Starting /dee2/code/volunteer_pipeline.sh ERR6133332 current disk space = 1548194172928 free memory = 1595651628 ERR6133332 SRAfilesize 5ed354b56d2fe2a689cb90ebd5ee6108 ERR6133332.sra ERR6133332.sra file validated ERR6133332 is single end ERR6133332 is conventional basespace ERR6133332 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133332_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 43 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.51125 37.0 37.0 37.0 37.0 37.0 2 36.59575 37.0 37.0 37.0 37.0 37.0 3 36.52525 37.0 37.0 37.0 37.0 37.0 4 36.4225 37.0 37.0 37.0 37.0 37.0 5 36.47625 37.0 37.0 37.0 37.0 37.0 6 36.527 37.0 37.0 37.0 37.0 37.0 7 38.6815 40.0 37.0 40.0 37.0 40.0 8 38.70025 40.0 37.0 40.0 37.0 40.0 9 38.71 40.0 37.0 40.0 37.0 40.0 10-11 38.7245 40.0 37.0 40.0 37.0 40.0 12-13 38.738125 40.0 37.0 40.0 37.0 40.0 14-15 38.704750000000004 40.0 37.0 40.0 37.0 40.0 16-17 38.6415 40.0 37.0 40.0 37.0 40.0 18-19 38.7485 40.0 37.0 40.0 37.0 40.0 20-21 38.5925 40.0 37.0 40.0 37.0 40.0 22-23 38.6005 40.0 37.0 40.0 37.0 40.0 24-25 38.564625 40.0 37.0 40.0 37.0 40.0 26-27 38.5055 40.0 37.0 40.0 37.0 40.0 28-29 38.487375 40.0 37.0 40.0 37.0 40.0 30-31 38.3905 40.0 37.0 40.0 37.0 40.0 32-33 38.41175 40.0 37.0 40.0 37.0 40.0 34-35 38.378625 40.0 37.0 40.0 37.0 40.0 36-37 38.208375000000004 40.0 37.0 40.0 37.0 40.0 38-39 38.02225 40.0 37.0 40.0 37.0 40.0 40-41 38.018249999999995 40.0 37.0 40.0 37.0 40.0 42-43 37.9015 38.5 37.0 40.0 37.0 40.0 44-45 37.644000000000005 37.0 37.0 40.0 33.0 40.0 46-47 37.506125 37.0 37.0 40.0 33.0 40.0 48-49 37.426125 37.0 37.0 40.0 33.0 40.0 50-51 37.197125 37.0 37.0 40.0 33.0 40.0 52-53 37.032250000000005 37.0 37.0 40.0 33.0 40.0 54-55 36.7675 37.0 37.0 37.0 33.0 40.0 56-57 36.597625 37.0 37.0 37.0 33.0 40.0 58-59 36.36525 37.0 37.0 37.0 33.0 40.0 60-61 36.144375 37.0 37.0 37.0 33.0 40.0 62-63 35.723124999999996 37.0 33.0 37.0 33.0 37.0 64-65 35.368375 37.0 33.0 37.0 33.0 37.0 66-67 35.179375 37.0 33.0 37.0 33.0 37.0 68-69 33.887625 35.0 33.0 37.0 30.0 37.0 70-71 33.60702730246602 33.0 33.0 37.0 30.0 37.0 72-73 34.0113559397878 33.0 33.0 37.0 33.0 37.0 74-75 33.887355130205854 33.0 33.0 37.0 33.0 37.0 76-77 33.67094858002198 33.0 33.0 37.0 27.0 37.0 78-79 33.26495661873845 33.0 33.0 37.0 27.0 37.0 80-81 32.92122823437526 33.0 33.0 37.0 27.0 37.0 82-83 32.818852861494264 33.0 33.0 37.0 27.0 37.0 84-85 32.309708202369436 33.0 33.0 35.0 27.0 37.0 86-87 32.02622767857143 33.0 33.0 33.0 27.0 37.0 88-89 31.9921875 33.0 33.0 33.0 27.0 37.0 90-91 31.231724330357146 33.0 30.0 33.0 24.5 37.0 92-93 30.315150669642858 33.0 27.0 33.0 22.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 3.0 21 2.0 22 3.0 23 5.0 24 3.0 25 5.0 26 13.0 27 11.0 28 18.0 29 25.0 30 34.0 31 49.0 32 60.0 33 88.0 34 211.0 35 616.0 36 1029.0 37 1481.0 38 317.0 39 27.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 62.875 10.549999999999999 8.5 18.075 2 44.574999999999996 27.625 17.45 10.35 3 30.675 36.199999999999996 18.375 14.75 4 31.924999999999997 25.650000000000002 22.7 19.725 5 24.65 27.175 27.525 20.65 6 19.3 33.725 29.375 17.599999999999998 7 29.525000000000002 26.825 24.224999999999998 19.425 8 27.950000000000003 27.725 27.425 16.900000000000002 9 24.2 26.424999999999997 30.15 19.225 10-11 23.549999999999997 27.325 29.025000000000002 20.1 12-13 24.3125 26.5125 29.95 19.225 14-15 22.0875 26.4125 32.2125 19.287499999999998 16-17 23.925 28.6625 27.6125 19.8 18-19 23.45 25.137500000000003 29.9875 21.425 20-21 23.9375 27.250000000000004 27.9125 20.9 22-23 25.825 25.45 27.212500000000002 21.512500000000003 24-25 24.0125 26.3 29.6625 20.025000000000002 26-27 23.05 25.575 31.112499999999997 20.2625 28-29 23.7625 26.875 28.475 20.8875 30-31 24.025 26.35 29.125 20.5 32-33 23.1875 26.75 29.799999999999997 20.2625 34-35 23.3375 27.287499999999998 29.175 20.200000000000003 36-37 23.3375 26.625 28.712500000000002 21.325 38-39 23.775 25.7875 30.412499999999998 20.025000000000002 40-41 24.9375 25.95 29.225 19.8875 42-43 23.3875 27.950000000000003 29.45 19.2125 44-45 22.2 26.687499999999996 30.0 21.1125 46-47 22.425 26.737499999999997 29.612500000000004 21.224999999999998 48-49 22.7625 26.35 31.612499999999997 19.275000000000002 50-51 22.625 27.05 30.3875 19.9375 52-53 23.5 27.900000000000002 28.5875 20.0125 54-55 23.849999999999998 28.512500000000003 28.849999999999998 18.787499999999998 56-57 23.7375 26.650000000000002 29.675 19.9375 58-59 23.1 27.500000000000004 29.2 20.200000000000003 60-61 24.587500000000002 26.8125 29.9375 18.6625 62-63 22.125 28.975 30.65 18.25 64-65 22.5125 28.712500000000002 29.2 19.575 66-67 22.875 28.825 28.962500000000002 19.3375 68-69 23.1375 28.225 28.762500000000003 19.875 70-71 24.040632054176072 26.686731878605467 28.91898670679709 20.353649360421368 72-73 24.119516846789573 27.806738715829628 29.434202161474886 18.639542275905914 74-75 23.63941191643023 27.418106783595565 29.404178488522053 19.538302811452155 76-77 22.883235485975213 26.810176125244617 30.39791258969341 19.908675799086758 78-79 23.44225426643736 25.704458261674823 30.612514882921023 20.24077258896679 80-81 23.017044691987653 28.89545027513086 29.60676419272581 18.480740840155686 82-83 22.15094854647195 27.3099495018425 29.725672171420776 20.813429780264777 84-85 23.12925170068027 25.531028738025825 31.25086769401638 20.088851867277523 86-87 21.554129464285715 28.334263392857146 30.41294642857143 19.698660714285715 88-89 20.633370535714285 30.13392857142857 30.203683035714285 19.029017857142858 90-91 22.963169642857142 29.129464285714285 28.976004464285715 18.931361607142858 92-93 20.940290178571427 30.440848214285715 29.617745535714285 19.001116071428573 >>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 0.5 18 1.0 19 1.0 20 1.0 21 3.0 22 5.0 23 5.5 24 9.0 25 13.5 26 12.5 27 15.0 28 25.0 29 31.5 30 42.0 31 55.0 32 69.0 33 84.5 34 107.0 35 128.0 36 148.0 37 197.0 38 220.0 39 201.5 40 220.5 41 240.5 42 248.0 43 259.5 44 220.5 45 185.0 46 175.0 47 166.5 48 157.5 49 152.0 50 150.5 51 140.0 52 127.0 53 135.0 54 133.0 55 93.5 56 68.5 57 65.0 58 49.0 59 21.0 60 11.5 61 15.0 62 14.0 63 9.0 64 6.5 65 8.0 66 9.0 67 4.5 68 2.0 69 4.0 70 2.5 71 0.0 72 0.5 73 0.5 74 0.0 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 0.0257864878803507 76-77 0.026085822355549758 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 26.0 71 28.0 72 27.0 73 30.0 74 22.0 75 25.0 76 17.0 77 27.0 78 37.0 79 20.0 80 31.0 81 30.0 82 33.0 83 28.0 84 35.0 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 3584.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 82.975 #Duplication Level Percentage of deduplicated Percentage of total 1 92.19644471226273 76.5 2 4.429044893040072 7.35 3 1.2051822838204278 3.0 4 0.6025911419102139 2.0 5 0.391684242241639 1.625 6 0.3615546851461284 1.7999999999999998 7 0.21090689966857487 1.225 8 0.06025911419102139 0.4 9 0.12051822838204278 0.8999999999999999 >10 0.42181379933714974 5.2 >50 0.0 0.0 >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 warn #Sequence Count Percentage Possible Source GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 28 0.7000000000000001 No Hit CAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCT 24 0.6 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 18 0.44999999999999996 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 17 0.42500000000000004 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 17 0.42500000000000004 No Hit CAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATAT 14 0.35000000000000003 No Hit GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGC 14 0.35000000000000003 No Hit CAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTG 12 0.3 No Hit TCAAAAGAGGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGGA 12 0.3 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 11 0.27499999999999997 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 11 0.27499999999999997 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 10 0.25 No Hit GGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTT 10 0.25 No Hit GTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAG 10 0.25 No Hit GTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAA 9 0.22499999999999998 No Hit GTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCT 9 0.22499999999999998 No Hit GGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGC 9 0.22499999999999998 No Hit GGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAA 9 0.22499999999999998 No Hit GGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAA 8 0.2 No Hit GGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGG 8 0.2 No Hit GGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGCTAAATACAG 7 0.17500000000000002 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 7 0.17500000000000002 No Hit GGGGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCT 7 0.17500000000000002 No Hit GGGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTA 7 0.17500000000000002 No Hit GTACTATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTT 7 0.17500000000000002 No Hit GGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGC 7 0.17500000000000002 No Hit GTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTC 7 0.17500000000000002 No Hit GGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAAGGCGATCAAATTC 6 0.15 No Hit GGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTT 6 0.15 No Hit GTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAA 6 0.15 No Hit GAAGTATGGAAGGCGATCAAATTCGAGTTCGCGCCGGTAGATACTATCGA 6 0.15 No Hit AGTCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAA 6 0.15 No Hit GAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGC 6 0.15 No Hit CAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAACGAAGGG 6 0.15 No Hit GGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGT 6 0.15 No Hit GGGCTCGAGGAGCATATGTACATTTGAACCCTGACTACACATATACACAC 6 0.15 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 6 0.15 No Hit GGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTCCT 6 0.15 No Hit AGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTG 6 0.15 No Hit CTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAA 5 0.125 No Hit CTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGT 5 0.125 No Hit GCAGCTTGCAAATGGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAA 5 0.125 No Hit GGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAAA 5 0.125 No Hit GAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTG 5 0.125 No Hit CTGTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTC 5 0.125 No Hit GGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAAATGGATTC 5 0.125 No Hit GGTATTAGTACTATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATC 5 0.125 No Hit CAAATAGGTCAACCTTTTAAACTGCCTGCTGAATCCATGAGCAGGCAAGA 5 0.125 No Hit GGGGCAGAGGGAATTTCCGGTGGAGCGGTGAAATGCATTGAGATCGGAAA 5 0.125 No Hit GGATACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATG 5 0.125 No Hit GGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAA 5 0.125 No Hit GGGCACTGTAGCCAGTGTGTCAGTCGTTGTTAAATTACAGGTTGAGATCA 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 0.025 0.0 0.0 0.0 0.0 24-25 0.025 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 0.025 0.0 0.0 0.0 0.0 32-33 0.025 0.0 0.0 0.0 0.0 34-35 0.025 0.0 0.0 0.0 0.0 36-37 0.025 0.0 0.0 0.0 0.0 38-39 0.025 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 0.025 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 pass >>END_MODULE Rejected 38072 READS because READLEN < 1 Read 38072 spots for ERR6133332.sra Written 38072 spots for ERR6133332.sra Rejected 38072 READS because READLEN < 1 Read 38072 spots for ERR6133332.sra Written 38072 spots for ERR6133332.sra Rejected 38072 READS because READLEN < 1 Read 38072 spots for ERR6133332.sra Written 38072 spots for ERR6133332.sra Rejected 38072 READS because READLEN < 1 Read 38072 spots for ERR6133332.sra Written 38072 spots for ERR6133332.sra Rejected 38072 READS because READLEN < 1 Read 38072 spots for ERR6133332.sra Written 38072 spots for ERR6133332.sra Rejected 38072 READS because READLEN < 1 Read 38072 spots for ERR6133332.sra Written 38072 spots for ERR6133332.sra Rejected 38072 READS because READLEN < 1 Read 38072 spots for ERR6133332.sra Written 38072 spots for ERR6133332.sra Rejected 38072 READS because READLEN < 1 Read 38072 spots for ERR6133332.sra Written 38072 spots for ERR6133332.sra Rejected 38072 READS because READLEN < 1 Read 38072 spots for ERR6133332.sra Written 38072 spots for ERR6133332.sra Rejected 38072 READS because READLEN < 1 Read 38072 spots for ERR6133332.sra Written 38072 spots for ERR6133332.sra Rejected 38072 READS because READLEN < 1 Read 38072 spots for ERR6133332.sra Written 38072 spots for ERR6133332.sra Rejected 38072 READS because READLEN < 1 Read 38072 spots for ERR6133332.sra Written 38072 spots for ERR6133332.sra Rejected 38072 READS because READLEN < 1 Read 38072 spots for ERR6133332.sra Written 38072 spots for ERR6133332.sra Rejected 38072 READS because READLEN < 1 Read 38072 spots for ERR6133332.sra Written 38072 spots for ERR6133332.sra Rejected 38085 READS because READLEN < 1 Read 38085 spots for ERR6133332.sra Written 38085 spots for ERR6133332.sra Rejected 38072 READS because READLEN < 1 Read 38072 spots for ERR6133332.sra Written 38072 spots for ERR6133332.sra Rejected 38072 READS because READLEN < 1 Read 38072 spots for ERR6133332.sra Written 38072 spots for ERR6133332.sra Rejected 38072 READS because READLEN < 1 Read 38072 spots for ERR6133332.sra Written 38072 spots for ERR6133332.sra Rejected 38072 READS because READLEN < 1 Read 38072 spots for ERR6133332.sra Written 38072 spots for ERR6133332.sra Rejected 38072 READS because READLEN < 1 Read 38072 spots for ERR6133332.sra Written 38072 spots for ERR6133332.sra SRR ids: ['ERR6133332.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_xmslxi_2 ERR6133332.sra spots: 761453 blocks: [[1, 38072], [38073, 76144], [76145, 114216], [114217, 152288], [152289, 190360], [190361, 228432], [228433, 266504], [266505, 304576], [304577, 342648], [342649, 380720], [380721, 418792], [418793, 456864], [456865, 494936], [494937, 533008], [533009, 571080], [571081, 609152], [609153, 647224], [647225, 685296], [685297, 723368], [723369, 761453]] ERR6133332 file size 165530 ERR6133332 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 ERR6133332 ERR6133332_1.fastq Input file: ERR6133332_1.fastq trimmed: ERR6133332-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 00:49:37 2024 >> started Sat Dec 7 00:49:37 2024 >> done (0.507s) 761453 reads processed; of these: 136 ( 0.02%) short reads filtered out after trimming by size control 6 ( 0.00%) empty reads filtered out after trimming by size control 761311 (99.98%) reads available; of these: 10987 ( 1.44%) trimmed reads available after processing 750324 (98.56%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 9 0.00% 19 16 0.00% 20 4 0.00% 21 10 0.00% 22 11 0.00% 23 5 0.00% 24 8 0.00% 25 3 0.00% 26 2 0.00% 27 8 0.00% 28 11 0.00% 29 10 0.00% 30 7 0.00% 31 7 0.00% 32 6 0.00% 33 6 0.00% 34 7 0.00% 35 23 0.00% 36 8 0.00% 37 7 0.00% 38 17 0.00% 39 17 0.00% 40 13 0.00% 41 9 0.00% 42 2 0.00% 43 3 0.00% 44 9 0.00% 45 3 0.00% 46 7 0.00% 47 3 0.00% 48 1 0.00% 49 3 0.00% 50 3 0.00% 51 13 0.00% 52 6 0.00% 53 6 0.00% 54 5 0.00% 55 3 0.00% 56 3 0.00% 57 9 0.00% 58 5 0.00% 59 8 0.00% 60 13 0.00% 61 5 0.00% 62 2 0.00% 63 1 0.00% 64 3 0.00% 65 0 0.00% 66 1 0.00% 67 5 0.00% 68 9 0.00% 69 30 0.00% 70 4884 0.64% 71 4699 0.62% 72 4830 0.63% 73 4822 0.63% 74 4438 0.58% 75 4408 0.58% 76 4457 0.59% 77 4585 0.60% 78 4779 0.63% 79 5131 0.67% 80 4998 0.66% 81 5740 0.75% 82 5925 0.78% 83 5591 0.73% 84 6077 0.80% 85 9 0.00% 86 19 0.00% 87 30 0.00% 88 79 0.01% 89 137 0.02% 90 388 0.05% 91 1356 0.18% 92 8088 1.06% 93 675456 88.72% 761311 reads passed initial QC criterion=sequence-density sequence-density=2.70 sequence-density-rank=1 fanout-score=2.01 fanout-score-rank=21 prefix-density=2.72 prefix-fanout=2.0 sequence=CAAGGCTAAATAC criterion=fanout-score sequence-density=0.09 sequence-density-rank=14 fanout-score=9.32 fanout-score-rank=1 prefix-density=0.51 prefix-fanout=1.7 sequence=TGCTGCAGCAGCTTAATTTGCATGCCAGGGACGCATGCAACGACCATCTACATATAGCTACTCGATCTACCGCTACCATGAACCGATCCAAGGCTAGCTGCACAAGCTAGGCCCTTATTTCCCTTTGTACGGGTGCATGCATGCCATCCCATGCCATGCTTGTAACCCCCCATAAATAAAATCGCCCTGGTTTAACTA 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 00:49:49 Started mapping on | Dec 07 00:49:49 Finished on | Dec 07 00:49:52 Mapping speed, Million of reads per hour | 913.57 Number of input reads | 761311 Average input read length | 91 UNIQUE READS: Uniquely mapped reads number | 462701 Uniquely mapped reads % | 60.78% Average mapped length | 90.55 Number of splices: Total | 15221 Number of splices: Annotated (sjdb) | 12224 Number of splices: GT/AG | 14602 Number of splices: GC/AG | 300 Number of splices: AT/AC | 23 Number of splices: Non-canonical | 296 Mismatch rate per base, % | 0.43% Deletion rate per base | 0.05% Deletion average length | 1.69 Insertion rate per base | 0.02% Insertion average length | 1.70 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 259677 % of reads mapped to multiple loci | 34.11% Number of reads mapped to too many loci | 18616 % of reads mapped to too many loci | 2.45% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 2.53% % of reads unmapped: other | 0.14% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 38933 38933 38933 N_multimapping 259677 259677 259677 N_noFeature 34981 38884 444032 N_ambiguous 17041 2241 88 UnstrandedReadsAssigned:410679 PositiveStrandReadsAssigned:421576 NegativeStrandReadsAssigned:18581 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=93 echo kmer=89 ERR6133332 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: ERR6133332-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 761,311 reads, 585,761 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 861 rounds 52973 ERR6133332.ke.tsv 35125 ERR6133332.se.tsv 88098 total ==> ERR6133332.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 10 16.7807 PNS24243 293 194 0 0 KQK14069 1603 1504 2 3.06158 KQK14071 474 375 0 0 ==> ERR6133332.se.tsv <== BRADI_1g14170v3 2 BRADI_1g53295v3 1 BRADI_1g59795v3 4 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 6 BRADI_1g74790v3 0 BRADI_1g09890v3 0 BRADI_1g77505v3 8 BRADI_1g48960v3 0 ERR6133332 completed mapping pipeline successfully