Starting /dee2/code/volunteer_pipeline.sh ERR6133315 current disk space = 1548187586560 free memory = 1410018140 ERR6133315 SRAfilesize a67a9f61a0ae3b11fcfbf436e785a2a4 ERR6133315.sra ERR6133315.sra file validated ERR6133315 is single end ERR6133315 is conventional basespace ERR6133315 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133315_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 44 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 35.19475 37.0 33.0 37.0 33.0 37.0 2 36.38 37.0 37.0 37.0 37.0 37.0 3 35.89125 37.0 37.0 37.0 33.0 37.0 4 35.417 37.0 37.0 37.0 33.0 37.0 5 35.37475 37.0 37.0 37.0 33.0 37.0 6 35.6465 37.0 37.0 37.0 33.0 37.0 7 37.4685 40.0 37.0 40.0 33.0 40.0 8 37.4935 40.0 37.0 40.0 33.0 40.0 9 37.606 40.0 37.0 40.0 33.0 40.0 10-11 37.575 38.5 37.0 40.0 33.0 40.0 12-13 37.565875000000005 40.0 37.0 40.0 33.0 40.0 14-15 37.431749999999994 37.0 37.0 40.0 33.0 40.0 16-17 37.37875 37.0 37.0 40.0 33.0 40.0 18-19 37.258875 37.0 37.0 40.0 33.0 40.0 20-21 37.099625 37.0 37.0 40.0 33.0 40.0 22-23 37.044875 37.0 37.0 40.0 33.0 40.0 24-25 37.1855 37.0 37.0 40.0 33.0 40.0 26-27 37.088125 37.0 37.0 40.0 33.0 40.0 28-29 36.98775 37.0 37.0 40.0 33.0 40.0 30-31 37.01649999999999 37.0 37.0 40.0 33.0 40.0 32-33 36.908625 37.0 37.0 40.0 33.0 40.0 34-35 36.672625 37.0 37.0 40.0 33.0 40.0 36-37 36.563625 37.0 37.0 40.0 33.0 40.0 38-39 36.470625 37.0 37.0 40.0 33.0 40.0 40-41 36.2375 37.0 37.0 40.0 33.0 40.0 42-43 36.0895 37.0 37.0 40.0 33.0 40.0 44-45 35.765 37.0 33.0 40.0 33.0 40.0 46-47 35.275499999999994 37.0 33.0 38.5 27.0 40.0 48-49 35.346875 37.0 33.0 37.0 27.0 40.0 50-51 35.23225 37.0 33.0 37.0 27.0 40.0 52-53 35.05175 37.0 33.0 37.0 27.0 40.0 54-55 34.844375 37.0 33.0 37.0 27.0 40.0 56-57 34.600875 37.0 33.0 37.0 27.0 40.0 58-59 32.321375 33.0 30.0 37.0 24.5 37.0 60-61 33.88825 37.0 33.0 37.0 27.0 37.0 62-63 34.137375 37.0 33.0 37.0 27.0 37.0 64-65 34.02025 37.0 33.0 37.0 27.0 37.0 66-67 33.777375000000006 37.0 33.0 37.0 27.0 37.0 68-69 33.240624999999994 35.0 33.0 37.0 27.0 37.0 70-71 33.35916278337531 35.0 33.0 37.0 27.0 37.0 72-73 33.67040309175789 37.0 33.0 37.0 27.0 37.0 74-75 33.698266652500834 37.0 33.0 37.0 27.0 37.0 76-77 33.65974302460234 37.0 33.0 37.0 27.0 37.0 78-79 33.539836265035106 37.0 33.0 37.0 27.0 37.0 80-81 33.45741960453927 37.0 33.0 37.0 27.0 37.0 82-83 33.17102127546826 37.0 33.0 37.0 27.0 37.0 84-85 33.02877751474527 33.0 33.0 37.0 27.0 37.0 86-87 32.99986157253599 35.0 33.0 37.0 27.0 37.0 88-89 33.0687984496124 37.0 33.0 37.0 27.0 37.0 90-91 32.81298449612403 33.0 33.0 37.0 27.0 37.0 92-93 32.736434108527135 33.0 33.0 37.0 27.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 12.0 21 9.0 22 23.0 23 26.0 24 40.0 25 39.0 26 30.0 27 50.0 28 57.0 29 81.0 30 100.0 31 110.0 32 143.0 33 184.0 34 299.0 35 482.0 36 775.0 37 903.0 38 615.0 39 22.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 83.325 4.075 5.1 7.5 2 64.4 20.549999999999997 10.0 5.050000000000001 3 32.65 37.95 16.6 12.8 4 31.7 26.525 21.375 20.4 5 21.75 30.875000000000004 30.025000000000002 17.349999999999998 6 20.4 37.2 26.775 15.625 7 36.199999999999996 26.85 21.175 15.775 8 29.349999999999998 27.900000000000002 25.75 17.0 9 24.425 27.85 27.525 20.200000000000003 10-11 23.575 28.287499999999998 28.9375 19.2 12-13 24.762500000000003 25.8 28.675 20.7625 14-15 21.099999999999998 29.212500000000002 30.062499999999996 19.625 16-17 24.575 30.7375 24.8625 19.825 18-19 23.8125 25.974999999999998 28.549999999999997 21.6625 20-21 24.228028503562946 26.690836354544317 27.903487935992 21.177647205900737 22-23 26.5625 23.974999999999998 28.425 21.0375 24-25 24.337500000000002 26.325 29.675 19.662499999999998 26-27 25.674999999999997 24.7875 30.612499999999997 18.925 28-29 25.025 26.85 28.812500000000004 19.3125 30-31 26.125 25.825 28.325 19.725 32-33 24.5625 27.0 29.037499999999998 19.400000000000002 34-35 24.00300037504688 27.715964495561945 27.603450431303912 20.677584698087262 36-37 24.4375 25.575 28.3875 21.6 38-39 25.468867216804203 26.281570392598148 28.707176794198553 19.5423855963991 40-41 24.0125 25.6 29.45 20.9375 42-43 24.1375 28.762500000000003 28.199999999999996 18.9 44-45 22.765345668208525 26.790848856107015 29.828728591073883 20.615076884610577 46-47 24.40305038129766 26.24078009751219 28.716089511188898 20.64008001000125 48-49 23.875 26.474999999999998 29.3375 20.3125 50-51 21.752719089886234 28.453556694586823 29.053631703962996 20.740092511563944 52-53 24.518629657414355 26.144036009002253 28.207051762940733 21.13028257064266 54-55 24.587500000000002 26.8125 29.849999999999998 18.75 56-57 23.6375 27.3 30.412499999999998 18.65 58-59 21.6875 27.712500000000002 30.7125 19.8875 60-61 25.775 25.974999999999998 29.2 19.05 62-63 22.400000000000002 28.8625 31.0 17.7375 64-65 22.3375 29.799999999999997 29.1375 18.725 66-67 23.9 30.2375 27.825 18.0375 68-69 22.537499999999998 26.787499999999998 28.9375 21.7375 70-71 23.161856963613552 27.791718946047677 29.573400250941027 19.47302383939774 72-73 25.371617329437175 25.42243679329183 29.691271757082966 19.514674120188033 74-75 23.84396796693361 26.94394213381555 29.411004908292433 19.801084990958408 76-77 22.641755944604128 25.476874836686697 30.729030572249805 21.152338646459366 78-79 24.429795649307845 26.24917600527357 29.41331575477917 19.90771259063942 80-81 23.15803523758676 29.05766150560598 29.21783235451148 18.56647090229578 82-83 23.45829937516979 25.726704699809833 31.078511274110298 19.73648465091008 84-85 21.70071783545003 25.469353948094977 32.523467697404755 20.306460519050248 86-87 22.051495016611295 26.785714285714285 30.661683277962346 20.50110741971207 88-89 21.22093023255814 31.173864894795127 29.318936877076414 18.28626799557032 90-91 23.477297895902545 29.858803986710964 28.72369878183832 17.940199335548172 92-93 21.760797342192692 32.07364341085272 27.505537098560357 18.660022148394244 >>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 0.5 18 0.0 19 0.0 20 0.5 21 2.5 22 3.5 23 6.5 24 11.0 25 10.0 26 13.0 27 17.5 28 25.5 29 32.5 30 42.0 31 56.0 32 74.5 33 92.5 34 112.0 35 136.5 36 150.5 37 184.0 38 200.5 39 189.0 40 198.5 41 199.0 42 197.0 43 205.0 44 190.0 45 182.0 46 189.5 47 173.0 48 160.0 49 159.5 50 175.0 51 152.0 52 110.0 53 115.0 54 125.0 55 100.5 56 62.5 57 55.5 58 48.5 59 36.0 60 29.5 61 23.0 62 19.5 63 17.0 64 10.0 65 12.0 66 14.0 67 11.0 68 10.0 69 9.5 70 10.5 71 11.0 72 9.5 73 6.0 74 4.0 75 3.5 76 1.5 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 0.0125 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 0.0125 36-37 0.0 38-39 0.025 40-41 0.0 42-43 0.0 44-45 0.0125 46-47 0.0125 48-49 0.0 50-51 0.0125 52-53 0.025 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 30.0 71 18.0 72 33.0 73 33.0 74 30.0 75 16.0 76 26.0 77 14.0 78 15.0 79 24.0 80 30.0 81 30.0 82 40.0 83 29.0 84 20.0 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 3612.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 81.025 #Duplication Level Percentage of deduplicated Percentage of total 1 92.90342486886763 75.275 2 3.949398333847578 6.4 3 0.8947855600123419 2.175 4 0.6479481641468683 2.1 5 0.49367479173094725 2.0 6 0.2776920703486578 1.35 7 0.09256402344955261 0.525 8 0.030854674483184203 0.2 9 0.061709348966368406 0.44999999999999996 >10 0.617093489663684 8.025 >50 0.030854674483184203 1.5 >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 TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 60 1.5 No Hit GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGC 49 1.225 No Hit GGGATGGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACGA 20 0.5 No Hit GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 20 0.5 No Hit GGGCATTCGTATTTCATAGTCAGAGGTGAAATTCTTGGATTTATGAAAGA 20 0.5 No Hit GGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGC 20 0.5 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 17 0.42500000000000004 No Hit GGACATTTCTTCGAACAAATTCGAATAGTGAGACGCATTAAAACGCAATT 16 0.4 No Hit GGGGATGGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACG 15 0.375 No Hit GGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGG 15 0.375 No Hit GGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCTGC 14 0.35000000000000003 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 13 0.325 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 12 0.3 No Hit GGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTT 12 0.3 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 12 0.3 No Hit GGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTCCT 12 0.3 No Hit GGGGCATTCGTATTTCATAGTCAGAGGTGAAATTCTTGGATTTATGAAAG 12 0.3 No Hit GTATTTAGCCTTGCAAGGTGGTCCTTGCTGATTCACACGGGATTCCACGT 11 0.27499999999999997 No Hit GGCGATCAAATTCGAGTTCGAGCCGGTAGATACTATCGATTAATAGATAA 11 0.27499999999999997 No Hit GGGAGTATTATGAAAGGAGATTAATCATAGATTATCAAAAACCCTAGAAA 10 0.25 No Hit GGAGTCCTGAACTAGCTGCAGCTTGTGAAGTATGGAAGGCGATCAAATTC 10 0.25 No Hit GAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGC 9 0.22499999999999998 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 9 0.22499999999999998 No Hit GGTTTTGAAAAGGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAA 8 0.2 No Hit GGATTGGTCTAGTCTTTCTCGTAGCTATTCTGAATTCTCTCATTTCATAA 7 0.17500000000000002 No Hit GTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCT 7 0.17500000000000002 No Hit GATACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGC 7 0.17500000000000002 No Hit GGGGTACTCTTTCTACACCTATATTTAGTATTAGTACCGAAATGCTTTAA 6 0.15 No Hit GGTGGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGC 6 0.15 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 6 0.15 No Hit GGGGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCT 6 0.15 No Hit GGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGGG 6 0.15 No Hit GGAGATTCCCAAATAGGTCAACCTTTTAAACTGCCTGCTGAATCCATGAG 6 0.15 No Hit TCAGTGTCGGCCCAGCAGAGTGCTTTCGCCGTTGGTGTTCTTTCCGATCT 6 0.15 No Hit GGCATTCGTATTTCATAGTCAGAGGTGAAATTCTTGGATTTATGAAAGAC 6 0.15 No Hit TCAAAAGAGGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGGA 6 0.15 No Hit GGAGGGTGAGAGCCCCGTCCGGCCCGGACCCTGTCGCCCCACGAGGCGCC 5 0.125 No Hit GTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAA 5 0.125 No Hit GAAGGCGATCAAATTCGAGTTCGAGCCGGTAGATACTATCGATTAATAGA 5 0.125 No Hit GGTCAACCTTTTAAACTGCCTGCTGAATCCATGAGCAGGCAAGAGACAAC 5 0.125 No Hit GTATGGAAGGCGATCAAATTCGAGTTCGAGCCGGTAGATACTATCGATTA 5 0.125 No Hit GTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCTGCA 5 0.125 No Hit GGGACAGTCGGGGGCATTCGTATTTCATAGTCAGAGGTGAAATTCTTGGA 5 0.125 No Hit GGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAATCCTCTTAACT 5 0.125 No Hit GGATACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATG 5 0.125 No Hit GGGTACTCTTTCTACACCTATATTTAGTATTAGTACCGAAATGCTTTAAA 5 0.125 No Hit GGGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTG 5 0.125 No Hit GTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTC 5 0.125 No Hit GCAGCTTGCAAATGGAGTCCTGAACTAGCTGCAGCTTGTGAAGTATGGAA 5 0.125 No Hit GGGTCGATGCCCGAGCGGTTAATGGGGACGGACTGTAAATTCGTTGACAA 5 0.125 No Hit GGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAA 5 0.125 No Hit GGGTGAGAGCCCCGTCCGGCCCGGACCCTGTCGCCCCACGAGGCGCCGTC 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 0.0625 0.0 0.0 0.0 0.0 22-23 0.1 0.0 0.0 0.0 0.0 24-25 0.1 0.0 0.0 0.0 0.0 26-27 0.1 0.0 0.0 0.0 0.0 28-29 0.1 0.0 0.0 0.0 0.0 30-31 0.1375 0.0 0.0 0.0 0.0 32-33 0.16249999999999998 0.0 0.0 0.0 0.0 34-35 0.1875 0.0 0.0 0.0 0.0 36-37 0.2375 0.0 0.0 0.0 0.0 38-39 0.25 0.0 0.0 0.0 0.0 40-41 0.3125 0.0 0.0 0.0 0.0 42-43 0.35 0.0 0.0 0.0 0.0 44-45 0.3625 0.0 0.0 0.0 0.0 46-47 0.375 0.0 0.0 0.0 0.0 48-49 0.375 0.0 0.0 0.0 0.0 50-51 0.375 0.0 0.0 0.0 0.0 52-53 0.375 0.0 0.0 0.0 0.0 54-55 0.375 0.0 0.0 0.0 0.0 56-57 0.3875 0.0 0.0 0.0 0.0 58-59 0.4 0.0 0.0 0.0 0.0 60-61 0.4 0.0 0.0 0.0 0.0 62-63 0.4 0.0 0.0 0.0 0.0 64-65 0.4 0.0 0.0 0.0 0.0 66-67 0.4 0.0 0.0 0.0 0.0 68-69 0.4 0.0 0.0 0.0 0.0 70-71 0.4 0.0 0.0 0.0 0.0 72-73 0.475 0.0 0.0 0.0 0.0 74-75 0.5 0.0 0.0 0.0 0.0 76-77 0.5 0.0 0.0 0.0 0.0 78-79 0.525 0.0 0.0 0.0 0.0 80-81 0.525 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Rejected 123945 READS because READLEN < 1 Read 123945 spots for ERR6133315.sra Written 123945 spots for ERR6133315.sra Rejected 123945 READS because READLEN < 1 Read 123945 spots for ERR6133315.sra Written 123945 spots for ERR6133315.sra Rejected 123945 READS because READLEN < 1 Read 123945 spots for ERR6133315.sra Written 123945 spots for ERR6133315.sra Rejected 123945 READS because READLEN < 1 Read 123945 spots for ERR6133315.sra Written 123945 spots for ERR6133315.sra Rejected 123945 READS because READLEN < 1 Read 123945 spots for ERR6133315.sra Written 123945 spots for ERR6133315.sra Rejected 123945 READS because READLEN < 1 Read 123945 spots for ERR6133315.sra Written 123945 spots for ERR6133315.sra Rejected 123956 READS because READLEN < 1 Read 123956 spots for ERR6133315.sra Written 123956 spots for ERR6133315.sra Rejected 123945 READS because READLEN < 1 Read 123945 spots for ERR6133315.sra Written 123945 spots for ERR6133315.sra Rejected 123945 READS because READLEN < 1 Read 123945 spots for ERR6133315.sra Written 123945 spots for ERR6133315.sra Rejected 123945 READS because READLEN < 1 Read 123945 spots for ERR6133315.sra Written 123945 spots for ERR6133315.sra Rejected 123945 READS because READLEN < 1 Read 123945 spots for ERR6133315.sra Written 123945 spots for ERR6133315.sra Rejected 123945 READS because READLEN < 1 Read 123945 spots for ERR6133315.sra Written 123945 spots for ERR6133315.sra Rejected 123945 READS because READLEN < 1 Read 123945 spots for ERR6133315.sra Written 123945 spots for ERR6133315.sra Rejected 123945 READS because READLEN < 1 Read 123945 spots for ERR6133315.sra Written 123945 spots for ERR6133315.sra Rejected 123945 READS because READLEN < 1 Read 123945 spots for ERR6133315.sra Written 123945 spots for ERR6133315.sra Rejected 123945 READS because READLEN < 1 Read 123945 spots for ERR6133315.sra Written 123945 spots for ERR6133315.sra Rejected 123945 READS because READLEN < 1 Read 123945 spots for ERR6133315.sra Written 123945 spots for ERR6133315.sra Rejected 123945 READS because READLEN < 1 Read 123945 spots for ERR6133315.sra Written 123945 spots for ERR6133315.sra Rejected 123945 READS because READLEN < 1 Read 123945 spots for ERR6133315.sra Written 123945 spots for ERR6133315.sra Rejected 123945 READS because READLEN < 1 Read 123945 spots for ERR6133315.sra Written 123945 spots for ERR6133315.sra SRR ids: ['ERR6133315.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_1wkqzvmw ERR6133315.sra spots: 2478911 blocks: [[1, 123945], [123946, 247890], [247891, 371835], [371836, 495780], [495781, 619725], [619726, 743670], [743671, 867615], [867616, 991560], [991561, 1115505], [1115506, 1239450], [1239451, 1363395], [1363396, 1487340], [1487341, 1611285], [1611286, 1735230], [1735231, 1859175], [1859176, 1983120], [1983121, 2107065], [2107066, 2231010], [2231011, 2354955], [2354956, 2478911]] ERR6133315 file size 542222 ERR6133315 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 ERR6133315 ERR6133315_1.fastq Input file: ERR6133315_1.fastq trimmed: ERR6133315-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 00:28:01 2024 >> started Sat Dec 7 00:28:03 2024 >> done (1.840s) 2478911 reads processed; of these: 1071 ( 0.04%) short reads filtered out after trimming by size control 93 ( 0.00%) empty reads filtered out after trimming by size control 2477747 (99.95%) reads available; of these: 46613 ( 1.88%) trimmed reads available after processing 2431134 (98.12%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 152 0.01% 19 388 0.02% 20 198 0.01% 21 249 0.01% 22 271 0.01% 23 64 0.00% 24 94 0.00% 25 49 0.00% 26 65 0.00% 27 76 0.00% 28 232 0.01% 29 137 0.01% 30 136 0.01% 31 230 0.01% 32 184 0.01% 33 82 0.00% 34 100 0.00% 35 771 0.03% 36 516 0.02% 37 147 0.01% 38 222 0.01% 39 813 0.03% 40 555 0.02% 41 311 0.01% 42 56 0.00% 43 44 0.00% 44 63 0.00% 45 40 0.00% 46 21 0.00% 47 27 0.00% 48 37 0.00% 49 46 0.00% 50 52 0.00% 51 224 0.01% 52 33 0.00% 53 28 0.00% 54 25 0.00% 55 35 0.00% 56 38 0.00% 57 55 0.00% 58 83 0.00% 59 33 0.00% 60 66 0.00% 61 32 0.00% 62 0 0.00% 63 3 0.00% 64 5 0.00% 65 3 0.00% 66 9 0.00% 67 14 0.00% 68 52 0.00% 69 195 0.01% 70 19167 0.77% 71 15517 0.63% 72 16371 0.66% 73 14226 0.57% 74 14825 0.60% 75 14152 0.57% 76 13765 0.56% 77 14289 0.58% 78 14407 0.58% 79 15798 0.64% 80 17955 0.72% 81 19456 0.79% 82 20386 0.82% 83 16185 0.65% 84 17080 0.69% 85 137 0.01% 86 198 0.01% 87 365 0.01% 88 616 0.02% 89 1064 0.04% 90 2219 0.09% 91 6851 0.28% 92 25180 1.02% 93 2190177 88.39% 2477747 reads passed initial QC criterion=sequence-density sequence-density=1.81 sequence-density-rank=1 fanout-score=1.95 fanout-score-rank=35 prefix-density=1.84 prefix-fanout=1.9 sequence=GACCGATAGCGAA criterion=fanout-score sequence-density=0.01 sequence-density-rank=44 fanout-score=41.03 fanout-score-rank=1 prefix-density=0.19 prefix-fanout=1.1 sequence=GAGAGGATAACTGCTGAAAGCATATAAGTAGTAAGCCCACCCCAAGATGAGTGCTCTCTCCTCCGACTTCCCTAGAGCCTCCGGTATCACAGCCGAGACAGCGACGGGTTCTCCACCCATACGGGGATGGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACGAGCCGTTTAAATAGGTGTCAAGTGGAAGTGCAGTGATGTATGCAGCTGAGGCATCCTAACGAACGAACGATTTGAACCTTGTTCCTACACGGCCTGATCAAATCGAT Started job on | Dec 07 00:28:35 Started mapping on | Dec 07 00:28:35 Finished on | Dec 07 00:28:49 Mapping speed, Million of reads per hour | 637.13 Number of input reads | 2477747 Average input read length | 91 UNIQUE READS: Uniquely mapped reads number | 1328391 Uniquely mapped reads % | 53.61% Average mapped length | 89.54 Number of splices: Total | 50564 Number of splices: Annotated (sjdb) | 38647 Number of splices: GT/AG | 46815 Number of splices: GC/AG | 1048 Number of splices: AT/AC | 57 Number of splices: Non-canonical | 2644 Mismatch rate per base, % | 1.85% Deletion rate per base | 0.17% Deletion average length | 2.14 Insertion rate per base | 0.10% Insertion average length | 1.93 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 684068 % of reads mapped to multiple loci | 27.61% Number of reads mapped to too many loci | 88884 % of reads mapped to too many loci | 3.59% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 14.95% % of reads unmapped: other | 0.25% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 465288 465288 465288 N_multimapping 684068 684068 684068 N_noFeature 122379 134762 1270101 N_ambiguous 52636 6813 155 UnstrandedReadsAssigned:1153376 PositiveStrandReadsAssigned:1186816 NegativeStrandReadsAssigned:58135 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=93 echo kmer=89 ERR6133315 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: ERR6133315-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 2,477,747 reads, 1,495,789 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 897 rounds 52973 ERR6133315.ke.tsv 35125 ERR6133315.se.tsv 88098 total ==> ERR6133315.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 17 11.0497 PNS24243 293 194 0 0 KQK14069 1603 1504 5 2.96467 KQK14071 474 375 0 0 ==> ERR6133315.se.tsv <== BRADI_1g14170v3 5 BRADI_1g53295v3 20 BRADI_1g59795v3 7 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 13 BRADI_1g74790v3 11 BRADI_1g09890v3 0 BRADI_1g77505v3 35 BRADI_1g48960v3 0 ERR6133315 completed mapping pipeline successfully