Starting /dee2/code/volunteer_pipeline.sh ERR6133553 current disk space = 1544488591360 free memory = 1600995624 ERR6133553 SRAfilesize 8c90c1aac9cd0ea324c741c9c9d72ee0 ERR6133553.sra ERR6133553.sra file validated ERR6133553 is single end ERR6133553 is conventional basespace ERR6133553 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133553_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 33.72525 33.0 33.0 37.0 27.0 37.0 2 35.84475 37.0 37.0 37.0 33.0 37.0 3 35.162 37.0 33.0 37.0 33.0 37.0 4 35.37675 37.0 37.0 37.0 33.0 37.0 5 35.30475 37.0 37.0 37.0 33.0 37.0 6 35.6735 37.0 37.0 37.0 33.0 37.0 7 37.48925 40.0 37.0 40.0 33.0 40.0 8 37.51125 40.0 37.0 40.0 33.0 40.0 9 37.51875 40.0 37.0 40.0 33.0 40.0 10-11 37.6335 40.0 37.0 40.0 33.0 40.0 12-13 37.52225 38.5 37.0 40.0 33.0 40.0 14-15 37.530249999999995 37.0 37.0 40.0 33.0 40.0 16-17 37.428125 37.0 37.0 40.0 33.0 40.0 18-19 37.321250000000006 37.0 37.0 40.0 33.0 40.0 20-21 37.124625 37.0 37.0 40.0 33.0 40.0 22-23 37.108125 37.0 37.0 40.0 33.0 40.0 24-25 37.20425 37.0 37.0 40.0 33.0 40.0 26-27 37.291 37.0 37.0 40.0 33.0 40.0 28-29 37.14525 37.0 37.0 40.0 33.0 40.0 30-31 37.039249999999996 37.0 37.0 40.0 33.0 40.0 32-33 36.919624999999996 37.0 37.0 40.0 33.0 40.0 34-35 36.766 37.0 37.0 40.0 33.0 40.0 36-37 36.512625 37.0 37.0 40.0 33.0 40.0 38-39 36.460875 37.0 37.0 40.0 33.0 40.0 40-41 36.165 37.0 37.0 40.0 33.0 40.0 42-43 36.077 37.0 37.0 40.0 33.0 40.0 44-45 35.80175 37.0 33.0 40.0 33.0 40.0 46-47 35.5075 37.0 33.0 37.0 33.0 40.0 48-49 35.5305 37.0 33.0 37.0 33.0 40.0 50-51 35.502125 37.0 33.0 37.0 33.0 40.0 52-53 35.174 37.0 33.0 37.0 27.0 40.0 54-55 35.18675 37.0 33.0 37.0 33.0 40.0 56-57 34.969625 37.0 33.0 37.0 30.0 40.0 58-59 34.19125 37.0 33.0 37.0 27.0 37.0 60-61 34.63325 37.0 33.0 37.0 27.0 37.0 62-63 34.512 37.0 33.0 37.0 27.0 37.0 64-65 34.44375 37.0 33.0 37.0 27.0 37.0 66-67 34.464375000000004 37.0 33.0 37.0 27.0 37.0 68-69 33.653 35.0 33.0 37.0 27.0 37.0 70-71 33.74506588176352 35.0 33.0 37.0 27.0 37.0 72-73 34.08030201206107 37.0 33.0 37.0 27.0 37.0 74-75 34.04010232606868 37.0 33.0 37.0 27.0 37.0 76-77 33.96570198384886 37.0 33.0 37.0 27.0 37.0 78-79 33.97759082837684 37.0 33.0 37.0 27.0 37.0 80-81 33.88367952798932 37.0 33.0 37.0 27.0 37.0 82-83 33.81597693619354 37.0 33.0 37.0 27.0 37.0 84-85 33.85571123980162 37.0 33.0 37.0 27.0 37.0 86-87 33.855232407166966 37.0 33.0 37.0 27.0 37.0 88-89 33.74396260711504 37.0 33.0 37.0 27.0 37.0 90-91 33.46027005972475 37.0 33.0 37.0 27.0 37.0 92-93 33.56881329524799 37.0 33.0 37.0 27.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 8.0 21 18.0 22 18.0 23 10.0 24 26.0 25 40.0 26 36.0 27 39.0 28 68.0 29 62.0 30 88.0 31 123.0 32 143.0 33 158.0 34 226.0 35 450.0 36 823.0 37 970.0 38 673.0 39 21.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 82.075 4.125 5.025 8.774999999999999 2 64.1 20.974999999999998 10.025 4.9 3 34.35 35.35 16.6 13.700000000000001 4 29.4 27.825 20.1 22.675 5 26.05 26.424999999999997 28.925 18.6 6 18.675 39.625 25.05 16.650000000000002 7 37.574999999999996 26.775 19.575 16.075 8 28.425 27.875 24.025 19.675 9 22.475 30.725 28.1 18.7 10-11 22.4875 29.75 29.475 18.2875 12-13 23.6125 28.749999999999996 26.387500000000003 21.25 14-15 20.3125 33.5875 27.9375 18.1625 16-17 24.9375 30.5 23.7625 20.8 18-19 24.315539442430303 26.515814476809602 30.16627078384798 19.002375296912113 20-21 26.278924327704818 24.853033145716072 29.9437148217636 18.92432770481551 22-23 28.5625 22.125 29.125 20.1875 24-25 23.3875 24.8125 29.862499999999997 21.9375 26-27 25.8625 23.5875 30.75 19.8 28-29 24.0375 27.85 29.099999999999998 19.0125 30-31 29.799999999999997 24.762500000000003 26.337500000000002 19.1 32-33 25.5 25.4 27.575 21.525 34-35 22.038774233896184 32.257661038148846 25.8036272670419 19.89993746091307 36-37 26.700000000000003 25.2125 24.6 23.4875 38-39 28.975 23.6625 28.575 18.787499999999998 40-41 25.243810952738183 23.680920230057513 30.17004251062766 20.905226306576644 42-43 25.747903367129805 29.76592815120791 25.82300663412192 18.66316184754037 44-45 24.056014003500874 26.894223555888974 30.34508627156789 18.704676169042262 46-47 26.5125 23.65 27.474999999999998 22.3625 48-49 25.275 24.712500000000002 28.575 21.4375 50-51 21.925 27.737499999999997 27.6 22.7375 52-53 24.684256596223584 25.459547330248846 25.397023883956482 24.45917218957109 54-55 23.8125 25.45 30.675 20.0625 56-57 27.55 27.3875 26.6125 18.45 58-59 22.875 26.0 31.05 20.075000000000003 60-61 28.575 26.450000000000003 26.987499999999997 17.9875 62-63 20.6125 28.462500000000002 31.924999999999997 19.0 64-65 20.6125 33.675 27.987499999999997 17.724999999999998 66-67 24.4375 29.4375 28.050000000000004 18.075 68-69 20.575 26.987499999999997 28.925 23.5125 70-71 22.81031031031031 28.065565565565564 27.164664664664667 21.95945945945946 72-73 26.67504714016342 24.839723444374606 28.74921433060968 19.736015084852294 74-75 24.71881713635789 29.306204979148237 28.750157967900925 17.22481991659295 76-77 22.3871131405378 25.279046169457132 26.357179096905124 25.976661593099948 78-79 25.50344124394596 26.49757838388988 29.429008411929647 18.569971960234515 80-81 21.665598975016014 33.91415759128763 27.46957078795644 16.95067264573991 82-83 23.058096096869768 25.60865644724977 28.15921679762978 23.17403065825068 84-85 21.915500259201657 25.116640746500778 32.128045619491964 20.839813374805598 86-87 20.462217605816672 27.07089067774604 28.95351856660608 23.513373149831214 88-89 19.241755388210855 29.109322253960013 30.615424565048038 21.033497792781095 90-91 25.590755647883668 29.04440405089587 27.239678005712804 18.12516229550766 92-93 20.812775902363022 29.732537003375747 28.901584004154763 20.553103090106468 >>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 14.0 18 15.0 19 2.5 20 2.5 21 5.5 22 6.5 23 4.5 24 9.5 25 9.5 26 6.5 27 12.0 28 22.0 29 28.0 30 29.0 31 40.5 32 55.5 33 68.5 34 77.5 35 82.0 36 104.0 37 150.5 38 200.0 39 196.0 40 197.5 41 205.0 42 207.0 43 229.0 44 189.0 45 164.5 46 182.0 47 166.0 48 145.5 49 140.5 50 160.5 51 154.0 52 126.5 53 134.5 54 195.0 55 167.0 56 69.0 57 52.0 58 48.0 59 36.5 60 31.0 61 32.0 62 26.0 63 18.5 64 16.0 65 19.5 66 15.0 67 13.5 68 15.5 69 11.5 70 10.0 71 9.0 72 5.5 73 1.5 74 2.0 75 2.5 76 1.5 77 0.5 78 1.0 79 1.0 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 0.0125 20-21 0.0625 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 0.0625 36-37 0.0 38-39 0.0 40-41 0.025 42-43 0.13749999999999998 44-45 0.025 46-47 0.0 48-49 0.0 50-51 0.0 52-53 0.0375 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 8.0 71 11.0 72 7.0 73 14.0 74 7.0 75 6.0 76 10.0 77 9.0 78 10.0 79 11.0 80 9.0 81 13.0 82 7.0 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 3851.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 72.15 #Duplication Level Percentage of deduplicated Percentage of total 1 91.75329175329175 66.2 2 4.261954261954262 6.15 3 1.5592515592515594 3.375 4 0.45045045045045046 1.3 5 0.5197505197505198 1.875 6 0.2079002079002079 0.8999999999999999 7 0.2772002772002772 1.4000000000000001 8 0.10395010395010396 0.6 9 0.10395010395010396 0.675 >10 0.6237006237006237 7.6499999999999995 >50 0.10395010395010396 4.675 >100 0.03465003465003465 5.2 >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 208 5.2 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 73 1.825 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 60 1.5 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 54 1.35 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 36 0.8999999999999999 No Hit GGAGTATCCTTGATATATAAATATATAGATAAATAGATTTAAATGGAAAA 30 0.75 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 25 0.625 No Hit GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 23 0.575 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 18 0.44999999999999996 No Hit GGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGG 17 0.42500000000000004 No Hit CAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCT 17 0.42500000000000004 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 17 0.42500000000000004 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 16 0.4 No Hit GGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAAATGGATTC 14 0.35000000000000003 No Hit GGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGGG 13 0.325 No Hit GGGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTG 13 0.325 No Hit CAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATAT 12 0.3 No Hit GTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAA 12 0.3 No Hit CAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTG 12 0.3 No Hit GGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAA 11 0.27499999999999997 No Hit GGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTT 10 0.25 No Hit GGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGC 10 0.25 No Hit GGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAA 9 0.22499999999999998 No Hit GGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTT 9 0.22499999999999998 No Hit GTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAG 9 0.22499999999999998 No Hit GGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCG 8 0.2 No Hit GGCCTGTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCG 8 0.2 No Hit GGGCCGGGTATCTCTCTGCATGTACGTATGCCTGTAATGTACGTAGCTAC 8 0.2 No Hit GTACTATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTT 7 0.17500000000000002 No Hit GGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGC 7 0.17500000000000002 No Hit GATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAAT 7 0.17500000000000002 No Hit GTACAAGCTCGTAACGAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAAT 7 0.17500000000000002 No Hit GGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGCA 7 0.17500000000000002 No Hit GGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAA 7 0.17500000000000002 No Hit GGTTTTGAAAAGGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAA 7 0.17500000000000002 No Hit GGATTTGTTAAATCAAATCCTTGGTTTAATAACGAACGGTGTTAACTTAC 7 0.17500000000000002 No Hit GGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTTGAAATCGGA 6 0.15 No Hit GTATTTAGCCTTGCAAGGTGGTCCTTGCTGATTCACACGGGATTCCACGT 6 0.15 No Hit GGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAAA 6 0.15 No Hit GGGACGCATGCAACGACCATCTACATATAGCTACTCGATCTACCGCTACC 6 0.15 No Hit GGAAAAGAGGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTTG 6 0.15 No Hit GGAAAAGAAAGCAAAAGCGATTCCCGTAGTAGCGGCGAGCGAAATGGGAG 6 0.15 No Hit TAATTAAGAATCAAGTCATCTCATTCTCATCTATGCAATTGCAAACACAA 5 0.125 No Hit GGTATTAGTACTATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATC 5 0.125 No Hit GGAGGGTGAGAGCCCCGTCCGGCCCGGACCCTGTCGCCCCACGAGGCGCC 5 0.125 No Hit GGGATGGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACGA 5 0.125 No Hit GCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCT 5 0.125 No Hit GGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAAA 5 0.125 No Hit GGGGATGGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACG 5 0.125 No Hit GGGAAATTAACAGTTGGAAAGGGCGATCGGTCTTGATCCCTCTGTGTTTC 5 0.125 No Hit AGTCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAA 5 0.125 No Hit CGAGGAAGGGCGTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAG 5 0.125 No Hit GGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAACCCTCTTAACT 5 0.125 No Hit GGGTTGTGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGA 5 0.125 No Hit GGGGAAGTACACCAGCGACGGCGAGGCCGCCGCCGCCAAGGAAGGCATGT 5 0.125 No Hit CACGAACGTAATGCTCACAACTTCCCTCTAGATCTAGCTGCTCTTGAAGT 5 0.125 No Hit AACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGA 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 0.0125 0.0 0.0 0.0 0.0 38-39 0.025 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 0.025 0.0 0.0 0.0 0.0 46-47 0.025 0.0 0.0 0.0 0.0 48-49 0.025 0.0 0.0 0.0 0.0 50-51 0.025 0.0 0.0 0.0 0.0 52-53 0.025 0.0 0.0 0.0 0.0 54-55 0.025 0.0 0.0 0.0 0.0 56-57 0.025 0.0 0.0 0.0 0.0 58-59 0.025 0.0 0.0 0.0 0.0 60-61 0.025 0.0 0.0 0.0 0.0 62-63 0.025 0.0 0.0 0.0 0.0 64-65 0.025 0.0 0.0 0.0 0.0 66-67 0.025 0.0 0.0 0.0 0.0 68-69 0.025 0.0 0.0 0.0 0.0 70-71 0.025 0.0 0.0 0.0 0.0 72-73 0.025 0.0 0.0 0.0 0.0 74-75 0.025 0.0 0.0 0.0 0.0 76-77 0.025 0.0 0.0 0.0 0.0 78-79 0.025 0.0 0.0 0.0 0.0 80-81 0.025 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content fail #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GGGAGAG 35 4.965841E-10 86.3 1 GGAGAGC 25 6.7847395E-7 86.299995 2 GCAATAC 25 6.7847395E-7 86.299995 7 GAGCAAT 25 6.7847395E-7 86.299995 5 AGAGCAA 25 6.7847395E-7 86.299995 4 GAGAGCA 25 6.7847395E-7 86.299995 3 AGCAATA 25 6.7847395E-7 86.299995 6 CAATACA 30 2.007393E-6 71.916664 8 AATACAA 30 2.007393E-6 71.916664 9 CATCACT 20 6.728844E-4 44.83117 82-83 ATCACTA 20 6.728844E-4 44.83117 84-85 AGCATCA 20 6.728844E-4 44.83117 80-81 CACTAGC 20 6.728844E-4 44.83117 86-87 TCACTAG 20 6.728844E-4 44.83117 84-85 ACTAGCT 20 6.728844E-4 44.83117 86-87 GCATCAC 20 6.728844E-4 44.83117 82-83 GAAAGCA 25 3.6202553E-5 44.83117 78-79 CGAAAGC 25 3.7637044E-5 44.541935 76-77 CCGAAAG 25 3.7637044E-5 44.541935 76-77 GTTGAGT 25 4.2225773E-5 43.6962 38-39 >>END_MODULE Rejected 334254 READS because READLEN < 1 Read 334254 spots for ERR6133553.sra Written 334254 spots for ERR6133553.sra Rejected 334254 READS because READLEN < 1 Read 334254 spots for ERR6133553.sra Written 334254 spots for ERR6133553.sra Rejected 334254 READS because READLEN < 1 Read 334254 spots for ERR6133553.sra Written 334254 spots for ERR6133553.sra Rejected 334254 READS because READLEN < 1 Read 334254 spots for ERR6133553.sra Written 334254 spots for ERR6133553.sra Rejected 334254 READS because READLEN < 1 Read 334254 spots for ERR6133553.sra Written 334254 spots for ERR6133553.sra Rejected 334254 READS because READLEN < 1 Read 334254 spots for ERR6133553.sra Written 334254 spots for ERR6133553.sra Rejected 334254 READS because READLEN < 1 Read 334254 spots for ERR6133553.sra Written 334254 spots for ERR6133553.sra Rejected 334254 READS because READLEN < 1 Read 334254 spots for ERR6133553.sra Written 334254 spots for ERR6133553.sra Rejected 334254 READS because READLEN < 1 Read 334254 spots for ERR6133553.sra Written 334254 spots for ERR6133553.sra Rejected 334254 READS because READLEN < 1 Read 334254 spots for ERR6133553.sra Written 334254 spots for ERR6133553.sra Rejected 334254 READS because READLEN < 1 Read 334254 spots for ERR6133553.sra Written 334254 spots for ERR6133553.sra Rejected 334258 READS because READLEN < 1 Read 334258 spots for ERR6133553.sra Written 334258 spots for ERR6133553.sra Rejected 334254 READS because READLEN < 1 Read 334254 spots for ERR6133553.sra Written 334254 spots for ERR6133553.sra Rejected 334254 READS because READLEN < 1 Read 334254 spots for ERR6133553.sra Written 334254 spots for ERR6133553.sra Rejected 334254 READS because READLEN < 1 Read 334254 spots for ERR6133553.sra Written 334254 spots for ERR6133553.sra Rejected 334254 READS because READLEN < 1 Read 334254 spots for ERR6133553.sra Written 334254 spots for ERR6133553.sra Rejected 334254 READS because READLEN < 1 Read 334254 spots for ERR6133553.sra Written 334254 spots for ERR6133553.sra Rejected 334254 READS because READLEN < 1 Read 334254 spots for ERR6133553.sra Written 334254 spots for ERR6133553.sra Rejected 334254 READS because READLEN < 1 Read 334254 spots for ERR6133553.sra Written 334254 spots for ERR6133553.sra Rejected 334254 READS because READLEN < 1 Read 334254 spots for ERR6133553.sra Written 334254 spots for ERR6133553.sra SRR ids: ['ERR6133553.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_g5a15poz ERR6133553.sra spots: 6685084 blocks: [[1, 334254], [334255, 668508], [668509, 1002762], [1002763, 1337016], [1337017, 1671270], [1671271, 2005524], [2005525, 2339778], [2339779, 2674032], [2674033, 3008286], [3008287, 3342540], [3342541, 3676794], [3676795, 4011048], [4011049, 4345302], [4345303, 4679556], [4679557, 5013810], [5013811, 5348064], [5348065, 5682318], [5682319, 6016572], [6016573, 6350826], [6350827, 6685084]] ERR6133553 file size 1478211 ERR6133553 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 ERR6133553 ERR6133553_1.fastq Input file: ERR6133553_1.fastq trimmed: ERR6133553-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 08:31:10 2024 >> started Sat Dec 7 08:31:13 2024 >> done (3.170s) 6685084 reads processed; of these: 198 ( 0.00%) short reads filtered out after trimming by size control 30 ( 0.00%) empty reads filtered out after trimming by size control 6684856 (100.00%) reads available; of these: 121602 ( 1.82%) trimmed reads available after processing 6563254 (98.18%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 15 0.00% 19 77 0.00% 20 12 0.00% 21 8 0.00% 22 20 0.00% 23 12 0.00% 24 7 0.00% 25 1 0.00% 26 6 0.00% 27 16 0.00% 28 18 0.00% 29 11 0.00% 30 10 0.00% 31 19 0.00% 32 30 0.00% 33 22 0.00% 34 27 0.00% 35 176 0.00% 36 923 0.01% 37 30 0.00% 38 41 0.00% 39 75 0.00% 40 93 0.00% 41 36 0.00% 42 7 0.00% 43 12 0.00% 44 19 0.00% 45 18 0.00% 46 16 0.00% 47 16 0.00% 48 18 0.00% 49 12 0.00% 50 18 0.00% 51 63 0.00% 52 12 0.00% 53 9 0.00% 54 8 0.00% 55 8 0.00% 56 12 0.00% 57 12 0.00% 58 16 0.00% 59 11 0.00% 60 19 0.00% 61 11 0.00% 62 8 0.00% 63 4 0.00% 64 8 0.00% 65 5 0.00% 66 19 0.00% 67 27 0.00% 68 58 0.00% 69 231 0.00% 70 16637 0.25% 71 15475 0.23% 72 16908 0.25% 73 14998 0.22% 74 15585 0.23% 75 15302 0.23% 76 14134 0.21% 77 15015 0.22% 78 16863 0.25% 79 18662 0.28% 80 18203 0.27% 81 22661 0.34% 82 24490 0.37% 83 22585 0.34% 84 21951 0.33% 85 247 0.00% 86 507 0.01% 87 821 0.01% 88 1577 0.02% 89 3078 0.05% 90 6874 0.10% 91 20111 0.30% 92 82304 1.23% 93 6297506 94.21% 6684856 reads passed initial QC criterion=sequence-density sequence-density=0.99 sequence-density-rank=1 fanout-score=2.00 fanout-score-rank=26 prefix-density=0.99 prefix-fanout=2.0 sequence=CAAGGCTAAATAC criterion=fanout-score sequence-density=0.01 sequence-density-rank=33 fanout-score=29.90 fanout-score-rank=1 prefix-density=0.06 prefix-fanout=3.1 sequence=AAGGAGAACGTGAAGAACGCGTCGTCGTCGCAGGGGAACATCACGCTCAGCGTCACCAAGAGCAAGCCGGAGACCGGGGAGGTCATCGGCGTCTTCGAGAGCGTGCAGCCGTCCGACACCGACCTCGGCGCCAAGGCGCCCAAGGACGTCAAGATCCAGGGCGTCTGGTACGCGCAGCTCGAGTCTAACTAGAAAAAGGATCGGTCGATCATCGGAGAAGAACACTTCCTCCGTGCATATGCGTGTACGTGGGTTGATCGGTGGAGAGAGAAAGGCAATGCGCCATGTGTGTATGTAGTAATGCGAACCTGGCCCCTGCTGTTGGTTGTAATTTTTAGCCTTTGTAATTTCTTCCTCACCAACTGGTATTGATCCCCCCATGAATCAG Started job on | Dec 07 08:31:26 Started mapping on | Dec 07 08:31:26 Finished on | Dec 07 08:31:34 Mapping speed, Million of reads per hour | 3008.19 Number of input reads | 6684856 Average input read length | 92 UNIQUE READS: Uniquely mapped reads number | 3861536 Uniquely mapped reads % | 57.77% Average mapped length | 91.91 Number of splices: Total | 162262 Number of splices: Annotated (sjdb) | 134344 Number of splices: GT/AG | 157037 Number of splices: GC/AG | 3692 Number of splices: AT/AC | 193 Number of splices: Non-canonical | 1340 Mismatch rate per base, % | 0.30% Deletion rate per base | 0.03% Deletion average length | 1.47 Insertion rate per base | 0.00% Insertion average length | 1.34 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 2637521 % of reads mapped to multiple loci | 39.46% Number of reads mapped to too many loci | 93285 % of reads mapped to too many loci | 1.40% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.29% % of reads unmapped: other | 0.10% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 185799 185799 185799 N_multimapping 2637521 2637521 2637521 N_noFeature 302877 344150 3691582 N_ambiguous 150060 21246 604 UnstrandedReadsAssigned:3408599 PositiveStrandReadsAssigned:3496140 NegativeStrandReadsAssigned:169350 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=93 echo kmer=89 ERR6133553 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: ERR6133553-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 6,684,856 reads, 5,037,507 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,054 rounds 52973 ERR6133553.ke.tsv 35125 ERR6133553.se.tsv 88098 total ==> ERR6133553.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 64 12.2278 PNS24243 293 194 0 0 KQK14069 1603 1504 187.079 32.606 KQK14071 474 375 0 0 ==> ERR6133553.se.tsv <== BRADI_1g14170v3 194 BRADI_1g53295v3 50 BRADI_1g59795v3 28 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 37 BRADI_1g74790v3 37 BRADI_1g09890v3 0 BRADI_1g77505v3 89 BRADI_1g48960v3 0 ERR6133553 completed mapping pipeline successfully