Starting /dee2/code/volunteer_pipeline.sh ERR6133471 current disk space = 1545006837760 free memory = 1512906388 ERR6133471 SRAfilesize 643713a057b598647f837aa9cf62c3f2 ERR6133471.sra ERR6133471.sra file validated ERR6133471 is single end ERR6133471 is conventional basespace ERR6133471 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133471_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 45 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 34.97875 37.0 33.0 37.0 33.0 37.0 2 36.204 37.0 37.0 37.0 33.0 37.0 3 35.22125 37.0 33.0 37.0 33.0 37.0 4 34.67675 37.0 33.0 37.0 27.0 37.0 5 34.681 37.0 33.0 37.0 27.0 37.0 6 34.98125 37.0 33.0 37.0 33.0 37.0 7 36.50225 37.0 37.0 40.0 33.0 40.0 8 36.667 37.0 37.0 40.0 33.0 40.0 9 36.946 37.0 37.0 40.0 33.0 40.0 10-11 36.920875 37.0 37.0 40.0 33.0 40.0 12-13 36.801125 37.0 37.0 40.0 33.0 40.0 14-15 36.71575 37.0 37.0 40.0 33.0 40.0 16-17 36.554875 37.0 37.0 40.0 33.0 40.0 18-19 36.301625 37.0 37.0 40.0 33.0 40.0 20-21 36.11775 37.0 35.0 40.0 33.0 40.0 22-23 35.745625000000004 37.0 33.0 40.0 33.0 40.0 24-25 35.928 37.0 33.0 40.0 33.0 40.0 26-27 36.218 37.0 37.0 40.0 33.0 40.0 28-29 36.08225 37.0 35.0 40.0 33.0 40.0 30-31 36.19125 37.0 37.0 40.0 33.0 40.0 32-33 36.069 37.0 33.0 40.0 33.0 40.0 34-35 35.944625 37.0 33.0 40.0 33.0 40.0 36-37 35.955 37.0 33.0 40.0 33.0 40.0 38-39 35.838125000000005 37.0 33.0 40.0 33.0 40.0 40-41 35.687625 37.0 33.0 40.0 33.0 40.0 42-43 35.571875 37.0 33.0 40.0 33.0 40.0 44-45 35.376374999999996 37.0 33.0 37.0 30.0 40.0 46-47 35.45275 37.0 33.0 37.0 33.0 40.0 48-49 35.503874999999994 37.0 33.0 37.0 33.0 40.0 50-51 35.329 37.0 33.0 37.0 33.0 40.0 52-53 35.11775 37.0 33.0 37.0 33.0 40.0 54-55 35.086375000000004 37.0 33.0 37.0 33.0 40.0 56-57 34.85925 37.0 33.0 37.0 33.0 38.5 58-59 34.415375 37.0 33.0 37.0 27.0 37.0 60-61 34.620374999999996 37.0 33.0 37.0 30.0 37.0 62-63 34.49525 37.0 33.0 37.0 27.0 37.0 64-65 34.268125 37.0 33.0 37.0 27.0 37.0 66-67 34.126374999999996 37.0 33.0 37.0 27.0 37.0 68-69 33.299875 35.0 33.0 37.0 27.0 37.0 70-71 33.42721795915811 35.0 33.0 37.0 27.0 37.0 72-73 33.87164609221169 37.0 33.0 37.0 27.0 37.0 74-75 33.92807718735449 37.0 33.0 37.0 27.0 37.0 76-77 34.01762498105792 37.0 33.0 37.0 27.0 37.0 78-79 33.87853312323681 37.0 33.0 37.0 27.0 37.0 80-81 33.77374745092733 37.0 33.0 37.0 27.0 37.0 82-83 33.64254421136063 37.0 33.0 37.0 27.0 37.0 84-85 33.516734055553485 35.0 33.0 37.0 27.0 37.0 86-87 33.400581702802754 33.0 33.0 37.0 27.0 37.0 88-89 33.563194077207825 37.0 33.0 37.0 27.0 37.0 90-91 33.28886832363828 33.0 33.0 37.0 27.0 37.0 92-93 33.3097567424643 33.0 33.0 37.0 27.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 8.0 21 10.0 22 24.0 23 20.0 24 23.0 25 36.0 26 46.0 27 47.0 28 66.0 29 79.0 30 117.0 31 147.0 32 180.0 33 190.0 34 329.0 35 491.0 36 880.0 37 864.0 38 430.0 39 13.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 87.175 3.025 3.5749999999999997 6.225 2 72.02499999999999 16.5 6.825 4.65 3 38.4 37.3 13.225000000000001 11.075 4 30.049999999999997 32.65 17.974999999999998 19.325 5 29.599999999999998 27.85 26.025 16.525000000000002 6 19.225 40.849999999999994 24.099999999999998 15.825 7 39.175 27.325 18.475 15.024999999999999 8 28.275 30.5 21.05 20.175 9 24.0 32.824999999999996 25.825 17.349999999999998 10-11 22.975 29.425 29.95 17.65 12-13 25.1 28.449999999999996 25.837500000000002 20.6125 14-15 21.05 36.175000000000004 25.575 17.2 16-17 25.15 29.525000000000002 23.375 21.95 18-19 24.76869217304326 25.868967241810452 30.120030007501875 19.24231057764441 20-21 26.682511883912934 24.36827620715537 30.122591943957964 18.82661996497373 22-23 29.125 22.675 27.925 20.275000000000002 24-25 23.2625 24.65 29.525000000000002 22.5625 26-27 25.8 24.712500000000002 29.075 20.4125 28-29 24.337500000000002 28.925 28.8625 17.875 30-31 30.7875 24.9875 25.337500000000002 18.8875 32-33 25.5125 24.875 27.3875 22.225 34-35 22.5625 32.175 24.6875 20.575 36-37 26.331582895723933 24.76869217304326 24.76869217304326 24.131032758189548 38-39 31.240620310155077 23.12406203101551 27.51375687843922 18.121560780390194 40-41 25.35633908477119 24.056014003500874 31.032758189547387 19.554888722180543 42-43 25.73612329282045 30.610199223154993 26.1746648289688 17.479012655055755 44-45 25.175087543771884 25.65032516258129 30.1775887943972 18.996998499249624 46-47 25.7 24.25 25.937500000000004 24.1125 48-49 26.075 24.1125 28.050000000000004 21.762500000000003 50-51 21.5375 28.6125 27.4125 22.4375 52-53 23.334168336673347 25.851703406813627 25.200400801603205 25.613727454909817 54-55 22.9057264316079 25.431357839459867 31.007751937984494 20.655163790947736 56-57 26.5875 27.787499999999998 26.737499999999997 18.8875 58-59 22.3625 27.3375 29.799999999999997 20.5 60-61 28.849999999999998 25.5125 27.437499999999996 18.2 62-63 20.5 27.950000000000003 32.0125 19.537499999999998 64-65 21.125 33.85 26.9625 18.0625 66-67 25.5125 30.725 26.125 17.6375 68-69 20.31503937992249 26.340792599074884 28.94111763970496 24.40305038129766 70-71 22.350143911900886 28.419471905894135 27.08046552371418 22.1499186584908 72-73 26.59025066129235 24.92757274215896 29.739261871772264 18.74291472477642 74-75 25.209337731540217 29.053539710733318 27.886323268206038 17.850799289520427 76-77 21.113096757722747 24.712790400816953 26.895583354608117 27.278529486852182 78-79 25.27952705307801 27.45148438504048 27.95270530780105 19.316283254080453 80-81 21.16580310880829 34.27461139896373 26.463730569948186 18.09585492227979 82-83 24.261051530211873 26.353648966780014 26.26209782893016 23.12320167407795 84-85 21.549221430456587 25.640010556875165 33.1353919239905 19.67537608867775 86-87 19.50026441036489 29.759386567953467 28.42411422527763 22.316234796404018 88-89 19.196192490745638 27.37969328397673 31.78212585933369 21.641988365943945 90-91 26.057641459545216 28.595980962453726 27.683765203595982 17.662612374405075 92-93 19.341618191433106 29.60074034902168 30.050237969328396 21.007403490216817 >>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 9.5 18 11.0 19 2.0 20 2.5 21 4.0 22 3.5 23 4.5 24 6.0 25 7.0 26 10.5 27 11.5 28 21.0 29 31.0 30 35.5 31 40.5 32 54.5 33 75.0 34 87.5 35 93.5 36 101.0 37 142.0 38 197.0 39 180.0 40 173.0 41 200.0 42 215.0 43 235.0 44 206.0 45 186.5 46 179.5 47 150.5 48 139.5 49 142.0 50 138.5 51 132.5 52 121.5 53 125.5 54 230.0 55 210.5 56 75.0 57 50.0 58 50.5 59 46.5 60 33.5 61 25.5 62 29.0 63 25.0 64 20.0 65 18.5 66 13.0 67 13.5 68 15.0 69 12.5 70 9.0 71 7.0 72 5.0 73 3.5 74 3.0 75 1.5 76 0.5 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 0.025 20-21 0.075 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 0.025 38-39 0.05 40-41 0.025 42-43 0.2375 44-45 0.05 46-47 0.0 48-49 0.0 50-51 0.0 52-53 0.2 54-55 0.025 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 0.0125 70-71 0.0 72-73 0.0 74-75 0.0 76-77 0.0 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 9.0 71 18.0 72 7.0 73 20.0 74 10.0 75 11.0 76 16.0 77 9.0 78 19.0 79 13.0 80 16.0 81 20.0 82 18.0 83 18.0 84 14.0 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 3782.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 73.925 #Duplication Level Percentage of deduplicated Percentage of total 1 92.56002705444708 68.425 2 4.328711531958065 6.4 3 0.7778153533987149 1.725 4 0.5410889414947582 1.6 5 0.4734528238079134 1.7500000000000002 6 0.3043625295908015 1.35 7 0.06763611768684477 0.35000000000000003 8 0.16909029421711194 1.0 9 0.0 0.0 >10 0.7439972945552925 10.9 >50 0.0 0.0 >100 0.033818058843422386 6.5 >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 GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGC 260 6.5 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 49 1.225 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 47 1.175 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 41 1.0250000000000001 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 36 0.8999999999999999 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 28 0.7000000000000001 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 23 0.575 No Hit GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 21 0.525 No Hit GGAGTATCCTTGATATATAAATATATAGATAAATAGATTTAAATGGAAAA 20 0.5 No Hit GGGATGGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACGA 15 0.375 No Hit GTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAA 14 0.35000000000000003 No Hit GGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTT 14 0.35000000000000003 No Hit GGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGG 13 0.325 No Hit CAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCT 13 0.325 No Hit GTATTTAGCCTTGCAAGGTGGTCCTTGCTGATTCACACGGGATTCCACGT 13 0.325 No Hit GGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTT 12 0.3 No Hit GGCCTGTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCG 12 0.3 No Hit GGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGC 11 0.27499999999999997 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 11 0.27499999999999997 No Hit GGGGATGGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACG 11 0.27499999999999997 No Hit GGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAA 11 0.27499999999999997 No Hit GGAAAAGAAAGCAAAAGCGATTCCCGTAGTAGCGGCGAGCGAAATGGGAG 11 0.27499999999999997 No Hit GGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAAGGCGATCAAATTC 10 0.25 No Hit GGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAAATGGATTC 8 0.2 No Hit GCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATC 8 0.2 No Hit GGGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTG 8 0.2 No Hit GGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGCA 8 0.2 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 8 0.2 No Hit GGTTTTGAAAAGGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAA 7 0.17500000000000002 No Hit CAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTG 7 0.17500000000000002 No Hit GAGGAAGGGCGTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAGC 6 0.15 No Hit GGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAA 6 0.15 No Hit GGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGGG 6 0.15 No Hit GTATGGAAGGCGATCAAATTCGAGTTCGCGCCGGTAGATACTATCGATTA 6 0.15 No Hit GGAGTCCCATATATATATGTATAAGATGCCAGCCCGGTTTCGTCAACCAT 6 0.15 No Hit GGGAGTATTATGAAAGGAGATTAATCATAGATTATCAAAAACCCTAGAAA 6 0.15 No Hit GGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAACCCTCTTAACT 6 0.15 No Hit GGGTTGTGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGA 6 0.15 No Hit CACGAACGTAATGCTCACAACTTCCCTCTAGATCTAGCTGCTCTTGAAGT 6 0.15 No Hit GGGAAAAGAGGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTT 5 0.125 No Hit GGCTTTAGAAGCCTGTGTACAAGCTCGTAACGAAGGGCGCGATCTTGCTC 5 0.125 No Hit GGGCTCGAGGAGCATATGTACATTTGAACCCTGACTACACATATACACAC 5 0.125 No Hit GGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCG 5 0.125 No Hit GGTTGTGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAG 5 0.125 No Hit GGATACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATG 5 0.125 No Hit GGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTCCT 5 0.125 No Hit GGGGTTGTGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTG 5 0.125 No Hit GGAAGAGCCCGAGCTGCTGCAGCAGGTTTTGAAAAGGGAATCGATCGTGA 5 0.125 No Hit GGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAAA 5 0.125 No Hit GTACAAGCTCGTAACGAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAAT 5 0.125 No Hit GAAGGAACAAACGAGGATAAGATAAAATTGCTTTAAATTTATTTTGCCCA 5 0.125 No Hit GGAAAAGAGGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTTG 5 0.125 No Hit GGGGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCT 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 0.0125 0.0 0.0 0.0 0.0 18-19 0.05 0.0 0.0 0.0 0.0 20-21 0.05 0.0 0.0 0.0 0.0 22-23 0.0625 0.0 0.0 0.0 0.0 24-25 0.075 0.0 0.0 0.0 0.0 26-27 0.075 0.0 0.0 0.0 0.0 28-29 0.075 0.0 0.0 0.0 0.0 30-31 0.075 0.0 0.0 0.0 0.0 32-33 0.075 0.0 0.0 0.0 0.0 34-35 0.075 0.0 0.0 0.0 0.0 36-37 0.075 0.0 0.0 0.0 0.0 38-39 0.075 0.0 0.0 0.0 0.0 40-41 0.1 0.0 0.0 0.0 0.0 42-43 0.1 0.0 0.0 0.0 0.0 44-45 0.1 0.0 0.0 0.0 0.0 46-47 0.1125 0.0 0.0 0.0 0.0 48-49 0.125 0.0 0.0 0.0 0.0 50-51 0.125 0.0 0.0 0.0 0.0 52-53 0.125 0.0 0.0 0.0 0.0 54-55 0.125 0.0 0.0 0.0 0.0 56-57 0.125 0.0 0.0 0.0 0.0 58-59 0.125 0.0 0.0 0.0 0.0 60-61 0.125 0.0 0.0 0.0 0.0 62-63 0.125 0.0 0.0 0.0 0.0 64-65 0.15 0.0 0.0 0.0 0.0 66-67 0.15 0.0 0.0 0.0 0.0 68-69 0.15 0.0 0.0 0.0 0.0 70-71 0.15 0.0 0.0 0.0 0.0 72-73 0.2 0.0 0.0 0.0 0.0 74-75 0.2 0.0 0.0 0.0 0.0 76-77 0.2 0.0 0.0 0.0 0.0 78-79 0.2 0.0 0.0 0.0 0.0 80-81 0.2 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GGAGGAA 15 9.197037E-4 85.825005 1 GGGAGAG 45 4.0017767E-11 76.288895 1 GCAATAC 50 1.0186341E-10 68.66 7 GAGAGCA 50 1.0186341E-10 68.66 3 CAATACA 45 3.807145E-9 66.75278 8 AATACAA 45 3.807145E-9 66.75278 9 GGAGAGC 55 2.382876E-10 62.418182 2 GAGCAAT 55 2.382876E-10 62.418182 5 AGAGCAA 55 2.382876E-10 62.418182 4 AGCAATA 55 2.382876E-10 62.418182 6 AGCATCA 45 2.1282176E-10 46.391895 80-81 AAAGCAT 45 2.1282176E-10 46.391895 78-79 TCACTAG 40 4.107278E-9 46.391888 84-85 CGAAAGC 45 2.4374458E-10 45.773335 76-77 GCCGAAA 45 2.7830538E-10 45.171055 74-75 AGTAGCC 45 3.3833203E-10 44.296776 70-71 CCAGTAG 45 3.8562575E-10 43.732487 68-69 GTCCAGT 45 4.110916E-10 43.455696 66-67 TGCCGCA 45 4.674803E-10 42.912502 44-45 GAAGCGG 45 4.674803E-10 42.912502 32-33 >>END_MODULE Rejected 128356 READS because READLEN < 1 Read 128356 spots for ERR6133471.sra Written 128356 spots for ERR6133471.sra Rejected 128356 READS because READLEN < 1 Read 128356 spots for ERR6133471.sra Written 128356 spots for ERR6133471.sra Rejected 128356 READS because READLEN < 1 Read 128356 spots for ERR6133471.sra Written 128356 spots for ERR6133471.sra Rejected 128356 READS because READLEN < 1 Read 128356 spots for ERR6133471.sra Written 128356 spots for ERR6133471.sra Rejected 128356 READS because READLEN < 1 Read 128356 spots for ERR6133471.sra Written 128356 spots for ERR6133471.sra Rejected 128356 READS because READLEN < 1 Read 128356 spots for ERR6133471.sra Written 128356 spots for ERR6133471.sra Rejected 128356 READS because READLEN < 1 Read 128356 spots for ERR6133471.sra Written 128356 spots for ERR6133471.sra Rejected 128356 READS because READLEN < 1 Read 128356 spots for ERR6133471.sra Written 128356 spots for ERR6133471.sra Rejected 128356 READS because READLEN < 1 Read 128356 spots for ERR6133471.sra Written 128356 spots for ERR6133471.sra Rejected 128356 READS because READLEN < 1 Read 128356 spots for ERR6133471.sra Written 128356 spots for ERR6133471.sra Rejected 128356 READS because READLEN < 1 Read 128356 spots for ERR6133471.sra Written 128356 spots for ERR6133471.sra Rejected 128356 READS because READLEN < 1 Read 128356 spots for ERR6133471.sra Written 128356 spots for ERR6133471.sra Rejected 128356 READS because READLEN < 1 Read 128356 spots for ERR6133471.sra Written 128356 spots for ERR6133471.sra Rejected 128356 READS because READLEN < 1 Read 128356 spots for ERR6133471.sra Written 128356 spots for ERR6133471.sra Rejected 128356 READS because READLEN < 1 Read 128356 spots for ERR6133471.sra Written 128356 spots for ERR6133471.sra Rejected 128358 READS because READLEN < 1 Read 128358 spots for ERR6133471.sra Written 128358 spots for ERR6133471.sra Rejected 128356 READS because READLEN < 1 Read 128356 spots for ERR6133471.sra Written 128356 spots for ERR6133471.sra Rejected 128356 READS because READLEN < 1 Read 128356 spots for ERR6133471.sra Written 128356 spots for ERR6133471.sra Rejected 128356 READS because READLEN < 1 Read 128356 spots for ERR6133471.sra Written 128356 spots for ERR6133471.sra Rejected 128356 READS because READLEN < 1 Read 128356 spots for ERR6133471.sra Written 128356 spots for ERR6133471.sra SRR ids: ['ERR6133471.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_lsmsq9hb ERR6133471.sra spots: 2567122 blocks: [[1, 128356], [128357, 256712], [256713, 385068], [385069, 513424], [513425, 641780], [641781, 770136], [770137, 898492], [898493, 1026848], [1026849, 1155204], [1155205, 1283560], [1283561, 1411916], [1411917, 1540272], [1540273, 1668628], [1668629, 1796984], [1796985, 1925340], [1925341, 2053696], [2053697, 2182052], [2182053, 2310408], [2310409, 2438764], [2438765, 2567122]] ERR6133471 file size 565000 ERR6133471 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 ERR6133471 ERR6133471_1.fastq Input file: ERR6133471_1.fastq trimmed: ERR6133471-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 06:46:47 2024 >> started Sat Dec 7 06:46:48 2024 >> done (1.708s) 2567122 reads processed; of these: 240 ( 0.01%) short reads filtered out after trimming by size control 18 ( 0.00%) empty reads filtered out after trimming by size control 2566864 (99.99%) reads available; of these: 35487 ( 1.38%) trimmed reads available after processing 2531377 (98.62%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 40 0.00% 19 66 0.00% 20 37 0.00% 21 60 0.00% 22 47 0.00% 23 16 0.00% 24 14 0.00% 25 10 0.00% 26 7 0.00% 27 17 0.00% 28 39 0.00% 29 100 0.00% 30 33 0.00% 31 45 0.00% 32 26 0.00% 33 25 0.00% 34 25 0.00% 35 154 0.01% 36 260 0.01% 37 26 0.00% 38 48 0.00% 39 219 0.01% 40 95 0.00% 41 62 0.00% 42 6 0.00% 43 12 0.00% 44 12 0.00% 45 10 0.00% 46 7 0.00% 47 9 0.00% 48 6 0.00% 49 14 0.00% 50 17 0.00% 51 24 0.00% 52 14 0.00% 53 6 0.00% 54 9 0.00% 55 10 0.00% 56 7 0.00% 57 16 0.00% 58 15 0.00% 59 11 0.00% 60 16 0.00% 61 8 0.00% 62 2 0.00% 63 1 0.00% 64 3 0.00% 65 5 0.00% 66 4 0.00% 67 12 0.00% 68 22 0.00% 69 108 0.00% 70 10306 0.40% 71 8629 0.34% 72 9151 0.36% 73 8471 0.33% 74 8704 0.34% 75 8740 0.34% 76 8053 0.31% 77 8086 0.32% 78 9362 0.36% 79 10276 0.40% 80 9635 0.38% 81 11113 0.43% 82 12220 0.48% 83 11096 0.43% 84 10280 0.40% 85 95 0.00% 86 142 0.01% 87 255 0.01% 88 458 0.02% 89 866 0.03% 90 1914 0.07% 91 5911 0.23% 92 22549 0.88% 93 2388695 93.06% 2566864 reads passed initial QC criterion=sequence-density sequence-density=1.07 sequence-density-rank=1 fanout-score=1.99 fanout-score-rank=32 prefix-density=1.07 prefix-fanout=2.0 sequence=CAAGGCTAAATAC criterion=fanout-score sequence-density=0.01 sequence-density-rank=41 fanout-score=113.48 fanout-score-rank=1 prefix-density=0.28 prefix-fanout=2.1 sequence=CAAGTGCGGAGAGGATAACTGCTGAAAGCATATAAGTAGTAAGCCCACCCCAAGATGAGTGCTCTCTCCTCCGACTTCCCTAGAGCCTCCGGTATCACAGCCGAGACAGCGACGGGTTCTCCACCCATACGGGGATGGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACGAGCCGTTTAAATAGGTGTCAAGTGGAAGTGCAGTGATGTATGCAGCTGAGGCATCCTAACGAACGAACGATTTGAACCTTGTTCCTACACGGCCTGATCAAATCGATCAGGCACTTGCCATCTATCTTCATTGTT Started job on | Dec 07 06:47:05 Started mapping on | Dec 07 06:47:05 Finished on | Dec 07 06:47:10 Mapping speed, Million of reads per hour | 1848.14 Number of input reads | 2566864 Average input read length | 92 UNIQUE READS: Uniquely mapped reads number | 1561553 Uniquely mapped reads % | 60.84% Average mapped length | 91.48 Number of splices: Total | 75665 Number of splices: Annotated (sjdb) | 63336 Number of splices: GT/AG | 72793 Number of splices: GC/AG | 1520 Number of splices: AT/AC | 69 Number of splices: Non-canonical | 1283 Mismatch rate per base, % | 0.44% Deletion rate per base | 0.04% Deletion average length | 1.85 Insertion rate per base | 0.02% Insertion average length | 1.93 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 934469 % of reads mapped to multiple loci | 36.41% Number of reads mapped to too many loci | 31791 % of reads mapped to too many loci | 1.24% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.43% % of reads unmapped: other | 0.09% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 70842 70842 70842 N_multimapping 934469 934469 934469 N_noFeature 130364 147658 1494229 N_ambiguous 58723 8736 309 UnstrandedReadsAssigned:1372466 PositiveStrandReadsAssigned:1405159 NegativeStrandReadsAssigned:67015 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=93 echo kmer=89 ERR6133471 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: ERR6133471-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 2,566,864 reads, 1,910,094 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 930 rounds 52973 ERR6133471.ke.tsv 35125 ERR6133471.se.tsv 88098 total ==> ERR6133471.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 73 37.1457 PNS24243 293 194 0 0 KQK14069 1603 1504 36.0787 16.7473 KQK14071 474 375 0 0 ==> ERR6133471.se.tsv <== BRADI_1g14170v3 43 BRADI_1g53295v3 6 BRADI_1g59795v3 8 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 28 BRADI_1g74790v3 12 BRADI_1g09890v3 0 BRADI_1g77505v3 31 BRADI_1g48960v3 0 ERR6133471 completed mapping pipeline successfully