Starting /dee2/code/volunteer_pipeline.sh SRR11389834 current disk space = 1544481079296 free memory = 1599781788 SRR11389834 SRAfilesize 4ce50d4dac2ed5f2236ac87d8b467a2a SRR11389834.sra SRR11389834.sra file validated SRR11389834 is paired end SRR11389834 is conventional basespace SRR11389834 read1 length is 47-76 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR11389834_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 47-76 %GC 47 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 31.10275 32.0 32.0 32.0 32.0 32.0 2 31.0375 32.0 32.0 32.0 32.0 32.0 3 30.925 32.0 32.0 32.0 32.0 32.0 4 31.048 32.0 32.0 32.0 32.0 32.0 5 31.10725 32.0 32.0 32.0 32.0 32.0 6 34.043 36.0 36.0 36.0 32.0 36.0 7 34.04575 36.0 36.0 36.0 32.0 36.0 8 33.89125 36.0 36.0 36.0 32.0 36.0 9 34.05025 36.0 36.0 36.0 32.0 36.0 10-11 34.006875 36.0 36.0 36.0 32.0 36.0 12-13 34.0295 36.0 36.0 36.0 32.0 36.0 14-15 33.977625 36.0 36.0 36.0 32.0 36.0 16-17 33.99025 36.0 36.0 36.0 32.0 36.0 18-19 34.03975 36.0 36.0 36.0 32.0 36.0 20-21 33.843500000000006 36.0 36.0 36.0 29.5 36.0 22-23 33.773375 36.0 36.0 36.0 32.0 36.0 24-25 33.853624999999994 36.0 36.0 36.0 32.0 36.0 26-27 33.702375 36.0 36.0 36.0 29.5 36.0 28-29 33.488875 36.0 36.0 36.0 26.5 36.0 30-31 33.523375 36.0 36.0 36.0 27.0 36.0 32-33 33.484875 36.0 36.0 36.0 26.5 36.0 34-35 33.402375000000006 36.0 36.0 36.0 24.0 36.0 36-37 33.245625000000004 36.0 36.0 36.0 17.5 36.0 38-39 33.32625 36.0 36.0 36.0 17.5 36.0 40-41 33.205875000000006 36.0 36.0 36.0 17.5 36.0 42-43 33.12375 36.0 36.0 36.0 17.5 36.0 44-45 32.902874999999995 36.0 36.0 36.0 14.0 36.0 46-47 33.02875 36.0 36.0 36.0 17.5 36.0 48-49 32.71630407601901 36.0 36.0 36.0 14.0 36.0 50-51 32.57943950720046 36.0 34.0 36.0 14.0 36.0 52-53 32.70797898949475 36.0 34.0 36.0 14.0 36.0 54-55 32.29909932449337 36.0 32.0 36.0 14.0 36.0 56-57 32.27983487615712 36.0 32.0 36.0 14.0 36.0 58-59 31.975974504652264 36.0 32.0 36.0 14.0 36.0 60-61 31.985364024850885 36.0 32.0 36.0 14.0 36.0 62-63 32.00763488709147 36.0 32.0 36.0 14.0 36.0 64-65 32.0717981285591 36.0 32.0 36.0 14.0 36.0 66-67 32.00025166374028 36.0 32.0 36.0 14.0 36.0 68-69 31.996001441793265 36.0 32.0 36.0 14.0 36.0 70-71 31.87900474856129 36.0 32.0 36.0 14.0 36.0 72-73 31.947259024574507 36.0 32.0 36.0 14.0 36.0 74-75 31.76222174969384 36.0 32.0 36.0 14.0 36.0 76 30.19538518794194 36.0 27.0 36.0 14.0 36.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 21 5.0 22 9.0 23 16.0 24 27.0 25 37.0 26 64.0 27 110.0 28 129.0 29 193.0 30 256.0 31 324.0 32 429.0 33 517.0 34 970.0 35 914.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 35.775 9.9 18.075 36.25 2 23.1 13.65 30.775000000000002 32.475 3 23.400000000000002 18.675 24.25 33.675 4 29.9 25.275 20.45 24.375 5 26.724999999999998 28.999999999999996 23.599999999999998 20.674999999999997 6 22.15 32.800000000000004 26.974999999999998 18.075 7 15.35 27.400000000000002 36.725 20.525 8 18.65 26.1 31.900000000000002 23.35 9 19.25 21.025 35.975 23.75 10-11 22.3 30.325000000000003 24.675 22.7 12-13 23.35 26.0125 27.1625 23.474999999999998 14-15 22.237499999999997 26.950000000000003 27.737499999999997 23.075000000000003 16-17 22.2 27.9125 26.9125 22.975 18-19 21.2625 26.2875 28.225 24.224999999999998 20-21 22.35 27.437499999999996 26.400000000000002 23.8125 22-23 22.175 26.125 27.650000000000002 24.05 24-25 21.224999999999998 26.0375 27.900000000000002 24.837500000000002 26-27 21.4 26.7125 26.700000000000003 25.1875 28-29 21.825 26.4125 27.6625 24.099999999999998 30-31 22.7125 27.200000000000003 26.575 23.5125 32-33 22.0625 26.924999999999997 26.974999999999998 24.0375 34-35 21.0 26.3625 27.8375 24.8 36-37 22.3125 26.450000000000003 26.187500000000004 25.05 38-39 22.7625 25.75 26.924999999999997 24.5625 40-41 21.8625 27.0 26.700000000000003 24.4375 42-43 22.1375 25.587500000000002 28.199999999999996 24.075 44-45 21.925 26.087500000000002 27.1625 24.825 46-47 22.25 24.887500000000003 28.4375 24.425 48-49 22.2430607651913 24.93123280820205 27.694423605901473 25.131282820705174 50-51 22.283356258596974 25.071901963236215 26.722520945354507 25.922220832812304 52-53 22.998999499749875 25.275137568784395 25.700350175087543 26.025512756378188 54-55 20.99074305729297 26.444833625218916 27.958468851638727 24.605954465849386 56-57 21.978984238178633 25.906930197648236 27.970978233675257 24.143107330497873 58-59 22.419617165019393 25.972726135368447 27.11122231952959 24.496434380082572 60-61 21.69941183831811 26.59241646852709 27.84382430234013 23.864347390814665 62-63 22.286215099536747 25.528984599974958 27.89532991110555 24.289470389382746 64-65 23.09619238476954 24.849699398797593 27.71793587174349 24.336172344689377 66-67 22.050896326939952 24.558104550582925 28.557101667293466 24.833897455183653 68-69 22.710163111668756 24.730238393977416 26.86323713927227 25.696361355081553 70-71 22.18314282125361 25.185278231377968 27.735209144579827 24.896369802788595 72-73 22.41183162684869 25.4582227278473 27.3163948931867 24.813550752117305 74-75 22.528491916247017 23.588656241717466 28.14736284124039 25.735489000795127 76 25.195385187941945 0.0 38.44436174171939 36.360253070338665 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 51.0 1 29.5 2 6.0 3 3.5 4 3.0 5 2.0 6 1.5 7 1.5 8 1.0 9 1.5 10 1.0 11 0.5 12 1.0 13 1.5 14 3.0 15 2.0 16 0.5 17 1.5 18 16.5 19 27.0 20 36.0 21 52.0 22 38.0 23 25.5 24 22.5 25 14.5 26 20.0 27 29.5 28 27.5 29 20.5 30 25.0 31 38.5 32 47.0 33 47.5 34 60.5 35 79.5 36 96.0 37 106.5 38 124.5 39 142.0 40 141.0 41 166.5 42 195.0 43 212.0 44 233.5 45 220.5 46 210.5 47 215.5 48 206.5 49 193.0 50 181.5 51 165.5 52 132.5 53 112.0 54 112.0 55 114.5 56 111.0 57 101.5 58 95.0 59 94.5 60 100.0 61 94.0 62 83.0 63 82.0 64 76.0 65 67.5 66 54.5 67 43.0 68 39.5 69 39.0 70 38.0 71 34.5 72 29.0 73 25.0 74 23.0 75 20.5 76 17.0 77 11.5 78 7.5 79 6.5 80 6.5 81 3.5 82 1.0 83 1.0 84 1.0 85 1.0 86 1.0 87 1.0 88 0.5 89 0.0 90 0.0 91 0.0 92 0.0 93 0.0 94 0.0 95 0.0 96 0.0 97 0.0 98 0.0 99 0.0 100 0.0 >>END_MODULE >>Per base N content pass #Base N-Count 1 0.0 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10-11 0.0 12-13 0.0 14-15 0.0 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 0.0 30-31 0.0 32-33 0.0 34-35 0.0 36-37 0.0 38-39 0.0 40-41 0.0 42-43 0.0 44-45 0.0 46-47 0.0 48-49 0.0 50-51 0.0 52-53 0.0 54-55 0.0 56-57 0.0 58-59 0.0 60-61 0.0 62-63 0.0 64-65 0.0 66-67 0.0 68-69 0.0 70-71 0.0 72-73 0.0 74-75 0.0 76 0.0 >>END_MODULE >>Sequence Length Distribution warn #Length Count 47 1.0 48 0.0 49 0.0 50 1.0 51 0.0 52 0.0 53 1.0 54 0.0 55 0.0 56 0.0 57 0.0 58 1.0 59 0.0 60 1.0 61 1.0 62 1.0 63 0.0 64 2.0 65 2.0 66 1.0 67 2.0 68 2.0 69 2.0 70 3.0 71 14.0 72 19.0 73 54.0 74 238.0 75 967.0 76 2687.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 92.95 #Duplication Level Percentage of deduplicated Percentage of total 1 96.79935449166219 89.97500000000001 2 2.097902097902098 3.9 3 0.5110274341043571 1.425 4 0.18827326519634213 0.7000000000000001 5 0.10758472296933834 0.5 6 0.10758472296933834 0.6 7 0.05379236148466917 0.35000000000000003 8 0.026896180742334585 0.2 9 0.0 0.0 >10 0.10758472296933834 2.35 >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 fail #Sequence Count Percentage Possible Source TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 41 1.0250000000000001 No Hit GTCAATTAGAAGAATAAAGAAGAATTACTGCATTTCGTAACTTATTTTTT 32 0.8 No Hit GCCGAGTTTAATTGCAGTCAATTAGAAGAATAAAGAAGAATTACTGCATT 11 0.27499999999999997 No Hit GCAGTCAATTAGAAGAATAAAGAAGAATTACTGCATTTCGTAACTTATTT 10 0.25 No Hit TTCGTAACTTATTTTTTCTCTTTTTATTTTGTTTCTTTTTATTTAGACCTTCTTCATATTTAGTTTTATCTATTA 8 0.2 No Hit GCGGCTAGTTCAGGACTCCATTTGCAAGCTGCTCGGATAATTTCATTACC 7 0.17500000000000002 No Hit GTTTTATCTATTAATCGATAGTATCTACCGGCGCGAACTCGAATTTGATC 7 0.17500000000000002 No Hit CCGGAGTTTATATTACATGCCCCTCTCCCAACGATAGTTGTAGTACTCTT 6 0.15 No Hit TGCAGTCAATTAGAAGAATAAAGAAGAATTACTGCATTTCGTAACTTATT 6 0.15 No Hit CCACCAAATTGTAATACAGAATCATCCCCAAAGATTTCGGTCAGAGCTGG 6 0.15 No Hit CTTCGTTACGAGCTTGTACACAGGCTTCTAAAGCCACTCGATTAGCTGCT 6 0.15 No Hit TCCATACTTCACAAGCTGCGGCTAGTTCAGGACTCCATTTGCAAGCTGCT 5 0.125 No Hit CAAAGATTTCGGTCAGAGCTGGCATATGCCAAACATGAATACCACCTGAAGCTACTGGTATAACACCTGGCATGG 5 0.125 No Hit CCGGGTTGTTGGGAGAGATCACATGCATAAATACAACATGAAACAAACGT 5 0.125 No Hit GTCAGGGTTCAAATGTACATATGCTCCTCGAGCCCATGTCGGTACATTCA 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 SRR11389834 read2 length is 47-76 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR11389834_2.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 47-76 %GC 50 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 29.88375 32.0 32.0 32.0 21.0 32.0 2 29.45975 32.0 32.0 32.0 14.0 32.0 3 29.5165 32.0 32.0 32.0 14.0 32.0 4 29.49775 32.0 32.0 32.0 14.0 32.0 5 29.49375 32.0 32.0 32.0 14.0 32.0 6 32.468 36.0 32.0 36.0 14.0 36.0 7 32.40375 36.0 32.0 36.0 14.0 36.0 8 32.17075 36.0 32.0 36.0 14.0 36.0 9 32.1155 36.0 32.0 36.0 14.0 36.0 10-11 32.071625 36.0 32.0 36.0 14.0 36.0 12-13 32.18625 36.0 32.0 36.0 14.0 36.0 14-15 32.207875 36.0 32.0 36.0 14.0 36.0 16-17 32.125625 36.0 32.0 36.0 14.0 36.0 18-19 31.949624999999997 36.0 32.0 36.0 14.0 36.0 20-21 31.93925 36.0 32.0 36.0 14.0 36.0 22-23 31.89075 36.0 32.0 36.0 14.0 36.0 24-25 31.809624999999997 36.0 32.0 36.0 14.0 36.0 26-27 31.740375 36.0 32.0 36.0 14.0 36.0 28-29 31.563499999999998 36.0 32.0 36.0 14.0 36.0 30-31 31.631125 36.0 32.0 36.0 14.0 36.0 32-33 31.572499999999998 36.0 32.0 36.0 14.0 36.0 34-35 31.712875 36.0 32.0 36.0 14.0 36.0 36-37 31.377625 36.0 32.0 36.0 14.0 36.0 38-39 31.37975 36.0 32.0 36.0 14.0 36.0 40-41 31.425874999999998 36.0 32.0 36.0 14.0 36.0 42-43 31.118375 36.0 32.0 36.0 14.0 36.0 44-45 31.198375 36.0 32.0 36.0 14.0 36.0 46-47 30.967875 36.0 32.0 36.0 14.0 36.0 48-49 30.91722930732683 36.0 32.0 36.0 14.0 36.0 50-51 31.02227141953072 36.0 32.0 36.0 14.0 36.0 52-53 30.738994497248626 36.0 32.0 36.0 14.0 36.0 54-55 30.75969477107831 36.0 32.0 36.0 14.0 36.0 56-57 30.42556917688266 36.0 27.0 36.0 14.0 36.0 58-59 30.540617894602132 36.0 27.0 36.0 14.0 36.0 60-61 30.418984848427904 36.0 27.0 36.0 14.0 36.0 62-63 30.251299626625013 36.0 27.0 36.0 14.0 36.0 64-65 30.47902975206238 36.0 27.0 36.0 14.0 36.0 66-67 30.211499753710868 36.0 27.0 36.0 14.0 36.0 68-69 30.07228216680067 36.0 27.0 36.0 14.0 36.0 70-71 30.289809038131427 36.0 27.0 36.0 14.0 36.0 72-73 30.14233541361121 36.0 27.0 36.0 14.0 36.0 74-75 30.052311084057735 36.0 27.0 36.0 14.0 36.0 76 28.96438146304098 32.0 21.0 36.0 14.0 36.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 14 12.0 15 17.0 16 38.0 17 19.0 18 30.0 19 14.0 20 15.0 21 22.0 22 35.0 23 41.0 24 63.0 25 85.0 26 138.0 27 156.0 28 218.0 29 258.0 30 355.0 31 356.0 32 481.0 33 646.0 34 684.0 35 317.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 34.775 16.650000000000002 15.775 32.800000000000004 2 31.525 23.1 23.775 21.6 3 28.525 27.900000000000002 20.275000000000002 23.3 4 31.924999999999997 30.599999999999998 17.625 19.85 5 30.45 31.6 20.825 17.125 6 24.95 33.650000000000006 21.349999999999998 20.05 7 23.9 18.725 33.324999999999996 24.05 8 26.5 22.975 24.75 25.775 9 24.7 23.150000000000002 25.650000000000002 26.5 10-11 28.000000000000004 29.075 19.2 23.724999999999998 12-13 27.6625 23.2625 23.875 25.2 14-15 26.1125 26.6125 24.275 23.0 16-17 27.55 24.5375 23.7625 24.15 18-19 25.887500000000003 25.0625 25.275 23.775 20-21 28.125 25.162499999999998 23.7625 22.95 22-23 27.800000000000004 26.5625 23.4125 22.225 24-25 25.95 26.2875 23.8875 23.875 26-27 27.325 26.150000000000002 24.337500000000002 22.1875 28-29 26.5875 26.0625 23.0125 24.337500000000002 30-31 26.6 25.912499999999998 23.9125 23.575 32-33 26.200000000000003 25.575 25.124999999999996 23.1 34-35 27.1125 24.975 24.0125 23.9 36-37 26.8125 24.8 24.4 23.9875 38-39 25.174999999999997 26.887499999999996 24.975 22.9625 40-41 27.2625 24.6 23.3125 24.825 42-43 26.5625 26.200000000000003 24.175 23.0625 44-45 26.2125 26.650000000000002 23.8125 23.325000000000003 46-47 25.7875 26.8625 23.7625 23.5875 48-49 26.144036009002253 24.968742185546386 24.981245311327832 23.905976494123532 50-51 26.12229586094785 25.63461297986745 24.45917218957109 23.783918969613605 52-53 25.87543771885943 26.17558779389695 23.411705852926463 24.537268634317158 54-55 26.932699524643482 26.207155366524894 23.967975981986488 22.892169126845133 56-57 26.032024018013512 26.36977733299975 24.69352014010508 22.904678508881663 58-59 26.66082822469661 25.84761666458151 24.408857750531716 23.082697360190167 60-61 25.55374796646227 26.417219371793266 24.752846952821926 23.276185708922537 62-63 26.655815700513337 26.893702266182544 23.588331037936648 22.86215099536747 64-65 26.76938494300388 26.005261180007516 23.675310033821873 23.55004384316673 66-67 25.159834524257242 26.914880280807317 23.530149178889307 24.39513601604613 68-69 25.821831869510664 26.461731493099123 24.454203262233378 23.26223337515684 70-71 26.28930817610063 26.742138364779873 23.660377358490567 23.30817610062893 72-73 26.33645806941981 26.60248289840385 24.246262984545226 22.814796047631113 74-75 26.732140454728913 24.175972016682362 25.373335127135743 23.718552401452982 76 30.180007659900422 0.0 33.97165836844121 35.84833397165837 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 36.0 1 19.5 2 2.5 3 1.0 4 0.0 5 0.0 6 0.5 7 1.5 8 2.0 9 1.5 10 0.5 11 1.0 12 2.0 13 2.0 14 2.0 15 1.5 16 2.0 17 3.5 18 8.0 19 14.0 20 14.0 21 10.0 22 11.0 23 13.5 24 17.0 25 21.5 26 17.5 27 15.0 28 21.0 29 23.5 30 21.5 31 29.5 32 41.0 33 43.0 34 45.0 35 68.0 36 94.0 37 101.0 38 112.0 39 122.0 40 135.5 41 154.0 42 168.0 43 183.5 44 175.5 45 175.0 46 188.0 47 198.0 48 194.0 49 174.0 50 171.0 51 160.5 52 127.5 53 112.0 54 118.0 55 117.5 56 116.0 57 110.5 58 114.5 59 137.5 60 135.5 61 122.5 62 118.0 63 109.5 64 98.0 65 89.0 66 83.0 67 70.0 68 67.0 69 58.5 70 42.5 71 36.5 72 36.5 73 40.0 74 35.0 75 29.5 76 24.5 77 16.0 78 13.0 79 12.0 80 12.0 81 8.5 82 8.0 83 10.5 84 5.5 85 3.0 86 4.0 87 3.5 88 3.0 89 1.5 90 2.5 91 3.0 92 2.0 93 2.0 94 2.0 95 1.5 96 1.0 97 1.5 98 1.5 99 6.0 100 11.0 >>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 0.0 7 0.0 8 0.0 9 0.0 10-11 0.0 12-13 0.0 14-15 0.0 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 0.0 30-31 0.0 32-33 0.0 34-35 0.0 36-37 0.0 38-39 0.0 40-41 0.0 42-43 0.0 44-45 0.0 46-47 0.0 48-49 0.0 50-51 0.0 52-53 0.0 54-55 0.0 56-57 0.0 58-59 0.0 60-61 0.0 62-63 0.0 64-65 0.0 66-67 0.0 68-69 0.0 70-71 0.0 72-73 0.0 74-75 0.0 76 0.0 >>END_MODULE >>Sequence Length Distribution warn #Length Count 47 1.0 48 0.0 49 0.0 50 1.0 51 0.0 52 0.0 53 1.0 54 0.0 55 0.0 56 0.0 57 0.0 58 1.0 59 0.0 60 1.0 61 1.0 62 1.0 63 1.0 64 1.0 65 2.0 66 1.0 67 2.0 68 2.0 69 3.0 70 12.0 71 11.0 72 22.0 73 70.0 74 299.0 75 956.0 76 2611.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 94.55 #Duplication Level Percentage of deduplicated Percentage of total 1 97.14436805922793 91.85 2 1.9037546271813854 3.5999999999999996 3 0.31729243786356426 0.8999999999999999 4 0.23796932839767318 0.8999999999999999 5 0.21152829190904282 1.0 6 0.026441036488630353 0.15 7 0.07932310946589106 0.525 8 0.0 0.0 9 0.0 0.0 >10 0.07932310946589106 1.075 >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 17 0.42500000000000004 No Hit GGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACA 14 0.35000000000000003 No Hit GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 12 0.3 No Hit GAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGA 7 0.17500000000000002 No Hit GAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTAC 7 0.17500000000000002 No Hit CCGGTACAGTAGTAGGTAAGTTAGAAGGGGAACGCGAAATCACTTTAGGT 7 0.17500000000000002 No Hit CCGGTAGATACTATCGATTAATAGATAAAACTAAATATGAAGAAGGTCTAAATAAAAAGAAACAAAATAAAAAG 6 0.15 No Hit CTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGGGGAAATGCA 5 0.125 No Hit TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 5 0.125 No Hit GTGGTATTCATGTTTGGCATATGCCAGCTCTGACCGAAATCTTTGGGGAT 5 0.125 No Hit CTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTG 5 0.125 No Hit TAGAAGGGGAACGCGAAATCACTTTAGGTTTTGTTGATTTATTGCGCGAC 5 0.125 No Hit AGTAGCTTCAGGTGGTATTCATGTTTGGCATATGCCAGCTCTGACCGAAATCTTTGGGGATGATTCTGTATTACA 5 0.125 No Hit AAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAAGGCGATCAAATTCG 5 0.125 No Hit GCCAGGTGTTATACCAGTAGCTTCAGGTGGTATTCATGTTTGGCATATGC 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 574689 spots for SRR11389834.sra Written 574689 spots for SRR11389834.sra Read 574689 spots for SRR11389834.sra Written 574689 spots for SRR11389834.sra Read 574689 spots for SRR11389834.sra Written 574689 spots for SRR11389834.sra Read 574689 spots for SRR11389834.sra Written 574689 spots for SRR11389834.sra Read 574689 spots for SRR11389834.sra Written 574689 spots for SRR11389834.sra Read 574689 spots for SRR11389834.sra Written 574689 spots for SRR11389834.sra Read 574689 spots for SRR11389834.sra Written 574689 spots for SRR11389834.sra Read 574689 spots for SRR11389834.sra Written 574689 spots for SRR11389834.sra Read 574689 spots for SRR11389834.sra Written 574689 spots for SRR11389834.sra Read 574689 spots for SRR11389834.sra Written 574689 spots for SRR11389834.sra Read 574689 spots for SRR11389834.sra Written 574689 spots for SRR11389834.sra Read 574689 spots for SRR11389834.sra Written 574689 spots for SRR11389834.sra Read 574689 spots for SRR11389834.sra Written 574689 spots for SRR11389834.sra Read 574689 spots for SRR11389834.sra Written 574689 spots for SRR11389834.sra Read 574689 spots for SRR11389834.sra Written 574689 spots for SRR11389834.sra Read 574689 spots for SRR11389834.sra Written 574689 spots for SRR11389834.sra Read 574689 spots for SRR11389834.sra Written 574689 spots for SRR11389834.sra Read 574689 spots for SRR11389834.sra Written 574689 spots for SRR11389834.sra Read 574689 spots for SRR11389834.sra Written 574689 spots for SRR11389834.sra Read 574695 spots for SRR11389834.sra Written 574695 spots for SRR11389834.sra SRR ids: ['SRR11389834.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_ulxgrs81 SRR11389834.sra spots: 11493786 blocks: [[1, 574689], [574690, 1149378], [1149379, 1724067], [1724068, 2298756], [2298757, 2873445], [2873446, 3448134], [3448135, 4022823], [4022824, 4597512], [4597513, 5172201], [5172202, 5746890], [5746891, 6321579], [6321580, 6896268], [6896269, 7470957], [7470958, 8045646], [8045647, 8620335], [8620336, 9195024], [9195025, 9769713], [9769714, 10344402], [10344403, 10919091], [10919092, 11493786]] SRR11389834 file size 2175371 SRR11389834 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 SRR11389834 SRR11389834_1.fastq SRR11389834_2.fastq Input file: SRR11389834_1.fastq Paired file: SRR11389834_2.fastq trimmed: SRR11389834-trimmed-pair1.fastq, SRR11389834-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 07:49:49 2024 >> started Sat Dec 7 07:49:59 2024 >> done (9.493s) 11493786 read pairs processed; of these: 3 ( 0.00%) short read pairs filtered out after trimming by size control 96327 ( 0.84%) empty read pairs filtered out after trimming by size control 11397456 (99.16%) read pairs available; of these: 109636 ( 0.96%) trimmed read pairs available after processing 11287820 (99.04%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 24 1 0.00% 25 0 0.00% 26 0 0.00% 27 0 0.00% 28 0 0.00% 29 0 0.00% 30 0 0.00% 31 3 0.00% 32 1 0.00% 33 2 0.00% 34 0 0.00% 35 195 0.00% 36 270 0.00% 37 283 0.00% 38 369 0.00% 39 422 0.00% 40 571 0.01% 41 663 0.01% 42 804 0.01% 43 938 0.01% 44 1045 0.01% 45 1181 0.01% 46 1226 0.01% 47 1383 0.01% 48 1572 0.01% 49 1745 0.02% 50 2033 0.02% 51 2303 0.02% 52 2556 0.02% 53 2831 0.02% 54 3112 0.03% 55 3405 0.03% 56 3896 0.03% 57 4427 0.04% 58 4841 0.04% 59 5294 0.05% 60 5802 0.05% 61 6081 0.05% 62 6819 0.06% 63 7498 0.07% 64 8417 0.07% 65 9322 0.08% 66 9911 0.09% 67 11072 0.10% 68 11365 0.10% 69 12379 0.11% 70 13559 0.12% 71 16027 0.14% 72 25283 0.22% 73 106731 0.94% 74 884757 7.76% 75 5071701 44.50% 76 5143360 45.13% 11397456 reads passed initial QC criterion=sequence-density sequence-density=1.15 sequence-density-rank=1 fanout-score=1.99 fanout-score-rank=20 prefix-density=1.13 prefix-fanout=2.0 sequence=TTCAAATGTACA criterion=fanout-score sequence-density=0.15 sequence-density-rank=20 fanout-score=5.46 fanout-score-rank=1 prefix-density=0.36 prefix-fanout=2.2 sequence=ACGCTGCCGAGACCAGCGCTGGCTGAGCGGCGGCCGATGGGGAGCCCGGCGGTGGA criterion=sequence-density sequence-density=1.01 sequence-density-rank=1 fanout-score=2.05 fanout-score-rank=24 prefix-density=1.04 prefix-fanout=2.0 sequence=GTGCAGTGCATCAGCTTCATCGCCTTCAAGCCACCGGGTTGTGAGGAGTCCGG criterion=fanout-score sequence-density=0.01 sequence-density-rank=27 fanout-score=8.18 fanout-score-rank=1 prefix-density=0.04 prefix-fanout=2.4 sequence=CCTCAAGCCAAAGCCTCTTGCTAAGCGTACCACACTATACAGACGTGCGCGCGCAGCCATGGCACCCACCGTGATGGCTTCCTCCGCCACCTCCGTGGC SRR11389834 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 07 07:50:30 Started mapping on | Dec 07 07:50:30 Finished on | Dec 07 07:51:35 Mapping speed, Million of reads per hour | 631.24 Number of input reads | 11397456 Average input read length | 150 UNIQUE READS: Uniquely mapped reads number | 8783481 Uniquely mapped reads % | 77.07% Average mapped length | 149.86 Number of splices: Total | 3174354 Number of splices: Annotated (sjdb) | 3010932 Number of splices: GT/AG | 3134359 Number of splices: GC/AG | 36157 Number of splices: AT/AC | 843 Number of splices: Non-canonical | 2995 Mismatch rate per base, % | 0.82% Deletion rate per base | 0.01% Deletion average length | 1.33 Insertion rate per base | 0.00% Insertion average length | 1.30 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 1642019 % of reads mapped to multiple loci | 14.41% Number of reads mapped to too many loci | 22565 % of reads mapped to too many loci | 0.20% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 7.09% % of reads unmapped: other | 1.24% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 971956 971956 971956 N_multimapping 1642019 1642019 1642019 N_noFeature 296508 8492698 410218 N_ambiguous 250981 1555 82826 UnstrandedReadsAssigned:8235992 PositiveStrandReadsAssigned:289228 NegativeStrandReadsAssigned:8290437 Dataset is classified negative stranded MeadianReadLen=76 20thPercentileLength=75 echo kmer=71 SRR11389834 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: SRR11389834-trimmed-pair1.fastq SRR11389834-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 11,397,456 reads, 10,086,537 reads pseudoaligned [quant] estimated average fragment length: 187.389 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,039 rounds 52973 SRR11389834.ke.tsv 35125 SRR11389834.se.tsv 88098 total ==> SRR11389834.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 749.74 0 0 PNS24247 1044 857.611 9.24292 1.43874 PNS24249 1928 1741.61 37.9316 2.90746 PNS24246 1044 857.611 9.24292 1.43874 PNS24248 1044 857.611 9.24292 1.43874 PNS24244 1471 1284.61 27.3396 2.84109 PNS24243 293 125.794 0 0 KQK14069 1603 1416.61 358.904 33.8214 KQK14071 474 290.203 13.6451 6.27681 ==> SRR11389834.se.tsv <== BRADI_1g14170v3 390 BRADI_1g53295v3 9 BRADI_1g59795v3 127 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 66 BRADI_1g74790v3 188 BRADI_1g09890v3 0 BRADI_1g77505v3 99 BRADI_1g48960v3 0 SRR11389834 completed mapping pipeline successfully