Starting /dee2/code/volunteer_pipeline.sh ERR6133409 current disk space = 1547542847488 free memory = 1601820336 ERR6133409 SRAfilesize 0ee90fe5f4e9444d7a248f73c47f2742 ERR6133409.sra ERR6133409.sra file validated ERR6133409 is single end ERR6133409 is conventional basespace ERR6133409 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133409_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 47 >>END_MODULE >>Per base sequence quality fail #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 29.85025 33.0 27.0 33.0 15.0 37.0 2 33.8375 37.0 33.0 37.0 27.0 37.0 3 33.365 33.0 33.0 37.0 27.0 37.0 4 33.16025 37.0 33.0 37.0 22.0 37.0 5 33.3785 37.0 33.0 37.0 22.0 37.0 6 33.2315 37.0 33.0 37.0 22.0 37.0 7 34.918 37.0 33.0 37.0 27.0 40.0 8 34.638 37.0 33.0 37.0 27.0 40.0 9 35.13175 37.0 33.0 37.0 33.0 40.0 10-11 34.9555 37.0 33.0 37.0 30.0 40.0 12-13 34.691874999999996 37.0 33.0 37.0 27.0 40.0 14-15 34.6285 37.0 33.0 37.0 27.0 40.0 16-17 34.437375 37.0 33.0 37.0 27.0 40.0 18-19 34.23225 37.0 33.0 37.0 27.0 40.0 20-21 33.535875 37.0 33.0 37.0 24.5 40.0 22-23 33.230125 37.0 33.0 37.0 22.0 40.0 24-25 33.2735 35.0 33.0 37.0 24.5 40.0 26-27 32.997125 35.0 33.0 37.0 22.0 40.0 28-29 32.663125 33.0 33.0 37.0 22.0 40.0 30-31 32.883125 33.0 33.0 37.0 22.0 40.0 32-33 31.99275 33.0 30.0 37.0 22.0 40.0 34-35 30.764375 33.0 27.0 37.0 15.0 38.5 36-37 30.472 33.0 27.0 37.0 15.0 37.0 38-39 31.13825 33.0 27.0 37.0 22.0 37.0 40-41 30.432375 33.0 27.0 37.0 15.0 37.0 42-43 30.308125 33.0 27.0 37.0 15.0 37.0 44-45 29.992 33.0 24.5 37.0 15.0 37.0 46-47 29.6705 33.0 27.0 37.0 15.0 37.0 48-49 29.480875 33.0 24.5 37.0 15.0 37.0 50-51 28.97975 33.0 22.0 37.0 15.0 37.0 52-53 29.019750000000002 33.0 24.5 37.0 15.0 37.0 54-55 29.176000000000002 33.0 27.0 35.0 15.0 37.0 56-57 28.4615 33.0 24.5 33.0 15.0 37.0 58-59 28.109375 33.0 27.0 33.0 15.0 37.0 60-61 28.088250000000002 33.0 27.0 33.0 15.0 37.0 62-63 27.879624999999997 33.0 22.0 33.0 15.0 37.0 64-65 27.275875 33.0 24.5 33.0 10.5 37.0 66-67 26.824125000000002 33.0 22.0 33.0 6.0 37.0 68-69 25.832875 27.0 18.5 33.0 10.5 35.0 70-71 28.214250908293664 33.0 27.0 33.0 15.0 35.0 72-73 28.316866363810053 33.0 27.0 33.0 15.0 37.0 74-75 28.205049623503037 33.0 27.0 33.0 15.0 37.0 76-77 28.390050341608816 33.0 27.0 33.0 15.0 37.0 78-79 27.248909570175492 33.0 24.5 33.0 10.5 37.0 80-81 26.275159234211714 33.0 22.0 33.0 6.0 37.0 82-83 25.748102961814546 33.0 22.0 33.0 2.0 37.0 84-85 25.288038516952625 33.0 18.5 33.0 2.0 37.0 86-87 24.414529914529915 30.0 15.0 33.0 2.0 37.0 88-89 23.907407407407405 30.0 10.5 33.0 2.0 37.0 90-91 22.555296555296557 27.0 2.0 33.0 2.0 35.0 92-93 21.267288267288265 27.0 2.0 33.0 2.0 33.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 107.0 21 135.0 22 149.0 23 192.0 24 198.0 25 225.0 26 232.0 27 232.0 28 236.0 29 240.0 30 237.0 31 259.0 32 305.0 33 281.0 34 280.0 35 304.0 36 208.0 37 157.0 38 22.0 39 1.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 76.875 6.525 5.800000000000001 10.8 2 61.575 19.475 11.55 7.3999999999999995 3 45.15 30.325000000000003 14.2 10.325 4 23.7 41.4 17.849999999999998 17.05 5 38.25 22.025 24.224999999999998 15.5 6 15.775 49.125 21.025 14.075 7 45.074999999999996 23.724999999999998 17.5 13.700000000000001 8 21.55 21.9 21.85 34.699999999999996 9 19.475 44.375 21.575 14.575 10-11 18.7375 32.300000000000004 33.324999999999996 15.6375 12-13 18.125 34.112500000000004 22.537499999999998 25.224999999999998 14-15 16.5875 44.1 23.7 15.6125 16-17 29.2 24.125 19.400000000000002 27.275 18-19 27.9375 20.8625 35.1875 16.0125 20-21 28.9 20.1125 34.5875 16.400000000000002 22-23 32.0125 18.912499999999998 32.725 16.35 24-25 19.675 19.825 33.1875 27.3125 26-27 28.525 19.2 25.7375 26.5375 28-29 19.2125 33.175 31.874999999999996 15.737499999999999 30-31 41.6875 21.8125 20.25 16.25 32-33 30.425 20.200000000000003 22.0875 27.287499999999998 34-35 18.3125 44.8125 20.325 16.55 36-37 29.525000000000002 22.037499999999998 20.4125 28.025 38-39 43.575 17.7625 22.3375 16.325 40-41 20.6625 19.6 43.7875 15.950000000000001 42-43 30.575000000000003 33.5 20.9 15.024999999999999 44-45 29.875 21.5375 32.5 16.0875 46-47 30.45 20.8125 21.3625 27.375 48-49 29.9375 19.4875 23.925 26.650000000000002 50-51 18.8 32.237500000000004 21.1125 27.85 52-53 19.5125 21.25 21.0 38.237500000000004 54-55 18.2 20.7875 34.2375 26.775 56-57 30.4625 31.574999999999996 22.175 15.787499999999998 58-59 18.525 32.425 32.3125 16.7375 60-61 40.387499999999996 21.2 21.975 16.4375 62-63 16.45 23.0625 34.575 25.912499999999998 64-65 17.2125 45.537499999999994 22.0125 15.2375 66-67 29.275000000000002 32.9875 21.3625 16.375 68-69 18.95 20.8 32.025 28.225 70-71 18.55837817544738 31.898385683894382 22.612939557001628 26.930296583656617 72-73 30.65528496108461 21.604318353000252 32.03615365302536 15.704243032889782 74-75 29.89781758546739 32.93805979563517 21.92506622934275 15.239056389554687 76-77 18.429385687143764 20.39265357821406 21.49461684610513 39.683343888537046 78-79 28.760330578512395 32.638270820089 21.51303242212333 17.08836617927527 80-81 17.844816566534575 47.07912565511952 21.104435638501855 13.971622139844051 82-83 28.560401389424932 20.81564389553583 21.330245722372315 29.29370899266692 84-85 17.756526234169037 29.51667097441199 34.466270354096665 18.260532437322304 86-87 17.52136752136752 33.65708365708366 21.21212121212121 27.609427609427613 88-89 16.23931623931624 22.83087283087283 33.72183372183372 27.20797720797721 90-91 30.212380212380214 32.452732452732455 21.147371147371146 16.187516187516188 92-93 16.174566174566174 24.553224553224553 32.23258223258224 27.03962703962704 >>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 1.0 17 3.5 18 5.5 19 3.0 20 1.5 21 2.5 22 3.5 23 5.0 24 3.5 25 2.5 26 3.0 27 7.0 28 21.0 29 29.5 30 27.0 31 29.5 32 42.0 33 47.0 34 44.5 35 60.5 36 97.0 37 148.0 38 188.5 39 182.0 40 171.5 41 162.0 42 156.5 43 169.0 44 156.5 45 133.5 46 135.5 47 135.5 48 110.0 49 98.0 50 94.5 51 100.0 52 114.0 53 170.0 54 454.0 55 477.0 56 191.5 57 113.5 58 84.5 59 40.5 60 23.5 61 18.5 62 12.5 63 10.0 64 8.0 65 7.5 66 7.5 67 5.5 68 4.5 69 5.0 70 4.0 71 2.0 72 3.0 73 4.0 74 2.0 75 0.0 76 0.0 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 0.0 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 0.0 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 9.0 71 4.0 72 8.0 73 9.0 74 13.0 75 5.0 76 9.0 77 7.0 78 7.0 79 11.0 80 13.0 81 14.0 82 9.0 83 5.0 84 16.0 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 3861.0 >>END_MODULE >>Sequence Duplication Levels warn #Total Deduplicated Percentage 61.625 #Duplication Level Percentage of deduplicated Percentage of total 1 91.27789046653145 56.25 2 4.300202839756592 5.3 3 1.460446247464503 2.7 4 0.4056795131845842 1.0 5 0.486815415821501 1.5 6 0.4056795131845842 1.5 7 0.2434077079107505 1.05 8 0.2839756592292089 1.4000000000000001 9 0.04056795131845842 0.22499999999999998 >10 1.054766734279919 10.775 >50 0.0 0.0 >100 0.0 0.0 >500 0.04056795131845842 18.3 >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 732 18.3 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 39 0.975 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 33 0.8250000000000001 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 31 0.775 No Hit GGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAAATGGATTC 24 0.6 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 22 0.5499999999999999 No Hit GGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCG 20 0.5 No Hit GGGTTGTGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGA 18 0.44999999999999996 No Hit GGGGTTGTGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTG 17 0.42500000000000004 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 16 0.4 No Hit GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 16 0.4 No Hit GGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGCA 15 0.375 No Hit TCAAAAGAGGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGGA 15 0.375 No Hit GGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGC 14 0.35000000000000003 No Hit GTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAA 14 0.35000000000000003 No Hit GTACTATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTT 13 0.325 No Hit CAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCT 13 0.325 No Hit GTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCT 13 0.325 No Hit GTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAG 13 0.325 No Hit GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGGGCCGC 12 0.3 No Hit GGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAAA 11 0.27499999999999997 No Hit GTATTAGTACTATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATCT 11 0.27499999999999997 No Hit GGGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTG 11 0.27499999999999997 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 10 0.25 No Hit CAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATAT 10 0.25 No Hit GGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGG 10 0.25 No Hit CAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTG 10 0.25 No Hit GGAAAAGAAAGCAAAAGCGATTCCCGTAGTAGCGGCGAGCGAAATGGGAG 9 0.22499999999999998 No Hit GGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAA 8 0.2 No Hit ATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGG 8 0.2 No Hit GGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTCCT 8 0.2 No Hit GAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGC 8 0.2 No Hit GGGAGAGCAATACAAGCTTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGC 8 0.2 No Hit TCTCATGGAGAGTTCGATCCTGGCTCAGGATGAACGCTGGCGGCATGCTT 8 0.2 No Hit GGATTTGTTAAATCAAATCCTTGGTTTAATAACGAACGGTGTTAACTTAC 8 0.2 No Hit CAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTT 7 0.17500000000000002 No Hit CTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGT 7 0.17500000000000002 No Hit GGCCTGTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCG 7 0.17500000000000002 No Hit GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGAGGTTGAGTGCCGC 7 0.17500000000000002 No Hit GGAGTATCCTTGATATATAAATATATAGATAAATAGATTTAAATGGAAAA 7 0.17500000000000002 No Hit GCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGT 7 0.17500000000000002 No Hit GTAGCATGGGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGC 6 0.15 No Hit GGGCTCGCGTCTGATTAGCTAGTTGGTGAGGCAATAGCTTACCAAGGCGA 6 0.15 No Hit GGCTTTAGAAGCCTGTGTACAAGCTCGTAACGAAGGGCGCGATCTTGCTC 6 0.15 No Hit GGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGGG 6 0.15 No Hit GAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAAAT 6 0.15 No Hit GATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAAT 6 0.15 No Hit GTACAAGCTCGTAACGAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAAT 6 0.15 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 6 0.15 No Hit GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGA 6 0.15 No Hit GGGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTA 6 0.15 No Hit GGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCG 5 0.125 No Hit GGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTT 5 0.125 No Hit GGTTGTGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAG 5 0.125 No Hit GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCAGC 5 0.125 No Hit GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGCGTGCCGC 5 0.125 No Hit GTGAAAACGGGGTTGTGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGA 5 0.125 No Hit GAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTG 5 0.125 No Hit GGAGCAGCCTAAACCGTGAAAACGGGGTTGTGGGAGAGCAATACAAGCGT 5 0.125 No Hit GTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTC 5 0.125 No Hit GCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCA 5 0.125 No Hit GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCGGC 5 0.125 No Hit GGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGC 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 0.0 0.0 0.0 0.0 0.0 38-39 0.0 0.0 0.0 0.0 0.0 40-41 0.0 0.0 0.0 0.0 0.0 42-43 0.0 0.0 0.0 0.0 0.0 44-45 0.0 0.0 0.0 0.0 0.0 46-47 0.0 0.0 0.0 0.0 0.0 48-49 0.0 0.0 0.0 0.0 0.0 50-51 0.0 0.0 0.0 0.0 0.0 52-53 0.0 0.0 0.0 0.0 0.0 54-55 0.0 0.0 0.0 0.0 0.0 56-57 0.0 0.0 0.0 0.0 0.0 58-59 0.0 0.0 0.0 0.0 0.0 60-61 0.0 0.0 0.0 0.0 0.0 62-63 0.0 0.0 0.0 0.0 0.0 64-65 0.0 0.0 0.0 0.0 0.0 66-67 0.0 0.0 0.0 0.0 0.0 68-69 0.0 0.0 0.0 0.0 0.0 70-71 0.0 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 GGAGAGC 105 0.0 82.40476 2 GCAATAC 105 0.0 82.40476 7 GGGAGAG 105 0.0 82.40476 1 CAATACA 105 0.0 82.40476 8 GAGCAAT 105 0.0 82.40476 5 AGAGCAA 105 0.0 82.40476 4 GAGAGCA 105 0.0 82.40476 3 AGCAATA 105 0.0 82.40476 6 AATACAA 115 0.0 75.23913 9 TCCAGTA 95 0.0 43.2625 68-69 GTCCAGT 95 0.0 43.2625 66-67 AGTCCAG 90 0.0 43.2625 66-67 CACTAGC 85 0.0 42.30405 86-87 TCACTAG 85 0.0 42.30405 84-85 CCGAAAG 85 0.0 42.30405 76-77 ATCACTA 75 0.0 41.951515 84-85 AGCATCA 75 0.0 41.951515 80-81 AAGCATC 75 0.0 41.951515 80-81 GCCGAAA 85 0.0 41.23306 74-75 AGTAGCC 100 0.0 41.099373 70-71 >>END_MODULE Rejected 110724 READS because READLEN < 1 Read 110724 spots for ERR6133409.sra Written 110724 spots for ERR6133409.sra Rejected 110724 READS because READLEN < 1 Read 110724 spots for ERR6133409.sra Written 110724 spots for ERR6133409.sra Rejected 110724 READS because READLEN < 1 Read 110724 spots for ERR6133409.sra Written 110724 spots for ERR6133409.sra Rejected 110724 READS because READLEN < 1 Read 110724 spots for ERR6133409.sra Written 110724 spots for ERR6133409.sra Rejected 110724 READS because READLEN < 1 Read 110724 spots for ERR6133409.sra Written 110724 spots for ERR6133409.sra Rejected 110724 READS because READLEN < 1 Read 110724 spots for ERR6133409.sra Written 110724 spots for ERR6133409.sra Rejected 110724 READS because READLEN < 1 Read 110724 spots for ERR6133409.sra Written 110724 spots for ERR6133409.sra Rejected 110724 READS because READLEN < 1 Read 110724 spots for ERR6133409.sra Written 110724 spots for ERR6133409.sra Rejected 110724 READS because READLEN < 1 Read 110724 spots for ERR6133409.sra Written 110724 spots for ERR6133409.sra Rejected 110724 READS because READLEN < 1 Read 110724 spots for ERR6133409.sra Written 110724 spots for ERR6133409.sra Rejected 110724 READS because READLEN < 1 Read 110724 spots for ERR6133409.sra Written 110724 spots for ERR6133409.sra Rejected 110724 READS because READLEN < 1 Read 110724 spots for ERR6133409.sra Written 110724 spots for ERR6133409.sra Rejected 110724 READS because READLEN < 1 Read 110724 spots for ERR6133409.sra Written 110724 spots for ERR6133409.sra Rejected 110724 READS because READLEN < 1 Read 110724 spots for ERR6133409.sra Written 110724 spots for ERR6133409.sra Rejected 110724 READS because READLEN < 1 Read 110724 spots for ERR6133409.sra Written 110724 spots for ERR6133409.sra Rejected 110730 READS because READLEN < 1 Read 110730 spots for ERR6133409.sra Written 110730 spots for ERR6133409.sra Rejected 110724 READS because READLEN < 1 Read 110724 spots for ERR6133409.sra Written 110724 spots for ERR6133409.sra Rejected 110724 READS because READLEN < 1 Read 110724 spots for ERR6133409.sra Written 110724 spots for ERR6133409.sra Rejected 110724 READS because READLEN < 1 Read 110724 spots for ERR6133409.sra Written 110724 spots for ERR6133409.sra Rejected 110724 READS because READLEN < 1 Read 110724 spots for ERR6133409.sra Written 110724 spots for ERR6133409.sra SRR ids: ['ERR6133409.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_3qbd5_nn ERR6133409.sra spots: 2214486 blocks: [[1, 110724], [110725, 221448], [221449, 332172], [332173, 442896], [442897, 553620], [553621, 664344], [664345, 775068], [775069, 885792], [885793, 996516], [996517, 1107240], [1107241, 1217964], [1217965, 1328688], [1328689, 1439412], [1439413, 1550136], [1550137, 1660860], [1660861, 1771584], [1771585, 1882308], [1882309, 1993032], [1993033, 2103756], [2103757, 2214486]] ERR6133409 file size 488094 ERR6133409 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 ERR6133409 ERR6133409_1.fastq Input file: ERR6133409_1.fastq trimmed: ERR6133409-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 03:33:43 2024 >> started Sat Dec 7 03:33:45 2024 >> done (1.553s) 2214486 reads processed; of these: 30 ( 0.00%) short reads filtered out after trimming by size control 1 ( 0.00%) empty reads filtered out after trimming by size control 2214455 (100.00%) reads available; of these: 591862 (26.73%) trimmed reads available after processing 1622593 (73.27%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 2 0.00% 19 5 0.00% 20 3 0.00% 21 1 0.00% 22 2 0.00% 23 0 0.00% 24 0 0.00% 25 3 0.00% 26 1 0.00% 27 2 0.00% 28 3 0.00% 29 9 0.00% 30 0 0.00% 31 3 0.00% 32 4 0.00% 33 5 0.00% 34 0 0.00% 35 5 0.00% 36 3 0.00% 37 3 0.00% 38 7 0.00% 39 14 0.00% 40 17 0.00% 41 6 0.00% 42 16 0.00% 43 13 0.00% 44 17 0.00% 45 26 0.00% 46 46 0.00% 47 53 0.00% 48 107 0.00% 49 128 0.01% 50 195 0.01% 51 256 0.01% 52 382 0.02% 53 551 0.02% 54 819 0.04% 55 960 0.04% 56 1408 0.06% 57 2113 0.10% 58 1545 0.07% 59 1948 0.09% 60 2355 0.11% 61 2821 0.13% 62 3077 0.14% 63 3386 0.15% 64 3822 0.17% 65 4167 0.19% 66 3999 0.18% 67 4593 0.21% 68 3618 0.16% 69 3414 0.15% 70 9536 0.43% 71 10508 0.47% 72 13114 0.59% 73 13205 0.60% 74 14642 0.66% 75 16214 0.73% 76 18795 0.85% 77 21935 0.99% 78 22272 1.01% 79 22072 1.00% 80 23353 1.05% 81 26279 1.19% 82 27915 1.26% 83 30598 1.38% 84 35767 1.62% 85 30487 1.38% 86 30314 1.37% 87 33978 1.53% 88 45955 2.08% 89 44113 1.99% 90 45370 2.05% 91 49099 2.22% 92 44263 2.00% 93 1538738 69.49% 2214455 reads passed initial QC criterion=sequence-density sequence-density=2.24 sequence-density-rank=1 fanout-score=2.05 fanout-score-rank=35 prefix-density=2.30 prefix-fanout=2.0 sequence=CAAGGCTAAATAC criterion=fanout-score sequence-density=0.13 sequence-density-rank=30 fanout-score=196.48 fanout-score-rank=1 prefix-density=24.78 prefix-fanout=1.0 sequence=GCGGTTGAGTGACGCACCCTAGA 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 03:34:07 Started mapping on | Dec 07 03:34:07 Finished on | Dec 07 03:34:15 Mapping speed, Million of reads per hour | 996.50 Number of input reads | 2214455 Average input read length | 89 UNIQUE READS: Uniquely mapped reads number | 737226 Uniquely mapped reads % | 33.29% Average mapped length | 88.87 Number of splices: Total | 39327 Number of splices: Annotated (sjdb) | 31024 Number of splices: GT/AG | 37536 Number of splices: GC/AG | 762 Number of splices: AT/AC | 28 Number of splices: Non-canonical | 1001 Mismatch rate per base, % | 0.85% Deletion rate per base | 0.04% Deletion average length | 1.77 Insertion rate per base | 0.02% Insertion average length | 1.82 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 1328725 % of reads mapped to multiple loci | 60.00% Number of reads mapped to too many loci | 48765 % of reads mapped to too many loci | 2.20% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 4.13% % of reads unmapped: other | 0.37% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 148504 148504 148504 N_multimapping 1328725 1328725 1328725 N_noFeature 65223 72930 703152 N_ambiguous 31497 5106 115 UnstrandedReadsAssigned:640506 PositiveStrandReadsAssigned:659190 NegativeStrandReadsAssigned:33959 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=86 echo kmer=81 ERR6133409 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: ERR6133409-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 2,214,455 reads, 1,203,550 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 875 rounds 52973 ERR6133409.ke.tsv 35125 ERR6133409.se.tsv 88098 total ==> ERR6133409.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 9 7.04986 PNS24243 293 194 0 0 KQK14069 1603 1504 5 3.57284 KQK14071 474 375 0 0 ==> ERR6133409.se.tsv <== BRADI_1g14170v3 5 BRADI_1g53295v3 23 BRADI_1g59795v3 6 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 5 BRADI_1g74790v3 8 BRADI_1g09890v3 0 BRADI_1g77505v3 21 BRADI_1g48960v3 0 ERR6133409 completed mapping pipeline successfully