Starting /dee2/code/volunteer_pipeline.sh ERR5052693 current disk space = 1525885018112 free memory = 1558557156 ERR5052693 SRAfilesize 11d92b3ebd2d6cc95f39c5b07afa1a9c ERR5052693.sra ERR5052693.sra file validated ERR5052693 is paired end ERR5052693 is conventional basespace ERR5052693 read1 length is 70 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR5052693_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 70 %GC 50 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 34.0985 35.0 35.0 35.0 35.0 35.0 2 34.542 35.0 35.0 35.0 35.0 35.0 3 34.59075 35.0 35.0 35.0 35.0 35.0 4 34.6405 35.0 35.0 35.0 35.0 35.0 5 34.69475 35.0 35.0 35.0 35.0 35.0 6 39.40325 40.0 40.0 40.0 39.0 40.0 7 39.47875 40.0 40.0 40.0 39.0 40.0 8 39.399 40.0 40.0 40.0 39.0 40.0 9 39.41875 40.0 40.0 40.0 39.0 40.0 10 39.39475 40.0 40.0 40.0 39.0 40.0 11 39.3765 40.0 40.0 40.0 39.0 40.0 12 39.4055 40.0 40.0 40.0 39.0 40.0 13 39.379 40.0 40.0 40.0 39.0 40.0 14 39.398 40.0 40.0 40.0 39.0 40.0 15 39.3405 40.0 40.0 40.0 39.0 40.0 16 39.3475 40.0 40.0 40.0 39.0 40.0 17 39.3265 40.0 40.0 40.0 39.0 40.0 18 39.3385 40.0 40.0 40.0 39.0 40.0 19 39.38825 40.0 40.0 40.0 39.0 40.0 20 39.3645 40.0 40.0 40.0 39.0 40.0 21 39.34175 40.0 40.0 40.0 39.0 40.0 22 39.3595 40.0 40.0 40.0 39.0 40.0 23 39.3325 40.0 40.0 40.0 39.0 40.0 24 39.36725 40.0 40.0 40.0 39.0 40.0 25 39.35275 40.0 40.0 40.0 39.0 40.0 26 39.362 40.0 40.0 40.0 39.0 40.0 27 39.29175 40.0 40.0 40.0 39.0 40.0 28 39.30925 40.0 40.0 40.0 39.0 40.0 29 39.2125 40.0 40.0 40.0 39.0 40.0 30 39.31775 40.0 40.0 40.0 39.0 40.0 31 39.33375 40.0 40.0 40.0 39.0 40.0 32 39.32875 40.0 40.0 40.0 39.0 40.0 33 39.339 40.0 40.0 40.0 39.0 40.0 34 39.38725 40.0 40.0 40.0 39.0 40.0 35 39.34875 40.0 40.0 40.0 39.0 40.0 36 39.41625 40.0 40.0 40.0 39.0 40.0 37 39.3835 40.0 40.0 40.0 39.0 40.0 38 39.2685 40.0 40.0 40.0 39.0 40.0 39 39.267 40.0 40.0 40.0 39.0 40.0 40 39.279 40.0 40.0 40.0 39.0 40.0 41 39.22975 40.0 40.0 40.0 39.0 40.0 42 39.27225 40.0 40.0 40.0 39.0 40.0 43 39.39675 40.0 40.0 40.0 39.0 40.0 44 39.34575 40.0 40.0 40.0 39.0 40.0 45 39.32225 40.0 40.0 40.0 39.0 40.0 46 39.2675 40.0 40.0 40.0 39.0 40.0 47 39.28275 40.0 40.0 40.0 39.0 40.0 48 39.30075 40.0 40.0 40.0 39.0 40.0 49 39.3215 40.0 40.0 40.0 39.0 40.0 50 39.3385 40.0 40.0 40.0 39.0 40.0 51 39.33575 40.0 40.0 40.0 39.0 40.0 52 39.2915 40.0 40.0 40.0 39.0 40.0 53 39.32025 40.0 40.0 40.0 39.0 40.0 54 39.3245 40.0 40.0 40.0 39.0 40.0 55 39.28325 40.0 40.0 40.0 39.0 40.0 56 39.3175 40.0 40.0 40.0 39.0 40.0 57 39.21 40.0 40.0 40.0 39.0 40.0 58 39.163 40.0 40.0 40.0 39.0 40.0 59 39.2775 40.0 40.0 40.0 39.0 40.0 60 39.288 40.0 40.0 40.0 39.0 40.0 61 39.28875 40.0 40.0 40.0 39.0 40.0 62 39.23725 40.0 40.0 40.0 39.0 40.0 63 39.29975 40.0 40.0 40.0 39.0 40.0 64 39.271 40.0 40.0 40.0 39.0 40.0 65 39.2795 40.0 40.0 40.0 39.0 40.0 66 39.3675 40.0 40.0 40.0 39.0 40.0 67 39.23975 40.0 40.0 40.0 39.0 40.0 68 39.29475 40.0 40.0 40.0 39.0 40.0 69 39.367 40.0 40.0 40.0 39.0 40.0 70 39.21325 40.0 40.0 40.0 39.0 40.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 23 1.0 24 2.0 25 4.0 26 7.0 27 4.0 28 11.0 29 9.0 30 22.0 31 27.0 32 33.0 33 32.0 34 33.0 35 47.0 36 80.0 37 105.0 38 255.0 39 3328.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 36.37057775515398 13.056757444642402 12.44591499109188 38.12674980911173 2 22.930732683170792 15.928982245561391 29.532383095773945 31.607901975493874 3 21.925 22.7 22.900000000000002 32.475 4 25.924999999999997 28.125 20.599999999999998 25.35 5 25.75 30.375000000000004 22.95 20.925 6 21.275 29.625 26.974999999999998 22.125 7 18.975 22.425 36.975 21.625 8 20.05 22.675 29.049999999999997 28.225 9 21.375 22.1 31.474999999999998 25.05 10 22.1 30.9 22.825 24.175 11 25.275 22.275 22.650000000000002 29.799999999999997 12 23.400000000000002 22.275 26.1 28.225 13 23.474999999999998 25.55 26.825 24.15 14 23.05 24.525 27.075 25.35 15 22.825 24.525 25.674999999999997 26.974999999999998 16 23.974999999999998 26.05 23.400000000000002 26.575 17 23.425 24.4 25.724999999999998 26.450000000000003 18 23.3 24.625 25.5 26.575 19 24.425 24.825 25.85 24.9 20 23.549999999999997 25.1 24.85 26.5 21 23.799999999999997 24.0 25.7 26.5 22 23.95 25.074999999999996 24.875 26.1 23 23.275000000000002 25.900000000000002 24.55 26.275 24 22.675 25.724999999999998 24.975 26.625 25 24.474999999999998 24.5 23.674999999999997 27.35 26 24.175 25.124999999999996 25.025 25.674999999999997 27 23.474999999999998 24.175 26.025 26.325 28 23.525 26.700000000000003 24.575 25.2 29 23.175 25.4 25.124999999999996 26.3 30 23.200000000000003 23.974999999999998 24.2 28.625 31 24.075 24.575 24.775 26.575 32 22.900000000000002 26.025 25.575 25.5 33 22.975 25.724999999999998 24.625 26.674999999999997 34 24.375 25.15 24.5 25.974999999999998 35 24.375 23.7 24.2 27.725 36 22.975 25.8 25.4 25.825 37 23.9 25.775 23.549999999999997 26.775 38 23.225 24.975 25.324999999999996 26.474999999999998 39 22.900000000000002 24.775 25.8 26.525 40 24.425 24.425 23.799999999999997 27.35 41 23.325000000000003 24.775 25.424999999999997 26.474999999999998 42 24.45 25.575 23.575 26.400000000000002 43 24.325 25.724999999999998 24.85 25.1 44 23.025000000000002 25.275 25.775 25.924999999999997 45 23.575 23.599999999999998 25.074999999999996 27.750000000000004 46 23.45 25.2 25.1 26.25 47 23.95 25.4 24.675 25.974999999999998 48 23.25581395348837 24.5311327831958 24.8062015503876 27.406851712928233 49 23.58089522380595 25.431357839459867 25.63140785196299 25.35633908477119 50 22.95573893473368 24.55613903475869 25.78144536134033 26.70667666916729 51 22.355588897224308 24.48112028007002 25.98149537384346 27.181795448862218 52 24.056014003500874 25.18129532383096 24.681170292573142 26.081520380095025 53 24.306076519129782 24.93123280820205 25.10627656914228 25.656414103525883 54 24.006001500375092 25.456364091022753 24.706176544136035 25.831457864466117 55 22.63631815907954 24.83741870935468 25.68784392196098 26.8384192096048 56 23.78689344672336 24.73736868434217 24.487243621810904 26.988494247123562 57 22.786393196598297 25.53776888444222 25.46273136568284 26.21310655327664 58 24.312156078039017 25.662831415707853 23.28664332166083 26.738369184592298 59 24.362181090545274 23.686843421710854 25.287643821910955 26.663331665832917 60 23.19239429572179 25.94445834375782 24.143107330497873 26.720040030022517 61 23.04804804804805 25.525525525525527 24.84984984984985 26.576576576576578 62 24.424424424424423 24.64964964964965 25.225225225225223 25.7007007007007 63 23.273273273273272 25.850850850850847 23.823823823823822 27.05205205205205 64 23.504380475594495 25.381727158948685 25.456821026282856 25.65707133917397 65 23.00375469336671 26.357947434292868 24.28035043804756 26.357947434292868 66 23.526460998244296 24.003009781790823 25.909204915976925 26.56132430398796 67 24.344758064516128 24.672379032258064 24.722782258064516 26.26008064516129 68 23.520368946963874 22.623622854214705 26.056879323597233 27.799128875224188 69 22.82967032967033 19.587912087912088 27.747252747252748 29.835164835164836 70 26.513493800145877 0.0 36.287381473377096 37.199124726477024 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 0.0 1 0.0 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10 0.0 11 0.0 12 0.0 13 0.0 14 0.0 15 0.0 16 0.5 17 1.0 18 0.5 19 0.0 20 0.0 21 0.0 22 1.0 23 2.0 24 1.0 25 2.0 26 3.5 27 3.0 28 5.5 29 15.0 30 22.0 31 26.0 32 31.0 33 32.0 34 40.5 35 68.0 36 104.0 37 121.0 38 125.5 39 151.5 40 173.0 41 190.0 42 234.0 43 261.0 44 246.0 45 244.0 46 259.0 47 261.0 48 242.5 49 221.0 50 218.0 51 209.5 52 204.5 53 208.0 54 183.5 55 148.5 56 130.5 57 123.0 58 109.0 59 104.0 60 113.0 61 103.0 62 94.0 63 95.0 64 90.5 65 85.0 66 79.0 67 74.0 68 62.5 69 49.0 70 47.0 71 41.5 72 30.5 73 25.0 74 21.0 75 18.0 76 12.5 77 6.0 78 5.0 79 3.0 80 2.0 81 2.5 82 1.5 83 0.0 84 0.0 85 0.0 86 0.0 87 0.0 88 0.0 89 0.0 90 0.0 91 0.0 92 0.0 93 0.0 94 0.0 95 0.0 96 0.0 97 0.0 98 0.0 99 0.0 100 0.0 >>END_MODULE >>Per base N content fail #Base N-Count 1 1.775 2 0.025 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 0.0 21 0.0 22 0.0 23 0.0 24 0.0 25 0.0 26 0.0 27 0.0 28 0.0 29 0.0 30 0.0 31 0.0 32 0.0 33 0.0 34 0.0 35 0.0 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 0.0 45 0.0 46 0.0 47 0.0 48 0.025 49 0.025 50 0.025 51 0.025 52 0.025 53 0.025 54 0.025 55 0.05 56 0.05 57 0.05 58 0.05 59 0.05 60 0.075 61 0.1 62 0.1 63 0.1 64 0.125 65 0.125 66 0.325 67 0.8 68 2.4250000000000003 69 9.0 70 31.45 >>END_MODULE >>Sequence Length Distribution pass #Length Count 70 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 99.575 #Duplication Level Percentage of deduplicated Percentage of total 1 99.59829274416269 99.175 2 0.37660055234747675 0.75 3 0.025106703489831784 0.075 4 0.0 0.0 5 0.0 0.0 6 0.0 0.0 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 pass >>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 >>END_MODULE >>Kmer Content pass >>END_MODULE ERR5052693 read2 length is 70 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR5052693_2.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 70 %GC 51 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 34.3645 35.0 35.0 35.0 33.0 35.0 2 34.25775 35.0 35.0 35.0 33.0 35.0 3 34.1095 35.0 35.0 35.0 33.0 35.0 4 34.05775 35.0 35.0 35.0 33.0 35.0 5 34.1415 35.0 35.0 35.0 33.0 35.0 6 38.80325 40.0 40.0 40.0 38.0 40.0 7 38.6525 40.0 40.0 40.0 38.0 40.0 8 38.6175 40.0 40.0 40.0 37.0 40.0 9 38.6775 40.0 40.0 40.0 38.0 40.0 10 38.7575 40.0 40.0 40.0 38.0 40.0 11 38.75675 40.0 40.0 40.0 38.0 40.0 12 38.77975 40.0 40.0 40.0 39.0 40.0 13 38.74825 40.0 40.0 40.0 38.0 40.0 14 38.74025 40.0 40.0 40.0 38.0 40.0 15 38.7955 40.0 40.0 40.0 38.0 40.0 16 38.70175 40.0 40.0 40.0 38.0 40.0 17 38.69175 40.0 40.0 40.0 38.0 40.0 18 38.7335 40.0 40.0 40.0 38.0 40.0 19 38.66975 40.0 40.0 40.0 38.0 40.0 20 38.77025 40.0 40.0 40.0 38.0 40.0 21 38.71625 40.0 40.0 40.0 38.0 40.0 22 38.7395 40.0 40.0 40.0 38.0 40.0 23 38.75675 40.0 40.0 40.0 39.0 40.0 24 38.74625 40.0 40.0 40.0 38.0 40.0 25 38.73 40.0 40.0 40.0 39.0 40.0 26 38.689 40.0 40.0 40.0 38.0 40.0 27 38.67725 40.0 40.0 40.0 38.0 40.0 28 38.702 40.0 40.0 40.0 38.0 40.0 29 38.68025 40.0 40.0 40.0 38.0 40.0 30 38.6805 40.0 40.0 40.0 38.0 40.0 31 38.71825 40.0 40.0 40.0 38.0 40.0 32 38.69825 40.0 40.0 40.0 38.0 40.0 33 38.675 40.0 40.0 40.0 38.0 40.0 34 38.698 40.0 40.0 40.0 38.0 40.0 35 38.67175 40.0 40.0 40.0 38.0 40.0 36 38.75975 40.0 40.0 40.0 38.0 40.0 37 38.6225 40.0 40.0 40.0 38.0 40.0 38 38.7025 40.0 40.0 40.0 38.0 40.0 39 38.65375 40.0 40.0 40.0 38.0 40.0 40 38.75 40.0 40.0 40.0 38.0 40.0 41 38.68925 40.0 40.0 40.0 38.0 40.0 42 38.6595 40.0 40.0 40.0 37.0 40.0 43 38.62075 40.0 40.0 40.0 38.0 40.0 44 38.621 40.0 40.0 40.0 37.0 40.0 45 38.67225 40.0 40.0 40.0 38.0 40.0 46 38.73825 40.0 40.0 40.0 38.0 40.0 47 38.6745 40.0 40.0 40.0 38.0 40.0 48 38.64125 40.0 40.0 40.0 38.0 40.0 49 38.6575 40.0 40.0 40.0 38.0 40.0 50 38.63975 40.0 40.0 40.0 38.0 40.0 51 38.61575 40.0 40.0 40.0 37.0 40.0 52 38.6285 40.0 40.0 40.0 38.0 40.0 53 38.51025 40.0 40.0 40.0 37.0 40.0 54 38.6125 40.0 40.0 40.0 37.0 40.0 55 38.6145 40.0 40.0 40.0 38.0 40.0 56 38.5075 40.0 40.0 40.0 37.0 40.0 57 38.63125 40.0 40.0 40.0 38.0 40.0 58 38.65975 40.0 40.0 40.0 37.0 40.0 59 38.5935 40.0 40.0 40.0 38.0 40.0 60 38.64725 40.0 40.0 40.0 38.0 40.0 61 38.64625 40.0 40.0 40.0 37.0 40.0 62 38.65275 40.0 40.0 40.0 38.0 40.0 63 38.60625 40.0 40.0 40.0 38.0 40.0 64 38.5955 40.0 40.0 40.0 37.0 40.0 65 38.56975 40.0 40.0 40.0 37.0 40.0 66 38.58 40.0 40.0 40.0 37.0 40.0 67 38.59225 40.0 40.0 40.0 37.0 40.0 68 38.6585 40.0 40.0 40.0 38.0 40.0 69 38.66175 40.0 40.0 40.0 38.0 40.0 70 38.60375 40.0 40.0 40.0 38.0 40.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 16 2.0 17 6.0 18 12.0 19 18.0 20 19.0 21 24.0 22 17.0 23 15.0 24 12.0 25 16.0 26 21.0 27 14.0 28 17.0 29 15.0 30 17.0 31 22.0 32 18.0 33 26.0 34 38.0 35 38.0 36 56.0 37 99.0 38 221.0 39 3257.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 35.675000000000004 17.724999999999998 15.775 30.825000000000003 2 29.549999999999997 22.45 26.0 22.0 3 23.1 24.2 28.775000000000002 23.925 4 26.875 28.4 19.75 24.975 5 27.700000000000003 32.175 19.475 20.65 6 23.43671835917959 30.115057528764382 22.836418209104554 23.611805902951478 7 22.675 17.75 34.4 25.174999999999997 8 23.075000000000003 20.1 24.6 32.225 9 24.6 22.225 27.0 26.174999999999997 10 25.85 28.499999999999996 21.825 23.825 11 28.15 22.075 21.099999999999998 28.675 12 27.575 21.275 24.075 27.075 13 25.5 23.225 25.6 25.674999999999997 14 26.55 23.5 25.374999999999996 24.575 15 25.674999999999997 24.5 25.074999999999996 24.75 16 26.6 24.349999999999998 23.849999999999998 25.2 17 26.150000000000002 24.7 23.400000000000002 25.75 18 26.974999999999998 23.674999999999997 23.3 26.05 19 26.125 24.725 22.725 26.424999999999997 20 26.525 24.7 23.625 25.15 21 24.9 25.124999999999996 25.224999999999998 24.75 22 25.6 24.025 23.775 26.6 23 26.5 25.4 24.05 24.05 24 26.525 24.3 24.975 24.2 25 25.8 24.25 23.95 26.0 26 25.974999999999998 24.75 23.525 25.75 27 26.025 24.099999999999998 25.650000000000002 24.224999999999998 28 25.55 24.15 24.55 25.75 29 26.25 25.025 24.325 24.4 30 27.425 23.549999999999997 25.05 23.974999999999998 31 26.650000000000002 24.45 23.549999999999997 25.35 32 26.3 24.975 23.9 24.825 33 25.674999999999997 25.15 24.925 24.25 34 27.55 24.125 24.224999999999998 24.099999999999998 35 27.375 24.575 22.45 25.6 36 24.8 26.674999999999997 24.45 24.075 37 26.85 23.400000000000002 24.85 24.9 38 27.325 25.025 23.1 24.55 39 24.675 24.775 24.474999999999998 26.075 40 26.950000000000003 24.95 24.375 23.724999999999998 41 27.825 24.525 22.775000000000002 24.875 42 26.625 25.174999999999997 24.275 23.925 43 26.025 25.474999999999998 24.05 24.45 44 26.424999999999997 24.95 24.0 24.625 45 25.674999999999997 25.55 24.15 24.625 46 25.575 25.974999999999998 23.35 25.1 47 26.400000000000002 25.674999999999997 23.674999999999997 24.25 48 25.506376594148538 25.681420355088775 24.15603900975244 24.656164041010253 49 26.756689172293076 23.705926481620406 24.356089022255563 25.18129532383096 50 27.506876719179797 23.680920230057513 23.48087021755439 25.331332833208304 51 25.331332833208304 24.681170292573142 25.10627656914228 24.88122030507627 52 26.60665166291573 23.23080770192548 24.681170292573142 25.481370342585645 53 28.307076769192296 25.056264066016503 23.25581395348837 23.380845211302827 54 26.081520380095025 24.256064016004 25.581395348837212 24.081020255063766 55 27.33866933466733 24.83741870935468 23.6368184092046 24.187093546773387 56 29.089544772386194 25.03751875937969 22.786393196598297 23.08654327163582 57 25.162581290645324 24.937468734367183 25.68784392196098 24.212106053026513 58 25.737868934467233 25.162581290645324 24.537268634317158 24.562281140570285 59 27.66383191595798 24.787393696848426 23.36168084042021 24.187093546773387 60 27.313656828414207 24.16208104052026 24.512256128064035 24.012006003001503 61 26.388194097048522 25.63781890945473 24.387193596798397 23.58679339669835 62 27.56378189094547 24.087043521760883 23.261630815407706 25.087543771885944 63 25.41270635317659 23.986993496748372 25.71285642821411 24.88744372186093 64 24.73736868434217 25.937968984492244 24.062031015507753 25.26263131565783 65 26.826826826826828 25.400400400400404 23.44844844844845 24.324324324324326 66 25.71428571428571 25.68922305764411 24.210526315789473 24.385964912280702 67 27.46532156368222 24.38839848675914 24.337957124842372 23.808322824716267 68 27.18621399176955 23.97119341563786 23.559670781893004 25.282921810699587 69 25.88888888888889 18.916666666666668 26.555555555555554 28.638888888888893 70 27.426002248032972 0.0 36.15586361933308 36.418134132633945 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 0.0 1 0.0 2 0.0 3 0.0 4 0.0 5 0.0 6 0.5 7 1.0 8 0.5 9 0.0 10 0.0 11 0.0 12 0.0 13 0.0 14 0.0 15 0.0 16 0.5 17 1.0 18 1.0 19 1.0 20 1.0 21 1.0 22 1.0 23 1.0 24 2.5 25 3.0 26 2.5 27 3.0 28 5.0 29 8.0 30 9.0 31 10.5 32 20.0 33 28.0 34 39.5 35 71.0 36 90.0 37 89.0 38 104.5 39 145.5 40 171.0 41 191.0 42 209.5 43 208.0 44 217.5 45 219.0 46 229.5 47 248.0 48 242.5 49 232.5 50 228.0 51 205.5 52 192.0 53 201.0 54 175.0 55 146.0 56 133.0 57 123.0 58 120.5 59 123.0 60 128.0 61 124.0 62 106.0 63 92.0 64 96.0 65 101.5 66 96.5 67 90.0 68 78.0 69 61.0 70 56.0 71 51.0 72 40.0 73 34.0 74 29.5 75 24.0 76 18.5 77 14.0 78 10.5 79 7.5 80 8.0 81 6.0 82 2.5 83 1.0 84 1.0 85 0.5 86 0.5 87 1.0 88 0.5 89 0.0 90 0.0 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 fail #Base N-Count 1 0.0 2 0.0 3 0.0 4 0.0 5 0.0 6 0.05 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 0.0 21 0.0 22 0.0 23 0.0 24 0.0 25 0.0 26 0.0 27 0.0 28 0.0 29 0.0 30 0.0 31 0.0 32 0.0 33 0.0 34 0.0 35 0.0 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 0.0 45 0.0 46 0.0 47 0.0 48 0.025 49 0.025 50 0.025 51 0.025 52 0.025 53 0.025 54 0.025 55 0.05 56 0.05 57 0.05 58 0.05 59 0.05 60 0.05 61 0.05 62 0.05 63 0.05 64 0.05 65 0.1 66 0.25 67 0.8750000000000001 68 2.8000000000000003 69 10.0 70 33.275 >>END_MODULE >>Sequence Length Distribution pass #Length Count 70 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 99.25 #Duplication Level Percentage of deduplicated Percentage of total 1 99.29471032745592 98.55000000000001 2 0.6801007556675063 1.35 3 0.0 0.0 4 0.025188916876574305 0.1 5 0.0 0.0 6 0.0 0.0 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 pass >>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 >>END_MODULE >>Kmer Content pass >>END_MODULE Read 528509 spots for ERR5052693.sra Written 528509 spots for ERR5052693.sra Read 528509 spots for ERR5052693.sra Written 528509 spots for ERR5052693.sra Read 528509 spots for ERR5052693.sra Written 528509 spots for ERR5052693.sra Read 528509 spots for ERR5052693.sra Written 528509 spots for ERR5052693.sra Read 528509 spots for ERR5052693.sra Written 528509 spots for ERR5052693.sra Read 528509 spots for ERR5052693.sra Written 528509 spots for ERR5052693.sra Read 528509 spots for ERR5052693.sra Written 528509 spots for ERR5052693.sra Read 528509 spots for ERR5052693.sra Written 528509 spots for ERR5052693.sra Read 528509 spots for ERR5052693.sra Written 528509 spots for ERR5052693.sra Read 528509 spots for ERR5052693.sra Written 528509 spots for ERR5052693.sra Read 528509 spots for ERR5052693.sra Written 528509 spots for ERR5052693.sra Read 528509 spots for ERR5052693.sra Written 528509 spots for ERR5052693.sra Read 528509 spots for ERR5052693.sra Written 528509 spots for ERR5052693.sra Read 528509 spots for ERR5052693.sra Written 528509 spots for ERR5052693.sra Read 528509 spots for ERR5052693.sra Written 528509 spots for ERR5052693.sra Read 528509 spots for ERR5052693.sra Written 528509 spots for ERR5052693.sra Read 528509 spots for ERR5052693.sra Written 528509 spots for ERR5052693.sra Read 528509 spots for ERR5052693.sra Written 528509 spots for ERR5052693.sra Read 528509 spots for ERR5052693.sra Written 528509 spots for ERR5052693.sra Read 528514 spots for ERR5052693.sra Written 528514 spots for ERR5052693.sra SRR ids: ['ERR5052693.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_4hc2_p9b ERR5052693.sra spots: 10570185 blocks: [[1, 528509], [528510, 1057018], [1057019, 1585527], [1585528, 2114036], [2114037, 2642545], [2642546, 3171054], [3171055, 3699563], [3699564, 4228072], [4228073, 4756581], [4756582, 5285090], [5285091, 5813599], [5813600, 6342108], [6342109, 6870617], [6870618, 7399126], [7399127, 7927635], [7927636, 8456144], [8456145, 8984653], [8984654, 9513162], [9513163, 10041671], [10041672, 10570185]] ERR5052693 file size 1877629 ERR5052693 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 ERR5052693 ERR5052693_1.fastq ERR5052693_2.fastq Input file: ERR5052693_1.fastq Paired file: ERR5052693_2.fastq trimmed: ERR5052693-trimmed-pair1.fastq, ERR5052693-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 Tue Dec 10 05:32:51 2024 >> started Tue Dec 10 05:32:59 2024 >> done (8.328s) 10570185 read pairs processed; of these: 0 ( 0.00%) short read pairs filtered out after trimming by size control 24 ( 0.00%) empty read pairs filtered out after trimming by size control 10570161 (100.00%) read pairs available; of these: 34 ( 0.00%) trimmed read pairs available after processing 10570127 (100.00%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 51 1 0.00% 52 2 0.00% 53 0 0.00% 54 0 0.00% 55 0 0.00% 56 0 0.00% 57 0 0.00% 58 0 0.00% 59 0 0.00% 60 0 0.00% 61 0 0.00% 62 3 0.00% 63 0 0.00% 64 0 0.00% 65 0 0.00% 66 0 0.00% 67 0 0.00% 68 0 0.00% 69 28 0.00% 70 10570127 100.00% 10570161 reads passed initial QC criterion=sequence-density sequence-density=0.07 sequence-density-rank=1 fanout-score=1.99 fanout-score-rank=31 prefix-density=0.06 prefix-fanout=2.0 sequence=CCGTCAATTCCTTT criterion=fanout-score sequence-density=0.05 sequence-density-rank=12 fanout-score=193.95 fanout-score-rank=1 prefix-density=0.43 prefix-fanout=22.5 sequence=CTTCTTCTTGTC criterion=sequence-density sequence-density=0.28 sequence-density-rank=1 fanout-score=2.19 fanout-score-rank=25 prefix-density=0.28 prefix-fanout=2.2 sequence=CGGTTCCGGTTC criterion=fanout-score sequence-density=0.06 sequence-density-rank=20 fanout-score=243.89 fanout-score-rank=1 prefix-density=0.65 prefix-fanout=21.5 sequence=CGCCGCCGCCGA ERR5052693 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 10 05:33:31 Started mapping on | Dec 10 05:33:31 Finished on | Dec 10 05:33:54 Mapping speed, Million of reads per hour | 1654.46 Number of input reads | 10570161 Average input read length | 139 UNIQUE READS: Uniquely mapped reads number | 9951326 Uniquely mapped reads % | 94.15% Average mapped length | 138.75 Number of splices: Total | 4906501 Number of splices: Annotated (sjdb) | 4665005 Number of splices: GT/AG | 4843178 Number of splices: GC/AG | 56311 Number of splices: AT/AC | 2304 Number of splices: Non-canonical | 4708 Mismatch rate per base, % | 0.23% Deletion rate per base | 0.01% Deletion average length | 1.89 Insertion rate per base | 0.00% Insertion average length | 1.74 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 188725 % of reads mapped to multiple loci | 1.79% Number of reads mapped to too many loci | 50397 % of reads mapped to too many loci | 0.48% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 2.28% % of reads unmapped: other | 1.31% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 430110 430110 430110 N_multimapping 188725 188725 188725 N_noFeature 322284 9711777 382755 N_ambiguous 212633 763 34046 UnstrandedReadsAssigned:9416409 PositiveStrandReadsAssigned:238786 NegativeStrandReadsAssigned:9534525 Dataset is classified negative stranded MeadianReadLen=70 20thPercentileLength=70 echo kmer=65 ERR5052693 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: ERR5052693-trimmed-pair1.fastq ERR5052693-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 10,570,161 reads, 9,753,760 reads pseudoaligned [quant] estimated average fragment length: 184.234 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,175 rounds 52973 ERR5052693.ke.tsv 35125 ERR5052693.se.tsv 88098 total ==> ERR5052693.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 753.039 0.0220322 0.00444292 PNS24247 1044 860.766 35.9521 6.34261 PNS24249 1928 1744.77 66.1724 5.75928 PNS24246 1044 860.766 35.9521 6.34261 PNS24248 1044 860.766 35.9521 6.34261 PNS24244 1471 1287.77 43.9491 5.18253 PNS24243 293 122.231 0 0 KQK14069 1603 1419.77 12640.4 1351.98 KQK14071 474 293.147 499.737 258.872 ==> ERR5052693.se.tsv <== BRADI_1g14170v3 14057 BRADI_1g53295v3 72 BRADI_1g59795v3 445 BRADI_1g07683v3 0 BRADI_1g00485v3 3 BRADI_1g20270v3 465 BRADI_1g74790v3 229 BRADI_1g09890v3 0 BRADI_1g77505v3 304 BRADI_1g48960v3 0 ERR5052693 completed mapping pipeline successfully