Starting /dee2/code/volunteer_pipeline.sh ERR6133354 current disk space = 1548298977280 free memory = 1597902620 ERR6133354 SRAfilesize b3ff46cd34a8e76a820be9d5631a3419 ERR6133354.sra ERR6133354.sra file validated ERR6133354 is single end ERR6133354 is conventional basespace ERR6133354 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133354_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 36.3105 37.0 37.0 37.0 33.0 37.0 2 36.68775 37.0 37.0 37.0 37.0 37.0 3 36.64825 37.0 37.0 37.0 37.0 37.0 4 36.31625 37.0 37.0 37.0 37.0 37.0 5 36.38275 37.0 37.0 37.0 37.0 37.0 6 36.52325 37.0 37.0 37.0 37.0 37.0 7 38.69925 40.0 37.0 40.0 37.0 40.0 8 38.72775 40.0 37.0 40.0 37.0 40.0 9 38.76075 40.0 37.0 40.0 37.0 40.0 10-11 38.758125 40.0 37.0 40.0 37.0 40.0 12-13 38.731 40.0 37.0 40.0 37.0 40.0 14-15 38.7475 40.0 37.0 40.0 37.0 40.0 16-17 38.692625 40.0 37.0 40.0 37.0 40.0 18-19 38.57225 40.0 37.0 40.0 37.0 40.0 20-21 38.54575 40.0 37.0 40.0 37.0 40.0 22-23 38.45075 40.0 37.0 40.0 37.0 40.0 24-25 38.390625 40.0 37.0 40.0 37.0 40.0 26-27 38.40475 40.0 37.0 40.0 37.0 40.0 28-29 38.467375000000004 40.0 37.0 40.0 37.0 40.0 30-31 38.397375 40.0 37.0 40.0 37.0 40.0 32-33 38.289375 40.0 37.0 40.0 37.0 40.0 34-35 38.18775 40.0 37.0 40.0 37.0 40.0 36-37 38.0935 40.0 37.0 40.0 37.0 40.0 38-39 38.078 40.0 37.0 40.0 37.0 40.0 40-41 37.90625 40.0 37.0 40.0 37.0 40.0 42-43 37.84975 37.0 37.0 40.0 37.0 40.0 44-45 37.697874999999996 37.0 37.0 40.0 35.0 40.0 46-47 37.586 37.0 37.0 40.0 35.0 40.0 48-49 37.36525 37.0 37.0 40.0 33.0 40.0 50-51 37.282875000000004 37.0 37.0 40.0 33.0 40.0 52-53 37.04475 37.0 37.0 40.0 33.0 40.0 54-55 36.876125 37.0 37.0 37.0 33.0 40.0 56-57 36.7305 37.0 37.0 37.0 33.0 40.0 58-59 36.549375 37.0 37.0 37.0 33.0 40.0 60-61 36.48575 37.0 37.0 37.0 33.0 40.0 62-63 36.207625 37.0 37.0 37.0 33.0 37.0 64-65 36.120625000000004 37.0 37.0 37.0 33.0 37.0 66-67 36.04025 37.0 37.0 37.0 33.0 37.0 68-69 35.10225 35.0 35.0 37.0 33.0 37.0 70-71 35.28285149572649 37.0 33.0 37.0 33.0 37.0 72-73 35.78370364807198 37.0 37.0 37.0 33.0 37.0 74-75 35.742995304423985 37.0 37.0 37.0 33.0 37.0 76-77 35.708948085676724 37.0 37.0 37.0 33.0 37.0 78-79 35.697620446726106 37.0 37.0 37.0 33.0 37.0 80-81 35.62640953459274 37.0 37.0 37.0 33.0 37.0 82-83 35.5408354838858 37.0 37.0 37.0 33.0 37.0 84-85 35.52514661095499 37.0 37.0 37.0 33.0 37.0 86-87 35.413854109961896 37.0 33.0 37.0 33.0 37.0 88-89 35.47005988023952 37.0 35.0 37.0 33.0 37.0 90-91 35.37683723462167 37.0 33.0 37.0 33.0 37.0 92-93 35.2559880239521 37.0 33.0 37.0 33.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 2.0 21 0.0 22 5.0 23 5.0 24 3.0 25 6.0 26 12.0 27 13.0 28 22.0 29 22.0 30 30.0 31 46.0 32 40.0 33 64.0 34 91.0 35 219.0 36 728.0 37 1131.0 38 1493.0 39 68.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 64.36609152288072 8.577144286071519 9.32733183295824 17.72943235808952 2 47.075 26.575 15.75 10.6 3 30.95 35.925000000000004 18.125 15.0 4 30.825000000000003 27.3 21.224999999999998 20.65 5 28.15 26.150000000000002 26.275 19.425 6 21.075 33.7 27.025 18.2 7 34.025 27.375 21.575 17.025000000000002 8 27.1 27.500000000000004 26.325 19.075 9 25.2 27.675 28.125 19.0 10-11 24.675 27.575 28.1375 19.6125 12-13 24.025 27.825 28.025 20.125 14-15 22.0125 29.45 29.1125 19.425 16-17 25.362499999999997 29.075 24.7375 20.825 18-19 24.3625 25.7 29.8375 20.1 20-21 27.0875 25.5 27.3 20.1125 22-23 27.8375 23.9875 27.0 21.175 24-25 23.95 26.075 29.4375 20.5375 26-27 26.187500000000004 24.05 28.537499999999998 21.224999999999998 28-29 24.8125 28.125 27.625 19.4375 30-31 26.737499999999997 25.8 27.925 19.537499999999998 32-33 25.074999999999996 24.3625 29.1375 21.425 34-35 22.975 29.562500000000004 27.175 20.2875 36-37 24.1375 26.1625 26.1 23.599999999999998 38-39 27.237499999999997 25.3 27.2625 20.200000000000003 40-41 24.4875 24.349999999999998 30.225 20.9375 42-43 26.375 28.4125 26.724999999999998 18.4875 44-45 23.375 27.6 28.249999999999996 20.775 46-47 25.4625 26.4125 26.887499999999996 21.2375 48-49 24.875 24.7375 29.049999999999997 21.337500000000002 50-51 22.6 27.5625 28.6875 21.15 52-53 24.8625 26.8625 27.3375 20.9375 54-55 24.675 27.85 28.4 19.075 56-57 24.85 28.425 27.55 19.175 58-59 24.6 28.1 28.1625 19.1375 60-61 28.349999999999998 26.787499999999998 26.5625 18.3 62-63 22.9625 28.037499999999998 30.099999999999998 18.9 64-65 22.15 31.5 28.075 18.275 66-67 24.474999999999998 29.2 27.2625 19.0625 68-69 22.8625 27.825 27.712500000000002 21.6 70-71 24.880922536976684 28.240160441213334 26.29731762346453 20.58159939834545 72-73 25.0950088674943 27.628578667342286 28.882695718267037 18.393716746896377 74-75 24.382123191189653 28.390318862850556 28.32629017799974 18.901267767960046 76-77 23.629073978272118 26.24159337816865 27.36678737713399 22.762545266425246 78-79 25.284202273618188 27.126617012936105 27.570887233764534 20.01829347968117 80-81 22.938689217758984 31.38213530655391 26.744186046511626 18.934989429175474 82-83 22.225201072386056 27.815013404825738 27.92225201072386 22.037533512064343 84-85 21.54868456739897 26.674803363167886 30.390561432058583 21.38595063737456 86-87 21.951551442569407 28.388677191072404 27.068590092542188 22.591181273816005 88-89 21.271094175285793 29.844855743059334 27.531301034295048 21.352749047359826 90-91 24.020141535111595 30.008165487207407 26.224823081110504 19.746869896570495 92-93 21.284703320631465 31.450734893848665 26.878062057702778 20.386499727817093 >>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 1.0 18 1.0 19 1.0 20 1.0 21 1.0 22 1.5 23 2.0 24 3.5 25 5.0 26 8.5 27 12.5 28 19.5 29 28.5 30 32.0 31 42.0 32 53.5 33 57.5 34 73.5 35 92.5 36 111.5 37 145.5 38 175.0 39 203.5 40 237.5 41 235.5 42 241.0 43 262.0 44 223.5 45 191.0 46 186.5 47 177.0 48 149.0 49 139.0 50 164.5 51 155.0 52 129.5 53 135.5 54 177.0 55 151.5 56 83.0 57 66.5 58 53.0 59 32.0 60 22.5 61 21.5 62 15.0 63 11.0 64 13.5 65 13.5 66 10.0 67 8.5 68 17.0 69 24.5 70 13.0 71 1.0 72 0.5 73 0.0 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 0.025 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 22.0 71 18.0 72 26.0 73 18.0 74 23.0 75 17.0 76 20.0 77 19.0 78 21.0 79 22.0 80 20.0 81 30.0 82 28.0 83 16.0 84 26.0 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 3674.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 76.325 #Duplication Level Percentage of deduplicated Percentage of total 1 91.90959711758926 70.15 2 4.094333442515558 6.25 3 1.342941369145103 3.075 4 0.8516213560432362 2.6 5 0.3930560104814936 1.5 6 0.22928267278087125 1.05 7 0.1965280052407468 1.05 8 0.06550933508024893 0.4 9 0.0982640026203734 0.675 >10 0.7861120209629872 10.65 >50 0.0 0.0 >100 0.03275466754012447 2.6 >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 104 2.6 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 41 1.0250000000000001 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 41 1.0250000000000001 No Hit CAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCT 39 0.975 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 24 0.6 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 24 0.6 No Hit CAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATAT 20 0.5 No Hit TCAAAAGAGGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGGA 20 0.5 No Hit CAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTG 19 0.475 No Hit GGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAA 16 0.4 No Hit GGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGC 15 0.375 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 14 0.35000000000000003 No Hit GGGTGAGAGCCCCGTCCGGCCCGGACCCTGTCGCCCCACGAGGCGCCGTC 14 0.35000000000000003 No Hit GGAGGGTGAGAGCCCCGTCCGGCCCGGACCCTGTCGCCCCACGAGGCGCC 13 0.325 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 13 0.325 No Hit GGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTCCT 13 0.325 No Hit CGAGGAAGGGCGTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAG 13 0.325 No Hit GGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTT 12 0.3 No Hit GGGGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCT 12 0.3 No Hit GGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGC 12 0.3 No Hit GTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAA 11 0.27499999999999997 No Hit GAGGAAGGGCGTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAGC 10 0.25 No Hit GGAAGGGCGTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAGCAT 10 0.25 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 10 0.25 No Hit GGGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTA 10 0.25 No Hit GGCCCGGACCCTGTCGCCCCACGAGGCGCCGTCAACGAGTCGGGTTGTTT 9 0.22499999999999998 No Hit AGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTG 9 0.22499999999999998 No Hit GTCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAAT 9 0.22499999999999998 No Hit GTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGGT 8 0.2 No Hit GGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGCA 8 0.2 No Hit GCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGGTATG 7 0.17500000000000002 No Hit GGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAAC 7 0.17500000000000002 No Hit CACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTTCGGGGAGT 7 0.17500000000000002 No Hit AGTCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAA 7 0.17500000000000002 No Hit GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 7 0.17500000000000002 No Hit GAACGTAATGCTCACAACTTCCCTCTAGATCTAGCTGCTCTTGAAGTTCC 7 0.17500000000000002 No Hit GGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAAA 6 0.15 No Hit GCAGCTTGCAAATGGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAA 6 0.15 No Hit GGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTTCGGGGA 6 0.15 No Hit GTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTC 6 0.15 No Hit GGGACGCATGCAACGACCATCTACATATAGCTACTCGATCTACCGCTACC 6 0.15 No Hit GAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGC 6 0.15 No Hit GGTTGAGTGCCGCACCCTAGATGGCTAAAGTCCAGTAGCCGAAAGCATCA 6 0.15 No Hit CGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGGTAT 5 0.125 No Hit CAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTT 5 0.125 No Hit GCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATC 5 0.125 No Hit CAAGCTCGTAACGAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAATTAT 5 0.125 No Hit GTAACGAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCA 5 0.125 No Hit CGAGTCGGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTC 5 0.125 No Hit GTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGCA 5 0.125 No Hit CTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGT 5 0.125 No Hit GTATTTAGCCTTGCAAGGTGGTCCTTGCTGATTCACACGGGATTCCACGT 5 0.125 No Hit GTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGGTATGGA 5 0.125 No Hit AACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGA 5 0.125 No Hit TCTCATGGAGAGTTCGATCCTGGCTCAGGATGAACGCTGGCGGCATGCTT 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 0.025 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 0.025 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 0.037500000000000006 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 0.0625 0.0 0.0 0.0 0.0 54-55 0.075 0.0 0.0 0.0 0.0 56-57 0.075 0.0 0.0 0.0 0.0 58-59 0.075 0.0 0.0 0.0 0.0 60-61 0.075 0.0 0.0 0.0 0.0 62-63 0.075 0.0 0.0 0.0 0.0 64-65 0.075 0.0 0.0 0.0 0.0 66-67 0.075 0.0 0.0 0.0 0.0 68-69 0.075 0.0 0.0 0.0 0.0 70-71 0.075 0.0 0.0 0.0 0.0 72-73 0.075 0.0 0.0 0.0 0.0 74-75 0.075 0.0 0.0 0.0 0.0 76-77 0.075 0.0 0.0 0.0 0.0 78-79 0.075 0.0 0.0 0.0 0.0 80-81 0.075 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Rejected 125474 READS because READLEN < 1 Read 125474 spots for ERR6133354.sra Written 125474 spots for ERR6133354.sra Rejected 125474 READS because READLEN < 1 Read 125474 spots for ERR6133354.sra Written 125474 spots for ERR6133354.sra Rejected 125474 READS because READLEN < 1 Read 125474 spots for ERR6133354.sra Written 125474 spots for ERR6133354.sra Rejected 125474 READS because READLEN < 1 Read 125474 spots for ERR6133354.sra Written 125474 spots for ERR6133354.sra Rejected 125474 READS because READLEN < 1 Read 125474 spots for ERR6133354.sra Written 125474 spots for ERR6133354.sra Rejected 125474 READS because READLEN < 1 Read 125474 spots for ERR6133354.sra Written 125474 spots for ERR6133354.sra Rejected 125474 READS because READLEN < 1 Read 125474 spots for ERR6133354.sra Written 125474 spots for ERR6133354.sra Rejected 125474 READS because READLEN < 1 Read 125474 spots for ERR6133354.sra Written 125474 spots for ERR6133354.sra Rejected 125474 READS because READLEN < 1 Read 125474 spots for ERR6133354.sra Written 125474 spots for ERR6133354.sra Rejected 125474 READS because READLEN < 1 Read 125474 spots for ERR6133354.sra Written 125474 spots for ERR6133354.sra Rejected 125474 READS because READLEN < 1 Read 125474 spots for ERR6133354.sra Written 125474 spots for ERR6133354.sra Rejected 125474 READS because READLEN < 1 Read 125474 spots for ERR6133354.sra Written 125474 spots for ERR6133354.sra Rejected 125474 READS because READLEN < 1 Read 125474 spots for ERR6133354.sra Written 125474 spots for ERR6133354.sra Rejected 125474 READS because READLEN < 1 Read 125474 spots for ERR6133354.sra Written 125474 spots for ERR6133354.sra Rejected 125474 READS because READLEN < 1 Read 125474 spots for ERR6133354.sra Written 125474 spots for ERR6133354.sra Rejected 125474 READS because READLEN < 1 Read 125474 spots for ERR6133354.sra Written 125474 spots for ERR6133354.sra Rejected 125474 READS because READLEN < 1 Read 125474 spots for ERR6133354.sra Written 125474 spots for ERR6133354.sra Rejected 125474 READS because READLEN < 1 Read 125474 spots for ERR6133354.sra Written 125474 spots for ERR6133354.sra Rejected 125474 READS because READLEN < 1 Read 125474 spots for ERR6133354.sra Written 125474 spots for ERR6133354.sra Rejected 125478 READS because READLEN < 1 Read 125478 spots for ERR6133354.sra Written 125478 spots for ERR6133354.sra SRR ids: ['ERR6133354.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_66801ycm ERR6133354.sra spots: 2509484 blocks: [[1, 125474], [125475, 250948], [250949, 376422], [376423, 501896], [501897, 627370], [627371, 752844], [752845, 878318], [878319, 1003792], [1003793, 1129266], [1129267, 1254740], [1254741, 1380214], [1380215, 1505688], [1505689, 1631162], [1631163, 1756636], [1756637, 1882110], [1882111, 2007584], [2007585, 2133058], [2133059, 2258532], [2258533, 2384006], [2384007, 2509484]] ERR6133354 file size 550126 ERR6133354 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 ERR6133354 ERR6133354_1.fastq Input file: ERR6133354_1.fastq trimmed: ERR6133354-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 01:16:37 2024 >> started Sat Dec 7 01:16:38 2024 >> done (1.329s) 2509484 reads processed; of these: 239 ( 0.01%) short reads filtered out after trimming by size control 17 ( 0.00%) empty reads filtered out after trimming by size control 2509228 (99.99%) reads available; of these: 16091 ( 0.64%) trimmed reads available after processing 2493137 (99.36%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 29 0.00% 19 47 0.00% 20 31 0.00% 21 26 0.00% 22 31 0.00% 23 20 0.00% 24 20 0.00% 25 21 0.00% 26 30 0.00% 27 28 0.00% 28 117 0.00% 29 189 0.01% 30 14 0.00% 31 39 0.00% 32 50 0.00% 33 32 0.00% 34 20 0.00% 35 81 0.00% 36 25 0.00% 37 22 0.00% 38 36 0.00% 39 86 0.00% 40 95 0.00% 41 34 0.00% 42 22 0.00% 43 36 0.00% 44 30 0.00% 45 25 0.00% 46 19 0.00% 47 17 0.00% 48 19 0.00% 49 18 0.00% 50 17 0.00% 51 119 0.00% 52 24 0.00% 53 14 0.00% 54 15 0.00% 55 13 0.00% 56 14 0.00% 57 38 0.00% 58 22 0.00% 59 26 0.00% 60 34 0.00% 61 16 0.00% 62 7 0.00% 63 8 0.00% 64 11 0.00% 65 14 0.00% 66 24 0.00% 67 29 0.00% 68 49 0.00% 69 94 0.00% 70 13618 0.54% 71 13359 0.53% 72 13932 0.56% 73 13241 0.53% 74 12622 0.50% 75 12199 0.49% 76 11967 0.48% 77 12901 0.51% 78 13018 0.52% 79 13351 0.53% 80 13627 0.54% 81 16898 0.67% 82 17431 0.69% 83 15557 0.62% 84 17759 0.71% 85 113 0.00% 86 152 0.01% 87 204 0.01% 88 339 0.01% 89 561 0.02% 90 1034 0.04% 91 2309 0.09% 92 7874 0.31% 93 2283265 90.99% 2509228 reads passed initial QC criterion=sequence-density sequence-density=3.77 sequence-density-rank=1 fanout-score=2.05 fanout-score-rank=26 prefix-density=3.83 prefix-fanout=2.0 sequence=CAAGGCTAAATAC criterion=fanout-score sequence-density=0.01 sequence-density-rank=35 fanout-score=65.06 fanout-score-rank=1 prefix-density=0.08 prefix-fanout=5.3 sequence=TTTTTTCCTTAGAAAAATAACTCAATCAAAATCCAATTATTTACTCTACAAGAACGAAATGCTTGTTATGCCTAATATACTTAGTTTAACCTGTATCTGTTTTAATTGTGTTCTTTATCCGACTAGTTTTTTCTTTGCTAAACTACCCGAAGCTTATGCTATTTTCAACCCAATCGTGGATGTTATGCCTGTCATACCTCTATTCTTTTTTCTATTAGCCTTTGTTTGGCAAGCTGCTGTAAGTTTTCGATGAAATCTTTACTACTCCGTCTGCCAAATTGAATGGTCTATTCATTCCAAAACCAA 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 01:17:16 Started mapping on | Dec 07 01:17:16 Finished on | Dec 07 01:17:24 Mapping speed, Million of reads per hour | 1129.15 Number of input reads | 2509228 Average input read length | 91 UNIQUE READS: Uniquely mapped reads number | 1247981 Uniquely mapped reads % | 49.74% Average mapped length | 90.60 Number of splices: Total | 43951 Number of splices: Annotated (sjdb) | 36027 Number of splices: GT/AG | 41227 Number of splices: GC/AG | 837 Number of splices: AT/AC | 48 Number of splices: Non-canonical | 1839 Mismatch rate per base, % | 0.43% Deletion rate per base | 0.05% Deletion average length | 1.67 Insertion rate per base | 0.03% Insertion average length | 1.53 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 1029818 % of reads mapped to multiple loci | 41.04% Number of reads mapped to too many loci | 127572 % of reads mapped to too many loci | 5.08% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 3.88% % of reads unmapped: other | 0.26% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 231429 231429 231429 N_multimapping 1029818 1029818 1029818 N_noFeature 105828 118455 1192764 N_ambiguous 49577 6962 228 UnstrandedReadsAssigned:1092576 PositiveStrandReadsAssigned:1122564 NegativeStrandReadsAssigned:54989 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=93 echo kmer=89 ERR6133354 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: ERR6133354-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 2,509,228 reads, 1,666,287 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 972 rounds 52973 ERR6133354.ke.tsv 35125 ERR6133354.se.tsv 88098 total ==> ERR6133354.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 36 21.0182 PNS24243 293 194 0 0 KQK14069 1603 1504 16 8.52156 KQK14071 474 375 0 0 ==> ERR6133354.se.tsv <== BRADI_1g14170v3 16 BRADI_1g53295v3 33 BRADI_1g59795v3 10 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 24 BRADI_1g74790v3 12 BRADI_1g09890v3 3 BRADI_1g77505v3 42 BRADI_1g48960v3 0 ERR6133354 completed mapping pipeline successfully