Starting /dee2/code/volunteer_pipeline.sh SRR1174006 current disk space = 1524476731392 free memory = 1418658288 SRR1174006 SRAfilesize 74dd88fac3a8af8b6b1b4dd4071ced68 SRR1174006.sra SRR1174006.sra file validated SRR1174006 is single end SRR1174006 is conventional basespace SRR1174006 read1 length is 42 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR1174006_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 32.20475 33.0 33.0 33.0 32.0 33.0 2 31.9775 33.0 32.0 34.0 30.0 34.0 3 32.01725 33.0 32.0 33.0 29.0 34.0 4 31.87075 33.0 32.0 33.0 29.0 34.0 5 31.63525 33.0 31.0 33.0 28.0 34.0 6 31.7905 33.0 32.0 33.0 29.0 34.0 7 31.76375 33.0 31.0 33.0 29.0 34.0 8 30.97075 32.0 30.0 33.0 26.0 34.0 9 31.40275 33.0 31.0 33.0 28.0 34.0 10 31.5115 33.0 31.0 33.0 28.0 34.0 11 31.0585 33.0 31.0 33.0 27.0 34.0 12 31.2285 33.0 31.0 33.0 27.0 34.0 13 31.05225 32.0 31.0 33.0 27.0 34.0 14 30.903 32.0 30.0 33.0 26.0 33.0 15 31.25275 33.0 31.0 33.0 27.0 34.0 16 30.9605 32.0 31.0 33.0 26.0 34.0 17 30.616 32.0 30.0 33.0 25.0 33.0 18 31.00225 32.0 31.0 33.0 27.0 33.0 19 31.04225 33.0 31.0 33.0 27.0 34.0 20 30.7165 32.0 30.0 33.0 26.0 33.0 21 30.61125 32.0 30.0 33.0 25.0 33.0 22 30.377 32.0 30.0 33.0 25.0 33.0 23 30.04 32.0 29.0 33.0 24.0 33.0 24 29.68725 31.0 29.0 33.0 23.0 33.0 25 29.6865 31.0 29.0 33.0 24.0 33.0 26 30.06575 32.0 30.0 33.0 25.0 33.0 27 29.081 31.0 28.0 33.0 22.0 33.0 28 29.17025 31.0 28.0 33.0 23.0 33.0 29 29.478 31.0 28.0 33.0 24.0 33.0 30 29.13825 31.0 28.0 33.0 22.0 33.0 31 28.3665 30.0 27.0 32.0 21.0 33.0 32 28.18425 30.0 27.0 32.0 21.0 33.0 33 28.6735 31.0 28.0 33.0 21.0 33.0 34 28.16225 31.0 27.0 33.0 21.0 33.0 35 28.098 30.0 27.0 32.0 21.0 33.0 36 27.763 30.0 26.0 32.0 20.0 33.0 37 28.4455 31.0 27.0 33.0 21.0 33.0 38 26.7935 29.0 24.0 32.0 19.0 33.0 39 27.74025 30.0 26.0 32.0 19.0 33.0 40 26.6185 30.0 24.0 32.0 17.0 33.0 41 26.563 29.0 25.0 32.0 18.0 33.0 42 25.84325 29.0 24.0 32.0 4.0 33.0 >>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 9.0 5 0.0 6 2.0 7 1.0 8 3.0 9 0.0 10 1.0 11 3.0 12 2.0 13 3.0 14 3.0 15 5.0 16 5.0 17 8.0 18 6.0 19 14.0 20 18.0 21 36.0 22 51.0 23 54.0 24 76.0 25 98.0 26 121.0 27 177.0 28 281.0 29 430.0 30 728.0 31 926.0 32 810.0 33 129.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 30.519645120405574 31.73637515842839 19.46768060836502 18.276299112801013 2 33.425 25.974999999999998 22.875 17.724999999999998 3 34.15853963490873 21.530382595648913 18.0545136284071 26.25656414103526 4 39.629722291718785 25.969477107830873 19.264448336252187 15.13635226419815 5 27.53188297074269 32.733183295823956 18.854713678419603 20.880220055013755 6 26.5 25.45 27.325 20.724999999999998 7 36.85921480370092 23.980995248812203 25.156289072268066 14.003500875218805 8 23.261630815407706 23.961980990495245 34.39219609804903 18.384192096048025 9 23.46760070052539 34.57593194896172 29.19689767325494 12.759569677257943 10 41.099999999999994 22.400000000000002 17.724999999999998 18.775 11 24.012006003001503 24.387193596798397 25.437718859429715 26.163081540770385 12 25.912956478239117 20.68534267133567 27.888944472236116 25.512756378189096 13 27.425 19.925 20.775 31.874999999999996 14 20.630157539384847 40.56014003500875 25.156289072268066 13.653413353338333 15 29.514757378689342 28.8144072036018 22.71135567783892 18.959479739869938 16 22.842131598699027 29.071803852889666 28.77157868401301 19.314485864398296 17 22.611305652826413 28.339169584792394 32.716358179089546 16.333166583291643 18 26.25 20.3 31.05 22.400000000000002 19 24.731182795698924 22.55563890972743 27.33183295823956 25.381345336334082 20 25.456364091022753 22.405601400350086 33.458364591147784 18.67966991747937 21 21.43035758939735 23.95598899724931 27.056764191047762 27.556889222305575 22 28.375 23.3 28.725 19.6 23 21.966474856142106 20.740555416562422 36.35226419814861 20.94070552914686 24 24.137068534267133 23.28664332166083 26.863431715857928 25.71285642821411 25 17.083541770885443 30.440220110055026 30.21510755377689 22.26113056528264 26 23.355838959739934 12.45311327831958 38.68467116779195 25.506376594148538 27 18.05902951475738 13.881940970485243 24.937468734367183 43.1215607803902 28 14.607303651825912 15.757878939469736 42.22111055527764 27.41370685342671 29 23.280820205051263 13.103275818954737 26.531632908227053 37.08427106776694 30 32.10802700675169 9.577394348587147 36.58414603650913 21.73043260815204 31 16.53326663331666 11.905952976488244 42.54627313656829 29.014507253626814 32 14.507253626813407 25.46273136568284 33.79189594797399 26.23811905952976 33 15.35767883941971 9.9799899949975 51.35067533766884 23.311655827913956 34 32.716358179089546 9.804902451225612 30.09004502251126 27.388694347173587 35 15.25 9.975000000000001 36.175000000000004 38.6 36 21.655413853463365 11.902975743935984 27.806951737934483 38.63465866466617 37 28.457114278569644 14.228557139284822 33.88347086771693 23.43085771442861 38 13.438438438438439 16.49149149149149 50.80080080080081 19.26926926926927 39 14.649999999999999 20.75 32.5 32.1 40 19.039279459594695 24.11808856642482 42.006504878658994 14.83612709532149 41 13.838838838838837 34.63463463463464 35.93593593593594 15.590590590590592 42 9.479739869934969 37.09354677338669 23.311655827913956 30.115057528764382 >>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 0.0 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 1.0 24 2.0 25 4.0 26 6.0 27 23.0 28 40.0 29 40.0 30 41.0 31 42.0 32 39.0 33 36.0 34 36.0 35 65.5 36 95.0 37 134.0 38 173.0 39 244.0 40 315.0 41 315.0 42 374.0 43 433.0 44 477.0 45 521.0 46 527.0 47 533.0 48 533.0 49 598.5 50 664.0 51 572.5 52 481.0 53 481.0 54 424.5 55 368.0 56 269.0 57 170.0 58 110.0 59 50.0 60 50.0 61 43.0 62 36.0 63 25.0 64 14.0 65 11.0 66 8.0 67 8.0 68 6.5 69 5.0 70 4.0 71 3.0 72 3.0 73 2.5 74 2.0 75 2.0 76 2.0 77 1.0 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 0.5 100 1.0 >>END_MODULE >>Per base N content pass #Base N-Count 1 1.375 2 0.0 3 0.025 4 0.075 5 0.025 6 0.0 7 0.025 8 0.05 9 0.075 10 0.0 11 0.05 12 0.05 13 0.0 14 0.025 15 0.05 16 0.075 17 0.05 18 0.0 19 0.025 20 0.025 21 0.025 22 0.0 23 0.075 24 0.05 25 0.05 26 0.025 27 0.05 28 0.05 29 0.025 30 0.025 31 0.05 32 0.05 33 0.05 34 0.05 35 0.0 36 0.025 37 0.025 38 0.1 39 0.0 40 0.075 41 0.1 42 0.05 >>END_MODULE >>Sequence Length Distribution pass #Length Count 42 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 72.1 #Duplication Level Percentage of deduplicated Percentage of total 1 92.19833564493759 66.475 2 3.3980582524271843 4.9 3 1.3176144244105408 2.85 4 0.6588072122052704 1.9 5 0.3120665742024965 1.125 6 0.3814147018030513 1.6500000000000001 7 0.13869625520110956 0.7000000000000001 8 0.13869625520110956 0.8 9 0.17337031900138697 1.125 >10 1.2135922330097086 15.225 >50 0.06934812760055478 3.25 >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 GGGGATGTAGCTCAGAATCTCGTATGCCGTCTTCTGCTTGAA 79 1.975 RNA PCR Primer, Index 40 (100% over 30bp) TCCGTCGTAGTCTAGGATCTCGTATGCCGTCTTCTGCTTGAA 51 1.275 RNA PCR Primer, Index 22 (96% over 28bp) GGGGATGTAGCTCAAAATCTCGTATGCCGTCTTCTGCTTGAA 42 1.05 RNA PCR Primer, Index 40 (96% over 30bp) GGCGGATGTAGCCAAGTGGAATCTCGTATGCCGTCTTCTGCT 37 0.9249999999999999 Illumina PCR Primer Index 8 (96% over 26bp) GGGGACGTAGCTCATAATCTCGTATGCCGTCTTCTGCTTGAA 31 0.775 RNA PCR Primer, Index 40 (96% over 30bp) ACGAACGATTTGAACATCTCGTATGCCGTCTTCTGCTTGAAA 24 0.6 Illumina PCR Primer Index 7 (96% over 28bp) ATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAA 24 0.6 Illumina Single End Adapter 1 (95% over 24bp) CTAACGAACGAACGATTTGAACATCTCGTATGCCGTCTTCTG 22 0.5499999999999999 RNA PCR Primer, Index 19 (96% over 25bp) AACGAACGATTTGAACATCTCGTATGCCGTCTTCTGCTTGAA 20 0.5 RNA PCR Primer, Index 19 (96% over 29bp) ACGAACGAACGATTTGAACATCTCGTATGCCGTCTTCTGCTT 19 0.475 Illumina PCR Primer Index 7 (96% over 27bp) CGAACGATTTGAACATCTCGTATGCCGTCTTCTGCTTGAAAA 19 0.475 RNA PCR Primer, Index 19 (96% over 29bp) CATCGAGTAGACCTTGTTATTGTGAGAATTCATCTCGTATGC 19 0.475 No Hit TTTGGATTGAAGGGAGCTCTGATCTCGTATGCCGTCTTCTGC 19 0.475 Illumina PCR Primer Index 9 (96% over 25bp) TAACGAACGAACGATTTGAACATCTCGTATGCCGTCTTCTGC 18 0.44999999999999996 Illumina PCR Primer Index 7 (96% over 25bp) AGCGGAGTAGAGCAGTATCTCGTATGCCGTCTTCTGCTTGAA 17 0.42500000000000004 Illumina PCR Primer Index 6 (96% over 28bp) AACGAACGAACGATTTGAACATCTCGTATGCCGTCTTCTGCT 17 0.42500000000000004 RNA PCR Primer, Index 19 (96% over 27bp) TAATTCATGATCTGGATCTCGTATGCCGTCTTCTGCTTGAAA 17 0.42500000000000004 RNA PCR Primer, Index 23 (96% over 28bp) GGGCCTGTAGCTCAGAGGAATCTCGTATGCCGTCTTCTGCTT 16 0.4 Illumina PCR Primer Index 12 (96% over 26bp) AGCGGAGTAGAGCAGTTATCTCGTATGCCGTCTTCTGCTTGA 16 0.4 Illumina PCR Primer Index 5 (96% over 29bp) GGGGATGTAGCTCAAATCTCGTATGCCGTCTTCTGCTTGAAA 15 0.375 TruSeq Adapter, Index 13 (96% over 28bp) GTCAGGATAGCTCAGTTGGTAGAGCAGAGGACTATCTCGTAT 15 0.375 No Hit GACACGACTCTCGGCAACGGATATCATCTCGTATGCCGTCTT 15 0.375 TruSeq Adapter, Index 7 (95% over 22bp) GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGATTGTGATCT 14 0.35000000000000003 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTATCTCGTATGCC 14 0.35000000000000003 No Hit GGGGATGTAGCTCAGATCTCGTATGCCGTCTTCTGCTTGAAA 14 0.35000000000000003 Illumina PCR Primer Index 9 (96% over 30bp) GGGGGTGTAGCTCATAATCTCGTATGCCGTCTTCTGCTTGAA 14 0.35000000000000003 Illumina PCR Primer Index 12 (96% over 27bp) GGGGATGTAGCTCAGATGGTATCTCGTATGCCGTCTTCTGCT 13 0.325 RNA PCR Primer, Index 34 (96% over 27bp) CGAACGAACGATTTGAACATCTCGTATGCCGTCTTCTGCTTG 13 0.325 RNA PCR Primer, Index 19 (96% over 29bp) GCGTCTGTAGTCCAACGGATCTCGTATGCCGTCTTCTGCTTG 13 0.325 TruSeq Adapter, Index 18 (96% over 27bp) GGGGATGTAGCTCAATCTCGTATGCCGTCTTCTGCTTGAAAA 13 0.325 RNA PCR Primer, Index 32 (96% over 29bp) GAACGAACGATTTGAACATCTCGTATGCCGTCTTCTGCTTGA 13 0.325 Illumina PCR Primer Index 7 (96% over 28bp) GGGATTGTAGTTCAATATCTCGTATGCCGTCTTCTGCTTGAA 12 0.3 Illumina PCR Primer Index 6 (96% over 29bp) AACGATTTGAACATCTCGTATGCCGTCTTCTGCTTGAAAAAA 12 0.3 Illumina PCR Primer Index 7 (96% over 28bp) TGACAGAAGAGAGTGAGCACATCTCGTATGCCGTCTTCTGCT 11 0.27499999999999997 Illumina PCR Primer Index 9 (96% over 25bp) CACGACTCTCGGCAACGATCTCGTATGCCGTCTTCTGCTTGA 11 0.27499999999999997 RNA PCR Primer, Index 36 (96% over 29bp) CACGACTCTCGGCAACGGATATCTATCTCGTATGCCGTCTTC 10 0.25 Illumina PCR Primer Index 2 (95% over 22bp) CCTAACGAACGAACGATTTGAACATCTCGTATGCCGTCTTCT 10 0.25 RNA PCR Primer, Index 19 (95% over 24bp) TCCTAACGAACGAACGATTTGAACATCTCGTATGCCGTCTTC 9 0.22499999999999998 Illumina PCR Primer Index 7 (95% over 22bp) GACACGACTCTCGGCAACGGATATCTCATCTCGTATGCCGTC 9 0.22499999999999998 No Hit AGGGCTATAGCTCAGTTCGGATCTCGTATGCCGTCTTCTGCT 9 0.22499999999999998 TruSeq Adapter, Index 9 (96% over 26bp) GACACGACTCTCGGCATCTCGTATGCCGTCTTCTGCTTGAAA 9 0.22499999999999998 Illumina PCR Primer Index 3 (96% over 29bp) GACACGACTCTCGGCAACGGATATCTATCTCGTATGCCGTCT 9 0.22499999999999998 No Hit TCTGTTGGGCATCTCGTATGCCGTCTTCTGCTTGAAAAAAAA 8 0.2 Illumina PCR Primer Index 3 (96% over 30bp) ATCCTAACGAACGAACGATTTGAACATCTCGTATGCCGTCTT 8 0.2 RNA PCR Primer, Index 19 (95% over 22bp) AGGGATGTAGCGCAGCTATCTCGTATGCCGTCTTCTGCTTGA 8 0.2 RNA PCR Primer, Index 38 (96% over 29bp) CACGACTCTCGGCAACGGATATCTCATCTCGTATGCCGTCTT 8 0.2 No Hit CACGACTCTCGGCAACGGATATCATCTCGTATGCCGTCTTCT 7 0.17500000000000002 TruSeq Adapter, Index 7 (95% over 24bp) GACACGACTCTCGGCAACGGAATCTCGTATGCCGTCTTCTGC 7 0.17500000000000002 RNA PCR Primer, Index 40 (96% over 25bp) ATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAACAA 7 0.17500000000000002 Illumina Single End Adapter 1 (95% over 24bp) AGCGGAGTAGAGCAGATCTCGTATGCCGTCTTCTGCTTGAAA 7 0.17500000000000002 Illumina PCR Primer Index 9 (100% over 27bp) CCACGTCGCACGGATTCGTATCTCGTATGCCGTCTTCTGCTT 6 0.15 Illumina PCR Primer Index 2 (96% over 26bp) GAACGATTTGAACATCTCGTATGCCGTCTTCTGCTTGAAAAA 6 0.15 RNA PCR Primer, Index 19 (96% over 29bp) TTGACAGAAGAGAGTGAGCACATCTCGTATGCCGTCTTCTGC 6 0.15 Illumina PCR Primer Index 9 (95% over 24bp) CACGACTCTCGGCAACGGATAATCTCGTATGCCGTCTTCTGC 6 0.15 TruSeq Adapter, Index 7 (96% over 25bp) CACGACTCTCGGCATCTCGTATGCCGTCTTCTGCTTGAAAAA 6 0.15 Illumina PCR Primer Index 3 (96% over 29bp) GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGATTGTATCTC 6 0.15 No Hit GCGTCTGTAGTCCAACGGTATCTCGTATGCCGTCTTCTGCTT 6 0.15 RNA PCR Primer, Index 31 (96% over 28bp) GACACGACTCTCGGCAACATCTCGTATGCCGTCTTCTGCTTG 6 0.15 Illumina PCR Primer Index 6 (96% over 28bp) GCGGCTGTAGCTCAGTTGGAATCTCGTATGCCGTCTTCTGCT 6 0.15 Illumina PCR Primer Index 12 (96% over 27bp) CGTCGCACGGATTCGTATCTCGTATGCCGTCTTCTGCTTGAA 6 0.15 Illumina PCR Primer Index 2 (96% over 27bp) AACCGTAGTAATTCTAGAGCATCTCGTATGCCGTCTTCTGCT 6 0.15 RNA PCR Primer, Index 43 (96% over 29bp) GGTAGTTCGACCGCGGAAATCTCGTATGCCGTCTTCTGCTTG 5 0.125 RNA PCR Primer, Index 48 (96% over 29bp) GACACGACTCTCGGCAACGGATATATCTCGTATGCCGTCTTC 5 0.125 Illumina PCR Primer Index 2 (95% over 23bp) GTCGTTGTAGTATAGTGGTAAGTATTCCCGCCTGTATCTCGT 5 0.125 No Hit ATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAT 5 0.125 Illumina Single End Adapter 1 (95% over 24bp) GTCGTTGTAGTATAGTGGTATCTCGTATGCCGTCTTCTGCTT 5 0.125 RNA PCR Primer, Index 34 (96% over 27bp) ATATTGGGTAGGTTGTGGTATTTCATTGCATCTCGTATGCCG 5 0.125 No Hit GGGGATGTAGCTCAAATGGTATCTCGTATGCCGTCTTCTGCT 5 0.125 RNA PCR Primer, Index 34 (96% over 27bp) ACGATTTGAACATCTCGTATGCCGTCTTCTGCTTGAAAAAAA 5 0.125 Illumina PCR Primer Index 7 (96% over 28bp) GTCGTTGTAGTATAATCTCGTATGCCGTCTTCTGCTTGAAAA 5 0.125 Illumina PCR Primer Index 12 (96% over 28bp) >>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 warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position AGCTCAG 20 0.0018889057 35.912502 9 TAGCTCA 25 1.2250376E-4 35.912502 8 GGCAACG 25 0.005640617 28.730001 11 TCGGCAA 25 0.005640617 28.730001 9 ACTCTCG 25 0.005640617 28.730001 5 CACGACT 25 0.005640617 28.730001 1 GAGTAGA 25 0.005640617 28.730001 5 CTCGGCA 25 0.005640617 28.730001 8 ACGACTC 25 0.005640617 28.730001 2 CGGCAAC 25 0.005640617 28.730001 10 GACTCTC 25 0.005640617 28.730001 4 CGACTCT 25 0.005640617 28.730001 3 GCTTGAA 135 7.9631456E-5 11.970834 36 TGCTTGA 160 3.8964907E-4 10.10039 35 CTGCTTG 170 6.043952E-4 9.626582 34 TCTGCTT 185 0.0013181871 8.846049 33 TTCTGCT 190 0.001683719 8.613258 32 CTTCTGC 210 0.0041957754 7.792948 31 CGTCTTC 290 1.350093E-4 7.430172 36 TCTTCTG 225 0.00783156 7.2734175 30 >>END_MODULE Read 523685 spots for SRR1174006.sra Written 523685 spots for SRR1174006.sra Read 523685 spots for SRR1174006.sra Written 523685 spots for SRR1174006.sra Read 523685 spots for SRR1174006.sra Written 523685 spots for SRR1174006.sra Read 523685 spots for SRR1174006.sra Written 523685 spots for SRR1174006.sra Read 523685 spots for SRR1174006.sra Written 523685 spots for SRR1174006.sra Read 523685 spots for SRR1174006.sra Written 523685 spots for SRR1174006.sra Read 523685 spots for SRR1174006.sra Written 523685 spots for SRR1174006.sra Read 523685 spots for SRR1174006.sra Written 523685 spots for SRR1174006.sra Read 523685 spots for SRR1174006.sra Written 523685 spots for SRR1174006.sra Read 523685 spots for SRR1174006.sra Written 523685 spots for SRR1174006.sra Read 523685 spots for SRR1174006.sra Written 523685 spots for SRR1174006.sra Read 523685 spots for SRR1174006.sra Written 523685 spots for SRR1174006.sra Read 523685 spots for SRR1174006.sra Written 523685 spots for SRR1174006.sra Read 523685 spots for SRR1174006.sra Written 523685 spots for SRR1174006.sra Read 523685 spots for SRR1174006.sra Written 523685 spots for SRR1174006.sra Read 523685 spots for SRR1174006.sra Written 523685 spots for SRR1174006.sra Read 523687 spots for SRR1174006.sra Written 523687 spots for SRR1174006.sra Read 523685 spots for SRR1174006.sra Written 523685 spots for SRR1174006.sra Read 523685 spots for SRR1174006.sra Written 523685 spots for SRR1174006.sra Read 523685 spots for SRR1174006.sra Written 523685 spots for SRR1174006.sra SRR ids: ['SRR1174006.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_yoejkyw9 SRR1174006.sra spots: 10473702 blocks: [[1, 523685], [523686, 1047370], [1047371, 1571055], [1571056, 2094740], [2094741, 2618425], [2618426, 3142110], [3142111, 3665795], [3665796, 4189480], [4189481, 4713165], [4713166, 5236850], [5236851, 5760535], [5760536, 6284220], [6284221, 6807905], [6807906, 7331590], [7331591, 7855275], [7855276, 8378960], [8378961, 8902645], [8902646, 9426330], [9426331, 9950015], [9950016, 10473702]] SRR1174006 file size 1459661 SRR1174006 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 SRR1174006 SRR1174006_1.fastq Input file: SRR1174006_1.fastq trimmed: SRR1174006-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 14:32:51 2024 >> started Mon Dec 9 14:33:14 2024 >> done (22.801s) 10473702 reads processed; of these: 32495 ( 0.31%) short reads filtered out after trimming by size control 20984 ( 0.20%) empty reads filtered out after trimming by size control 10420223 (99.49%) reads available; of these: 1399557 (13.43%) trimmed reads available after processing 9020666 (86.57%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 4224 0.04% 19 5490 0.05% 20 6717 0.06% 21 7423 0.07% 22 10196 0.10% 23 14447 0.14% 24 17447 0.17% 25 19035 0.18% 26 27910 0.27% 27 44971 0.43% 28 39743 0.38% 29 49296 0.47% 30 53433 0.51% 31 50942 0.49% 32 44133 0.42% 33 37886 0.36% 34 35238 0.34% 35 38744 0.37% 36 56345 0.54% 37 87805 0.84% 38 111474 1.07% 39 120723 1.16% 40 206852 1.99% 41 309083 2.97% 42 9020666 86.57% 10420223 reads passed initial QC criterion=sequence-density sequence-density=84.20 sequence-density-rank=1 fanout-score=34.33 fanout-score-rank=1 prefix-density=85.76 prefix-fanout=33.7 sequence=ATCTCGTATGCCGTCTTCTGCTTGAAAAA criterion=fanout-score sequence-density=84.20 sequence-density-rank=1 fanout-score=34.33 fanout-score-rank=1 prefix-density=85.76 prefix-fanout=33.7 sequence=ATCTCGTATGCCGTCTTCTGCTTGAAAAA 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 ATCTCGTATGCCGTCTTCTGCTTGAAAAA -o SRR1174006 - Input file: STDIN trimmed: SRR1174006-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): ATCTCGTATGCCGTCTTCTGCTTGAAAAA -- 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 14:33:52 2024 >> started Mon Dec 9 14:34:29 2024 >> done (37.043s) 10175041 reads processed; of these: 3524700 (34.64%) short reads filtered out after trimming by size control 312419 ( 3.07%) empty reads filtered out after trimming by size control 6337922 (62.29%) reads available; of these: 6059385 (95.61%) trimmed reads available after processing 278537 ( 4.39%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 336618 5.31% 19 411508 6.49% 20 474555 7.49% 21 532431 8.40% 22 306469 4.84% 23 402074 6.34% 24 1824510 28.79% 25 246809 3.89% 26 177909 2.81% 27 152109 2.40% 28 127741 2.02% 29 160309 2.53% 30 168494 2.66% 31 170405 2.69% 32 116897 1.84% 33 151419 2.39% 34 98223 1.55% 35 98492 1.55% 36 81792 1.29% 37 62174 0.98% 38 51869 0.82% 39 21201 0.33% 40 6253 0.10% 41 7191 0.11% 42 150470 2.37% criterion=sequence-density sequence-density=2.49 sequence-density-rank=1 fanout-score=1.00 fanout-score-rank=10 prefix-density=0.03 prefix-fanout=1.0 sequence=GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGATTGTGA criterion=fanout-score sequence-density=1.11 sequence-density-rank=5 fanout-score=37.88 fanout-score-rank=1 prefix-density=1.17 prefix-fanout=36.2 sequence=TCGTATGCCGTCTTCTGCTTGAAAAA Started job on | Dec 09 14:36:29 Started mapping on | Dec 09 14:36:29 Finished on | Dec 09 14:38:46 Mapping speed, Million of reads per hour | 172.99 Number of input reads | 6583104 Average input read length | 25 UNIQUE READS: Uniquely mapped reads number | 1919684 Uniquely mapped reads % | 29.16% Average mapped length | 23.81 Number of splices: Total | 27766 Number of splices: Annotated (sjdb) | 5742 Number of splices: GT/AG | 26291 Number of splices: GC/AG | 664 Number of splices: AT/AC | 11 Number of splices: Non-canonical | 800 Mismatch rate per base, % | 0.19% Deletion rate per base | 0.00% 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 | 2182390 % of reads mapped to multiple loci | 33.15% Number of reads mapped to too many loci | 2012855 % of reads mapped to too many loci | 30.58% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 5.73% % of reads unmapped: other | 1.38% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 2481030 2481030 2481030 N_multimapping 2182390 2182390 2182390 N_noFeature 1486475 1620322 1780264 N_ambiguous 9971 4061 592 UnstrandedReadsAssigned:423238 PositiveStrandReadsAssigned:295301 NegativeStrandReadsAssigned:138828 Dataset is classified unstranded MeadianReadLen=24 20thPercentileLength=21 echo kmer=19 SRR1174006 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: SRR1174006-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 6,583,104 reads, 1,847,038 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,063 rounds 52973 SRR1174006.ke.tsv 35125 SRR1174006.se.tsv 88098 total ==> SRR1174006.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 5 0.840145 PNS24243 293 194 0 0 KQK14069 1603 1504 25.2637 3.87247 KQK14071 474 375 0 0 ==> SRR1174006.se.tsv <== BRADI_1g14170v3 27 BRADI_1g53295v3 10 BRADI_1g59795v3 0 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 1 BRADI_1g74790v3 43 BRADI_1g09890v3 1 BRADI_1g77505v3 0 BRADI_1g48960v3 0 SRR1174006 completed mapping pipeline successfully