Starting /dee2/code/volunteer_pipeline.sh ERR6133350 current disk space = 1548393394176 free memory = 1379439400 ERR6133350 SRAfilesize cdc63a174d6c5101a8c519775b4d25ad ERR6133350.sra ERR6133350.sra file validated ERR6133350 is single end ERR6133350 is conventional basespace ERR6133350 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133350_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 70-93 %GC 43 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.39675 37.0 37.0 37.0 33.0 37.0 2 36.6245 37.0 37.0 37.0 37.0 37.0 3 36.45125 37.0 37.0 37.0 37.0 37.0 4 36.39175 37.0 37.0 37.0 37.0 37.0 5 36.433 37.0 37.0 37.0 37.0 37.0 6 36.4935 37.0 37.0 37.0 37.0 37.0 7 38.61875 40.0 37.0 40.0 37.0 40.0 8 38.75775 40.0 37.0 40.0 37.0 40.0 9 38.7515 40.0 37.0 40.0 37.0 40.0 10-11 38.745999999999995 40.0 37.0 40.0 37.0 40.0 12-13 38.722125000000005 40.0 37.0 40.0 37.0 40.0 14-15 38.635125 40.0 37.0 40.0 37.0 40.0 16-17 38.685625 40.0 37.0 40.0 37.0 40.0 18-19 38.747749999999996 40.0 37.0 40.0 37.0 40.0 20-21 38.405125 40.0 37.0 40.0 37.0 40.0 22-23 38.592 40.0 37.0 40.0 37.0 40.0 24-25 38.593999999999994 40.0 37.0 40.0 37.0 40.0 26-27 38.464124999999996 40.0 37.0 40.0 37.0 40.0 28-29 38.43075 40.0 37.0 40.0 37.0 40.0 30-31 38.35825 40.0 37.0 40.0 37.0 40.0 32-33 38.34725 40.0 37.0 40.0 37.0 40.0 34-35 38.314375 40.0 37.0 40.0 37.0 40.0 36-37 38.15575 40.0 37.0 40.0 37.0 40.0 38-39 37.910624999999996 40.0 37.0 40.0 37.0 40.0 40-41 37.865 40.0 37.0 40.0 37.0 40.0 42-43 37.815250000000006 38.5 37.0 40.0 35.0 40.0 44-45 37.573625 37.0 37.0 40.0 33.0 40.0 46-47 37.380250000000004 37.0 37.0 40.0 33.0 40.0 48-49 37.318749999999994 37.0 37.0 40.0 33.0 40.0 50-51 37.074625 37.0 37.0 40.0 33.0 40.0 52-53 36.9075 37.0 37.0 40.0 33.0 40.0 54-55 36.729124999999996 37.0 37.0 37.0 33.0 40.0 56-57 36.582125000000005 37.0 37.0 37.0 33.0 40.0 58-59 36.290125 37.0 37.0 37.0 33.0 40.0 60-61 36.063375 37.0 37.0 37.0 33.0 40.0 62-63 35.5655 37.0 33.0 37.0 33.0 37.0 64-65 35.288250000000005 37.0 33.0 37.0 33.0 37.0 66-67 35.145624999999995 37.0 33.0 37.0 33.0 37.0 68-69 33.803124999999994 35.0 33.0 37.0 30.0 37.0 70-71 33.58594181197877 33.0 33.0 37.0 30.0 37.0 72-73 34.132801271545866 33.0 33.0 37.0 33.0 37.0 74-75 34.03208230394425 33.0 33.0 37.0 33.0 37.0 76-77 33.69158581262339 33.0 33.0 37.0 27.0 37.0 78-79 33.38409055317635 33.0 33.0 37.0 27.0 37.0 80-81 33.01242879396888 33.0 33.0 37.0 27.0 37.0 82-83 32.87551684190938 33.0 33.0 37.0 27.0 37.0 84-85 32.186607010863014 33.0 33.0 35.0 27.0 37.0 86-87 31.95415683962264 33.0 33.0 33.0 27.0 37.0 88-89 31.932340801886795 33.0 33.0 33.0 27.0 37.0 90-91 31.349646226415093 33.0 27.0 33.0 27.0 37.0 92-93 30.34375 33.0 27.0 33.0 22.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 2.0 21 6.0 22 2.0 23 7.0 24 7.0 25 6.0 26 11.0 27 11.0 28 15.0 29 21.0 30 22.0 31 57.0 32 77.0 33 98.0 34 220.0 35 570.0 36 1009.0 37 1447.0 38 376.0 39 36.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 63.375 9.225 8.025 19.375 2 45.800000000000004 25.4 17.95 10.85 3 30.675 35.675000000000004 18.85 14.799999999999999 4 29.875 25.45 23.75 20.925 5 21.875 28.325 28.675 21.125 6 20.0 31.624999999999996 29.45 18.925 7 29.4 26.85 24.55 19.2 8 27.1 27.075 27.700000000000003 18.125 9 24.975 25.474999999999998 29.2 20.349999999999998 10-11 24.1375 27.750000000000004 28.712500000000002 19.400000000000002 12-13 24.6125 27.237499999999997 30.075000000000003 18.075 14-15 22.412499999999998 25.7625 32.2875 19.537499999999998 16-17 23.025000000000002 28.5875 28.3375 20.05 18-19 23.674999999999997 25.874999999999996 29.599999999999998 20.849999999999998 20-21 23.6875 26.025 29.125 21.1625 22-23 24.4875 26.474999999999998 28.3625 20.674999999999997 24-25 23.9125 26.1625 29.725 20.200000000000003 26-27 23.25 25.775 30.4375 20.5375 28-29 23.674999999999997 26.450000000000003 29.037499999999998 20.837500000000002 30-31 22.9375 27.8375 29.675 19.55 32-33 23.0 26.137500000000003 31.4 19.4625 34-35 23.3875 26.55 29.675 20.3875 36-37 23.2125 28.025 28.1 20.6625 38-39 23.35 26.724999999999998 30.4 19.525000000000002 40-41 24.2375 26.1125 29.075 20.575 42-43 23.625 27.125 30.125 19.125 44-45 22.400000000000002 28.3125 29.4 19.8875 46-47 22.925 29.1875 28.487499999999997 19.400000000000002 48-49 22.6875 27.037499999999998 30.125 20.150000000000002 50-51 22.2 28.7 30.162499999999998 18.9375 52-53 23.275000000000002 28.8375 28.9125 18.975 54-55 22.95 29.299999999999997 29.65 18.099999999999998 56-57 22.675 28.462500000000002 29.325000000000003 19.537499999999998 58-59 22.7625 27.5625 29.1375 20.5375 60-61 24.25 27.3875 29.6875 18.675 62-63 22.45 29.525000000000002 30.2125 17.8125 64-65 22.45 30.049999999999997 29.3375 18.1625 66-67 22.8125 28.212500000000002 29.1875 19.787499999999998 68-69 21.337500000000002 29.725 29.7875 19.15 70-71 24.632399145406563 27.346990071635034 29.961040593188386 18.059570189770014 72-73 23.408624229979466 27.938911704312115 29.53028747433265 19.12217659137577 74-75 22.62449353025748 28.57142857142857 29.499411841589335 19.304666056724614 76-77 22.29612877477717 27.803645071172014 29.360117067979246 20.54010908607157 78-79 23.58120005417852 26.533929297033726 30.786942977109575 19.097927671678182 80-81 22.243794203300514 30.592150880599085 28.09596449868257 19.068090417417835 82-83 20.92097782831154 28.29732802728823 30.17339397384878 20.60830017055145 84-85 22.623574144486692 26.367358876864582 31.105586428780345 19.903480549868384 86-87 22.37617924528302 30.2623820754717 27.962853773584907 19.39858490566038 88-89 20.81367924528302 31.589033018867923 28.891509433962266 18.70577830188679 90-91 21.90448113207547 30.940448113207548 28.287146226415093 18.867924528301888 92-93 19.472287735849054 34.31603773584906 27.505896226415093 18.70577830188679 >>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 1.0 18 2.5 19 2.5 20 1.5 21 1.5 22 6.5 23 11.5 24 11.0 25 10.5 26 18.0 27 33.5 28 42.0 29 42.0 30 52.0 31 65.5 32 73.0 33 84.0 34 107.5 35 137.5 36 162.5 37 198.0 38 221.0 39 214.0 40 225.0 41 240.0 42 242.0 43 242.0 44 211.5 45 182.0 46 172.5 47 154.5 48 139.5 49 144.5 50 138.0 51 124.5 52 125.5 53 137.0 54 120.5 55 87.0 56 74.0 57 66.0 58 53.0 59 30.5 60 17.0 61 10.5 62 7.5 63 4.5 64 5.5 65 7.5 66 4.0 67 2.5 68 4.0 69 5.0 70 3.5 71 2.0 72 1.0 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 0.0 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 0.013068478829064296 76-77 0.013301409949454644 78-79 0.0 80-81 0.0 82-83 0.0 84-85 0.0 86-87 0.0 88-89 0.0 90-91 0.0 92-93 0.0 >>END_MODULE >>Sequence Length Distribution warn #Length Count 70 43.0 71 40.0 72 42.0 73 37.0 74 24.0 75 41.0 76 28.0 77 36.0 78 35.0 79 49.0 80 39.0 81 47.0 82 42.0 83 51.0 84 54.0 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 3392.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 81.675 #Duplication Level Percentage of deduplicated Percentage of total 1 91.6131007040098 74.825 2 4.468931741659015 7.3 3 1.5916743189470461 3.9 4 0.6121824303642486 2.0 5 0.33670033670033667 1.375 6 0.4591368227731864 2.25 7 0.09182736455463728 0.525 8 0.21426385062748698 1.4000000000000001 9 0.18365472910927455 1.35 >10 0.42852770125497397 5.075 >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 GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 21 0.525 No Hit CAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCT 20 0.5 No Hit GGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGC 19 0.475 No Hit GGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTCCT 19 0.475 No Hit GGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAA 17 0.42500000000000004 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 15 0.375 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 13 0.325 No Hit GTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTC 13 0.325 No Hit GTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAG 12 0.3 No Hit GTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAA 11 0.27499999999999997 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 11 0.27499999999999997 No Hit GCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGGTATG 11 0.27499999999999997 No Hit GGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTT 11 0.27499999999999997 No Hit CAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATAT 10 0.25 No Hit GGGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTT 9 0.22499999999999998 No Hit GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 9 0.22499999999999998 No Hit GGGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTA 9 0.22499999999999998 No Hit GGAGATTCCCAAATAGGTCAACCTTTTAAACTGCCTGCTGAATCCATGAG 9 0.22499999999999998 No Hit CAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTG 9 0.22499999999999998 No Hit GAACGTAATGCTCACAACTTCCCTCTAGATCTAGCTGCTCTTGAAGTTCC 9 0.22499999999999998 No Hit GGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGCTAAATACAG 8 0.2 No Hit GTATTAGTACTATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATCT 8 0.2 No Hit GGGGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCT 8 0.2 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 8 0.2 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 8 0.2 No Hit GGAAGACATTGTCAGGTGGGGAGTTTGGCTGGGGCGGCACATCTGTTAAA 8 0.2 No Hit TCAAAAGAGGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGGA 8 0.2 No Hit GGAGTTTGGCTGGGGCGGCACATCTGTTAAAAGATAACGCAGGTGTCCTA 7 0.17500000000000002 No Hit GGGGTTGTACTTGTGATGCGTAATTTGGTCATCTTGTGACCAAAAGACAT 7 0.17500000000000002 No Hit GGGCACTGTAGCCAGTGTGTCAGTCGTTGTTAAATTACAGGTTGAGATCA 7 0.17500000000000002 No Hit GGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAAGGCGATCAAATTC 6 0.15 No Hit GGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCG 6 0.15 No Hit GTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAA 6 0.15 No Hit CGGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGG 6 0.15 No Hit GGGCCTGTTATCTCTATCAATATGATTCTAATTCGTCAGATATTATTTAT 6 0.15 No Hit GAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTCCTG 6 0.15 No Hit GGTGGATACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAA 6 0.15 No Hit GGGCATTCGTATTTCATAGTCAGAGGTGAAATTCTTGGATTTATGAAAGA 6 0.15 No Hit CAAATAGGTCAACCTTTTAAACTGCCTGCTGAATCCATGAGCAGGCAAGA 6 0.15 No Hit GTACTATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTT 6 0.15 No Hit GGATACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATG 6 0.15 No Hit AGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTG 6 0.15 No Hit CACGAACGTAATGCTCACAACTTCCCTCTAGATCTAGCTGCTCTTGAAGT 6 0.15 No Hit GGTTGAGATCATCAGCGTACTCCGATGGGAGGTGGACATCAGAAAGTATA 6 0.15 No Hit GTGAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTA 6 0.15 No Hit AACGTAATGCTCACAACTTCCCTCTAGATCTAGCTGCTCTTGAAGTTCCC 5 0.125 No Hit GGAAGAGCCCGAGCTGCTGCAGCAGGTTTTGAAAAGGGAATCGATCGTGA 5 0.125 No Hit CAAAAGAGGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGGAA 5 0.125 No Hit GGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGC 5 0.125 No Hit CTGTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTC 5 0.125 No Hit CAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGCTAAATACAGGCGAGAG 5 0.125 No Hit CGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGGTAT 5 0.125 No Hit CTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGT 5 0.125 No Hit CAACGAGTCGGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCC 5 0.125 No Hit GCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAACGA 5 0.125 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 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 10-11 0.0 0.0 0.0 0.0 0.0 12-13 0.0 0.0 0.0 0.0 0.0 14-15 0.0 0.0 0.0 0.0 0.0 16-17 0.0 0.0 0.0 0.0 0.0 18-19 0.0 0.0 0.0 0.0 0.0 20-21 0.0 0.0 0.0 0.0 0.0 22-23 0.0 0.0 0.0 0.0 0.0 24-25 0.0 0.0 0.0 0.0 0.0 26-27 0.0 0.0 0.0 0.0 0.0 28-29 0.0 0.0 0.0 0.0 0.0 30-31 0.0 0.0 0.0 0.0 0.0 32-33 0.0 0.0 0.0 0.0 0.0 34-35 0.0 0.0 0.0 0.0 0.0 36-37 0.0 0.0 0.0 0.0 0.0 38-39 0.0125 0.0 0.0 0.0 0.0 40-41 0.025 0.0 0.0 0.0 0.0 42-43 0.025 0.0 0.0 0.0 0.0 44-45 0.05 0.0 0.0 0.0 0.0 46-47 0.05 0.0 0.0 0.0 0.0 48-49 0.05 0.0 0.0 0.0 0.0 50-51 0.05 0.0 0.0 0.0 0.0 52-53 0.075 0.0 0.0 0.0 0.0 54-55 0.075 0.0 0.0 0.0 0.0 56-57 0.075 0.0 0.0 0.0 0.0 58-59 0.075 0.0 0.0 0.0 0.0 60-61 0.1 0.0 0.0 0.0 0.0 62-63 0.1 0.0 0.0 0.0 0.0 64-65 0.1 0.0 0.0 0.0 0.0 66-67 0.1 0.0 0.0 0.0 0.0 68-69 0.1 0.0 0.0 0.0 0.0 70-71 0.125 0.0 0.0 0.0 0.0 72-73 0.125 0.0 0.0 0.0 0.0 74-75 0.125 0.0 0.0 0.0 0.0 76-77 0.125 0.0 0.0 0.0 0.0 78-79 0.125 0.0 0.0 0.0 0.0 80-81 0.125 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Rejected 118186 READS because READLEN < 1 Read 118186 spots for ERR6133350.sra Written 118186 spots for ERR6133350.sra Rejected 118186 READS because READLEN < 1 Read 118186 spots for ERR6133350.sra Written 118186 spots for ERR6133350.sra Rejected 118186 READS because READLEN < 1 Read 118186 spots for ERR6133350.sra Written 118186 spots for ERR6133350.sra Rejected 118186 READS because READLEN < 1 Read 118186 spots for ERR6133350.sra Written 118186 spots for ERR6133350.sra Rejected 118186 READS because READLEN < 1 Read 118186 spots for ERR6133350.sra Written 118186 spots for ERR6133350.sra Rejected 118186 READS because READLEN < 1 Read 118186 spots for ERR6133350.sra Written 118186 spots for ERR6133350.sra Rejected 118186 READS because READLEN < 1 Read 118186 spots for ERR6133350.sra Written 118186 spots for ERR6133350.sra Rejected 118186 READS because READLEN < 1 Read 118186 spots for ERR6133350.sra Written 118186 spots for ERR6133350.sra Rejected 118186 READS because READLEN < 1 Read 118186 spots for ERR6133350.sra Written 118186 spots for ERR6133350.sra Rejected 118186 READS because READLEN < 1 Read 118186 spots for ERR6133350.sra Written 118186 spots for ERR6133350.sra Rejected 118186 READS because READLEN < 1 Read 118186 spots for ERR6133350.sra Written 118186 spots for ERR6133350.sra Rejected 118186 READS because READLEN < 1 Read 118186 spots for ERR6133350.sra Written 118186 spots for ERR6133350.sra Rejected 118186 READS because READLEN < 1 Read 118186 spots for ERR6133350.sra Written 118186 spots for ERR6133350.sra Rejected 118186 READS because READLEN < 1 Read 118186 spots for ERR6133350.sra Written 118186 spots for ERR6133350.sra Rejected 118186 READS because READLEN < 1 Read 118186 spots for ERR6133350.sra Written 118186 spots for ERR6133350.sra Rejected 118186 READS because READLEN < 1 Read 118186 spots for ERR6133350.sra Written 118186 spots for ERR6133350.sra Rejected 118186 READS because READLEN < 1 Read 118186 spots for ERR6133350.sra Written 118186 spots for ERR6133350.sra Rejected 118200 READS because READLEN < 1 Read 118200 spots for ERR6133350.sra Written 118200 spots for ERR6133350.sra Rejected 118186 READS because READLEN < 1 Read 118186 spots for ERR6133350.sra Written 118186 spots for ERR6133350.sra Rejected 118186 READS because READLEN < 1 Read 118186 spots for ERR6133350.sra Written 118186 spots for ERR6133350.sra SRR ids: ['ERR6133350.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_4_bblww5 ERR6133350.sra spots: 2363734 blocks: [[1, 118186], [118187, 236372], [236373, 354558], [354559, 472744], [472745, 590930], [590931, 709116], [709117, 827302], [827303, 945488], [945489, 1063674], [1063675, 1181860], [1181861, 1300046], [1300047, 1418232], [1418233, 1536418], [1536419, 1654604], [1654605, 1772790], [1772791, 1890976], [1890977, 2009162], [2009163, 2127348], [2127349, 2245534], [2245535, 2363734]] ERR6133350 file size 513681 ERR6133350 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 ERR6133350 ERR6133350_1.fastq Input file: ERR6133350_1.fastq trimmed: ERR6133350-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 Sat Dec 7 01:12:44 2024 >> started Sat Dec 7 01:12:46 2024 >> done (1.642s) 2363734 reads processed; of these: 531 ( 0.02%) short reads filtered out after trimming by size control 19 ( 0.00%) empty reads filtered out after trimming by size control 2363184 (99.98%) reads available; of these: 33714 ( 1.43%) trimmed reads available after processing 2329470 (98.57%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 39 0.00% 19 52 0.00% 20 46 0.00% 21 25 0.00% 22 42 0.00% 23 27 0.00% 24 19 0.00% 25 19 0.00% 26 25 0.00% 27 24 0.00% 28 69 0.00% 29 25 0.00% 30 30 0.00% 31 34 0.00% 32 53 0.00% 33 32 0.00% 34 23 0.00% 35 37 0.00% 36 23 0.00% 37 30 0.00% 38 36 0.00% 39 74 0.00% 40 91 0.00% 41 33 0.00% 42 18 0.00% 43 23 0.00% 44 32 0.00% 45 23 0.00% 46 21 0.00% 47 11 0.00% 48 15 0.00% 49 13 0.00% 50 17 0.00% 51 93 0.00% 52 25 0.00% 53 10 0.00% 54 15 0.00% 55 19 0.00% 56 12 0.00% 57 38 0.00% 58 20 0.00% 59 21 0.00% 60 29 0.00% 61 18 0.00% 62 2 0.00% 63 1 0.00% 64 5 0.00% 65 8 0.00% 66 8 0.00% 67 12 0.00% 68 22 0.00% 69 104 0.00% 70 22974 0.97% 71 21964 0.93% 72 23538 1.00% 73 21601 0.91% 74 20645 0.87% 75 19898 0.84% 76 19386 0.82% 77 20702 0.88% 78 20935 0.89% 79 21598 0.91% 80 21046 0.89% 81 25947 1.10% 82 27354 1.16% 83 23639 1.00% 84 28208 1.19% 85 22 0.00% 86 54 0.00% 87 99 0.00% 88 198 0.01% 89 508 0.02% 90 1189 0.05% 91 3963 0.17% 92 23669 1.00% 93 1992504 84.31% 2363184 reads passed initial QC criterion=sequence-density sequence-density=4.55 sequence-density-rank=1 fanout-score=2.01 fanout-score-rank=36 prefix-density=4.59 prefix-fanout=2.0 sequence=CAAGGCTAAATAC criterion=fanout-score sequence-density=0.03 sequence-density-rank=25 fanout-score=39.22 fanout-score-rank=1 prefix-density=0.16 prefix-fanout=7.2 sequence=TTTCCTTTTTTCCTTAGAAAAATAACTCAATCAAAATCCAATTATTTACTCTACAAGAACGAAATGCTTGTTATGCCTAATATACTTAGTTTAACCTGTATCTGTTTTAATTGTGTTCTTTATCCGACTAGTTTTTTCTTTGCTAAACTACCCGAAGCTTATGCTATTTTCAACCCAATCGTGGATTTTATGCCTGTCATACCTCTATTCTTTTTTCTATTAGCCTTTGTTTGGCAAGCTGCTGTAAGTTTTCGATGAAATCTTTACTACTCCGTCTGCCAAATTGAATGGTCTATTCATTCCAAAACCAAAAAAA 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: 0 (0.00%) aligned 0 times 0 (0.00%) aligned exactly 1 time 1 (100.00%) aligned >1 times 100.00% overall alignment rate Potential adapter found in reference sequence. Continuing without clipping. Started job on | Dec 07 01:13:06 Started mapping on | Dec 07 01:13:06 Finished on | Dec 07 01:13:13 Mapping speed, Million of reads per hour | 1215.35 Number of input reads | 2363184 Average input read length | 90 UNIQUE READS: Uniquely mapped reads number | 1402875 Uniquely mapped reads % | 59.36% Average mapped length | 89.66 Number of splices: Total | 33644 Number of splices: Annotated (sjdb) | 26006 Number of splices: GT/AG | 31645 Number of splices: GC/AG | 840 Number of splices: AT/AC | 25 Number of splices: Non-canonical | 1134 Mismatch rate per base, % | 0.40% Deletion rate per base | 0.04% Deletion average length | 1.63 Insertion rate per base | 0.02% Insertion average length | 1.64 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 792648 % of reads mapped to multiple loci | 33.54% Number of reads mapped to too many loci | 108389 % of reads mapped to too many loci | 4.59% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 2.28% % of reads unmapped: other | 0.23% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 167661 167661 167661 N_multimapping 792648 792648 792648 N_noFeature 124730 139125 1344065 N_ambiguous 52586 8121 274 UnstrandedReadsAssigned:1225559 PositiveStrandReadsAssigned:1255629 NegativeStrandReadsAssigned:58536 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=93 echo kmer=89 ERR6133350 Starting Kallisto single end mapping to ensembl reference transcriptome. kmer=31 [quant] fragment length distribution is truncated gaussian with mean = 100, sd = 20 [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 single-end mode [quant] will process file 1: ERR6133350-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 2,363,184 reads, 1,693,660 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 967 rounds 52973 ERR6133350.ke.tsv 35125 ERR6133350.se.tsv 88098 total ==> ERR6133350.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 14 8.22857 PNS24243 293 194 0 0 KQK14069 1603 1504 8 4.28936 KQK14071 474 375 0 0 ==> ERR6133350.se.tsv <== BRADI_1g14170v3 9 BRADI_1g53295v3 3 BRADI_1g59795v3 17 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 8 BRADI_1g74790v3 6 BRADI_1g09890v3 0 BRADI_1g77505v3 21 BRADI_1g48960v3 0 ERR6133350 completed mapping pipeline successfully