Starting /dee2/code/volunteer_pipeline.sh ERR6133473 current disk space = 1544965206016 free memory = 1480442264 ERR6133473 SRAfilesize 3604fb8e6915bead621a8d426ce51344 ERR6133473.sra ERR6133473.sra file validated ERR6133473 is single end ERR6133473 is conventional basespace ERR6133473 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133473_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 35.0865 37.0 33.0 37.0 33.0 37.0 2 36.246 37.0 37.0 37.0 33.0 37.0 3 35.48625 37.0 33.0 37.0 33.0 37.0 4 34.89375 37.0 37.0 37.0 33.0 37.0 5 34.792 37.0 37.0 37.0 27.0 37.0 6 35.24475 37.0 37.0 37.0 33.0 37.0 7 36.75975 37.0 37.0 40.0 33.0 40.0 8 36.8735 37.0 37.0 40.0 33.0 40.0 9 37.13775 37.0 37.0 40.0 33.0 40.0 10-11 37.035875000000004 37.0 37.0 40.0 33.0 40.0 12-13 36.956375 37.0 37.0 40.0 33.0 40.0 14-15 36.89475 37.0 37.0 40.0 33.0 40.0 16-17 36.725375 37.0 37.0 40.0 33.0 40.0 18-19 36.428375 37.0 37.0 40.0 33.0 40.0 20-21 36.2785 37.0 37.0 40.0 33.0 40.0 22-23 35.96025 37.0 35.0 40.0 33.0 40.0 24-25 36.105500000000006 37.0 35.0 40.0 33.0 40.0 26-27 36.4 37.0 37.0 40.0 33.0 40.0 28-29 36.284000000000006 37.0 37.0 40.0 33.0 40.0 30-31 36.36125 37.0 37.0 40.0 33.0 40.0 32-33 36.3505 37.0 37.0 40.0 33.0 40.0 34-35 36.301125 37.0 37.0 40.0 33.0 40.0 36-37 36.24925 37.0 37.0 40.0 33.0 40.0 38-39 36.127875 37.0 37.0 40.0 33.0 40.0 40-41 36.014875 37.0 37.0 40.0 33.0 40.0 42-43 35.917874999999995 37.0 35.0 40.0 33.0 40.0 44-45 35.673249999999996 37.0 33.0 38.5 33.0 40.0 46-47 35.648375 37.0 33.0 37.0 33.0 40.0 48-49 35.674875 37.0 33.0 37.0 33.0 40.0 50-51 35.45 37.0 33.0 37.0 33.0 40.0 52-53 35.10725 37.0 33.0 37.0 33.0 40.0 54-55 35.06625 37.0 33.0 37.0 33.0 40.0 56-57 34.895624999999995 37.0 33.0 37.0 30.0 38.5 58-59 34.454125 37.0 33.0 37.0 27.0 37.0 60-61 34.575375 37.0 33.0 37.0 30.0 37.0 62-63 34.495875 37.0 33.0 37.0 27.0 37.0 64-65 34.34625 37.0 33.0 37.0 27.0 37.0 66-67 34.0555 37.0 33.0 37.0 27.0 37.0 68-69 33.24525 35.0 33.0 37.0 27.0 37.0 70-71 33.44243201754386 35.0 33.0 37.0 27.0 37.0 72-73 33.84639006308504 37.0 33.0 37.0 27.0 37.0 74-75 33.86200073549546 37.0 33.0 37.0 27.0 37.0 76-77 33.927652035570325 37.0 33.0 37.0 27.0 37.0 78-79 33.9672289466907 37.0 33.0 37.0 27.0 37.0 80-81 33.85501272422401 37.0 33.0 37.0 27.0 37.0 82-83 33.64976092401938 37.0 33.0 37.0 27.0 37.0 84-85 33.556288279149 37.0 33.0 37.0 27.0 37.0 86-87 33.424861587134195 35.0 33.0 37.0 27.0 37.0 88-89 33.53282362246243 37.0 33.0 37.0 27.0 37.0 90-91 33.26918006854733 33.0 33.0 37.0 27.0 37.0 92-93 33.2469021882415 33.0 33.0 37.0 27.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 9.0 21 20.0 22 16.0 23 15.0 24 27.0 25 30.0 26 46.0 27 50.0 28 66.0 29 75.0 30 117.0 31 116.0 32 161.0 33 211.0 34 280.0 35 480.0 36 860.0 37 926.0 38 480.0 39 15.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 88.47500000000001 2.35 2.475 6.7 2 72.89999999999999 16.175 6.425 4.5 3 35.225 40.875 13.625000000000002 10.274999999999999 4 33.625 29.575000000000003 19.475 17.325 5 25.15 30.525000000000002 26.575 17.75 6 20.3 38.05 26.05 15.6 7 34.35 29.25 20.474999999999998 15.925 8 29.725 30.75 23.200000000000003 16.325 9 24.8 30.875000000000004 27.325 17.0 10-11 25.362499999999997 28.1875 29.212500000000002 17.2375 12-13 27.125 27.500000000000004 27.962500000000002 17.4125 14-15 22.0 31.7375 28.6375 17.625 16-17 24.65 31.162499999999998 25.674999999999997 18.512500000000003 18-19 23.7125 27.325 28.7375 20.225 20-21 24.362181090545274 25.887943971985994 29.964982491245625 19.78489244622311 22-23 25.924999999999997 23.7125 28.999999999999996 21.3625 24-25 24.95 25.25 28.962500000000002 20.837500000000002 26-27 24.3875 24.975 31.0125 19.625 28-29 24.6625 27.0625 29.525000000000002 18.75 30-31 26.625 25.85 27.750000000000004 19.775000000000002 32-33 23.6875 26.900000000000002 28.825 20.5875 34-35 25.0125 27.325 27.6125 20.05 36-37 24.8625 25.525 28.425 21.1875 38-39 26.153269158644832 25.603200400050007 30.366295786973375 17.87723465433179 40-41 26.325 24.4125 29.7375 19.525000000000002 42-43 24.76846057571965 28.473091364205256 28.498122653316642 18.260325406758447 44-45 22.702837854731843 25.57819727465933 32.11651456432054 19.602450306288286 46-47 25.112499999999997 24.6875 27.6625 22.537499999999998 48-49 24.4875 24.9125 31.45 19.15 50-51 23.925 26.787499999999998 29.7125 19.575 52-53 23.562570462232244 28.15983965927596 27.333082800952024 20.94450707753977 54-55 22.230557639409852 27.59439859964991 30.720180045011254 19.454863715928983 56-57 26.25 25.8625 28.95 18.9375 58-59 23.4125 26.5375 28.9125 21.1375 60-61 25.087500000000002 25.3125 30.5 19.1 62-63 21.25 27.200000000000003 32.125 19.425 64-65 23.474999999999998 28.125 29.862499999999997 18.5375 66-67 24.1625 27.9375 29.6625 18.2375 68-69 21.95 26.6625 29.7125 21.675 70-71 23.829787234042556 26.758448060075096 29.036295369211512 20.375469336670836 72-73 25.39762686190356 24.160565513759153 30.459479929310778 19.98232769502651 74-75 23.132530120481928 26.924540266328474 30.019023462270134 19.923906150919468 76-77 22.8567778203654 25.7953238788808 29.99872237127891 21.349175929474896 78-79 22.373665938022373 27.182718271827184 31.400282885431402 19.043332904719044 80-81 22.06645898234683 30.08826583592939 30.192107995846314 17.653167185877468 82-83 22.037883736120182 26.623122142390592 30.097975179621162 21.24101894186806 84-85 23.050624589086127 24.957264957264957 32.00525969756739 19.986850756081527 86-87 21.31558133403638 27.959398892697074 31.465858159767997 19.25916161349855 88-89 20.564197205378328 28.67123648826786 32.059056156076984 18.705510150276826 90-91 24.597943580279463 27.102557342472977 29.58080674927498 18.71869232797258 92-93 20.867387292380702 29.303981017664114 30.4903770102821 19.33825467967308 >>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 1.0 16 2.5 17 8.0 18 8.5 19 2.0 20 1.0 21 3.0 22 4.5 23 5.0 24 6.0 25 6.0 26 9.0 27 16.0 28 27.5 29 36.0 30 42.0 31 50.0 32 60.0 33 85.0 34 94.5 35 109.5 36 130.0 37 158.0 38 198.5 39 200.0 40 208.0 41 218.0 42 209.5 43 208.0 44 202.5 45 203.5 46 201.0 47 177.5 48 160.5 49 162.5 50 148.5 51 124.0 52 118.5 53 127.0 54 132.5 55 92.5 56 51.0 57 46.5 58 43.0 59 35.0 60 29.5 61 24.5 62 24.0 63 26.5 64 20.0 65 13.0 66 8.0 67 8.0 68 13.0 69 13.0 70 9.5 71 8.0 72 5.5 73 2.0 74 2.0 75 3.0 76 2.0 77 0.5 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 0.05 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 0.0125 40-41 0.0 42-43 0.125 44-45 0.0125 46-47 0.0 48-49 0.0 50-51 0.0 52-53 0.21250000000000002 54-55 0.025 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 10.0 71 21.0 72 16.0 73 4.0 74 13.0 75 18.0 76 9.0 77 15.0 78 11.0 79 23.0 80 16.0 81 12.0 82 9.0 83 11.0 84 19.0 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 3793.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 79.975 #Duplication Level Percentage of deduplicated Percentage of total 1 92.71647389809316 74.15 2 3.8762113160362612 6.2 3 1.312910284463895 3.15 4 0.5314160675211004 1.7000000000000002 5 0.5001562988433885 2.0 6 0.09377930603313535 0.44999999999999996 7 0.15629884338855893 0.8750000000000001 8 0.09377930603313535 0.6 9 0.15629884338855893 1.125 >10 0.5314160675211004 8.075000000000001 >50 0.03125976867771178 1.675 >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 GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGC 67 1.675 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 46 1.15 No Hit GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 34 0.8500000000000001 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 27 0.675 No Hit GGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGG 25 0.625 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 21 0.525 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 20 0.5 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 18 0.44999999999999996 No Hit GGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTT 17 0.42500000000000004 No Hit GGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTT 15 0.375 No Hit GGAGTATCCTTGATATATAAATATATAGATAAATAGATTTAAATGGAAAA 14 0.35000000000000003 No Hit GTATTTAGCCTTGCAAGGTGGTCCTTGCTGATTCACACGGGATTCCACGT 14 0.35000000000000003 No Hit CAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCT 13 0.325 No Hit GGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAA 13 0.325 No Hit GGAAAAGAGGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTTG 13 0.325 No Hit GTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAA 12 0.3 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 11 0.27499999999999997 No Hit GGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAA 10 0.25 No Hit GGGAAAAGAGGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTT 9 0.22499999999999998 No Hit GGGATGGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACGA 9 0.22499999999999998 No Hit GGAAGAGCCCGAGCTGCTGCAGCAGGTTTTGAAAAGGGAATCGATCGTGA 9 0.22499999999999998 No Hit GGAAGGCGATCAAATTCGAGTTCGCGCCGGTAGATACTATCGATTAATAG 9 0.22499999999999998 No Hit GGGCCATTTGTGGCATGCAGGAAGAGCCCGAGCTGCTGCAGCAGGTTTTG 9 0.22499999999999998 No Hit GGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAAGGCGATCAAATTC 8 0.2 No Hit GGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGC 8 0.2 No Hit GGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGGG 8 0.2 No Hit GGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAAA 7 0.17500000000000002 No Hit GGGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTT 7 0.17500000000000002 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 7 0.17500000000000002 No Hit GTACAAGCTCGTAACGAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAAT 7 0.17500000000000002 No Hit GGTTTTGAAAAGGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAA 7 0.17500000000000002 No Hit GGTGGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGC 6 0.15 No Hit GGCCTGTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCG 6 0.15 No Hit GGGCCGGGTATCTCTCTGCATGTACGTATGCCTGTAATGTACGTAGCTAC 6 0.15 No Hit GGGAAAGAATCAATATACTTTTAATGTCGAATCAGGATTCACTAAGACAG 5 0.125 No Hit GGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCG 5 0.125 No Hit GGACATTTCTTCGAAAAAATTCGAATAGTGAGACGCATTAAAACGCAATT 5 0.125 No Hit GGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTA 5 0.125 No Hit GGAATAAGAATAAATCGCAACTCCTTTCCACTACACATAAAAATTGATTT 5 0.125 No Hit GAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGC 5 0.125 No Hit GGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAAATGGATTC 5 0.125 No Hit GGTGGGGCAATGGGCATTCCGTTGAGTTTGTATGGTGGGTGCTGTTTTGC 5 0.125 No Hit GGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTG 5 0.125 No Hit GGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGC 5 0.125 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 5 0.125 No Hit GGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTCCT 5 0.125 No Hit GGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAACCCTCTTAACT 5 0.125 No Hit GGGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTG 5 0.125 No Hit CAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTG 5 0.125 No Hit GGAAAAGAAAGCAAAAGCGATTCCCGTAGTAGCGGCGAGCGAAATGGGAG 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 0.025 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 0.05 0.0 0.0 0.0 0.0 74-75 0.05 0.0 0.0 0.0 0.0 76-77 0.05 0.0 0.0 0.0 0.0 78-79 0.05 0.0 0.0 0.0 0.0 80-81 0.0625 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position AATACAA 25 0.0068019433 51.817497 9 TAGCCGA 20 7.1509025E-4 44.28846 72-73 >>END_MODULE Rejected 132718 READS because READLEN < 1 Read 132718 spots for ERR6133473.sra Written 132718 spots for ERR6133473.sra Rejected 132718 READS because READLEN < 1 Read 132718 spots for ERR6133473.sra Written 132718 spots for ERR6133473.sra Rejected 132718 READS because READLEN < 1 Read 132718 spots for ERR6133473.sra Written 132718 spots for ERR6133473.sra Rejected 132718 READS because READLEN < 1 Read 132718 spots for ERR6133473.sra Written 132718 spots for ERR6133473.sra Rejected 132718 READS because READLEN < 1 Read 132718 spots for ERR6133473.sra Written 132718 spots for ERR6133473.sra Rejected 132718 READS because READLEN < 1 Read 132718 spots for ERR6133473.sra Written 132718 spots for ERR6133473.sra Rejected 132718 READS because READLEN < 1 Read 132718 spots for ERR6133473.sra Written 132718 spots for ERR6133473.sra Rejected 132718 READS because READLEN < 1 Read 132718 spots for ERR6133473.sra Written 132718 spots for ERR6133473.sra Rejected 132718 READS because READLEN < 1 Read 132718 spots for ERR6133473.sra Written 132718 spots for ERR6133473.sra Rejected 132718 READS because READLEN < 1 Read 132718 spots for ERR6133473.sra Written 132718 spots for ERR6133473.sra Rejected 132718 READS because READLEN < 1 Read 132718 spots for ERR6133473.sra Written 132718 spots for ERR6133473.sra Rejected 132718 READS because READLEN < 1 Read 132718 spots for ERR6133473.sra Written 132718 spots for ERR6133473.sra Rejected 132718 READS because READLEN < 1 Read 132718 spots for ERR6133473.sra Written 132718 spots for ERR6133473.sra Rejected 132718 READS because READLEN < 1 Read 132718 spots for ERR6133473.sra Written 132718 spots for ERR6133473.sra Rejected 132718 READS because READLEN < 1 Read 132718 spots for ERR6133473.sra Written 132718 spots for ERR6133473.sra Rejected 132718 READS because READLEN < 1 Read 132718 spots for ERR6133473.sra Written 132718 spots for ERR6133473.sra Rejected 132718 READS because READLEN < 1 Read 132718 spots for ERR6133473.sra Written 132718 spots for ERR6133473.sra Rejected 132718 READS because READLEN < 1 Read 132718 spots for ERR6133473.sra Written 132718 spots for ERR6133473.sra Rejected 132718 READS because READLEN < 1 Read 132718 spots for ERR6133473.sra Written 132718 spots for ERR6133473.sra Rejected 132733 READS because READLEN < 1 Read 132733 spots for ERR6133473.sra Written 132733 spots for ERR6133473.sra SRR ids: ['ERR6133473.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_q3aq5fhv ERR6133473.sra spots: 2654375 blocks: [[1, 132718], [132719, 265436], [265437, 398154], [398155, 530872], [530873, 663590], [663591, 796308], [796309, 929026], [929027, 1061744], [1061745, 1194462], [1194463, 1327180], [1327181, 1459898], [1459899, 1592616], [1592617, 1725334], [1725335, 1858052], [1858053, 1990770], [1990771, 2123488], [2123489, 2256206], [2256207, 2388924], [2388925, 2521642], [2521643, 2654375]] ERR6133473 file size 583919 ERR6133473 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 ERR6133473 ERR6133473_1.fastq Input file: ERR6133473_1.fastq trimmed: ERR6133473-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 06:48:54 2024 >> started Sat Dec 7 06:49:00 2024 >> done (6.337s) 2654375 reads processed; of these: 100 ( 0.00%) short reads filtered out after trimming by size control 28 ( 0.00%) empty reads filtered out after trimming by size control 2654247 (100.00%) reads available; of these: 36600 ( 1.38%) trimmed reads available after processing 2617647 (98.62%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 13 0.00% 19 36 0.00% 20 11 0.00% 21 16 0.00% 22 22 0.00% 23 5 0.00% 24 7 0.00% 25 4 0.00% 26 1 0.00% 27 4 0.00% 28 19 0.00% 29 15 0.00% 30 8 0.00% 31 19 0.00% 32 14 0.00% 33 10 0.00% 34 15 0.00% 35 91 0.00% 36 299 0.01% 37 20 0.00% 38 18 0.00% 39 106 0.00% 40 66 0.00% 41 26 0.00% 42 10 0.00% 43 15 0.00% 44 13 0.00% 45 7 0.00% 46 6 0.00% 47 7 0.00% 48 12 0.00% 49 7 0.00% 50 12 0.00% 51 24 0.00% 52 13 0.00% 53 6 0.00% 54 7 0.00% 55 5 0.00% 56 11 0.00% 57 10 0.00% 58 9 0.00% 59 9 0.00% 60 13 0.00% 61 8 0.00% 62 1 0.00% 63 3 0.00% 64 8 0.00% 65 5 0.00% 66 8 0.00% 67 10 0.00% 68 34 0.00% 69 100 0.00% 70 10148 0.38% 71 10078 0.38% 72 10647 0.40% 73 9789 0.37% 74 10143 0.38% 75 10156 0.38% 76 8865 0.33% 77 9353 0.35% 78 10508 0.40% 79 11894 0.45% 80 10726 0.40% 81 11321 0.43% 82 12749 0.48% 83 13121 0.49% 84 11188 0.42% 85 102 0.00% 86 198 0.01% 87 271 0.01% 88 486 0.02% 89 933 0.04% 90 1951 0.07% 91 6087 0.23% 92 23743 0.89% 93 2458572 92.63% 2654247 reads passed initial QC criterion=sequence-density sequence-density=0.70 sequence-density-rank=1 fanout-score=1.96 fanout-score-rank=36 prefix-density=0.70 prefix-fanout=2.0 sequence=CAAGGCTAAATAC criterion=fanout-score sequence-density=0.02 sequence-density-rank=30 fanout-score=168.02 fanout-score-rank=1 prefix-density=0.48 prefix-fanout=6.6 sequence=GAAGAAGAAAAGTTTTCTCAACATGGGGAGGAAGTCCCTCCGAAATTTGATTTGTTATTGTATTGTAAGGGGCTTTTTTAGTATTTATCTAAAGGAAGGAACAAACGAGGATAAGATAAAATTTCTTTAAATTTATTTTGCCCAAGTGGGATATATGGCATACTATTCTTTCCATTTTCATCTTTTTTTCTATTCCACTCCATCTAGATATAAGAAAGAACCCAATGCAATGAAATTCCACTAATATACAATACAAAAAAGAAGAATAGATACAGGGTCTCAAACCTTGCTATAGAGTTTTTGCTT Started job on | Dec 07 06:49:40 Started mapping on | Dec 07 06:49:40 Finished on | Dec 07 06:50:24 Mapping speed, Million of reads per hour | 217.17 Number of input reads | 2654247 Average input read length | 92 UNIQUE READS: Uniquely mapped reads number | 1836549 Uniquely mapped reads % | 69.19% Average mapped length | 91.49 Number of splices: Total | 69503 Number of splices: Annotated (sjdb) | 57829 Number of splices: GT/AG | 66567 Number of splices: GC/AG | 1731 Number of splices: AT/AC | 31 Number of splices: Non-canonical | 1174 Mismatch rate per base, % | 0.44% Deletion rate per base | 0.04% Deletion average length | 1.77 Insertion rate per base | 0.02% Insertion average length | 1.85 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 755149 % of reads mapped to multiple loci | 28.45% Number of reads mapped to too many loci | 28341 % of reads mapped to too many loci | 1.07% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.21% % of reads unmapped: other | 0.08% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 62549 62549 62549 N_multimapping 755149 755149 755149 N_noFeature 144992 162970 1753502 N_ambiguous 73903 8686 323 UnstrandedReadsAssigned:1617654 PositiveStrandReadsAssigned:1664893 NegativeStrandReadsAssigned:82724 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=93 echo kmer=89 ERR6133473 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: ERR6133473-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 2,654,247 reads, 2,150,807 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,008 rounds 52973 ERR6133473.ke.tsv 35125 ERR6133473.se.tsv 88098 total ==> ERR6133473.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 65 29.7635 PNS24243 293 194 0 0 KQK14069 1603 1504 6 2.50627 KQK14071 474 375 0 0 ==> ERR6133473.se.tsv <== BRADI_1g14170v3 6 BRADI_1g53295v3 15 BRADI_1g59795v3 24 BRADI_1g07683v3 1 BRADI_1g00485v3 0 BRADI_1g20270v3 36 BRADI_1g74790v3 23 BRADI_1g09890v3 0 BRADI_1g77505v3 66 BRADI_1g48960v3 0 ERR6133473 completed mapping pipeline successfully