Starting /dee2/code/volunteer_pipeline.sh ERR6133345 current disk space = 1548108668928 free memory = 1598846160 ERR6133345 SRAfilesize 10d8085fd49eb9b2c876571e40a8cff9 ERR6133345.sra ERR6133345.sra file validated ERR6133345 is single end ERR6133345 is conventional basespace ERR6133345 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133345_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 46 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.118 37.0 37.0 37.0 33.0 37.0 2 36.51125 37.0 37.0 37.0 37.0 37.0 3 36.5225 37.0 37.0 37.0 37.0 37.0 4 36.22225 37.0 37.0 37.0 33.0 37.0 5 36.2695 37.0 37.0 37.0 33.0 37.0 6 36.36175 37.0 37.0 37.0 37.0 37.0 7 38.534 40.0 37.0 40.0 37.0 40.0 8 38.611 40.0 37.0 40.0 37.0 40.0 9 38.6205 40.0 37.0 40.0 37.0 40.0 10-11 38.553375 40.0 37.0 40.0 37.0 40.0 12-13 38.499375 40.0 37.0 40.0 37.0 40.0 14-15 38.5065 40.0 37.0 40.0 37.0 40.0 16-17 38.456875 40.0 37.0 40.0 37.0 40.0 18-19 38.430875 40.0 37.0 40.0 37.0 40.0 20-21 38.317125 40.0 37.0 40.0 37.0 40.0 22-23 38.275875 40.0 37.0 40.0 37.0 40.0 24-25 38.228750000000005 40.0 37.0 40.0 37.0 40.0 26-27 38.17275 40.0 37.0 40.0 37.0 40.0 28-29 38.21775 40.0 37.0 40.0 37.0 40.0 30-31 38.19725 40.0 37.0 40.0 37.0 40.0 32-33 38.038875000000004 40.0 37.0 40.0 37.0 40.0 34-35 37.911 40.0 37.0 40.0 35.0 40.0 36-37 37.791624999999996 40.0 37.0 40.0 35.0 40.0 38-39 37.7885 38.5 37.0 40.0 37.0 40.0 40-41 37.544875 37.0 37.0 40.0 33.0 40.0 42-43 37.495374999999996 37.0 37.0 40.0 33.0 40.0 44-45 37.34825 37.0 37.0 40.0 33.0 40.0 46-47 37.197125 37.0 37.0 40.0 33.0 40.0 48-49 37.028625000000005 37.0 37.0 40.0 33.0 40.0 50-51 36.9465 37.0 37.0 40.0 33.0 40.0 52-53 36.832750000000004 37.0 37.0 38.5 33.0 40.0 54-55 36.725375 37.0 37.0 37.0 33.0 40.0 56-57 36.599625 37.0 37.0 37.0 33.0 40.0 58-59 36.362875 37.0 37.0 37.0 33.0 40.0 60-61 36.311625 37.0 37.0 37.0 33.0 38.5 62-63 36.15712499999999 37.0 37.0 37.0 33.0 37.0 64-65 35.996125 37.0 37.0 37.0 33.0 37.0 66-67 35.854625 37.0 37.0 37.0 33.0 37.0 68-69 34.871875 35.0 35.0 37.0 33.0 37.0 70-71 35.17530262162843 37.0 33.0 37.0 33.0 37.0 72-73 35.60463484860051 37.0 37.0 37.0 33.0 37.0 74-75 35.498565626074715 37.0 37.0 37.0 33.0 37.0 76-77 35.58054720849831 37.0 37.0 37.0 33.0 37.0 78-79 35.64605466424302 37.0 37.0 37.0 33.0 37.0 80-81 35.5571552140179 37.0 37.0 37.0 33.0 37.0 82-83 35.40923211079485 37.0 37.0 37.0 33.0 37.0 84-85 35.40035352478838 37.0 33.0 37.0 33.0 37.0 86-87 35.31070608495982 37.0 33.0 37.0 33.0 37.0 88-89 35.40944316877153 37.0 33.0 37.0 33.0 37.0 90-91 35.312715269804826 37.0 33.0 37.0 33.0 37.0 92-93 35.24354190585534 37.0 33.0 37.0 33.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 4.0 21 4.0 22 6.0 23 7.0 24 10.0 25 11.0 26 14.0 27 15.0 28 16.0 29 23.0 30 41.0 31 31.0 32 58.0 33 64.0 34 119.0 35 197.0 36 869.0 37 1089.0 38 1350.0 39 72.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 68.22500000000001 8.225 8.725 14.825 2 51.7 24.275 14.899999999999999 9.125 3 35.125 35.875 15.174999999999999 13.825000000000001 4 29.175 31.95 19.900000000000002 18.975 5 28.075 26.900000000000002 26.450000000000003 18.575 6 20.525 38.074999999999996 23.7 17.7 7 38.525 25.025 19.950000000000003 16.5 8 27.175 26.224999999999998 24.9 21.7 9 25.1 31.35 25.15 18.4 10-11 23.925 29.6375 27.987499999999997 18.45 12-13 23.5625 29.9375 25.162499999999998 21.337500000000002 14-15 21.4 33.3625 26.2125 19.025 16-17 26.737499999999997 28.875 22.325 22.0625 18-19 26.4625 23.7 29.7 20.1375 20-21 26.700000000000003 24.5125 28.325 20.4625 22-23 29.362500000000004 23.7375 26.474999999999998 20.424999999999997 24-25 23.5625 25.825 27.700000000000003 22.912499999999998 26-27 27.150000000000002 24.6625 26.25 21.9375 28-29 24.1125 27.775 27.725 20.3875 30-31 30.412499999999998 25.4625 24.9375 19.1875 32-33 28.537499999999998 23.75 25.900000000000002 21.8125 34-35 23.05 32.675 23.799999999999997 20.474999999999998 36-37 26.4625 26.887499999999996 22.6375 24.0125 38-39 31.786920095035637 23.558834562961113 24.896836313617605 19.757409028385645 40-41 24.9125 24.1375 30.9375 20.0125 42-43 27.8375 31.8 23.3 17.0625 44-45 24.337500000000002 27.462500000000002 28.799999999999997 19.400000000000002 46-47 28.7375 25.05 23.7125 22.5 48-49 25.9875 23.75 26.5 23.7625 50-51 21.575 29.8375 26.087500000000002 22.5 52-53 24.224999999999998 27.775 23.9875 24.0125 54-55 23.5 26.775 26.974999999999998 22.75 56-57 25.7125 30.15 24.7875 19.35 58-59 22.475 30.3875 27.9125 19.225 60-61 31.474999999999998 26.4625 22.925 19.1375 62-63 22.325 27.825 29.7875 20.0625 64-65 22.004003002251686 36.177132849637225 24.931198398799097 16.887665749311985 66-67 25.44386096524131 31.407851962990748 24.518629657414355 18.629657414353588 68-69 21.7875 27.487499999999997 27.6 23.125 70-71 24.726998870340154 29.797916405171332 24.237479603363877 21.237605121124638 72-73 28.547770700636942 26.292993630573246 28.02547770700637 17.133757961783438 74-75 26.266683944538034 30.15420500194376 25.670597382402487 17.90851367111572 76-77 23.24295867333509 24.769676230586995 25.309291918926036 26.678073177151884 78-79 27.69663674125687 29.813747822591452 24.31997856090044 18.16963687525124 80-81 22.82016348773842 35.55858310626703 24.291553133514988 17.329700272479563 82-83 24.975568895714087 26.804411559402485 24.975568895714087 23.244450649169345 84-85 21.765796605334476 27.271430609042934 29.467978890315216 21.494793895307374 86-87 20.92422502870264 31.917336394948336 23.493111366245696 23.665327210103328 88-89 20.62284730195178 30.597014925373134 26.406429391504016 22.373708381171067 90-91 24.899540757749712 33.19460390355913 22.63203214695752 19.273823191733637 92-93 20.33582089552239 33.13719862227325 25.516647531572907 21.010332950631458 >>END_MODULE >>Per sequence GC content fail #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 1.5 19 2.5 20 4.5 21 2.5 22 1.5 23 2.0 24 4.0 25 8.0 26 8.5 27 13.5 28 17.5 29 18.0 30 25.5 31 34.0 32 43.0 33 55.0 34 68.5 35 77.0 36 108.0 37 157.0 38 174.0 39 163.5 40 184.5 41 201.0 42 204.0 43 218.0 44 183.0 45 164.5 46 161.5 47 149.0 48 136.0 49 125.0 50 153.5 51 180.5 52 167.0 53 191.5 54 294.5 55 259.5 56 124.0 57 83.0 58 76.5 59 46.5 60 22.5 61 20.0 62 16.5 63 13.5 64 10.5 65 10.0 66 6.5 67 5.0 68 12.5 69 16.5 70 10.0 71 4.0 72 2.0 73 0.5 74 0.5 75 0.5 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 0.0 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 0.0375 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 0.075 66-67 0.025 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 0.028518465706544985 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 33.0 71 25.0 72 34.0 73 31.0 74 37.0 75 28.0 76 26.0 77 41.0 78 27.0 79 28.0 80 40.0 81 45.0 82 47.0 83 29.0 84 45.0 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 3484.0 >>END_MODULE >>Sequence Duplication Levels warn #Total Deduplicated Percentage 66.7 #Duplication Level Percentage of deduplicated Percentage of total 1 88.41829085457272 58.975 2 5.7721139430284865 7.7 3 2.136431784107946 4.275 4 0.8620689655172413 2.3 5 0.4497751124437781 1.5 6 0.4122938530734633 1.6500000000000001 7 0.4122938530734633 1.925 8 0.29985007496251875 1.6 9 0.29985007496251875 1.7999999999999998 >10 0.8995502248875562 12.049999999999999 >50 0.0 0.0 >100 0.037481259370314844 6.225 >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 249 6.225 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 49 1.225 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 32 0.8 No Hit GGAAAAGAAAGCAAAAGCGATTCCCGTAGTAGCGGCGAGCGAAATGGGAG 31 0.775 No Hit GGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAA 29 0.7250000000000001 No Hit GGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGC 28 0.7000000000000001 No Hit GGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTCCT 26 0.65 No Hit CAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCT 26 0.65 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 25 0.625 No Hit GGGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTA 22 0.5499999999999999 No Hit GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 21 0.525 No Hit CAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTG 21 0.525 No Hit CAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATAT 20 0.5 No Hit TCAAAAGAGGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGGA 20 0.5 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 16 0.4 No Hit GGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTT 14 0.35000000000000003 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 14 0.35000000000000003 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 13 0.325 No Hit GGGTTGTGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGA 13 0.325 No Hit GGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGCA 11 0.27499999999999997 No Hit GGGGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCT 11 0.27499999999999997 No Hit GGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGCTAAATACAG 10 0.25 No Hit GGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCG 10 0.25 No Hit GTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTC 10 0.25 No Hit GGGTGAGAGCCCCGTCCGGCCCGGACCCTGTCGCCCCACGAGGCGCCGTC 10 0.25 No Hit GAGGAAGGGCGTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAGC 9 0.22499999999999998 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 9 0.22499999999999998 No Hit GGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGG 9 0.22499999999999998 No Hit GGAAGGGCGTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAGCAT 9 0.22499999999999998 No Hit GGTCAACCTTTTAAACTGCCTGCTGAATCCATGAGCAGGCAAGAGACAAC 9 0.22499999999999998 No Hit GGGGTTGTGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTG 9 0.22499999999999998 No Hit CACGAACGTAATGCTCACAACTTCCCTCTAGATCTAGCTGCTCTTGAAGT 9 0.22499999999999998 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 9 0.22499999999999998 No Hit CGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGGTAT 8 0.2 No Hit GAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTG 8 0.2 No Hit GTATTAGTACTATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATCT 8 0.2 No Hit CGAGGAAGGGCGTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAG 8 0.2 No Hit AACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGA 8 0.2 No Hit GAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGC 8 0.2 No Hit TCTCATGGAGAGTTCGATCCTGGCTCAGGATGAACGCTGGCGGCATGCTT 8 0.2 No Hit AAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCC 8 0.2 No Hit GGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAAGGCGATCAAATTC 7 0.17500000000000002 No Hit GGAGGGTGAGAGCCCCGTCCGGCCCGGACCCTGTCGCCCCACGAGGCGCC 7 0.17500000000000002 No Hit GTACTATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTT 7 0.17500000000000002 No Hit GGCGAAGCGGTTGAGTGCCGCACCCTAGATGGCTAAAGTCCAGTAGCCGA 7 0.17500000000000002 No Hit GCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCT 7 0.17500000000000002 No Hit CAACGAGTCGGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCC 7 0.17500000000000002 No Hit GCAGCTTGCAAATGGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAA 7 0.17500000000000002 No Hit GATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGC 7 0.17500000000000002 No Hit GGAGCAGCCTAAACCGTGAAAACGGGGTTGTGGGAGAGCAATACAAGCGT 7 0.17500000000000002 No Hit GGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGC 7 0.17500000000000002 No Hit GGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGCT 7 0.17500000000000002 No Hit GGGCGTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAGCATAGAT 6 0.15 No Hit GTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAA 6 0.15 No Hit GGAGATTCCCAAATAGGTCAACCTTTTAAACTGCCTGCTGAATCCATGAG 6 0.15 No Hit GACCCGAGTAGCATGGGGCACGTGGAATCCCGTGTGAATCAGCAAGGACC 6 0.15 No Hit AACGTAATGCTCACAACTTCCCTCTAGATCTAGCTGCTCTTGAAGTTCCC 6 0.15 No Hit CTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGT 6 0.15 No Hit GAAGCCTGTGTACAAGCTCGTAACGAAGGGCGCGATCTTGCTCGTGAAGG 6 0.15 No Hit GTAATGCACGAACGTAATGCTCACAACTTCCCTCTAGATCTAGCTGCTCT 6 0.15 No Hit GAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTCCTG 6 0.15 No Hit GGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAA 6 0.15 No Hit CTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATATCATC 6 0.15 No Hit GGAGTTTGGCTGGGGCGGCACATCTGTTAAAAGATAACGCAGGTGTCCTA 5 0.125 No Hit CAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTT 5 0.125 No Hit GGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGGAAGGGCGTA 5 0.125 No Hit GGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTT 5 0.125 No Hit CACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTTCGGGGAGT 5 0.125 No Hit GGGAATTTCCGGTGGAGCGGTGAAATGCATTGAGATCGGAAAGAACACCA 5 0.125 No Hit CAAATCGGGCGGTAGACTCCGTCCAAGGCTAAATACAGGCGAGAGACCGATAGCGAACAAGTACCGCGAGGG 5 0.125 No Hit GTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAA 5 0.125 No Hit GTGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCC 5 0.125 No Hit GTACAAGCTCGTAACGAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAAT 5 0.125 No Hit GGCCCGGACCCTGTCGCCCCACGAGGCGCCGTCAACGAGTCGGGTTGTTT 5 0.125 No Hit GATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAG 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 0.025 0.0 0.0 0.0 0.0 28-29 0.025 0.0 0.0 0.0 0.0 30-31 0.05 0.0 0.0 0.0 0.0 32-33 0.05 0.0 0.0 0.0 0.0 34-35 0.125 0.0 0.0 0.0 0.0 36-37 0.125 0.0 0.0 0.0 0.0 38-39 0.125 0.0 0.0 0.0 0.0 40-41 0.1375 0.0 0.0 0.0 0.0 42-43 0.15 0.0 0.0 0.0 0.0 44-45 0.15 0.0 0.0 0.0 0.0 46-47 0.15 0.0 0.0 0.0 0.0 48-49 0.15 0.0 0.0 0.0 0.0 50-51 0.15 0.0 0.0 0.0 0.0 52-53 0.15 0.0 0.0 0.0 0.0 54-55 0.15 0.0 0.0 0.0 0.0 56-57 0.15 0.0 0.0 0.0 0.0 58-59 0.15 0.0 0.0 0.0 0.0 60-61 0.15 0.0 0.0 0.0 0.0 62-63 0.15 0.0 0.0 0.0 0.0 64-65 0.16249999999999998 0.0 0.0 0.0 0.0 66-67 0.1875 0.0 0.0 0.0 0.0 68-69 0.2 0.0 0.0 0.0 0.0 70-71 0.2 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 fail #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GGAGAGC 70 1.2412238E-7 42.931248 2 GCAATAC 70 1.2412238E-7 42.931248 7 GAGCAAT 70 1.2412238E-7 42.931248 5 AGCAATA 70 1.2412238E-7 42.931248 6 ATCACTA 50 5.18412E-10 42.34315 84-85 CACTAGC 50 5.18412E-10 42.34315 86-87 ACTAGCT 40 2.0254447E-7 41.166954 86-87 GGGAGAG 75 2.1355481E-7 40.069164 1 AGAGCAA 75 2.1355481E-7 40.069164 4 AATACAA 65 4.0110044E-6 39.62885 9 GCATCAC 55 1.3187673E-9 38.493774 82-83 GAGAGCA 80 3.5456287E-7 37.564842 3 CAATACA 70 6.675882E-6 36.798214 8 AAGCATC 60 3.094101E-9 35.285957 80-81 CATCACT 50 1.1649336E-6 32.933563 82-83 TCACTAG 50 1.1649336E-6 32.933563 84-85 CAGTAGC 60 6.852133E-9 32.606014 70-71 TCCAGTA 60 6.852133E-9 32.606014 68-69 AGTCCAG 60 7.2996045E-9 32.400944 66-67 ATGGCTA 60 7.774361E-9 32.198437 58-59 >>END_MODULE Rejected 42831 READS because READLEN < 1 Read 42831 spots for ERR6133345.sra Written 42831 spots for ERR6133345.sra Rejected 42831 READS because READLEN < 1 Read 42831 spots for ERR6133345.sra Written 42831 spots for ERR6133345.sra Rejected 42831 READS because READLEN < 1 Read 42831 spots for ERR6133345.sra Written 42831 spots for ERR6133345.sra Rejected 42831 READS because READLEN < 1 Read 42831 spots for ERR6133345.sra Written 42831 spots for ERR6133345.sra Rejected 42831 READS because READLEN < 1 Read 42831 spots for ERR6133345.sra Written 42831 spots for ERR6133345.sra Rejected 42831 READS because READLEN < 1 Read 42831 spots for ERR6133345.sra Written 42831 spots for ERR6133345.sra Rejected 42831 READS because READLEN < 1 Read 42831 spots for ERR6133345.sra Written 42831 spots for ERR6133345.sra Rejected 42831 READS because READLEN < 1 Read 42831 spots for ERR6133345.sra Written 42831 spots for ERR6133345.sra Rejected 42831 READS because READLEN < 1 Read 42831 spots for ERR6133345.sra Written 42831 spots for ERR6133345.sra Rejected 42831 READS because READLEN < 1 Read 42831 spots for ERR6133345.sra Written 42831 spots for ERR6133345.sra Rejected 42831 READS because READLEN < 1 Read 42831 spots for ERR6133345.sra Written 42831 spots for ERR6133345.sra Rejected 42831 READS because READLEN < 1 Read 42831 spots for ERR6133345.sra Written 42831 spots for ERR6133345.sra Rejected 42831 READS because READLEN < 1 Read 42831 spots for ERR6133345.sra Written 42831 spots for ERR6133345.sra Rejected 42831 READS because READLEN < 1 Read 42831 spots for ERR6133345.sra Written 42831 spots for ERR6133345.sra Rejected 42831 READS because READLEN < 1 Read 42831 spots for ERR6133345.sra Written 42831 spots for ERR6133345.sra Rejected 42831 READS because READLEN < 1 Read 42831 spots for ERR6133345.sra Written 42831 spots for ERR6133345.sra Rejected 42831 READS because READLEN < 1 Read 42831 spots for ERR6133345.sra Written 42831 spots for ERR6133345.sra Rejected 42831 READS because READLEN < 1 Read 42831 spots for ERR6133345.sra Written 42831 spots for ERR6133345.sra Rejected 42831 READS because READLEN < 1 Read 42831 spots for ERR6133345.sra Written 42831 spots for ERR6133345.sra Rejected 42837 READS because READLEN < 1 Read 42837 spots for ERR6133345.sra Written 42837 spots for ERR6133345.sra SRR ids: ['ERR6133345.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_y8cf068l ERR6133345.sra spots: 856626 blocks: [[1, 42831], [42832, 85662], [85663, 128493], [128494, 171324], [171325, 214155], [214156, 256986], [256987, 299817], [299818, 342648], [342649, 385479], [385480, 428310], [428311, 471141], [471142, 513972], [513973, 556803], [556804, 599634], [599635, 642465], [642466, 685296], [685297, 728127], [728128, 770958], [770959, 813789], [813790, 856626]] ERR6133345 file size 185653 ERR6133345 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 ERR6133345 ERR6133345_1.fastq Input file: ERR6133345_1.fastq trimmed: ERR6133345-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 01:06:16 2024 >> started Sat Dec 7 01:06:17 2024 >> done (0.601s) 856626 reads processed; of these: 186 ( 0.02%) short reads filtered out after trimming by size control 5 ( 0.00%) empty reads filtered out after trimming by size control 856435 (99.98%) reads available; of these: 6840 ( 0.80%) trimmed reads available after processing 849595 (99.20%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 10 0.00% 19 24 0.00% 20 24 0.00% 21 20 0.00% 22 21 0.00% 23 13 0.00% 24 16 0.00% 25 10 0.00% 26 16 0.00% 27 7 0.00% 28 25 0.00% 29 136 0.02% 30 12 0.00% 31 16 0.00% 32 25 0.00% 33 799 0.09% 34 18 0.00% 35 49 0.01% 36 10 0.00% 37 14 0.00% 38 28 0.00% 39 51 0.01% 40 74 0.01% 41 22 0.00% 42 11 0.00% 43 17 0.00% 44 19 0.00% 45 22 0.00% 46 9 0.00% 47 2 0.00% 48 8 0.00% 49 7 0.00% 50 11 0.00% 51 61 0.01% 52 9 0.00% 53 2 0.00% 54 11 0.00% 55 6 0.00% 56 8 0.00% 57 10 0.00% 58 14 0.00% 59 16 0.00% 60 16 0.00% 61 14 0.00% 62 1 0.00% 63 5 0.00% 64 4 0.00% 65 2 0.00% 66 9 0.00% 67 1 0.00% 68 23 0.00% 69 48 0.01% 70 6836 0.80% 71 6414 0.75% 72 6999 0.82% 73 6584 0.77% 74 6181 0.72% 75 5918 0.69% 76 5543 0.65% 77 6240 0.73% 78 6437 0.75% 79 6661 0.78% 80 6636 0.77% 81 8695 1.02% 82 8852 1.03% 83 7562 0.88% 84 9178 1.07% 85 47 0.01% 86 46 0.01% 87 60 0.01% 88 106 0.01% 89 174 0.02% 90 360 0.04% 91 759 0.09% 92 2691 0.31% 93 745650 87.06% 856435 reads passed initial QC criterion=sequence-density sequence-density=6.39 sequence-density-rank=1 fanout-score=2.03 fanout-score-rank=20 prefix-density=6.45 prefix-fanout=2.0 sequence=CAAGGCTAAATAC criterion=fanout-score sequence-density=0.14 sequence-density-rank=10 fanout-score=92.65 fanout-score-rank=1 prefix-density=6.41 prefix-fanout=2.0 sequence=AAGGCTAAATATAGGCGAGAGAC 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 01:06:30 Started mapping on | Dec 07 01:06:30 Finished on | Dec 07 01:06:34 Mapping speed, Million of reads per hour | 770.79 Number of input reads | 856435 Average input read length | 90 UNIQUE READS: Uniquely mapped reads number | 348566 Uniquely mapped reads % | 40.70% Average mapped length | 89.45 Number of splices: Total | 12331 Number of splices: Annotated (sjdb) | 9943 Number of splices: GT/AG | 11543 Number of splices: GC/AG | 282 Number of splices: AT/AC | 13 Number of splices: Non-canonical | 493 Mismatch rate per base, % | 0.45% Deletion rate per base | 0.04% Deletion average length | 1.74 Insertion rate per base | 0.02% Insertion average length | 1.93 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 426128 % of reads mapped to multiple loci | 49.76% Number of reads mapped to too many loci | 50216 % of reads mapped to too many loci | 5.86% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 3.30% % of reads unmapped: other | 0.38% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 81741 81741 81741 N_multimapping 426128 426128 426128 N_noFeature 29940 33427 333392 N_ambiguous 13532 1838 61 UnstrandedReadsAssigned:305094 PositiveStrandReadsAssigned:313301 NegativeStrandReadsAssigned:15113 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=93 echo kmer=89 ERR6133345 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: ERR6133345-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 856,435 reads, 485,914 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 861 rounds 52973 ERR6133345.ke.tsv 35125 ERR6133345.se.tsv 88098 total ==> ERR6133345.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 4 8.10978 PNS24243 293 194 0 0 KQK14069 1603 1504 5 9.24752 KQK14071 474 375 0 0 ==> ERR6133345.se.tsv <== BRADI_1g14170v3 5 BRADI_1g53295v3 4 BRADI_1g59795v3 3 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 1 BRADI_1g74790v3 5 BRADI_1g09890v3 0 BRADI_1g77505v3 7 BRADI_1g48960v3 0 ERR6133345 completed mapping pipeline successfully