Starting /dee2/code/volunteer_pipeline.sh SRR1174000 current disk space = 1524693315584 free memory = 1404373448 SRR1174000 SRAfilesize 97ce21df33a35c814c9867a9f3ce60ca SRR1174000.sra SRR1174000.sra file validated SRR1174000 is single end SRR1174000 is conventional basespace SRR1174000 read1 length is 42 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR1174000_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 42 %GC 47 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 30.75775 32.0 30.0 33.0 27.0 33.0 2 29.2915 31.0 28.0 33.0 23.0 33.0 3 28.73 30.0 27.0 32.0 23.0 33.0 4 28.055 29.0 26.0 32.0 21.0 33.0 5 28.0155 29.0 26.0 32.0 20.0 33.0 6 29.59225 31.0 28.0 33.0 24.0 33.0 7 28.57525 30.0 26.0 32.0 21.0 33.0 8 30.167 31.0 29.0 33.0 25.0 34.0 9 30.74125 32.0 30.0 33.0 27.0 33.0 10 29.7175 31.0 28.0 33.0 24.0 33.0 11 28.47825 29.0 26.0 32.0 22.0 33.0 12 22.9535 27.0 13.0 32.0 5.0 34.0 13 28.7845 30.0 26.0 32.0 22.0 33.0 14 30.97275 32.0 30.0 33.0 27.0 34.0 15 30.13475 32.0 29.0 33.0 24.0 34.0 16 30.58275 32.0 29.0 33.0 26.0 34.0 17 30.70725 32.0 29.0 33.0 26.0 34.0 18 30.0505 32.0 29.0 33.0 23.0 34.0 19 29.2425 31.0 28.0 33.0 23.0 33.0 20 29.67825 31.0 28.0 33.0 23.0 34.0 21 29.88975 31.0 28.0 33.0 24.0 34.0 22 30.6365 32.0 29.0 33.0 26.0 34.0 23 29.968 31.0 29.0 33.0 24.0 33.0 24 29.98825 32.0 29.0 33.0 24.0 34.0 25 29.3215 31.0 28.0 33.0 22.0 33.0 26 29.0245 31.0 27.0 33.0 22.0 33.0 27 29.384 31.0 28.0 33.0 24.0 33.0 28 29.38875 31.0 27.0 33.0 24.0 33.0 29 28.31975 30.0 26.0 32.0 21.0 33.0 30 28.408 30.0 27.0 32.0 21.0 33.0 31 27.45575 29.0 25.0 32.0 20.0 33.0 32 29.36675 32.0 28.0 33.0 23.0 34.0 33 29.482 32.0 29.0 33.0 23.0 34.0 34 27.83675 30.0 26.0 32.0 20.0 33.0 35 27.89475 30.0 26.0 33.0 20.0 33.0 36 27.30375 30.0 25.0 33.0 17.0 33.0 37 27.37825 30.0 26.0 33.0 18.0 33.0 38 27.39525 31.0 25.0 33.0 17.0 34.0 39 28.138 31.0 28.0 33.0 18.0 33.0 40 25.92275 29.0 23.0 32.0 10.0 33.0 41 26.49475 29.0 24.0 32.0 16.0 33.0 42 27.98725 32.0 27.0 33.0 4.0 34.0 >>END_MODULE >>Per tile sequence quality pass #Tile Base Mean 1 1 0.0 1 2 0.0 1 3 0.0 1 4 0.0 1 5 0.0 1 6 0.0 1 7 0.0 1 8 0.0 1 9 0.0 1 10 0.0 1 11 0.0 1 12 0.0 1 13 0.0 1 14 0.0 1 15 0.0 1 16 0.0 1 17 0.0 1 18 0.0 1 19 0.0 1 20 0.0 1 21 0.0 1 22 0.0 1 23 0.0 1 24 0.0 1 25 0.0 1 26 0.0 1 27 0.0 1 28 0.0 1 29 0.0 1 30 0.0 1 31 0.0 1 32 0.0 1 33 0.0 1 34 0.0 1 35 0.0 1 36 0.0 1 37 0.0 1 38 0.0 1 39 0.0 1 40 0.0 1 41 0.0 1 42 0.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 4 1.0 5 0.0 6 0.0 7 1.0 8 0.0 9 0.0 10 1.0 11 2.0 12 2.0 13 1.0 14 3.0 15 1.0 16 4.0 17 1.0 18 7.0 19 8.0 20 17.0 21 21.0 22 38.0 23 71.0 24 96.0 25 150.0 26 248.0 27 396.0 28 677.0 29 864.0 30 747.0 31 465.0 32 158.0 33 20.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 42.699999999999996 33.675 12.775 10.85 2 57.432432432432435 15.89089089089089 15.965965965965967 10.71071071071071 3 38.15 15.049999999999999 8.7 38.1 4 53.5 19.125 12.725 14.649999999999999 5 36.95 30.325000000000003 12.174999999999999 20.549999999999997 6 18.2 37.2 28.000000000000004 16.6 7 47.775 18.275 23.674999999999997 10.274999999999999 8 22.375 18.45 49.425000000000004 9.75 9 12.625 51.4 27.125 8.85 10 55.05 25.275 10.25 9.425 11 21.2 26.1 16.5 36.199999999999996 12 22.923504165614744 19.84347387023479 28.906841706639735 28.32618025751073 13 17.299999999999997 15.6 11.975 55.125 14 9.175 66.175 16.875 7.775 15 31.25 35.875 20.599999999999998 12.275 16 19.875 34.150000000000006 35.525 10.45 17 16.025 33.1 41.9 8.975 18 31.55 16.55 33.525 18.375 19 24.706176544136035 19.579894973743436 24.356089022255563 31.357839459864966 20 15.625 29.299999999999997 36.575 18.5 21 12.3 23.95 24.625 39.125 22 30.175 17.849999999999998 30.625000000000004 21.349999999999998 23 17.9 14.975 47.099999999999994 20.025000000000002 24 17.75 32.324999999999996 30.775000000000002 19.15 25 18.85 22.400000000000002 35.125 23.625 26 41.175 11.575000000000001 27.250000000000004 20.0 27 18.534267133566786 18.18409204602301 23.23661830915458 40.04502251125563 28 11.627906976744185 24.5311327831958 25.78144536134033 38.05951487871968 29 35.40466048609371 12.728639438737158 25.63267351540967 26.23402655975946 30 31.690140845070424 10.890342052313883 38.60663983903421 18.81287726358149 31 11.721887550200803 11.495983935742972 28.13755020080321 48.644578313253014 32 13.15 15.575 36.85 34.425 33 17.4 10.625 52.949999999999996 19.025 34 16.04104104104104 10.51051051051051 34.83483483483483 38.61361361361361 35 10.99949773982923 8.9904570567554 45.605223505775996 34.40482169763938 36 27.633894895649984 9.42921800352024 38.923811918531555 24.013075182298216 37 17.87962729790985 9.97229916897507 36.06144547972803 36.08662805338705 38 8.901705115346038 10.481444332998997 53.309929789368105 27.30692076228686 39 17.471839799749684 13.391739674593243 51.83979974968711 17.296620775969963 40 37.828371278458846 18.11358518889167 29.597197898423815 14.460845634225668 41 15.036459642946944 41.061101332662815 24.013075182298216 19.889363842092028 42 7.949685534591194 46.314465408805034 29.61006289308176 16.12578616352201 >>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 0.0 17 0.0 18 0.0 19 0.0 20 1.0 21 2.0 22 2.0 23 1.0 24 0.0 25 13.0 26 26.0 27 63.5 28 101.0 29 101.0 30 77.5 31 54.0 32 45.5 33 37.0 34 37.0 35 34.5 36 32.0 37 52.0 38 72.0 39 108.0 40 144.0 41 144.0 42 252.0 43 360.0 44 453.0 45 546.0 46 592.5 47 639.0 48 639.0 49 796.5 50 954.0 51 661.5 52 369.0 53 369.0 54 449.0 55 529.0 56 305.0 57 81.0 58 52.0 59 23.0 60 23.0 61 21.0 62 19.0 63 13.5 64 8.0 65 4.0 66 0.0 67 0.0 68 2.0 69 4.0 70 2.0 71 0.0 72 0.0 73 0.0 74 0.0 75 0.0 76 0.0 77 0.0 78 0.0 79 0.0 80 0.0 81 0.0 82 0.0 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 pass #Base N-Count 1 0.0 2 0.1 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 0.975 13 0.0 14 0.0 15 0.0 16 0.0 17 0.0 18 0.0 19 0.025 20 0.0 21 0.0 22 0.0 23 0.0 24 0.0 25 0.0 26 0.0 27 0.05 28 0.025 29 0.22499999999999998 30 0.6 31 0.4 32 0.0 33 0.0 34 0.1 35 0.44999999999999996 36 0.575 37 0.7250000000000001 38 0.3 39 0.125 40 0.075 41 0.575 42 0.625 >>END_MODULE >>Sequence Length Distribution pass #Length Count 42 4000.0 >>END_MODULE >>Sequence Duplication Levels fail #Total Deduplicated Percentage 42.5 #Duplication Level Percentage of deduplicated Percentage of total 1 86.23529411764706 36.65 2 5.294117647058823 4.5 3 2.411764705882353 3.075 4 1.0 1.7000000000000002 5 0.6470588235294118 1.375 6 0.5882352941176471 1.5 7 0.35294117647058826 1.05 8 0.411764705882353 1.4000000000000001 9 0.2352941176470588 0.8999999999999999 >10 2.3529411764705883 21.375 >50 0.1176470588235294 3.325 >100 0.35294117647058826 23.150000000000002 >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 GGCGGATGTAGCCAAGTGGAATCTCGTATGCCGTCTTCTGCT 240 6.0 Illumina PCR Primer Index 8 (96% over 26bp) GGGGATGTAGCTCAAAATCTCGTATGCCGTCTTCTGCTTGAA 159 3.975 RNA PCR Primer, Index 40 (96% over 30bp) GGGGACGTAGCTCATAATCTCGTATGCCGTCTTCTGCTTGAA 149 3.7249999999999996 RNA PCR Primer, Index 40 (96% over 30bp) AGCGGAGTAGAGCAGTTATCTCGTATGCCGTCTTCTGCTTGA 145 3.6249999999999996 Illumina PCR Primer Index 5 (96% over 29bp) GGGCCTGTAGCTCAGAGGAATCTCGTATGCCGTCTTCTGCTT 121 3.025 Illumina PCR Primer Index 12 (96% over 26bp) AGCGGAGTAGAGCAGTATCTCGTATGCCGTCTTCTGCTTGAA 112 2.8000000000000003 Illumina PCR Primer Index 6 (96% over 28bp) TAACGAACGAACGATTTGAACATCTCGTATGCCGTCTTCTGC 77 1.925 Illumina PCR Primer Index 7 (96% over 25bp) AACGAACGAACGATTTGAACATCTCGTATGCCGTCTTCTGCT 56 1.4000000000000001 RNA PCR Primer, Index 19 (96% over 27bp) ATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAA 48 1.2 Illumina Single End Adapter 1 (95% over 24bp) AGCGGAGTAGAGCAGATCTCGTATGCCGTCTTCTGCTTGAAA 44 1.0999999999999999 Illumina PCR Primer Index 9 (100% over 27bp) GGCGGATGTAGACAAGTGGAATCTCGTATGCCGTCTTCTGCT 42 1.05 Illumina PCR Primer Index 12 (96% over 26bp) ACGAACGATTTGAACATCTCGTATGCCGTCTTCTGCTTGAAA 36 0.8999999999999999 Illumina PCR Primer Index 7 (96% over 28bp) GGGGGTGTAGCTCATAATCTCGTATGCCGTCTTCTGCTTGAA 34 0.8500000000000001 Illumina PCR Primer Index 12 (96% over 27bp) CGAACGATTTGAACATCTCGTATGCCGTCTTCTGCTTGAAAA 33 0.8250000000000001 RNA PCR Primer, Index 19 (96% over 29bp) GGGGATGTAGCTCAGAATCTCGTATGCCGTCTTCTGCTTGAA 32 0.8 RNA PCR Primer, Index 40 (100% over 30bp) ACGAACGAACGATTTGAACATCTCGTATGCCGTCTTCTGCTT 32 0.8 Illumina PCR Primer Index 7 (96% over 27bp) GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCATCTCGTAT 30 0.75 No Hit GGGGATGTAGCACAAAATCTCGTATGCCGTCTTCTGCTTGAA 30 0.75 Illumina PCR Primer Index 6 (96% over 28bp) GGGGACGTAGCACATAATCTCGTATGCCGTCTTCTGCTTGAA 29 0.7250000000000001 Illumina PCR Primer Index 12 (96% over 27bp) TCCGTCGTAGTCTAGGATCTCGTATGCCGTCTTCTGCTTGAA 26 0.65 RNA PCR Primer, Index 22 (96% over 28bp) CTAACGAACGAACGATTTGAACATCTCGTATGCCGTCTTCTG 26 0.65 RNA PCR Primer, Index 19 (96% over 25bp) AACGAACGATTTGAACATCTCGTATGCCGTCTTCTGCTTGAA 24 0.6 RNA PCR Primer, Index 19 (96% over 29bp) GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGATTATCTCGT 23 0.575 No Hit CGAACGAACGATTTGAACATCTCGTATGCCGTCTTCTGCTTG 23 0.575 RNA PCR Primer, Index 19 (96% over 29bp) GGGGATGTAGCGCAAAATCTCGTATGCCGTCTTCTGCTTGAA 23 0.575 Illumina PCR Primer Index 6 (96% over 28bp) AGGGATGTAGCGCAGCATCTCGTATGCCGTCTTCTGCTTGAA 18 0.44999999999999996 TruSeq Adapter, Index 18 (96% over 28bp) GGGATTGTAGTTCAATATCTCGTATGCCGTCTTCTGCTTGAA 18 0.44999999999999996 Illumina PCR Primer Index 6 (96% over 29bp) AGGCATCCTAACGAACGAACGATTTGAACATCTCGTATGCCG 17 0.42500000000000004 No Hit GTCAGGATAGCTCAGTTGGTAGAGCAGAGGACTATCTCGTAT 17 0.42500000000000004 No Hit AGCGGAGTAGACCAGTTATCTCGTATGCCGTCTTCTGCTTGA 16 0.4 Illumina PCR Primer Index 5 (96% over 29bp) ATAGTCGGCTCCAATCTCGTATGCCGTCTTCTGCTTGAAAAA 15 0.375 Illumina Paired End PCR Primer 2 (96% over 27bp) CATCCTAACGAACGAACGATTTGAACATCTCGTATGCCGTCT 15 0.375 No Hit GGCGGATGTAGTCAAGTGGAATCTCGTATGCCGTCTTCTGCT 15 0.375 Illumina PCR Primer Index 12 (96% over 26bp) GAACGAACGATTTGAACATCTCGTATGCCGTCTTCTGCTTGA 15 0.375 Illumina PCR Primer Index 7 (96% over 28bp) GGGCCTGTAGCGCAGAGGAATCTCGTATGCCGTCTTCTGCTT 15 0.375 Illumina PCR Primer Index 12 (96% over 26bp) TCCTAACGAACGAACGATTTGAACATCTCGTATGCCGTCTTC 14 0.35000000000000003 Illumina PCR Primer Index 7 (95% over 22bp) TGAGGCATCCTAACGAACGAACGATTTGAACATCTCGTATGC 14 0.35000000000000003 No Hit AGCGGAGTAGAGCAATCTCGTATGCCGTCTTCTGCTTGAAAA 14 0.35000000000000003 Illumina PCR Primer Index 4 (96% over 29bp) TGGGCCTGTAGCTCAGAGGAATCTCGTATGCCGTCTTCTGCT 14 0.35000000000000003 RNA PCR Primer, Index 3 (96% over 26bp) GGGCCTGTAGCACAGAGGAATCTCGTATGCCGTCTTCTGCTT 14 0.35000000000000003 Illumina PCR Primer Index 3 (96% over 27bp) TAATTCATGATCTGGATCTCGTATGCCGTCTTCTGCTTGAAA 13 0.325 RNA PCR Primer, Index 23 (96% over 28bp) AGGGCTATAGCTCAGTTCGGATCTCGTATGCCGTCTTCTGCT 12 0.3 TruSeq Adapter, Index 9 (96% over 26bp) GGGGACGTAGCGCATAATCTCGTATGCCGTCTTCTGCTTGAA 12 0.3 Illumina PCR Primer Index 7 (96% over 27bp) AGCGGAGTAGATCAGTTATCTCGTATGCCGTCTTCTGCTTGA 11 0.27499999999999997 Illumina PCR Primer Index 5 (96% over 29bp) TATAGTCGGCTCCAATCTCGTATGCCGTCTTCTGCTTGAAAA 11 0.27499999999999997 Illumina PCR Primer Index 4 (96% over 28bp) TGACAGAAGAGAGTGAGCACATCTCGTATGCCGTCTTCTGCT 10 0.25 Illumina PCR Primer Index 9 (96% over 25bp) GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCCATCTCGTA 10 0.25 No Hit AGCGGAGTAGAACAGTATCTCGTATGCCGTCTTCTGCTTGAA 10 0.25 Illumina PCR Primer Index 6 (96% over 28bp) GTCAGGATAGCTCAGTTGGATCTCGTATGCCGTCTTCTGCTT 9 0.22499999999999998 RNA PCR Primer, Index 21 (96% over 27bp) CCTAACGAACGAACGATTTGAACATCTCGTATGCCGTCTTCT 9 0.22499999999999998 RNA PCR Primer, Index 19 (95% over 24bp) ATCTCGTATGCAGTCTTCTGCTTGAAAAAAAAAAAAAAAAAA 9 0.22499999999999998 Illumina Paired End PCR Primer 2 (95% over 24bp) GATAGTCGGCTCCAATCTCGTATGCCGTCTTCTGCTTGAAAA 9 0.22499999999999998 Illumina PCR Primer Index 4 (96% over 28bp) AGCGGAGTAGACCAGTATCTCGTATGCCGTCTTCTGCTTGAA 8 0.2 RNA PCR Primer, Index 40 (96% over 28bp) CTAACGAACGATTTGAACATCTCGTATGCCGTCTTCTGCTTG 8 0.2 RNA PCR Primer, Index 19 (96% over 29bp) GGCGGATGTAGNCAAGTGGAATCTCGTATGCCGTCTTCTGCT 8 0.2 Illumina PCR Primer Index 12 (96% over 26bp) GTCAGGATAGCTCAGTTGGTAGAGCAGAGGACATCTCGTATG 8 0.2 No Hit AGCGGAGTAGAACAGTTATCTCGTATGCCGTCTTCTGCTTGA 8 0.2 Illumina PCR Primer Index 10 (96% over 27bp) GCATCCTAACGAACGAACGATTTGAACATCTCGTATGCCGTC 8 0.2 No Hit AACGAACGATTCGAACATCTCGTATGCCGTCTTCTGCTTGAA 8 0.2 Illumina PCR Primer Index 11 (96% over 27bp) ATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAC 7 0.17500000000000002 Illumina Single End Adapter 1 (95% over 24bp) ATCCTAACGAACGAACGATTTGAACATCTCGTATGCCGTCTT 7 0.17500000000000002 RNA PCR Primer, Index 19 (95% over 22bp) ACGAACGAACGCTTTGAACATCTCGTATGCCGTCTTCTGCTT 7 0.17500000000000002 RNA PCR Primer, Index 19 (96% over 28bp) GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGATTGATCTCG 7 0.17500000000000002 No Hit GCCTTGATGGTGAAATGGTAGACACGCGAGACTCAATCTCGT 7 0.17500000000000002 No Hit GGGTCGATGCCCGAGCGGTTAATGGGGACGGACTGTATCTCG 7 0.17500000000000002 No Hit AAGGAAGCTATAAGATCTCGTATGCCGTCTTCTGCTTGAAAA 6 0.15 RNA PCR Primer, Index 44 (96% over 31bp) GGGATTGTAGTACAATTGGTCAGAGCACCGCCCATCTCGTAT 6 0.15 No Hit AGCGGAGTAGATCAGTATCTCGTATGCCGTCTTCTGCTTGAA 6 0.15 Illumina PCR Primer Index 6 (96% over 28bp) CATCGAGTAGACCTTGTTATTGTGAGAATTCATCTCGTATGC 6 0.15 No Hit GAGGCATCCTAACGAACGAACGATTTGAACATCTCGTATGCC 6 0.15 No Hit GTCAGGATAGCTCAGTATCTCGTATGCCGTCTTCTGCTTGAA 6 0.15 RNA PCR Primer, Index 40 (96% over 30bp) ATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAATAAA 6 0.15 Illumina Single End Adapter 1 (95% over 24bp) GGGATTGTAGTTCAAATCTCGTATGCCGTCTTCTGCTTGAAA 6 0.15 RNA PCR Primer, Index 13 (96% over 29bp) GGCGGATGTAGCCAAGTGGAATCTCGTATGCCGTCTTCTTCT 6 0.15 TruSeq Adapter, Index 8 (95% over 24bp) AGCGGAGTAGAATCTCGTATGCCGTCTTCTGCTTGAAAAAAA 6 0.15 RNA PCR Primer, Index 40 (96% over 28bp) GGGGATGTAGCACAGAATCTCGTATGCCGTCTTCTGCTTGAA 5 0.125 RNA PCR Primer, Index 40 (96% over 30bp) ACGAACGATTTAAACATCTCGTATGCCGTCTTCTGCTTGAAA 5 0.125 RNA PCR Primer, Index 28 (96% over 28bp) AACGAACGAACTATTTGAACATCTCGTATGCCGTCTTCTGCT 5 0.125 RNA PCR Primer, Index 19 (96% over 27bp) CGAACGAACGACTTGAACATCTCGTATGCCGTCTTCTGCTTG 5 0.125 Illumina PCR Primer Index 7 (96% over 28bp) GCGGATGTAGCCAAGTGGAATCTCGTATGCCGTCTTCTGCTT 5 0.125 Illumina PCR Primer Index 8 (96% over 27bp) AGGGATGTAGCGCAGATCTCGTATGCCGTCTTCTGCTTGAAA 5 0.125 Illumina PCR Primer Index 9 (100% over 27bp) TAACGAACGAAAGATTTGAACATCTCGTATGCCGTCTTCTGC 5 0.125 Illumina PCR Primer Index 7 (96% over 25bp) CATCGGTTCAAATCCGATAGTCGGCTCCAATCTCGTATGCCG 5 0.125 No Hit ACGAACGATTTCAACATCTCGTATGCCGTCTTCTGCTTGAAA 5 0.125 Illumina PCR Primer Index 6 (96% over 28bp) TAGATATTTCAGGTTGTGTGGAATCTCGTATGCCGTCTTCTG 5 0.125 Illumina PCR Primer Index 8 (95% over 24bp) GGGGATGTAGCGCAGAATCTCGTATGCCGTCTTCTGCTTGAA 5 0.125 RNA PCR Primer, Index 40 (96% over 30bp) >>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 >>END_MODULE >>Kmer Content fail #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position CGGAGTA 55 7.2759576E-12 36.0 3 CAGTTAT 40 3.1324817E-8 36.0 13 AGCTCAA 25 1.2076046E-4 36.0 9 AGCCAAG 20 0.001866456 36.0 10 AGTAGAG 50 1.2187229E-10 36.0 6 TAGCCAA 20 0.001866456 36.0 9 AGTGGAA 30 7.761133E-6 36.0 15 CGGATGT 30 7.761133E-6 36.0 3 GCGGATG 30 7.761133E-6 36.0 2 GCGGAGT 55 7.2759576E-12 36.0 2 AGCAGTT 35 4.9512164E-7 36.0 11 AGAATCT 20 0.001866456 36.0 14 GAGCAGT 45 1.9645086E-9 36.0 10 GCAGTTA 35 4.9512164E-7 36.0 12 TCAAAAT 20 0.001866456 36.0 12 AGCGGAG 55 7.2759576E-12 36.0 1 TGTAGCC 20 0.001866456 36.0 7 GGGATGT 55 7.2759576E-12 36.0 2 TGGAATC 25 1.2076046E-4 36.0 17 AAAATCT 25 1.2076046E-4 36.0 14 >>END_MODULE Read 399352 spots for SRR1174000.sra Written 399352 spots for SRR1174000.sra Read 399352 spots for SRR1174000.sra Written 399352 spots for SRR1174000.sra Read 399352 spots for SRR1174000.sra Written 399352 spots for SRR1174000.sra Read 399352 spots for SRR1174000.sra Written 399352 spots for SRR1174000.sra Read 399352 spots for SRR1174000.sra Written 399352 spots for SRR1174000.sra Read 399352 spots for SRR1174000.sra Written 399352 spots for SRR1174000.sra Read 399352 spots for SRR1174000.sra Written 399352 spots for SRR1174000.sra Read 399352 spots for SRR1174000.sra Written 399352 spots for SRR1174000.sra Read 399352 spots for SRR1174000.sra Written 399352 spots for SRR1174000.sra Read 399352 spots for SRR1174000.sra Written 399352 spots for SRR1174000.sra Read 399364 spots for SRR1174000.sra Written 399364 spots for SRR1174000.sra Read 399352 spots for SRR1174000.sra Written 399352 spots for SRR1174000.sra Read 399352 spots for SRR1174000.sra Written 399352 spots for SRR1174000.sra Read 399352 spots for SRR1174000.sra Written 399352 spots for SRR1174000.sra Read 399352 spots for SRR1174000.sra Written 399352 spots for SRR1174000.sra Read 399352 spots for SRR1174000.sra Written 399352 spots for SRR1174000.sra Read 399352 spots for SRR1174000.sra Written 399352 spots for SRR1174000.sra Read 399352 spots for SRR1174000.sra Written 399352 spots for SRR1174000.sra Read 399352 spots for SRR1174000.sra Written 399352 spots for SRR1174000.sra Read 399352 spots for SRR1174000.sra Written 399352 spots for SRR1174000.sra SRR ids: ['SRR1174000.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_gdxxgjqr SRR1174000.sra spots: 7987052 blocks: [[1, 399352], [399353, 798704], [798705, 1198056], [1198057, 1597408], [1597409, 1996760], [1996761, 2396112], [2396113, 2795464], [2795465, 3194816], [3194817, 3594168], [3594169, 3993520], [3993521, 4392872], [4392873, 4792224], [4792225, 5191576], [5191577, 5590928], [5590929, 5990280], [5990281, 6389632], [6389633, 6788984], [6788985, 7188336], [7188337, 7587688], [7587689, 7987052]] SRR1174000 file size 1112566 SRR1174000 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 SRR1174000 SRR1174000_1.fastq Input file: SRR1174000_1.fastq trimmed: SRR1174000-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -- 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 -- minimum overlap length for adapter detection (-k): inf -- number of concurrent threads (-t): 20 Mon Dec 9 14:02:47 2024 >> started Mon Dec 9 14:03:06 2024 >> done (18.981s) 7987052 reads processed; of these: 6734 ( 0.08%) short reads filtered out after trimming by size control 3368 ( 0.04%) empty reads filtered out after trimming by size control 7976950 (99.87%) reads available; of these: 815847 (10.23%) trimmed reads available after processing 7161103 (89.77%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 867 0.01% 19 1126 0.01% 20 1436 0.02% 21 1663 0.02% 22 2071 0.03% 23 3411 0.04% 24 5597 0.07% 25 7803 0.10% 26 11100 0.14% 27 17183 0.22% 28 16612 0.21% 29 22554 0.28% 30 32732 0.41% 31 46047 0.58% 32 55088 0.69% 33 62235 0.78% 34 63510 0.80% 35 36736 0.46% 36 27548 0.35% 37 32143 0.40% 38 39241 0.49% 39 58522 0.73% 40 106447 1.33% 41 164175 2.06% 42 7161103 89.77% 7976950 reads passed initial QC criterion=sequence-density sequence-density=84.26 sequence-density-rank=1 fanout-score=11.49 fanout-score-rank=5 prefix-density=83.63 prefix-fanout=11.5 sequence=ATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAA criterion=fanout-score sequence-density=5.00 sequence-density-rank=3 fanout-score=27.90 fanout-score-rank=1 prefix-density=5.19 prefix-fanout=26.9 sequence=GCATCTCGTATG Potential 3prime adapter identified. Now checking if in reference sequence Warning: gzbuffer added in zlib v1.2.3.5. Unable to change buffer size from default of 8192. 1 reads; of these: 1 (100.00%) were unpaired; of these: 1 (100.00%) aligned 0 times 0 (0.00%) aligned exactly 1 time 0 (0.00%) aligned >1 times 0.00% overall alignment rate Adapter seq not found in reference. Now shuffling file before clipping skewer v0.2.2 [April 4, 2016] COMMAND LINE: skewer -f sanger -l 18 -t 20 -x ATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAA -o SRR1174000 - Input file: STDIN trimmed: SRR1174000-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): ATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAA -- maximum error ratio allowed (-r): 0.100 -- maximum indel error ratio allowed (-d): 0.030 -- minimum read length allowed after trimming (-l): 18 -- file format (-f): Sanger/Illumina 1.8+ FASTQ -- minimum overlap length for adapter detection (-k): 3 -- number of concurrent threads (-t): 20 Mon Dec 9 14:04:11 2024 >> started Mon Dec 9 14:04:41 2024 >> done (29.664s) 7789257 reads processed; of these: 3057129 (39.25%) short reads filtered out after trimming by size control 405373 ( 5.20%) empty reads filtered out after trimming by size control 4326755 (55.55%) reads available; of these: 4177724 (96.56%) trimmed reads available after processing 149031 ( 3.44%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 184554 4.27% 19 588556 13.60% 20 1017529 23.52% 21 347569 8.03% 22 159764 3.69% 23 146593 3.39% 24 548142 12.67% 25 98280 2.27% 26 79461 1.84% 27 66626 1.54% 28 55900 1.29% 29 117853 2.72% 30 116429 2.69% 31 106070 2.45% 32 95375 2.20% 33 196462 4.54% 34 90277 2.09% 35 102339 2.37% 36 60768 1.40% 37 21815 0.50% 38 13108 0.30% 39 4471 0.10% 40 2755 0.06% 41 4034 0.09% 42 102025 2.36% criterion=sequence-density sequence-density=3.58 sequence-density-rank=1 fanout-score=0.00 fanout-score-rank=13 prefix-density=0.00 prefix-fanout=1.0 sequence=GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCC criterion=fanout-score sequence-density=0.01 sequence-density-rank=34 fanout-score=181.98 fanout-score-rank=1 prefix-density=1.32 prefix-fanout=1.9 sequence=GGCATCCTAACTAACGAACGATT Started job on | Dec 09 14:06:09 Started mapping on | Dec 09 14:06:10 Finished on | Dec 09 14:08:35 Mapping speed, Million of reads per hour | 112.08 Number of input reads | 4514448 Average input read length | 24 UNIQUE READS: Uniquely mapped reads number | 660014 Uniquely mapped reads % | 14.62% Average mapped length | 23.74 Number of splices: Total | 13002 Number of splices: Annotated (sjdb) | 685 Number of splices: GT/AG | 11921 Number of splices: GC/AG | 532 Number of splices: AT/AC | 15 Number of splices: Non-canonical | 534 Mismatch rate per base, % | 0.42% Deletion rate per base | 0.01% Deletion average length | 1.21 Insertion rate per base | 0.00% Insertion average length | 1.00 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 3140545 % of reads mapped to multiple loci | 69.57% Number of reads mapped to too many loci | 403318 % of reads mapped to too many loci | 8.93% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 6.31% % of reads unmapped: other | 0.57% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 713889 713889 713889 N_multimapping 3140545 3140545 3140545 N_noFeature 513097 564426 606221 N_ambiguous 4834 2146 372 UnstrandedReadsAssigned:142083 PositiveStrandReadsAssigned:93442 NegativeStrandReadsAssigned:53421 Dataset is classified unstranded MeadianReadLen=22 20thPercentileLength=20 echo kmer=19 SRR1174000 Starting Kallisto single end mapping to ensembl reference transcriptome. kmer=19 [quant] fragment length distribution is truncated gaussian with mean = 100, sd = 20 [index] k-mer length: 19 [index] number of targets: 52,972 [index] number of k-mers: 65,492,969 [index] number of equivalence classes: 320,172 [quant] running in single-end mode [quant] will process file 1: SRR1174000-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 4,514,448 reads, 1,579,896 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 894 rounds 52973 SRR1174000.ke.tsv 35125 SRR1174000.se.tsv 88098 total ==> SRR1174000.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 837 0 0 PNS24247 1044 945 0 0 PNS24249 1928 1829 0 0 PNS24246 1044 945 0 0 PNS24248 1044 945 0 0 PNS24244 1471 1372 0 0 PNS24243 293 194 0 0 KQK14069 1603 1504 13.4111 0.745915 KQK14071 474 375 1.27624 0.28469 ==> SRR1174000.se.tsv <== BRADI_1g14170v3 12 BRADI_1g53295v3 3 BRADI_1g59795v3 0 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 17 BRADI_1g74790v3 7 BRADI_1g09890v3 0 BRADI_1g77505v3 0 BRADI_1g48960v3 0 SRR1174000 completed mapping pipeline successfully