Starting /dee2/code/volunteer_pipeline.sh ERR6133499 current disk space = 1544473976832 free memory = 1601187032 ERR6133499 SRAfilesize 3728703386531e086683f0b6bfd699a7 ERR6133499.sra ERR6133499.sra file validated ERR6133499 is single end ERR6133499 is conventional basespace ERR6133499 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133499_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 35.44625 37.0 33.0 37.0 33.0 37.0 2 36.5395 37.0 37.0 37.0 37.0 37.0 3 35.828 37.0 37.0 37.0 33.0 37.0 4 35.21175 37.0 37.0 37.0 33.0 37.0 5 35.2415 37.0 37.0 37.0 33.0 37.0 6 35.62025 37.0 37.0 37.0 33.0 37.0 7 37.23575 37.0 37.0 40.0 33.0 40.0 8 37.31625 37.0 37.0 40.0 33.0 40.0 9 37.414 37.0 37.0 40.0 33.0 40.0 10-11 37.38175 37.0 37.0 40.0 33.0 40.0 12-13 37.289874999999995 37.0 37.0 40.0 33.0 40.0 14-15 37.235375000000005 37.0 37.0 40.0 33.0 40.0 16-17 37.10425 37.0 37.0 40.0 33.0 40.0 18-19 36.96825 37.0 37.0 40.0 33.0 40.0 20-21 36.679 37.0 37.0 40.0 33.0 40.0 22-23 36.69725 37.0 37.0 40.0 33.0 40.0 24-25 36.5685 37.0 37.0 40.0 33.0 40.0 26-27 36.855625 37.0 37.0 40.0 33.0 40.0 28-29 36.796125 37.0 37.0 40.0 33.0 40.0 30-31 36.605625 37.0 37.0 40.0 33.0 40.0 32-33 36.643625 37.0 37.0 40.0 33.0 40.0 34-35 36.578 37.0 37.0 40.0 33.0 40.0 36-37 36.453500000000005 37.0 37.0 40.0 33.0 40.0 38-39 36.422625 37.0 37.0 40.0 33.0 40.0 40-41 36.151375 37.0 37.0 40.0 33.0 40.0 42-43 36.1445 37.0 37.0 40.0 33.0 40.0 44-45 36.161625 37.0 37.0 40.0 33.0 40.0 46-47 36.012625 37.0 37.0 37.0 33.0 40.0 48-49 35.94725 37.0 37.0 37.0 33.0 40.0 50-51 35.752125 37.0 33.0 37.0 33.0 40.0 52-53 35.54375 37.0 33.0 37.0 33.0 40.0 54-55 35.450625 37.0 33.0 37.0 33.0 40.0 56-57 35.309124999999995 37.0 33.0 37.0 33.0 37.0 58-59 34.352125 37.0 33.0 37.0 27.0 37.0 60-61 34.819 37.0 33.0 37.0 33.0 37.0 62-63 34.650875 37.0 33.0 37.0 33.0 37.0 64-65 34.59375 37.0 33.0 37.0 33.0 37.0 66-67 34.593125 37.0 33.0 37.0 33.0 37.0 68-69 33.8105 35.0 33.0 37.0 30.0 37.0 70-71 33.999318941679235 35.0 33.0 37.0 27.0 37.0 72-73 34.325454701441316 37.0 33.0 37.0 33.0 37.0 74-75 34.25231455043887 37.0 33.0 37.0 33.0 37.0 76-77 34.196627542122854 37.0 33.0 37.0 30.0 37.0 78-79 34.1066533066533 37.0 33.0 37.0 27.0 37.0 80-81 34.02263864672234 37.0 33.0 37.0 27.0 37.0 82-83 33.93585648884151 37.0 33.0 37.0 27.0 37.0 84-85 33.76069547904217 37.0 33.0 37.0 27.0 37.0 86-87 33.57361148020196 37.0 33.0 37.0 27.0 37.0 88-89 33.71791124103109 37.0 33.0 37.0 27.0 37.0 90-91 33.50292319957481 37.0 33.0 37.0 27.0 37.0 92-93 33.49747541854903 35.0 33.0 37.0 27.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 12.0 21 9.0 22 11.0 23 13.0 24 22.0 25 25.0 26 27.0 27 37.0 28 43.0 29 52.0 30 90.0 31 123.0 32 150.0 33 192.0 34 270.0 35 504.0 36 906.0 37 951.0 38 544.0 39 19.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 89.9 2.725 2.0500000000000003 5.325 2 75.75 14.299999999999999 6.2 3.75 3 37.875 38.45 13.375 10.299999999999999 4 31.825 31.15 18.7 18.325 5 25.974999999999998 32.5 24.775 16.75 6 20.1 39.1 24.625 16.175 7 36.15 29.725 19.475 14.649999999999999 8 30.025000000000002 29.7 22.650000000000002 17.625 9 26.275 29.025000000000002 27.575 17.125 10-11 25.662499999999998 28.9125 27.5125 17.9125 12-13 27.650000000000002 26.687499999999996 27.650000000000002 18.0125 14-15 22.8125 30.325000000000003 28.15 18.712500000000002 16-17 25.1 31.2125 25.324999999999996 18.3625 18-19 24.925 26.400000000000002 27.525 21.15 20-21 25.9875 25.887500000000003 27.500000000000004 20.625 22-23 27.375 23.150000000000002 27.650000000000002 21.825 24-25 25.55 24.712500000000002 28.6125 21.125 26-27 24.95 25.2 30.325000000000003 19.525000000000002 28-29 24.637500000000003 27.0 28.712500000000002 19.650000000000002 30-31 27.8375 25.837500000000002 27.3 19.025 32-33 24.637500000000003 27.375 27.0625 20.925 34-35 25.3 27.3375 27.437499999999996 19.925 36-37 25.2 24.95 27.3875 22.4625 38-39 27.336419366946078 24.671587639184285 30.251470036281745 17.74052295758789 40-41 25.625312656328163 25.912956478239117 28.83941970985493 19.62231115557779 42-43 25.528191023877984 28.803600450056255 26.60332541567696 19.0648831103888 44-45 24.087500000000002 24.725 30.725 20.4625 46-47 24.762500000000003 24.637500000000003 28.4375 22.162499999999998 48-49 25.05 25.275 29.099999999999998 20.575 50-51 23.775 27.187499999999996 28.65 20.3875 52-53 24.5995995995996 26.413913913913913 27.87787787787788 21.10860860860861 54-55 23.9875 27.250000000000004 29.462500000000002 19.3 56-57 25.75 26.1625 28.712500000000002 19.375 58-59 23.7 25.874999999999996 30.0 20.424999999999997 60-61 25.662499999999998 25.5 29.3875 19.45 62-63 21.912499999999998 27.975 30.925000000000004 19.1875 64-65 23.6875 28.1375 29.612500000000004 18.5625 66-67 24.5 28.787499999999998 28.525 18.1875 68-69 22.1375 27.0 29.349999999999998 21.512500000000003 70-71 24.3920782150915 26.20957633492103 28.77914264226623 20.619202807721233 72-73 26.51591712986357 24.82314300151592 29.547751389590704 19.113188479029812 74-75 24.591836734693878 27.32142857142857 28.660714285714285 19.426020408163268 76-77 21.71794871794872 25.551282051282055 30.19230769230769 22.538461538461537 78-79 24.593338497288926 25.910147172734316 29.847663310095534 19.648851019881228 80-81 22.682831443097378 28.78373093468909 30.295919697562248 18.237517924651282 82-83 23.279378865640215 24.358468219502566 30.54349256481116 21.81866035004606 84-85 23.421750663129973 24.244031830238725 32.320954907161806 20.0132625994695 86-87 23.00026574541589 27.1326069625299 30.52086101514749 19.346266276906725 88-89 21.963858623438746 28.567632208344406 30.34812649481796 19.120382673398883 90-91 26.787137921870848 27.5046505447781 28.673930374701033 17.034281158650014 92-93 21.03374966781823 30.427850119585436 28.87323943661972 19.665160775976613 >>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 0.0 17 6.5 18 8.0 19 2.0 20 2.5 21 2.5 22 1.5 23 4.0 24 5.0 25 5.0 26 10.0 27 11.5 28 16.0 29 25.0 30 30.0 31 36.5 32 51.5 33 67.5 34 81.0 35 99.0 36 126.0 37 145.0 38 177.0 39 199.0 40 194.0 41 206.0 42 205.5 43 193.5 44 192.0 45 202.5 46 207.5 47 191.5 48 170.5 49 159.5 50 158.5 51 138.0 52 124.5 53 145.5 54 164.5 55 126.0 56 65.5 57 51.5 58 51.0 59 39.5 60 28.0 61 25.5 62 24.5 63 24.0 64 23.0 65 22.5 66 19.0 67 12.0 68 11.5 69 8.5 70 4.5 71 6.0 72 6.0 73 5.0 74 3.0 75 2.0 76 1.0 77 1.0 78 1.0 79 0.0 80 0.0 81 0.0 82 0.0 83 0.5 84 0.5 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 0.08750000000000001 40-41 0.05 42-43 0.0125 44-45 0.0 46-47 0.0 48-49 0.0 50-51 0.0 52-53 0.1 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 22.0 71 10.0 72 20.0 73 23.0 74 10.0 75 10.0 76 10.0 77 10.0 78 24.0 79 15.0 80 21.0 81 15.0 82 21.0 83 12.0 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 3763.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 81.27499999999999 #Duplication Level Percentage of deduplicated Percentage of total 1 92.98677330052291 75.575 2 4.152568440479852 6.75 3 1.2611504152568442 3.075 4 0.3998769609350969 1.3 5 0.30759766225776686 1.25 6 0.09227929867733005 0.44999999999999996 7 0.15379883112888343 0.8750000000000001 8 0.09227929867733005 0.6 9 0.030759766225776686 0.22499999999999998 >10 0.492156259612427 7.75 >50 0.030759766225776686 2.15 >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 86 2.15 No Hit GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 49 1.225 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 29 0.7250000000000001 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 25 0.625 No Hit GGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGG 25 0.625 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 24 0.6 No Hit GGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTT 21 0.525 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 17 0.42500000000000004 No Hit GGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAA 15 0.375 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 15 0.375 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 14 0.35000000000000003 No Hit GGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGC 14 0.35000000000000003 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 14 0.35000000000000003 No Hit GGAGTATCCTTGATATATAAATATATAGATAAATAGATTTAAATGGAAAA 13 0.325 No Hit GAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGC 12 0.3 No Hit GGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGGG 12 0.3 No Hit GGGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTG 11 0.27499999999999997 No Hit GGAAGAGCCCGAGCTGCTGCAGCAGGTTTTGAAAAGGGAATCGATCGTGA 9 0.22499999999999998 No Hit GGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAA 8 0.2 No Hit GGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGC 8 0.2 No Hit GGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAA 8 0.2 No Hit GGGAAAAGAGGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTT 7 0.17500000000000002 No Hit GGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAAGGCGATCAAATTC 7 0.17500000000000002 No Hit GTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAA 7 0.17500000000000002 No Hit GGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAAA 7 0.17500000000000002 No Hit GGGCCATTTGTGGCATGCAGGAAGAGCCCGAGCTGCTGCAGCAGGTTTTG 7 0.17500000000000002 No Hit GGTGGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGC 6 0.15 No Hit GGGGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCT 6 0.15 No Hit GGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTT 6 0.15 No Hit GGCTTTAGAAGCCTGTGTACAAGCTCGTAACGAAGGGCGCGATCTTGCTC 5 0.125 No Hit GGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGGAAGGGCGTA 5 0.125 No Hit GGGGATGGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACG 5 0.125 No Hit GGCCTGTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCG 5 0.125 No Hit GCAGCTTGCAAATGGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAA 5 0.125 No Hit GGGAAACAACGAGGTCATCATCGACATGATATATTGCTGCTATTTTCCAC 5 0.125 No Hit GTAACGAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCA 5 0.125 No Hit GGAAGGCGATCAAATTCGAGTTCGCGCCGGTAGATACTATCGATTAATAG 5 0.125 No Hit GTATTTAGCCTTGCAAGGTGGTCCTTGCTGATTCACACGGGATTCCACGT 5 0.125 No Hit GGTTTTGAAAAGGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAA 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 0.025 0.0 0.0 0.0 0.0 40-41 0.037500000000000006 0.0 0.0 0.0 0.0 42-43 0.05 0.0 0.0 0.0 0.0 44-45 0.05 0.0 0.0 0.0 0.0 46-47 0.05 0.0 0.0 0.0 0.0 48-49 0.05 0.0 0.0 0.0 0.0 50-51 0.05 0.0 0.0 0.0 0.0 52-53 0.05 0.0 0.0 0.0 0.0 54-55 0.05 0.0 0.0 0.0 0.0 56-57 0.0625 0.0 0.0125 0.0 0.0 58-59 0.075 0.0 0.025 0.0 0.0 60-61 0.075 0.0 0.025 0.0 0.0 62-63 0.075 0.0 0.025 0.0 0.0 64-65 0.075 0.0 0.025 0.0 0.0 66-67 0.1 0.0 0.025 0.0 0.0 68-69 0.1 0.0 0.025 0.0 0.0 70-71 0.1 0.0 0.025 0.0 0.0 72-73 0.1 0.0 0.025 0.0 0.0 74-75 0.1 0.0 0.025 0.0 0.0 76-77 0.1 0.0 0.025 0.0 0.0 78-79 0.1 0.0 0.025 0.0 0.0 80-81 0.1 0.0 0.025 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position AATTTCA 25 0.0068019433 51.817497 7 CAATTTC 25 0.0068019433 51.817497 6 GGATTCA 25 0.0068019433 51.817497 1 TTTCAAC 25 0.0068019433 51.817497 9 TCAATTT 25 0.0068019433 51.817497 5 GATTCAA 25 0.0068019433 51.817497 2 ATTTCAA 25 0.0068019433 51.817497 8 TATCATC 30 0.005935565 28.787502 62-63 ATATCAT 30 0.005935565 28.787502 62-63 >>END_MODULE Rejected 170909 READS because READLEN < 1 Read 170909 spots for ERR6133499.sra Written 170909 spots for ERR6133499.sra Rejected 170909 READS because READLEN < 1 Read 170909 spots for ERR6133499.sra Written 170909 spots for ERR6133499.sra Rejected 170909 READS because READLEN < 1 Read 170909 spots for ERR6133499.sra Written 170909 spots for ERR6133499.sra Rejected 170909 READS because READLEN < 1 Read 170909 spots for ERR6133499.sra Written 170909 spots for ERR6133499.sra Rejected 170909 READS because READLEN < 1 Read 170909 spots for ERR6133499.sra Written 170909 spots for ERR6133499.sra Rejected 170909 READS because READLEN < 1 Read 170909 spots for ERR6133499.sra Written 170909 spots for ERR6133499.sra Rejected 170909 READS because READLEN < 1 Read 170909 spots for ERR6133499.sra Written 170909 spots for ERR6133499.sra Rejected 170909 READS because READLEN < 1 Read 170909 spots for ERR6133499.sra Written 170909 spots for ERR6133499.sra Rejected 170909 READS because READLEN < 1 Read 170909 spots for ERR6133499.sra Written 170909 spots for ERR6133499.sra Rejected 170909 READS because READLEN < 1 Read 170909 spots for ERR6133499.sra Written 170909 spots for ERR6133499.sra Rejected 170909 READS because READLEN < 1 Read 170909 spots for ERR6133499.sra Written 170909 spots for ERR6133499.sra Rejected 170909 READS because READLEN < 1 Read 170909 spots for ERR6133499.sra Written 170909 spots for ERR6133499.sra Rejected 170909 READS because READLEN < 1 Read 170909 spots for ERR6133499.sra Written 170909 spots for ERR6133499.sra Rejected 170909 READS because READLEN < 1 Read 170909 spots for ERR6133499.sra Written 170909 spots for ERR6133499.sra Rejected 170909 READS because READLEN < 1 Read 170909 spots for ERR6133499.sra Written 170909 spots for ERR6133499.sra Rejected 170909 READS because READLEN < 1 Read 170909 spots for ERR6133499.sra Written 170909 spots for ERR6133499.sra Rejected 170912 READS because READLEN < 1 Read 170912 spots for ERR6133499.sra Written 170912 spots for ERR6133499.sra Rejected 170909 READS because READLEN < 1 Read 170909 spots for ERR6133499.sra Written 170909 spots for ERR6133499.sra Rejected 170909 READS because READLEN < 1 Read 170909 spots for ERR6133499.sra Written 170909 spots for ERR6133499.sra Rejected 170909 READS because READLEN < 1 Read 170909 spots for ERR6133499.sra Written 170909 spots for ERR6133499.sra SRR ids: ['ERR6133499.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_nv4j20z3 ERR6133499.sra spots: 3418183 blocks: [[1, 170909], [170910, 341818], [341819, 512727], [512728, 683636], [683637, 854545], [854546, 1025454], [1025455, 1196363], [1196364, 1367272], [1367273, 1538181], [1538182, 1709090], [1709091, 1879999], [1880000, 2050908], [2050909, 2221817], [2221818, 2392726], [2392727, 2563635], [2563636, 2734544], [2734545, 2905453], [2905454, 3076362], [3076363, 3247271], [3247272, 3418183]] ERR6133499 file size 751052 ERR6133499 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 ERR6133499 ERR6133499_1.fastq Input file: ERR6133499_1.fastq trimmed: ERR6133499-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 07:24:50 2024 >> started Sat Dec 7 07:24:52 2024 >> done (1.649s) 3418183 reads processed; of these: 333 ( 0.01%) short reads filtered out after trimming by size control 50 ( 0.00%) empty reads filtered out after trimming by size control 3417800 (99.99%) reads available; of these: 52555 ( 1.54%) trimmed reads available after processing 3365245 (98.46%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 80 0.00% 19 137 0.00% 20 39 0.00% 21 35 0.00% 22 54 0.00% 23 26 0.00% 24 28 0.00% 25 10 0.00% 26 21 0.00% 27 25 0.00% 28 36 0.00% 29 85 0.00% 30 30 0.00% 31 37 0.00% 32 62 0.00% 33 30 0.00% 34 31 0.00% 35 332 0.01% 36 362 0.01% 37 32 0.00% 38 69 0.00% 39 189 0.01% 40 213 0.01% 41 71 0.00% 42 21 0.00% 43 15 0.00% 44 25 0.00% 45 20 0.00% 46 13 0.00% 47 9 0.00% 48 15 0.00% 49 9 0.00% 50 9 0.00% 51 86 0.00% 52 29 0.00% 53 12 0.00% 54 8 0.00% 55 11 0.00% 56 15 0.00% 57 10 0.00% 58 16 0.00% 59 7 0.00% 60 25 0.00% 61 17 0.00% 62 1 0.00% 63 3 0.00% 64 6 0.00% 65 12 0.00% 66 11 0.00% 67 15 0.00% 68 43 0.00% 69 124 0.00% 70 17045 0.50% 71 16398 0.48% 72 17749 0.52% 73 16035 0.47% 74 15702 0.46% 75 15907 0.47% 76 13929 0.41% 77 15207 0.44% 78 16471 0.48% 79 18613 0.54% 80 16319 0.48% 81 18052 0.53% 82 20063 0.59% 83 20519 0.60% 84 16504 0.48% 85 131 0.00% 86 191 0.01% 87 313 0.01% 88 550 0.02% 89 1029 0.03% 90 2126 0.06% 91 6693 0.20% 92 35134 1.03% 93 3114499 91.13% 3417800 reads passed initial QC criterion=sequence-density sequence-density=0.75 sequence-density-rank=1 fanout-score=1.94 fanout-score-rank=32 prefix-density=0.75 prefix-fanout=1.9 sequence=CAAGGCTAAATAC criterion=fanout-score sequence-density=0.01 sequence-density-rank=26 fanout-score=289.68 fanout-score-rank=1 prefix-density=0.61 prefix-fanout=7.1 sequence=GAAGAAGAAAAGTTTTCTCAACATGGGGAGGAAGTCCCTCCGAAATTTGATTTGTTATTGTATTGTAAGGGGCTTTTTTAGTATTTATCTAAAGGAAGGAACAAACGAGGATAAGATAAAATTGCTTTAAATTTATTTTGCCCAAGTGGGATATATGGCATACTATTCTTTCCATTTTCATCTTTTTTTCTATTCCACTCCATCTAGATATAAGAAAGAACCCAATGCAATGAAATTCCACTAATATACAATACAAAAAAGAAGAA Started job on | Dec 07 07:25:05 Started mapping on | Dec 07 07:25:05 Finished on | Dec 07 07:25:10 Mapping speed, Million of reads per hour | 2460.82 Number of input reads | 3417800 Average input read length | 91 UNIQUE READS: Uniquely mapped reads number | 2519024 Uniquely mapped reads % | 73.70% Average mapped length | 91.28 Number of splices: Total | 100663 Number of splices: Annotated (sjdb) | 82777 Number of splices: GT/AG | 95922 Number of splices: GC/AG | 2673 Number of splices: AT/AC | 47 Number of splices: Non-canonical | 2021 Mismatch rate per base, % | 0.43% Deletion rate per base | 0.04% Deletion average length | 1.79 Insertion rate per base | 0.02% Insertion average length | 2.02 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 815282 % of reads mapped to multiple loci | 23.85% Number of reads mapped to too many loci | 30548 % of reads mapped to too many loci | 0.89% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.49% % of reads unmapped: other | 0.06% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 83494 83494 83494 N_multimapping 815282 815282 815282 N_noFeature 159037 183305 2403607 N_ambiguous 101372 10128 357 UnstrandedReadsAssigned:2258615 PositiveStrandReadsAssigned:2325591 NegativeStrandReadsAssigned:115060 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=93 echo kmer=89 ERR6133499 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: ERR6133499-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 3,417,800 reads, 2,833,472 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,054 rounds 52973 ERR6133499.ke.tsv 35125 ERR6133499.se.tsv 88098 total ==> ERR6133499.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 97 33.6773 PNS24243 293 194 0 0 KQK14069 1603 1504 14 4.43404 KQK14071 474 375 0 0 ==> ERR6133499.se.tsv <== BRADI_1g14170v3 14 BRADI_1g53295v3 26 BRADI_1g59795v3 22 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 37 BRADI_1g74790v3 19 BRADI_1g09890v3 0 BRADI_1g77505v3 73 BRADI_1g48960v3 0 ERR6133499 completed mapping pipeline successfully