63 2.0 64 1.0 65 0.0 66 0.0 67 1.0 68 1.0 69 1.0 70 2.0 71 6.0 72 18.0 73 61.0 74 254.0 75 941.0 76 2703.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 92.825 #Duplication Level Percentage of deduplicated Percentage of total 1 95.01750605978992 88.2 2 3.555076757339079 6.6000000000000005 3 0.8079719903043361 2.25 4 0.3501211957985456 1.3 5 0.13466199838405601 0.625 6 0.08079719903043361 0.44999999999999996 7 0.0 0.0 8 0.026932399676811204 0.2 9 0.0 0.0 >10 0.026932399676811204 0.375 >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 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 15 0.375 No Hit CAAAGATTTCGGTCAGAGCTGGCATATGCCAAACATGAATACCACCTGAAGCTACTGGTATAACACCTGGCATGG 8 0.2 No Hit CTTCAAATAGATCTAATGGATAAGCTACATAACAGATCCATTGACTGTCTTCCCCAGGAACAGGCTCGATGTGAT 6 0.15 No Hit CTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATT 6 0.15 No Hit CCAAGGATGTCCTAAAGTTCCTCCACCAAATTGTAATACAGAATCATCCCCAAAGATTTCGGTCAGAGCTGGCAT 6 0.15 No Hit CCAGGAACAGGCTCGATGTGATAGCATCGTCCTTTGTAACGATCAAGACT 5 0.125 No Hit GTCCATGTACCAGTAGAAGATTCGGCAGCTACTGCAGCCCCTGCTTCTTCGGGCGGAACCCCAGGTTGAGGAGAT 5 0.125 No Hit CCTAAAGTTCCTCCACCAAATTGTAATACAGAATCATCCCCAAAGATTTC 5 0.125 No Hit CCCGACTGTCCCTATTAATCATTACTCCGATCCCGAAGGCCAACACAATA 5 0.125 No Hit GTCCTAAAGTTCCTCCACCAAATTGTAATACAGAATCATCCCCAAAGATT 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 SRR19784175 read2 length is 41-76 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR19784175_2.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 41-76 %GC 53 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 30.46475 32.0 32.0 32.0 32.0 32.0 2 30.3145 32.0 32.0 32.0 21.0 32.0 3 30.52375 32.0 32.0 32.0 32.0 32.0 4 30.4445 32.0 32.0 32.0 32.0 32.0 5 30.39775 32.0 32.0 32.0 21.0 32.0 6 33.645 36.0 36.0 36.0 21.0 36.0 7 33.8365 36.0 36.0 36.0 32.0 36.0 8 33.67025 36.0 36.0 36.0 27.0 36.0 9 33.74125 36.0 36.0 36.0 32.0 36.0 10-11 33.699125 36.0 36.0 36.0 27.0 36.0 12-13 33.512625 36.0 36.0 36.0 27.0 36.0 14-15 33.59525 36.0 36.0 36.0 29.5 36.0 16-17 33.530249999999995 36.0 36.0 36.0 29.5 36.0 18-19 33.398125 36.0 36.0 36.0 21.0 36.0 20-21 33.575625 36.0 36.0 36.0 27.0 36.0 22-23 33.88175 36.0 36.0 36.0 32.0 36.0 24-25 33.650875 36.0 36.0 36.0 32.0 36.0 26-27 33.600625 36.0 36.0 36.0 29.5 36.0 28-29 33.290625 36.0 36.0 36.0 21.0 36.0 30-31 33.4475 36.0 36.0 36.0 27.0 36.0 32-33 33.48375 36.0 36.0 36.0 27.0 36.0 34-35 33.570875 36.0 36.0 36.0 27.0 36.0 36-37 33.456 36.0 36.0 36.0 24.0 36.0 38-39 33.545874999999995 36.0 36.0 36.0 24.0 36.0 40-41 33.502250000000004 36.0 36.0 36.0 27.0 36.0 42-43 33.47949487371843 36.0 36.0 36.0 27.0 36.0 44-45 33.44336084021005 36.0 36.0 36.0 21.0 36.0 46-47 33.55501375343836 36.0 36.0 36.0 24.0 36.0 48-49 33.36734183545886 36.0 36.0 36.0 21.0 36.0 50-51 33.387471867966994 36.0 36.0 36.0 21.0 36.0 52-53 33.47586896724181 36.0 36.0 36.0 24.0 36.0 54-55 33.385971492873225 36.0 36.0 36.0 21.0 36.0 56-57 33.40724174321336 36.0 36.0 36.0 21.0 36.0 58-59 33.232607607607605 36.0 36.0 36.0 17.5 36.0 60-61 33.206206206206204 36.0 36.0 36.0 21.0 36.0 62-63 33.3227424859152 36.0 36.0 36.0 21.0 36.0 64-65 33.12459582952532 36.0 36.0 36.0 21.0 36.0 66-67 33.19802104208417 36.0 36.0 36.0 17.5 36.0 68-69 33.18474473348073 36.0 36.0 36.0 17.5 36.0 70-71 33.1391980130054 36.0 36.0 36.0 21.0 36.0 72-73 33.06738587473427 36.0 36.0 36.0 14.0 36.0 74-75 33.31706171163928 36.0 36.0 36.0 21.0 36.0 76 32.71727941176471 36.0 36.0 36.0 14.0 36.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 14 6.0 15 15.0 16 14.0 17 20.0 18 18.0 19 17.0 20 17.0 21 30.0 22 17.0 23 38.0 24 35.0 25 36.0 26 62.0 27 64.0 28 76.0 29 95.0 30 118.0 31 176.0 32 203.0 33 346.0 34 631.0 35 1966.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 32.369942196531795 16.511686353355117 11.937672782106057 39.18069866800703 2 25.5 24.325 25.575 24.6 3 24.575 24.675 22.900000000000002 27.85 4 28.225 27.450000000000003 16.475 27.85 5 29.099999999999998 28.449999999999996 19.275000000000002 23.175 6 24.975 33.550000000000004 18.425 23.05 7 23.724999999999998 18.725 30.049999999999997 27.500000000000004 8 24.06805103827871 21.966474856142106 22.66700025018764 31.298473855391546 9 24.95 22.575 25.775 26.700000000000003 10-11 28.20352544068008 26.940867608451057 18.977372171521438 25.87823477934742 12-13 27.5625 22.650000000000002 21.4875 28.299999999999997 14-15 26.2125 25.4 22.237499999999997 26.150000000000002 16-17 27.17023675310034 22.585494175122133 22.36001503194288 27.884254039834648 18-19 27.533508706000248 23.66278341475636 22.66065388951522 26.14305398972817 20-21 27.131782945736433 23.88097024256064 22.918229557389346 26.069017254313575 22-23 26.825 23.3875 22.5 27.287499999999998 24-25 26.778347293411674 23.952994124265533 22.86535816977122 26.403300412551566 26-27 26.8951713785339 25.55666750062547 21.878909181886414 25.66925193895422 28-29 26.70347596938135 24.607855439829336 20.993851173296523 27.694817417492786 30-31 25.71892973243311 26.106526631657918 21.530382595648913 26.644161040260066 32-33 27.05 24.175 22.575 26.200000000000003 34-35 27.6 24.5125 20.974999999999998 26.9125 36-37 26.319079769942487 24.381095273818453 22.005501375343837 27.294323580895224 38-39 26.611590937539116 25.547627988484166 21.667292527224934 26.173488546751784 40-41 27.342184368737477 23.960420841683366 21.956412825651302 26.740981963927858 42-43 26.499372647427855 24.37892095357591 22.634880803011292 26.486825595984943 44-45 26.81522283425138 24.43665498247371 22.946920380570855 25.801201802704053 46-47 26.897586594973117 24.296611229210953 22.283356258596974 26.522445917218956 48-49 26.687578419071517 24.178168130489336 22.371392722710162 26.76286072772898 50-51 27.408242515345112 24.58975322560441 21.896530126518854 26.10547413253163 52-53 26.872577216456172 24.14655495810929 22.1833187445292 26.79754908090534 54-55 27.081770442610654 24.831207801950487 22.1055263815954 25.98149537384346 56-57 27.336419366946078 24.32128112098086 21.944201176029026 26.39809833604404 58-59 27.187146981297854 23.96134052968495 21.70202083594829 27.149491653068907 60-61 26.566227244193346 24.33145009416196 22.159447583176398 26.942875078468298 62-63 27.039218143089837 24.78386167146974 21.67648164390427 26.50043854153615 64-65 27.89328657314629 24.423847695390783 21.59318637274549 26.089679358717433 66-67 27.45490981963928 24.949899799599198 21.8436873747495 25.751503006012022 68-69 27.036851341188267 24.69290549009777 22.724993732765103 25.545249435948858 70-71 27.056603773584904 25.069182389937104 22.050314465408803 25.82389937106918 72-73 25.76275477908596 24.674009368274465 22.787694644891758 26.775541207747818 74-75 27.431388222755132 22.675193178790302 23.514521715960566 26.378896882494008 76 31.874999999999996 0.0 31.25 36.875 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 25.0 1 19.5 2 10.5 3 5.5 4 4.0 5 3.5 6 3.0 7 4.5 8 6.0 9 8.0 10 10.0 11 7.0 12 4.0 13 3.0 14 1.5 15 1.0 16 1.5 17 2.0 18 2.0 19 2.0 20 1.5 21 2.0 22 2.5 23 2.0 24 1.5 25 3.5 26 7.5 27 8.0 28 8.0 29 8.5 30 8.5 31 12.5 32 17.5 33 20.0 34 32.5 35 52.0 36 67.0 37 78.0 38 96.5 39 113.0 40 109.0 41 108.5 42 121.5 43 134.5 44 155.5 45 159.0 46 149.5 47 144.5 48 132.5 49 133.0 50 132.5 51 130.5 52 133.0 53 128.0 54 121.5 55 131.0 56 132.5 57 141.5 58 162.5 59 156.0 60 152.5 61 147.5 62 136.0 63 131.5 64 125.0 65 124.0 66 113.5 67 95.0 68 94.0 69 99.5 70 90.0 71 80.0 72 77.5 73 72.0 74 66.0 75 58.5 76 49.0 77 41.5 78 31.0 79 21.0 80 18.0 81 13.0 82 9.0 83 8.0 84 5.5 85 5.5 86 4.0 87 0.5 88 1.5 89 2.0 90 1.0 91 0.5 92 1.0 93 0.5 94 0.0 95 1.0 96 2.0 97 1.5 98 2.0 99 2.0 100 1.0 >>END_MODULE >>Per base N content pass #Base N-Count 1 0.525 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.075 9 0.0 10-11 0.0125 12-13 0.0 14-15 0.0 16-17 0.21250000000000002 18-19 0.21250000000000002 20-21 0.025 22-23 0.0 24-25 0.0125 26-27 0.075 28-29 0.3875 30-31 0.025 32-33 0.0 34-35 0.0 36-37 0.025 38-39 0.13749999999999998 40-41 0.2 42-43 0.3500875218804701 44-45 0.12503125781445362 46-47 0.012503125781445362 48-49 0.3500875218804701 50-51 0.1875468867216804 52-53 0.012503125781445362 54-55 0.0 56-57 0.025015634771732333 58-59 0.3128128128128128 60-61 0.33783783783783783 62-63 0.12514078338130397 64-65 0.012523481527864746 66-67 0.0 68-69 0.012532898859506203 70-71 0.3009781790820165 72-73 0.3029155622870125 74-75 0.013320900492873319 76 0.0 >>END_MODULE >>Sequence Length Distribution warn #Length Count 41 1.0 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 1.0 56 1.0 57 1.0 58 0.0 59 0.0 60 0.0 61 0.0 62 1.0 63 2.0 64 1.0 65 0.0 66 0.0 67 2.0 68 1.0 69 1.0 70 2.0 71 12.0 72 25.0 73 48.0 74 295.0 75 886.0 76 2720.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 93.95 #Duplication Level Percentage of deduplicated Percentage of total 1 95.47631718999467 89.7 2 3.3794571580627992 6.35 3 0.7184672698243746 2.025 4 0.2394890899414582 0.8999999999999999 5 0.10643959552953698 0.5 6 0.0 0.0 7 0.07982969664715274 0.525 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 ATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGGGGAAAT 7 0.17500000000000002 No Hit GGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACA 7 0.17500000000000002 No Hit AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 7 0.17500000000000002 No Hit CTTTTTCACTCAGGACTGGGTATCCATGCCAGGTGTTATACCAGTAGCTT 5 0.125 No Hit CCTCTTGCTAAGCGTACCACACTATACAGACGTGCGCGCGCAGCCATGGCACCCACCGTGATGGCTTCCTCCGCC 5 0.125 No Hit CTTGATTTTACCAAAGATGATGAAAACGTAAACTCACAACCATTTATGCG 5 0.125 No Hit CTGCCAGTAGTCATATGCTTGTCTCAAAGATTAAGCCATGCATGTGCAAG 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 0.025 0.0 0.0 0.0 37 0.0 0.025 0.0 0.0 0.0 38 0.0 0.025 0.0 0.0 0.0 39 0.0 0.025 0.0 0.0 0.0 40 0.0 0.025 0.0 0.0 0.0 41 0.0 0.025 0.0 0.0 0.0 42 0.0 0.025 0.0 0.0 0.0 43 0.0 0.025 0.0 0.0 0.0 44 0.0 0.025 0.0 0.0 0.0 45 0.0 0.025 0.0 0.0 0.0 46 0.0 0.025 0.0 0.0 0.0 47 0.0 0.025 0.0 0.0 0.0 48 0.0 0.025 0.0 0.0 0.0 49 0.0 0.025 0.0 0.0 0.0 50 0.0 0.025 0.0 0.0 0.0 51 0.0 0.025 0.0 0.0 0.0 52 0.0 0.025 0.0 0.0 0.0 53 0.0 0.025 0.0 0.0 0.0 54 0.0 0.025 0.0 0.0 0.0 55 0.0 0.025 0.0 0.0 0.0 56 0.0 0.025 0.0 0.0 0.0 57 0.0 0.025 0.0 0.0 0.0 58 0.0 0.025 0.0 0.0 0.0 59 0.0 0.025 0.0 0.0 0.0 60 0.0 0.025 0.0 0.0 0.0 61 0.0 0.025 0.0 0.0 0.0 62 0.0 0.025 0.0 0.0 0.0 63 0.0 0.025 0.0 0.0 0.0 64 0.0 0.025 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Read 1931725 spots for SRR19784175.sra Written 1931725 spots for SRR19784175.sra Read 1931725 spots for SRR19784175.sra Written 1931725 spots for SRR19784175.sra Read 1931725 spots for SRR19784175.sra Written 1931725 spots for SRR19784175.sra Read 1931725 spots for SRR19784175.sra Written 1931725 spots for SRR19784175.sra Read 1931725 spots for SRR19784175.sra Written 1931725 spots for SRR19784175.sra Read 1931725 spots for SRR19784175.sra Written 1931725 spots for SRR19784175.sra Read 1931725 spots for SRR19784175.sra Written 1931725 spots for SRR19784175.sra Read 1931725 spots for SRR19784175.sra Written 1931725 spots for SRR19784175.sra Read 1931725 spots for SRR19784175.sra Written 1931725 spots for SRR19784175.sra Read 1931725 spots for SRR19784175.sra Written 1931725 spots for SRR19784175.sra Read 1931725 spots for SRR19784175.sra Written 1931725 spots for SRR19784175.sra Read 1931725 spots for SRR19784175.sra Written 1931725 spots for SRR19784175.sra Read 1931737 spots for SRR19784175.sra Written 1931737 spots for SRR19784175.sra Read 1931725 spots for SRR19784175.sra Written 1931725 spots for SRR19784175.sra Read 1931725 spots for SRR19784175.sra Written 1931725 spots for SRR19784175.sra Read 1931725 spots for SRR19784175.sra Written 1931725 spots for SRR19784175.sra Read 1931725 spots for SRR19784175.sra Written 1931725 spots for SRR19784175.sra Read 1931725 spots for SRR19784175.sra Written 1931725 spots for SRR19784175.sra Read 1931725 spots for SRR19784175.sra Written 1931725 spots for SRR19784175.sra Read 1931725 spots for SRR19784175.sra Written 1931725 spots for SRR19784175.sra SRR ids: ['SRR19784175.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_riwyemjx SRR19784175.sra spots: 38634512 blocks: [[1, 1931725], [1931726, 3863450], [3863451, 5795175], [5795176, 7726900], [7726901, 9658625], [9658626, 11590350], [11590351, 13522075], [13522076, 15453800], [15453801, 17385525], [17385526, 19317250], [19317251, 21248975], [21248976, 23180700], [23180701, 25112425], [25112426, 27044150], [27044151, 28975875], [28975876, 30907600], [30907601, 32839325], [32839326, 34771050], [34771051, 36702775], [36702776, 38634512]] SRR19784175 file size 7371311 SRR19784175 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 SRR19784175 SRR19784175_1.fastq SRR19784175_2.fastq Input file: SRR19784175_1.fastq Paired file: SRR19784175_2.fastq trimmed: SRR19784175-trimmed-pair1.fastq, SRR19784175-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 13:34:03 2024 >> started Fri Dec 6 13:34:58 2024 >> done (54.465s) 38634512 read pairs processed; of these: 1 ( 0.00%) short read pairs filtered out after trimming by size control 38360 ( 0.10%) empty read pairs filtered out after trimming by size control 38596151 (99.90%) read pairs available; of these: 54241 ( 0.14%) trimmed read pairs available after processing 38541910 (99.86%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 2 0.00% 19 2 0.00% 20 10 0.00% 21 5 0.00% 22 31 0.00% 23 54 0.00% 24 82 0.00% 25 104 0.00% 26 112 0.00% 27 161 0.00% 28 193 0.00% 29 223 0.00% 30 297 0.00% 31 781 0.00% 32 916 0.00% 33 398 0.00% 34 1154 0.00% 35 767 0.00% 36 774 0.00% 37 912 0.00% 38 937 0.00% 39 1056 0.00% 40 1154 0.00% 41 1302 0.00% 42 1385 0.00% 43 1454 0.00% 44 1649 0.00% 45 1645 0.00% 46 1801 0.00% 47 1948 0.01% 48 2176 0.01% 49 2353 0.01% 50 2505 0.01% 51 2918 0.01% 52 3232 0.01% 53 3570 0.01% 54 3688 0.01% 55 4185 0.01% 56 4449 0.01% 57 4713 0.01% 58 5174 0.01% 59 5775 0.01% 60 6249 0.02% 61 6654 0.02% 62 7620 0.02% 63 8317 0.02% 64 9080 0.02% 65 9840 0.03% 66 10567 0.03% 67 11681 0.03% 68 12596 0.03% 69 14193 0.04% 70 19558 0.05% 71 22380 0.06% 72 46330 0.12% 73 292123 0.76% 74 2384389 6.18% 75 17009885 44.07% 76 18658642 48.34% 38596151 reads passed initial QC criterion=sequence-density sequence-density=0.54 sequence-density-rank=1 fanout-score=1.98 fanout-score-rank=28 prefix-density=0.51 prefix-fanout=2.0 sequence=TTCAAATGTACA criterion=fanout-score sequence-density=0.14 sequence-density-rank=28 fanout-score=69.66 fanout-score-rank=1 prefix-density=0.91 prefix-fanout=10.4 sequence=GGCGGCGGCGAACCGCCCCCGTCGCCGCGATCCGAACACTTCACCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGCATTCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCTATATACTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCGTCGCCTAAACGGCGATAGTCCCTCTAAGAAGCTAGCTGCGGAGGGATGGCTCCGCATAGCTAGTTAGCAGGCTGAGGTCTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCATGCACCACCACCCATAGAATCAAGAAAGAGCTCTCAGTCTGTCAATCCTTGCTATGTCTGGACCTGGTAAG criterion=sequence-density sequence-density=0.49 sequence-density-rank=1 fanout-score=3.84 fanout-score-rank=13 prefix-density=0.55 prefix-fanout=3.4 sequence=GAGTTCAGCAAGGTCGGCTTCGTCTTCCGCGAGCACAACAGCTC criterion=fanout-score sequence-density=0.01 sequence-density-rank=38 fanout-score=74.05 fanout-score-rank=1 prefix-density=0.51 prefix-fanout=1.9 sequence=CCGCTCCAACACTTCAGTTCTCACTCCACAGCTCAGAGTCAGAGCTACTAGCAATGGCAGCGGCGACCATGGCGCTCTCCTCCCCCGCGATGGCCGGCACCCCGGTGAAGGTCTCCAGGGCCACCCCCTTCGGCGAGGGCCGCATCACCATGCGCAAGAC SRR19784175 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 06 13:35:35 Started mapping on | Dec 06 13:35:36 Finished on | Dec 06 13:38:23 Mapping speed, Million of reads per hour | 832.01 Number of input reads | 38596151 Average input read length | 151 UNIQUE READS: Uniquely mapped reads number | 28021651 Uniquely mapped reads % | 72.60% Average mapped length | 150.52 Number of splices: Total | 9460932 Number of splices: Annotated (sjdb) | 9047801 Number of splices: GT/AG | 9337322 Number of splices: GC/AG | 108007 Number of splices: AT/AC | 2067 Number of splices: Non-canonical | 13536 Mismatch rate per base, % | 0.38% Deletion rate per base | 0.01% Deletion average length | 1.78 Insertion rate per base | 0.00% Insertion average length | 1.83 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 5758806 % of reads mapped to multiple loci | 14.92% Number of reads mapped to too many loci | 1005852 % of reads mapped to too many loci | 2.61% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 4.04% % of reads unmapped: other | 5.83% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 4815701 4815701 4815701 N_multimapping 5758806 5758806 5758806 N_noFeature 878880 26856802 1613210 N_ambiguous 607259 4222 186008 UnstrandedReadsAssigned:26535512 PositiveStrandReadsAssigned:1160627 NegativeStrandReadsAssigned:26222433 Dataset is classified negative stranded MeadianReadLen=76 20thPercentileLength=75 echo kmer=71 SRR19784175 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: SRR19784175-trimmed-pair1.fastq SRR19784175-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 38,596,151 reads, 31,201,645 reads pseudoaligned [quant] estimated average fragment length: 160.119 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,158 rounds 52973 SRR19784175.ke.tsv 35125 SRR19784175.se.tsv 88098 total ==> SRR19784175.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 776.948 0 0 PNS24247 1044 884.881 29.5962 1.38304 PNS24249 1928 1768.88 149.069 3.48476 PNS24246 1044 884.881 29.5962 1.38304 PNS24248 1044 884.881 29.5962 1.38304 PNS24244 1471 1311.88 47.1423 1.48593 PNS24243 293 138.84 0 0 KQK14069 1603 1443.88 14468.1 414.346 KQK14071 474 315.568 2063.83 270.436 ==> SRR19784175.se.tsv <== BRADI_1g14170v3 17380 BRADI_1g53295v3 24 BRADI_1g59795v3 589 BRADI_1g07683v3 0 BRADI_1g00485v3 3 BRADI_1g20270v3 381 BRADI_1g74790v3 127 BRADI_1g09890v3 0 BRADI_1g77505v3 175 BRADI_1g48960v3 0 SRR19784175 completed mapping pipeline successfully