Starting /dee2/code/volunteer_pipeline.sh ERR6133524 current disk space = 1544423219200 free memory = 1441228444 ERR6133524 SRAfilesize efb857a6e8b1f067ba6f15e72f738530 ERR6133524.sra ERR6133524.sra file validated ERR6133524 is single end ERR6133524 is conventional basespace ERR6133524 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133524_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 36.64175 37.0 37.0 37.0 37.0 37.0 2 36.81475 37.0 37.0 37.0 37.0 37.0 3 36.55525 37.0 37.0 37.0 37.0 37.0 4 35.90825 37.0 37.0 37.0 33.0 37.0 5 36.01175 37.0 37.0 37.0 33.0 37.0 6 36.29825 37.0 37.0 37.0 33.0 37.0 7 38.28775 40.0 37.0 40.0 37.0 40.0 8 38.3195 40.0 37.0 40.0 37.0 40.0 9 38.34625 40.0 37.0 40.0 37.0 40.0 10-11 38.3095 40.0 37.0 40.0 37.0 40.0 12-13 38.19075 40.0 37.0 40.0 37.0 40.0 14-15 38.174625 40.0 37.0 40.0 37.0 40.0 16-17 38.123999999999995 40.0 37.0 40.0 37.0 40.0 18-19 38.101375 40.0 37.0 40.0 37.0 40.0 20-21 38.0095 40.0 37.0 40.0 37.0 40.0 22-23 38.186125000000004 40.0 37.0 40.0 37.0 40.0 24-25 38.018125 40.0 37.0 40.0 37.0 40.0 26-27 37.987875 40.0 37.0 40.0 37.0 40.0 28-29 37.973 40.0 37.0 40.0 37.0 40.0 30-31 37.991125 40.0 37.0 40.0 37.0 40.0 32-33 38.023125 40.0 37.0 40.0 37.0 40.0 34-35 37.961 38.5 37.0 40.0 37.0 40.0 36-37 37.902125 37.0 37.0 40.0 37.0 40.0 38-39 37.801625 37.0 37.0 40.0 37.0 40.0 40-41 37.627250000000004 37.0 37.0 40.0 37.0 40.0 42-43 37.5845 37.0 37.0 40.0 37.0 40.0 44-45 37.325375 37.0 37.0 40.0 35.0 40.0 46-47 37.16975 37.0 37.0 40.0 33.0 40.0 48-49 37.05525 37.0 37.0 38.5 33.0 40.0 50-51 36.901625 37.0 37.0 37.0 33.0 40.0 52-53 36.43875 37.0 37.0 37.0 33.0 40.0 54-55 36.41575 37.0 37.0 37.0 33.0 40.0 56-57 36.250125 37.0 37.0 37.0 33.0 38.5 58-59 35.897125 37.0 37.0 37.0 33.0 37.0 60-61 35.95075 37.0 37.0 37.0 33.0 37.0 62-63 35.827625 37.0 37.0 37.0 33.0 37.0 64-65 35.769375 37.0 37.0 37.0 33.0 37.0 66-67 35.740875 37.0 37.0 37.0 33.0 37.0 68-69 34.84975 35.0 35.0 37.0 33.0 37.0 70-71 34.984483040201 37.0 33.0 37.0 33.0 37.0 72-73 35.48384576915968 37.0 33.0 37.0 33.0 37.0 74-75 35.44516952136283 37.0 33.0 37.0 33.0 37.0 76-77 35.41452316812899 37.0 33.0 37.0 33.0 37.0 78-79 35.362916843010474 37.0 33.0 37.0 33.0 37.0 80-81 35.296889903842455 37.0 33.0 37.0 33.0 37.0 82-83 35.10821842502651 37.0 33.0 37.0 33.0 37.0 84-85 34.93074903126688 37.0 33.0 37.0 33.0 37.0 86-87 34.84741721854304 37.0 33.0 37.0 33.0 37.0 88-89 34.91562913907285 37.0 33.0 37.0 33.0 37.0 90-91 34.878807947019865 37.0 33.0 37.0 33.0 37.0 92-93 34.81854304635762 37.0 33.0 37.0 33.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 21 5.0 22 3.0 23 4.0 24 5.0 25 5.0 26 10.0 27 14.0 28 23.0 29 22.0 30 25.0 31 44.0 32 50.0 33 69.0 34 116.0 35 306.0 36 1121.0 37 1381.0 38 776.0 39 21.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 88.6 2.9250000000000003 2.825 5.65 2 74.97500000000001 14.799999999999999 6.4750000000000005 3.75 3 35.4 39.324999999999996 13.225000000000001 12.049999999999999 4 32.925 29.025000000000002 18.4 19.650000000000002 5 25.1 30.725 26.325 17.849999999999998 6 20.3 38.2 24.625 16.875 7 34.175 28.599999999999998 21.15 16.075 8 30.099999999999998 31.65 23.5 14.75 9 27.800000000000004 27.975 26.3 17.925 10-11 25.324999999999996 27.900000000000002 28.549999999999997 18.224999999999998 12-13 28.6625 25.7625 27.487499999999997 18.087500000000002 14-15 21.7 31.6875 29.099999999999998 17.5125 16-17 23.2375 32.625 25.4 18.7375 18-19 22.8625 28.375 27.5625 21.2 20-21 24.953095684803 26.391494684177612 28.55534709193246 20.10006253908693 22-23 26.8 24.212500000000002 27.55 21.4375 24-25 25.85 26.424999999999997 28.4125 19.3125 26-27 26.2875 25.424999999999997 30.25 18.0375 28-29 25.85 26.674999999999997 27.1125 20.3625 30-31 26.95336917114639 25.978247280910118 26.828353544193025 20.24003000375047 32-33 23.849999999999998 28.425 28.1875 19.537499999999998 34-35 24.349999999999998 26.075 27.975 21.6 36-37 23.3625 25.224999999999998 29.912499999999998 21.5 38-39 25.7875 25.35 30.562499999999996 18.3 40-41 26.969242310577645 26.156539134783696 26.76919229807452 20.10502625656414 42-43 25.05 29.312500000000004 26.6625 18.975 44-45 22.975 27.037499999999998 28.525 21.462500000000002 46-47 24.349999999999998 25.4875 28.012500000000003 22.15 48-49 25.137500000000003 24.9 30.975 18.987499999999997 50-51 25.4375 27.474999999999998 28.875 18.212500000000002 52-53 25.24479035902586 29.16143610343962 26.18629173989455 19.40748179763997 54-55 23.5125 29.675 28.012500000000003 18.8 56-57 25.2125 26.3625 27.1375 21.2875 58-59 24.8125 26.125 27.6125 21.45 60-61 23.5625 26.887499999999996 29.4375 20.1125 62-63 23.075000000000003 28.8375 30.3 17.7875 64-65 23.625 28.65 28.4375 19.287499999999998 66-67 23.599999999999998 28.3375 28.7 19.3625 68-69 23.0625 27.325 27.2625 22.35 70-71 24.837092731829575 27.380952380952383 27.644110275689222 20.13784461152882 72-73 26.093533341737047 25.211143325349806 28.223874952729105 20.47144838018404 74-75 23.857287963433215 28.059928897917725 27.92026409344845 20.162519045200607 76-77 22.46228586039376 27.703912042955764 28.56047046791102 21.273331628739452 78-79 23.742765273311896 25.594855305466236 30.559485530546628 20.10289389067524 80-81 24.607193870925855 28.61965978444358 28.86638098948189 17.906765355148682 82-83 23.750164020469754 26.623802650570795 29.79923894502034 19.826794383939117 84-85 23.71760973030143 24.25965097831835 30.51295610787943 21.509783183500794 86-87 22.450331125827812 27.09933774834437 31.13907284768212 19.311258278145697 88-89 21.311258278145694 29.562913907284766 30.317880794701985 18.807947019867548 90-91 26.079470198675498 27.933774834437088 27.072847682119207 18.91390728476821 92-93 23.24503311258278 30.741721854304636 27.52317880794702 18.490066225165563 >>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 3.5 18 4.5 19 1.0 20 1.0 21 3.0 22 3.0 23 6.5 24 9.5 25 6.5 26 8.0 27 11.0 28 16.0 29 22.0 30 23.0 31 30.5 32 45.0 33 57.5 34 66.5 35 82.0 36 121.5 37 162.5 38 183.0 39 172.5 40 185.5 41 213.0 42 205.5 43 202.0 44 190.5 45 177.0 46 235.0 47 250.0 48 202.0 49 190.0 50 183.0 51 176.5 52 163.0 53 168.5 54 145.5 55 82.5 56 55.0 57 56.0 58 43.5 59 29.5 60 24.5 61 18.0 62 15.5 63 12.0 64 12.5 65 13.0 66 9.5 67 11.5 68 9.0 69 4.5 70 3.5 71 3.0 72 2.0 73 0.5 74 1.0 75 1.5 76 0.5 77 0.5 78 0.5 79 0.5 80 0.5 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 0.0625 22-23 0.0 24-25 0.0 26-27 0.0 28-29 0.0 30-31 0.0125 32-33 0.0 34-35 0.0 36-37 0.0 38-39 0.0 40-41 0.025 42-43 0.0 44-45 0.0 46-47 0.0 48-49 0.0 50-51 0.0 52-53 0.42500000000000004 54-55 0.0 56-57 0.0 58-59 0.0 60-61 0.0 62-63 0.0 64-65 0.0 66-67 0.0 68-69 0.0 70-71 0.0 72-73 0.0 74-75 0.0 76-77 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 20.0 71 8.0 72 11.0 73 15.0 74 16.0 75 15.0 76 8.0 77 8.0 78 23.0 79 18.0 80 15.0 81 24.0 82 17.0 83 13.0 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 3775.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 76.64999999999999 #Duplication Level Percentage of deduplicated Percentage of total 1 91.51989562948467 70.15 2 5.185909980430528 7.95 3 1.0437051532941943 2.4 4 0.4892367906066536 1.5 5 0.42400521852576645 1.625 6 0.228310502283105 1.05 7 0.16307893020221786 0.8750000000000001 8 0.09784735812133072 0.6 9 0.06523157208088715 0.44999999999999996 >10 0.7827788649706457 13.4 >50 0.0 0.0 >100 0.0 0.0 >500 0.0 0.0 >1k 0.0 0.0 >5k 0.0 0.0 >10k+ 0.0 0.0 >>END_MODULE >>Overrepresented sequences fail #Sequence Count Percentage Possible Source GGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGG 49 1.225 No Hit GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 46 1.15 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 33 0.8250000000000001 No Hit GGCCTGTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCG 33 0.8250000000000001 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 30 0.75 No Hit GGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGGG 29 0.7250000000000001 No Hit GGGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTG 28 0.7000000000000001 No Hit GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGC 28 0.7000000000000001 No Hit GTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAA 26 0.65 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 26 0.65 No Hit GGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTT 24 0.6 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 24 0.6 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 23 0.575 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 16 0.4 No Hit GGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTT 15 0.375 No Hit GGCTGCTTGGCCTGTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTA 14 0.35000000000000003 No Hit GTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCT 14 0.35000000000000003 No Hit GGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAA 14 0.35000000000000003 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 13 0.325 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 11 0.27499999999999997 No Hit GGAAGAGACTTATAATATTGTGGCTGCTCATGGTTATTTTGGCCGATTAA 10 0.25 No Hit GGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCG 10 0.25 No Hit GGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTCCT 10 0.25 No Hit GGGCAAGGAGAAGTACAAGTGCGGATCCAACGTCTTCTGGAAATGGTGAA 10 0.25 No Hit GGGATGGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACGA 9 0.22499999999999998 No Hit GGTGGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGC 9 0.22499999999999998 No Hit GGGAAAAGAGGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTT 8 0.2 No Hit GGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGC 8 0.2 No Hit GTATGGAAGGCGATCAAATTCGAGTTCGCGCCGGTAGATACTATCGATTA 8 0.2 No Hit GGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAAGGCGATCAAATTC 7 0.17500000000000002 No Hit GGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAA 7 0.17500000000000002 No Hit GGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTG 7 0.17500000000000002 No Hit GGAGTATCCTTGATATATAAATATATAGATAAATAGATTTAAATGGAAAA 7 0.17500000000000002 No Hit GGTTTTGAAAAGGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAA 7 0.17500000000000002 No Hit GGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAA 6 0.15 No Hit GGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGT 6 0.15 No Hit CAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATAT 6 0.15 No Hit GGGGATGGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACG 6 0.15 No Hit GGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAAA 6 0.15 No Hit GGAGAAGTACAAGTGCGGATCCAACGTCTTCTGGAAATGGTGAAGATGAT 6 0.15 No Hit GAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGC 6 0.15 No Hit GCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATC 5 0.125 No Hit GGGGCAGAGGGAATTTCCGGTGGAGCGGTGAAATGCATTGAGATCGGAAA 5 0.125 No Hit GGAAGGGCGTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAGCAT 5 0.125 No Hit GGATACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATG 5 0.125 No Hit GGGAGTATTATGAAAGGAGATTAATCATAGATTATCAAAAACCCTAGAAA 5 0.125 No Hit GGAGTACGGTAGGGGCAGAGGGAATTTCCGGTGGAGCGGTGAAATGCATT 5 0.125 No Hit GGAATAAGAATAAATCGCAACTCCTTTCCACTACACATAAAAATTGATTT 5 0.125 No Hit GGATTTGAAGAAAAAAAAGACTTCGATTCATTTTCTATTTATTTCGTTAG 5 0.125 No Hit GGCATATGCCAGCTCTGACCGAAATCTTTGGGGATGATTCTGTATTACAA 5 0.125 No Hit GGAAAAGAGGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTTG 5 0.125 No Hit GGGCACTGTAGCCAGTGTGTCAGTCGTTGTTAAATTACAGGTTGAGATCA 5 0.125 No Hit GGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTG 5 0.125 No Hit GGAAAAGAAAGCAAAAGCGATTCCCGTAGTAGCGGCGAGCGAAATGGGAG 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 0.025 0.0 0.0 0.0 0.0 22-23 0.025 0.0 0.0 0.0 0.0 24-25 0.025 0.0 0.0 0.0 0.0 26-27 0.025 0.0 0.0 0.0 0.0 28-29 0.025 0.0 0.0 0.0 0.0 30-31 0.025 0.0 0.0 0.0 0.0 32-33 0.025 0.0 0.0 0.0 0.0 34-35 0.025 0.0 0.0 0.0 0.0 36-37 0.037500000000000006 0.0 0.0 0.0 0.0 38-39 0.0625 0.0 0.0 0.0 0.0 40-41 0.0875 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 0.1 0.0 0.0 0.0 0.0 48-49 0.1 0.0 0.0 0.0 0.0 50-51 0.1 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 0.125 0.0 0.0 0.0 0.0 66-67 0.1375 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 0.1875 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 GGCGTGG 15 9.309663E-4 85.5625 2 GGGCGTG 20 0.002916316 64.171875 1 >>END_MODULE Rejected 71228 READS because READLEN < 1 Read 71228 spots for ERR6133524.sra Written 71228 spots for ERR6133524.sra Rejected 71228 READS because READLEN < 1 Read 71228 spots for ERR6133524.sra Written 71228 spots for ERR6133524.sra Rejected 71228 READS because READLEN < 1 Read 71228 spots for ERR6133524.sra Written 71228 spots for ERR6133524.sra Rejected 71228 READS because READLEN < 1 Read 71228 spots for ERR6133524.sra Written 71228 spots for ERR6133524.sra Rejected 71228 READS because READLEN < 1 Read 71228 spots for ERR6133524.sra Written 71228 spots for ERR6133524.sra Rejected 71228 READS because READLEN < 1 Read 71228 spots for ERR6133524.sra Written 71228 spots for ERR6133524.sra Rejected 71228 READS because READLEN < 1 Read 71228 spots for ERR6133524.sra Written 71228 spots for ERR6133524.sra Rejected 71228 READS because READLEN < 1 Read 71228 spots for ERR6133524.sra Written 71228 spots for ERR6133524.sra Rejected 71228 READS because READLEN < 1 Read 71228 spots for ERR6133524.sra Written 71228 spots for ERR6133524.sra Rejected 71228 READS because READLEN < 1 Read 71228 spots for ERR6133524.sra Written 71228 spots for ERR6133524.sra Rejected 71228 READS because READLEN < 1 Read 71228 spots for ERR6133524.sra Written 71228 spots for ERR6133524.sra Rejected 71228 READS because READLEN < 1 Read 71228 spots for ERR6133524.sra Written 71228 spots for ERR6133524.sra Rejected 71228 READS because READLEN < 1 Read 71228 spots for ERR6133524.sra Written 71228 spots for ERR6133524.sra Rejected 71228 READS because READLEN < 1 Read 71228 spots for ERR6133524.sra Written 71228 spots for ERR6133524.sra Rejected 71228 READS because READLEN < 1 Read 71228 spots for ERR6133524.sra Written 71228 spots for ERR6133524.sra Rejected 71228 READS because READLEN < 1 Read 71228 spots for ERR6133524.sra Written 71228 spots for ERR6133524.sra Rejected 71228 READS because READLEN < 1 Read 71228 spots for ERR6133524.sra Written 71228 spots for ERR6133524.sra Rejected 71228 READS because READLEN < 1 Read 71228 spots for ERR6133524.sra Written 71228 spots for ERR6133524.sra Rejected 71232 READS because READLEN < 1 Read 71232 spots for ERR6133524.sra Written 71232 spots for ERR6133524.sra Rejected 71228 READS because READLEN < 1 Read 71228 spots for ERR6133524.sra Written 71228 spots for ERR6133524.sra SRR ids: ['ERR6133524.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_hjj4yd8z ERR6133524.sra spots: 1424564 blocks: [[1, 71228], [71229, 142456], [142457, 213684], [213685, 284912], [284913, 356140], [356141, 427368], [427369, 498596], [498597, 569824], [569825, 641052], [641053, 712280], [712281, 783508], [783509, 854736], [854737, 925964], [925965, 997192], [997193, 1068420], [1068421, 1139648], [1139649, 1210876], [1210877, 1282104], [1282105, 1353332], [1353333, 1424564]] ERR6133524 file size 312209 ERR6133524 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 ERR6133524 ERR6133524_1.fastq Input file: ERR6133524_1.fastq trimmed: ERR6133524-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 07:54:40 2024 >> started Sat Dec 7 07:54:46 2024 >> done (5.895s) 1424564 reads processed; of these: 300 ( 0.02%) short reads filtered out after trimming by size control 12 ( 0.00%) empty reads filtered out after trimming by size control 1424252 (99.98%) reads available; of these: 7458 ( 0.52%) trimmed reads available after processing 1416794 (99.48%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 49 0.00% 19 107 0.01% 20 32 0.00% 21 23 0.00% 22 27 0.00% 23 8 0.00% 24 12 0.00% 25 10 0.00% 26 12 0.00% 27 15 0.00% 28 17 0.00% 29 137 0.01% 30 11 0.00% 31 18 0.00% 32 35 0.00% 33 17 0.00% 34 16 0.00% 35 131 0.01% 36 190 0.01% 37 10 0.00% 38 57 0.00% 39 89 0.01% 40 97 0.01% 41 31 0.00% 42 7 0.00% 43 12 0.00% 44 16 0.00% 45 15 0.00% 46 6 0.00% 47 7 0.00% 48 1 0.00% 49 6 0.00% 50 11 0.00% 51 74 0.01% 52 16 0.00% 53 7 0.00% 54 2 0.00% 55 5 0.00% 56 8 0.00% 57 11 0.00% 58 12 0.00% 59 7 0.00% 60 18 0.00% 61 9 0.00% 62 0 0.00% 63 2 0.00% 64 1 0.00% 65 3 0.00% 66 3 0.00% 67 5 0.00% 68 11 0.00% 69 48 0.00% 70 6757 0.47% 71 5944 0.42% 72 6157 0.43% 73 5612 0.39% 74 5851 0.41% 75 5644 0.40% 76 4812 0.34% 77 5024 0.35% 78 5680 0.40% 79 6409 0.45% 80 5600 0.39% 81 6772 0.48% 82 7265 0.51% 83 6686 0.47% 84 5961 0.42% 85 26 0.00% 86 25 0.00% 87 61 0.00% 88 116 0.01% 89 163 0.01% 90 378 0.03% 91 1035 0.07% 92 3851 0.27% 93 1326949 93.17% 1424252 reads passed initial QC criterion=sequence-density sequence-density=1.03 sequence-density-rank=1 fanout-score=1.96 fanout-score-rank=29 prefix-density=1.03 prefix-fanout=2.0 sequence=CAAGGCTAAATAC criterion=fanout-score sequence-density=0.02 sequence-density-rank=29 fanout-score=48.18 fanout-score-rank=1 prefix-density=0.15 prefix-fanout=6.5 sequence=AAAAGAAGGGGTGTTCCATCTCCGGACGACGATCCTGCCTGCAGAGGAAGACATGCCGGCGATCATGTCGAGCTTCAAGAAGTTCAACGACTCATTCATGGAGCAATACCAAGACTACTCCAGGCTGTGATGTGAAGAGGGAAACAACGAGGTCATCATCGACATGATATATTGCTGCTATTTTCCACCAGCGATTAAAAGTTAAAAAATTTAGCTGTAAGCTGTAACTATCTTGAAGAAACTAAACTGGTTGCTGTGCTT Started job on | Dec 07 07:56:17 Started mapping on | Dec 07 07:56:18 Finished on | Dec 07 07:57:00 Mapping speed, Million of reads per hour | 122.08 Number of input reads | 1424252 Average input read length | 91 UNIQUE READS: Uniquely mapped reads number | 934951 Uniquely mapped reads % | 65.65% Average mapped length | 91.46 Number of splices: Total | 61308 Number of splices: Annotated (sjdb) | 52322 Number of splices: GT/AG | 59541 Number of splices: GC/AG | 1197 Number of splices: AT/AC | 26 Number of splices: Non-canonical | 544 Mismatch rate per base, % | 0.41% Deletion rate per base | 0.04% Deletion average length | 1.84 Insertion rate per base | 0.02% Insertion average length | 1.87 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 430905 % of reads mapped to multiple loci | 30.25% Number of reads mapped to too many loci | 13973 % of reads mapped to too many loci | 0.98% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 3.07% % of reads unmapped: other | 0.05% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 58396 58396 58396 N_multimapping 430905 430905 430905 N_noFeature 66628 75699 894135 N_ambiguous 36879 5051 196 UnstrandedReadsAssigned:831444 PositiveStrandReadsAssigned:854201 NegativeStrandReadsAssigned:40620 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=93 echo kmer=89 ERR6133524 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: ERR6133524-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 1,424,252 reads, 1,159,355 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 896 rounds 52973 ERR6133524.ke.tsv 35125 ERR6133524.se.tsv 88098 total ==> ERR6133524.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 36 30.1417 PNS24243 293 194 0 0 KQK14069 1603 1504 30 22.9136 KQK14071 474 375 0 0 ==> ERR6133524.se.tsv <== BRADI_1g14170v3 30 BRADI_1g53295v3 3 BRADI_1g59795v3 3 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 18 BRADI_1g74790v3 9 BRADI_1g09890v3 0 BRADI_1g77505v3 19 BRADI_1g48960v3 0 ERR6133524 completed mapping pipeline successfully