Starting /dee2/code/volunteer_pipeline.sh ERR6133522 current disk space = 1544430514176 free memory = 1599178976 ERR6133522 SRAfilesize 715fe63d7b82dfa138c700d5fd654b10 ERR6133522.sra ERR6133522.sra file validated ERR6133522 is single end ERR6133522 is conventional basespace ERR6133522 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133522_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 36.60225 37.0 37.0 37.0 37.0 37.0 2 36.79725 37.0 37.0 37.0 37.0 37.0 3 36.50825 37.0 37.0 37.0 37.0 37.0 4 35.9915 37.0 37.0 37.0 33.0 37.0 5 36.03275 37.0 37.0 37.0 33.0 37.0 6 36.331 37.0 37.0 37.0 37.0 37.0 7 38.3445 40.0 37.0 40.0 37.0 40.0 8 38.33 40.0 37.0 40.0 37.0 40.0 9 38.37625 40.0 37.0 40.0 37.0 40.0 10-11 38.288375 40.0 37.0 40.0 37.0 40.0 12-13 38.236625000000004 40.0 37.0 40.0 37.0 40.0 14-15 38.211 40.0 37.0 40.0 37.0 40.0 16-17 38.127250000000004 40.0 37.0 40.0 37.0 40.0 18-19 38.079 40.0 37.0 40.0 37.0 40.0 20-21 37.970625 40.0 37.0 40.0 35.0 40.0 22-23 38.188125 40.0 37.0 40.0 37.0 40.0 24-25 38.109624999999994 40.0 37.0 40.0 37.0 40.0 26-27 37.972375 40.0 37.0 40.0 35.0 40.0 28-29 37.92775 40.0 37.0 40.0 37.0 40.0 30-31 38.019999999999996 40.0 37.0 40.0 37.0 40.0 32-33 38.086749999999995 40.0 37.0 40.0 37.0 40.0 34-35 38.015375000000006 40.0 37.0 40.0 37.0 40.0 36-37 37.883125 37.0 37.0 40.0 37.0 40.0 38-39 37.79425 37.0 37.0 40.0 37.0 40.0 40-41 37.646625 37.0 37.0 40.0 37.0 40.0 42-43 37.57025 37.0 37.0 40.0 37.0 40.0 44-45 37.351625 37.0 37.0 40.0 35.0 40.0 46-47 37.184875 37.0 37.0 40.0 33.0 40.0 48-49 37.06325 37.0 37.0 38.5 33.0 40.0 50-51 36.8465 37.0 37.0 37.0 33.0 40.0 52-53 36.39675 37.0 37.0 37.0 33.0 40.0 54-55 36.414625 37.0 37.0 37.0 33.0 40.0 56-57 36.254374999999996 37.0 37.0 37.0 33.0 38.5 58-59 35.92175 37.0 37.0 37.0 33.0 37.0 60-61 36.02975 37.0 37.0 37.0 33.0 37.0 62-63 35.87675 37.0 37.0 37.0 33.0 37.0 64-65 35.82825 37.0 37.0 37.0 33.0 37.0 66-67 35.793 37.0 37.0 37.0 33.0 37.0 68-69 34.939125000000004 35.0 35.0 37.0 33.0 37.0 70-71 35.105519332161684 37.0 33.0 37.0 33.0 37.0 72-73 35.51621412611448 37.0 33.0 37.0 33.0 37.0 74-75 35.49252329013886 37.0 35.0 37.0 33.0 37.0 76-77 35.50136854240385 37.0 33.0 37.0 33.0 37.0 78-79 35.41186365618823 37.0 33.0 37.0 33.0 37.0 80-81 35.31811198373698 37.0 33.0 37.0 33.0 37.0 82-83 35.143754210510565 37.0 33.0 37.0 33.0 37.0 84-85 35.0006992394397 37.0 33.0 37.0 33.0 37.0 86-87 34.96625686633534 37.0 33.0 37.0 33.0 37.0 88-89 34.88739210044468 37.0 33.0 37.0 33.0 37.0 90-91 34.88778446246403 37.0 33.0 37.0 33.0 37.0 92-93 34.81572063824222 37.0 33.0 37.0 33.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 2.0 21 6.0 22 8.0 23 5.0 24 5.0 25 3.0 26 3.0 27 13.0 28 15.0 29 23.0 30 33.0 31 35.0 32 55.0 33 61.0 34 114.0 35 295.0 36 1116.0 37 1420.0 38 766.0 39 22.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 87.825 2.475 3.325 6.375 2 73.125 16.225 7.049999999999999 3.5999999999999996 3 36.05 38.525 13.625000000000002 11.799999999999999 4 33.0 29.599999999999998 17.95 19.45 5 24.5 30.525000000000002 28.525 16.45 6 19.15 38.925 26.450000000000003 15.475 7 37.675 28.7 19.025 14.6 8 28.050000000000004 31.7 23.575 16.675 9 25.874999999999996 29.099999999999998 27.500000000000004 17.525 10-11 24.4875 28.6125 27.875 19.025 12-13 27.125 26.6625 28.012500000000003 18.2 14-15 22.35 32.7875 27.8125 17.05 16-17 23.4125 32.15 25.0375 19.400000000000002 18-19 22.165270658832352 28.153519189898734 28.291036379547442 21.390173771721464 20-21 23.973973973973976 28.22822822822823 28.153153153153156 19.644644644644647 22-23 27.500000000000004 23.4125 27.925 21.1625 24-25 26.775 25.525 27.375 20.325 26-27 25.8625 25.8625 31.075000000000003 17.2 28-29 27.1 28.050000000000004 26.400000000000002 18.45 30-31 27.294323580895224 26.51912978244561 27.494373593398347 18.692173043260816 32-33 23.875 27.950000000000003 27.200000000000003 20.974999999999998 34-35 23.9375 27.437499999999996 26.937499999999996 21.6875 36-37 24.2875 25.7 28.712500000000002 21.3 38-39 26.3625 25.9625 30.2375 17.4375 40-41 28.325 24.7375 25.937500000000004 21.0 42-43 25.662499999999998 30.125 25.387500000000003 18.825 44-45 22.6 27.725 28.4125 21.2625 46-47 23.974999999999998 24.2875 28.0875 23.65 48-49 24.025 25.1875 31.7625 19.025 50-51 24.525 27.237499999999997 28.5625 19.675 52-53 24.984322087043772 28.84735983945817 26.26363978427192 19.904678289226137 54-55 24.1125 30.599999999999998 27.8375 17.45 56-57 26.1625 25.7625 27.8375 20.2375 58-59 24.5625 24.575 28.9125 21.95 60-61 24.762500000000003 26.400000000000002 28.9375 19.900000000000002 62-63 21.587500000000002 29.549999999999997 31.2 17.6625 64-65 23.625 29.5 27.8125 19.0625 66-67 23.4625 28.762500000000003 28.3375 19.4375 68-69 21.85 27.6 27.1 23.45 70-71 24.677439559063007 27.157710134034822 26.982337467117624 21.182512839784543 72-73 26.2700113450145 25.185932182024455 27.80789108786084 20.736165385100215 74-75 23.261117445838085 28.683643734955023 28.683643734955023 19.37159508425187 76-77 23.011218765935748 27.689954105048443 28.467618561958187 20.831208567057622 78-79 24.118476727785616 25.567380433388898 30.19617899730735 20.117963841518144 80-81 23.540028361479955 30.024494005414464 28.79979373469125 17.635683898414335 82-83 23.637071651090345 26.20716510903427 29.672897196261683 20.482866043613708 84-85 24.392474523125163 23.151293441337863 31.578259733472695 20.87797230206428 86-87 21.91995814805127 27.543813758828144 31.192780538843838 19.343447554276747 88-89 20.612084750196182 30.970442061208477 29.453308919696575 18.96416426889877 90-91 26.1443892231232 26.222861626994508 28.995553230447292 18.637195919434998 92-93 23.43709128956317 30.5911587758305 27.91001831022757 18.06173162437876 >>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 0.5 17 8.0 18 10.0 19 3.0 20 1.5 21 2.0 22 2.5 23 7.0 24 7.5 25 5.0 26 8.5 27 13.5 28 22.0 29 28.5 30 32.0 31 40.0 32 46.5 33 52.5 34 58.5 35 68.5 36 111.5 37 146.5 38 168.5 39 176.0 40 180.0 41 193.5 42 210.0 43 231.0 44 204.0 45 201.5 46 262.0 47 258.5 48 198.0 49 163.5 50 165.0 51 178.0 52 158.0 53 165.0 54 158.0 55 92.0 56 59.5 57 59.5 58 48.0 59 29.0 60 19.5 61 15.5 62 10.5 63 10.5 64 12.5 65 12.0 66 10.0 67 8.0 68 7.0 69 8.5 70 6.0 71 2.0 72 1.5 73 0.5 74 0.0 75 0.0 76 0.0 77 0.0 78 0.0 79 0.5 80 0.5 81 0.5 82 1.0 83 0.5 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 0.0125 20-21 0.1 22-23 0.0 24-25 0.0 26-27 0.0 28-29 0.0 30-31 0.025 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 0.3375 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 17.0 71 12.0 72 9.0 73 10.0 74 11.0 75 14.0 76 10.0 77 14.0 78 7.0 79 11.0 80 13.0 81 14.0 82 12.0 83 15.0 84 8.0 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 3823.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 70.475 #Duplication Level Percentage of deduplicated Percentage of total 1 90.10287335934729 63.5 2 5.39198297268535 7.6 3 1.4189428875487762 3.0 4 0.7804185881518269 2.1999999999999997 5 0.4966300106420717 1.7500000000000002 6 0.35473572188719404 1.5 7 0.31926214969847466 1.575 8 0.2128414331323164 1.2 9 0.0354735721887194 0.22499999999999998 >10 0.8158921603405462 14.374999999999998 >50 0.0709471443774388 3.075 >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 68 1.7000000000000002 No Hit GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 55 1.375 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 48 1.2 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 45 1.125 No Hit GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGC 43 1.075 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 40 1.0 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 40 1.0 No Hit GTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAA 37 0.9249999999999999 No Hit GGGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTG 32 0.8 No Hit GGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTT 31 0.775 No Hit GGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTT 30 0.75 No Hit GGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGGG 27 0.675 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 26 0.65 No Hit GGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAA 26 0.65 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 20 0.5 No Hit GGCCTGTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCG 18 0.44999999999999996 No Hit GGAGTATCCTTGATATATAAATATATAGATAAATAGATTTAAATGGAAAA 16 0.4 No Hit GGGATGGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACGA 13 0.325 No Hit GGGGATGGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACG 13 0.325 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 13 0.325 No Hit CAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCT 13 0.325 No Hit GGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAA 12 0.3 No Hit GGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCG 12 0.3 No Hit GGAAGAGACTTATAATATTGTGGCTGCTCATGGTTATTTTGGCCGATTAA 10 0.25 No Hit GGAAAAGAAAGCAAAAGCGATTCCCGTAGTAGCGGCGAGCGAAATGGGAG 10 0.25 No Hit GAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGC 9 0.22499999999999998 No Hit GGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAA 8 0.2 No Hit CAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATAT 8 0.2 No Hit GGAAGGGCGTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAGCAT 8 0.2 No Hit GGAAGAGCCCGAGCTGCTGCAGCAGGTTTTGAAAAGGGAATCGATCGTGA 8 0.2 No Hit GGAATAAGAATAAATCGCAACTCCTTTCCACTACACATAAAAATTGATTT 8 0.2 No Hit GGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGC 8 0.2 No Hit GGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAAGGCGATCAAATTC 7 0.17500000000000002 No Hit GGTATTAGTACTATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATC 7 0.17500000000000002 No Hit GGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGT 7 0.17500000000000002 No Hit GGTGGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGC 7 0.17500000000000002 No Hit GGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTCCT 7 0.17500000000000002 No Hit GAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAAT 7 0.17500000000000002 No Hit GGGATTACGACGAGAAAGAAGAAGAAGAAGAAACGCATGGTGCCCTGCTT 7 0.17500000000000002 No Hit GGAGAAGTACAAGTGCGGATCCAACGTCTTCTGGAAATGGTGAAGATGAT 7 0.17500000000000002 No Hit GGGGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCT 7 0.17500000000000002 No Hit GGGGGAGAAGTCTTATGTTATATATGGTAATCGCCTTGCCTATAGTGCCC 6 0.15 No Hit GGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAAATGGATTC 6 0.15 No Hit GGGAAAAGAGGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTT 6 0.15 No Hit GCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATC 6 0.15 No Hit GGCTGCTTGGCCTGTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTA 6 0.15 No Hit GGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACGAGCCGT 6 0.15 No Hit GGTCAAGAGGAAGAGACTTATAATATTGTGGCTGCTCATGGTTATTTTGG 6 0.15 No Hit GTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCT 6 0.15 No Hit GGAAAAGAGGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTTG 6 0.15 No Hit GGTTTTGAAAAGGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAA 6 0.15 No Hit GAGGAAGGGCGTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAGC 5 0.125 No Hit GGAGTGGGGGTGCCATACGCAAAAAGGAAGCGACTCATAGAATGGCAGAG 5 0.125 No Hit GGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGC 5 0.125 No Hit GGATACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATG 5 0.125 No Hit GGGAGGGGCTTGGCTACAATTCCGAATACGCTATTACATGTTTGCGCTAG 5 0.125 No Hit GGGAGTATTATGAAAGGAGATTAATCATAGATTATCAAAAACCCTAGAAA 5 0.125 No Hit GGGGGTGCCATACGCAAAAAGGAAGCGACTCATAGAATGGCAGAGGCAAA 5 0.125 No Hit GGCATATGCCAGCTCTGACCGAAATCTTTGGGGATGATTCTGTATTACAA 5 0.125 No Hit GGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAACCCTCTTAACT 5 0.125 No Hit GGGCTTGGCTACAATTCCGAATACGCTATTACATGTTTGCGCTAGTTTTT 5 0.125 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 5 0.125 No Hit GGGCCATTTGTGGCATGCAGGAAGAGCCCGAGCTGCTGCAGCAGGTTTTG 5 0.125 No Hit GGTGGATACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAA 5 0.125 No Hit GGAGAACGAGTCTTGCACTATGCTGTTGCCCGTCTACCAGTTGACTACGA 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 0.025 0.0 0.0 0.0 0.0 16-17 0.025 0.0 0.0 0.0 0.0 18-19 0.025 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 0.0625 0.0 0.0 0.0 0.0 38-39 0.1125 0.0 0.0 0.0 0.0 40-41 0.125 0.0 0.0 0.0 0.0 42-43 0.125 0.0 0.0 0.0 0.0 44-45 0.125 0.0 0.0 0.0 0.0 46-47 0.125 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 0.125 0.0 0.0 0.0 0.0 66-67 0.125 0.0 0.0 0.0 0.0 68-69 0.125 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 warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position CTAGGCA 15 8.910033E-4 86.5125 4 AGGCACC 15 8.910033E-4 86.5125 6 TACCTAG 15 8.910033E-4 86.5125 1 ACCTAGG 15 8.910033E-4 86.5125 2 CCTAGGC 15 8.910033E-4 86.5125 3 TAGGCAC 15 8.910033E-4 86.5125 5 GGCACCC 20 0.0027914012 64.88438 7 CACCCAG 20 0.0027914012 64.88438 9 GCACCCA 20 0.0027914012 64.88438 8 GATATCA 25 0.006755406 51.907497 6 TGATATC 25 0.006755406 51.907497 5 CTGATAT 25 0.006755406 51.907497 4 GCTGATA 25 0.006755406 51.907497 3 GGGCTGA 25 0.006755406 51.907497 1 >>END_MODULE Rejected 79915 READS because READLEN < 1 Read 79915 spots for ERR6133522.sra Written 79915 spots for ERR6133522.sra Rejected 79915 READS because READLEN < 1 Read 79915 spots for ERR6133522.sra Written 79915 spots for ERR6133522.sra Rejected 79915 READS because READLEN < 1 Read 79915 spots for ERR6133522.sra Written 79915 spots for ERR6133522.sra Rejected 79915 READS because READLEN < 1 Read 79915 spots for ERR6133522.sra Written 79915 spots for ERR6133522.sra Rejected 79915 READS because READLEN < 1 Read 79915 spots for ERR6133522.sra Written 79915 spots for ERR6133522.sra Rejected 79915 READS because READLEN < 1 Read 79915 spots for ERR6133522.sra Written 79915 spots for ERR6133522.sra Rejected 79915 READS because READLEN < 1 Read 79915 spots for ERR6133522.sra Written 79915 spots for ERR6133522.sra Rejected 79915 READS because READLEN < 1 Read 79915 spots for ERR6133522.sra Written 79915 spots for ERR6133522.sra Rejected 79915 READS because READLEN < 1 Read 79915 spots for ERR6133522.sra Written 79915 spots for ERR6133522.sra Rejected 79915 READS because READLEN < 1 Read 79915 spots for ERR6133522.sra Written 79915 spots for ERR6133522.sra Rejected 79915 READS because READLEN < 1 Read 79915 spots for ERR6133522.sra Written 79915 spots for ERR6133522.sra Rejected 79915 READS because READLEN < 1 Read 79915 spots for ERR6133522.sra Written 79915 spots for ERR6133522.sra Rejected 79915 READS because READLEN < 1 Read 79915 spots for ERR6133522.sra Written 79915 spots for ERR6133522.sra Rejected 79915 READS because READLEN < 1 Read 79915 spots for ERR6133522.sra Written 79915 spots for ERR6133522.sra Rejected 79915 READS because READLEN < 1 Read 79915 spots for ERR6133522.sra Written 79915 spots for ERR6133522.sra Rejected 79915 READS because READLEN < 1 Read 79915 spots for ERR6133522.sra Written 79915 spots for ERR6133522.sra Rejected 79915 READS because READLEN < 1 Read 79915 spots for ERR6133522.sra Written 79915 spots for ERR6133522.sra Rejected 79915 READS because READLEN < 1 Read 79915 spots for ERR6133522.sra Written 79915 spots for ERR6133522.sra Rejected 79915 READS because READLEN < 1 Read 79915 spots for ERR6133522.sra Written 79915 spots for ERR6133522.sra Rejected 79923 READS because READLEN < 1 Read 79923 spots for ERR6133522.sra Written 79923 spots for ERR6133522.sra SRR ids: ['ERR6133522.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_glo4ex0o ERR6133522.sra spots: 1598308 blocks: [[1, 79915], [79916, 159830], [159831, 239745], [239746, 319660], [319661, 399575], [399576, 479490], [479491, 559405], [559406, 639320], [639321, 719235], [719236, 799150], [799151, 879065], [879066, 958980], [958981, 1038895], [1038896, 1118810], [1118811, 1198725], [1198726, 1278640], [1278641, 1358555], [1358556, 1438470], [1438471, 1518385], [1518386, 1598308]] ERR6133522 file size 351188 ERR6133522 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 ERR6133522 ERR6133522_1.fastq Input file: ERR6133522_1.fastq trimmed: ERR6133522-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 07:52:22 2024 >> started Sat Dec 7 07:52:23 2024 >> done (0.954s) 1598308 reads processed; of these: 866 ( 0.05%) short reads filtered out after trimming by size control 18 ( 0.00%) empty reads filtered out after trimming by size control 1597424 (99.94%) reads available; of these: 8303 ( 0.52%) trimmed reads available after processing 1589121 (99.48%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 57 0.00% 19 90 0.01% 20 34 0.00% 21 43 0.00% 22 43 0.00% 23 18 0.00% 24 18 0.00% 25 14 0.00% 26 4 0.00% 27 17 0.00% 28 28 0.00% 29 89 0.01% 30 20 0.00% 31 26 0.00% 32 33 0.00% 33 14 0.00% 34 21 0.00% 35 156 0.01% 36 206 0.01% 37 21 0.00% 38 34 0.00% 39 89 0.01% 40 112 0.01% 41 41 0.00% 42 5 0.00% 43 9 0.00% 44 13 0.00% 45 7 0.00% 46 5 0.00% 47 8 0.00% 48 5 0.00% 49 4 0.00% 50 8 0.00% 51 56 0.00% 52 18 0.00% 53 9 0.00% 54 3 0.00% 55 5 0.00% 56 5 0.00% 57 10 0.00% 58 8 0.00% 59 5 0.00% 60 8 0.00% 61 12 0.00% 62 1 0.00% 63 0 0.00% 64 1 0.00% 65 1 0.00% 66 2 0.00% 67 7 0.00% 68 7 0.00% 69 35 0.00% 70 6381 0.40% 71 5112 0.32% 72 5544 0.35% 73 4713 0.30% 74 4876 0.31% 75 4793 0.30% 76 4200 0.26% 77 4396 0.28% 78 4979 0.31% 79 5800 0.36% 80 5094 0.32% 81 5974 0.37% 82 6930 0.43% 83 6223 0.39% 84 5473 0.34% 85 27 0.00% 86 43 0.00% 87 78 0.00% 88 134 0.01% 89 230 0.01% 90 444 0.03% 91 1103 0.07% 92 4416 0.28% 93 1508976 94.46% 1597424 reads passed initial QC criterion=sequence-density sequence-density=0.90 sequence-density-rank=1 fanout-score=1.94 fanout-score-rank=30 prefix-density=0.90 prefix-fanout=1.9 sequence=CAAGGCTAAATAC criterion=fanout-score sequence-density=0.01 sequence-density-rank=28 fanout-score=42.83 fanout-score-rank=1 prefix-density=0.22 prefix-fanout=2.4 sequence=CAAGGAAGGCGTCGCCAACGGAACCCTCAAGCTCGTGGGCGGCCACTACGACTTCGTCTCCGGCAAGTTCGACACATGGGAGCTCTAAGTCCTCTCATCCGGTTAACTCCTATACATACAACGTATACTTATACATACAGATATGGAGATGACCCTACAGATCGATCCATTGATGTGGATGCGATGCCATGGAGTATATGTACTCGCTATTTTCCAGTACTGCATGCCGGATGGCTCGATGTGAATTTGTAATAAGCAATAGAAGTTTCTACCATTTTCTGACGTGGGGTTGTACTTGTGATGCGTAATTTGGTCATCTTGTGACCAAAAGACATCAACTATATAATTATAATACCATTTTCATCAAGACTCT Started job on | Dec 07 07:52:34 Started mapping on | Dec 07 07:52:34 Finished on | Dec 07 07:52:38 Mapping speed, Million of reads per hour | 1437.68 Number of input reads | 1597424 Average input read length | 92 UNIQUE READS: Uniquely mapped reads number | 967474 Uniquely mapped reads % | 60.56% Average mapped length | 91.75 Number of splices: Total | 58581 Number of splices: Annotated (sjdb) | 49796 Number of splices: GT/AG | 57198 Number of splices: GC/AG | 1056 Number of splices: AT/AC | 32 Number of splices: Non-canonical | 295 Mismatch rate per base, % | 0.25% Deletion rate per base | 0.03% Deletion average length | 1.62 Insertion rate per base | 0.01% Insertion average length | 1.76 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 584344 % of reads mapped to multiple loci | 36.58% Number of reads mapped to too many loci | 13416 % of reads mapped to too many loci | 0.84% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.97% % of reads unmapped: other | 0.04% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 45606 45606 45606 N_multimapping 584344 584344 584344 N_noFeature 72381 81528 925204 N_ambiguous 38603 5486 158 UnstrandedReadsAssigned:856490 PositiveStrandReadsAssigned:880460 NegativeStrandReadsAssigned:42112 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=93 echo kmer=89 ERR6133522 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: ERR6133522-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 1,597,424 reads, 1,296,325 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 891 rounds 52973 ERR6133522.ke.tsv 35125 ERR6133522.se.tsv 88098 total ==> ERR6133522.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 42 30.6937 PNS24243 293 194 0 0 KQK14069 1603 1504 87 57.9997 KQK14071 474 375 0 0 ==> ERR6133522.se.tsv <== BRADI_1g14170v3 86 BRADI_1g53295v3 9 BRADI_1g59795v3 9 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 12 BRADI_1g74790v3 3 BRADI_1g09890v3 0 BRADI_1g77505v3 19 BRADI_1g48960v3 0 ERR6133522 completed mapping pipeline successfully