Starting /dee2/code/volunteer_pipeline.sh ERR6133573 current disk space = 1544430776320 free memory = 1598228520 ERR6133573 SRAfilesize f2561b247edc06253154d244ec30b000 ERR6133573.sra ERR6133573.sra file validated ERR6133573 is single end ERR6133573 is conventional basespace ERR6133573 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133573_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 35.344 37.0 33.0 37.0 33.0 37.0 2 36.4955 37.0 37.0 37.0 37.0 37.0 3 35.98725 37.0 37.0 37.0 33.0 37.0 4 35.378 37.0 37.0 37.0 33.0 37.0 5 35.11175 37.0 37.0 37.0 33.0 37.0 6 35.61725 37.0 37.0 37.0 33.0 37.0 7 37.3935 37.0 37.0 40.0 33.0 40.0 8 37.4645 37.0 37.0 40.0 33.0 40.0 9 37.6075 40.0 37.0 40.0 33.0 40.0 10-11 37.51475 38.5 37.0 40.0 33.0 40.0 12-13 37.421625 37.0 37.0 40.0 33.0 40.0 14-15 37.436 37.0 37.0 40.0 33.0 40.0 16-17 37.261250000000004 37.0 37.0 40.0 33.0 40.0 18-19 37.285875000000004 37.0 37.0 40.0 33.0 40.0 20-21 37.23225 37.0 37.0 40.0 33.0 40.0 22-23 37.225750000000005 37.0 37.0 40.0 33.0 40.0 24-25 37.314625 37.0 37.0 40.0 33.0 40.0 26-27 37.31075 37.0 37.0 40.0 33.0 40.0 28-29 37.2745 37.0 37.0 40.0 33.0 40.0 30-31 37.108000000000004 37.0 37.0 40.0 33.0 40.0 32-33 36.915 37.0 37.0 40.0 33.0 40.0 34-35 36.79425 37.0 37.0 40.0 33.0 40.0 36-37 36.781 37.0 37.0 40.0 33.0 40.0 38-39 36.52875 37.0 37.0 40.0 33.0 40.0 40-41 36.45762499999999 37.0 37.0 40.0 33.0 40.0 42-43 36.256 37.0 37.0 40.0 33.0 40.0 44-45 35.947625 37.0 35.0 40.0 33.0 40.0 46-47 35.758750000000006 37.0 33.0 37.0 33.0 40.0 48-49 35.617374999999996 37.0 33.0 37.0 33.0 40.0 50-51 35.510000000000005 37.0 33.0 37.0 33.0 40.0 52-53 35.173875 37.0 33.0 37.0 33.0 40.0 54-55 35.109624999999994 37.0 33.0 37.0 33.0 40.0 56-57 34.879625000000004 37.0 33.0 37.0 27.0 38.5 58-59 33.806375 37.0 33.0 37.0 27.0 37.0 60-61 34.38675 37.0 33.0 37.0 27.0 37.0 62-63 34.37625 37.0 33.0 37.0 27.0 37.0 64-65 34.379875 37.0 33.0 37.0 27.0 37.0 66-67 34.456999999999994 37.0 33.0 37.0 27.0 37.0 68-69 33.71425 35.0 33.0 37.0 27.0 37.0 70-71 33.69583862384172 35.0 33.0 37.0 27.0 37.0 72-73 34.12834876068275 37.0 33.0 37.0 27.0 37.0 74-75 33.88391728887051 37.0 33.0 37.0 27.0 37.0 76-77 34.04734067838638 37.0 33.0 37.0 27.0 37.0 78-79 34.08427080172125 37.0 33.0 37.0 27.0 37.0 80-81 33.92392470414697 37.0 33.0 37.0 27.0 37.0 82-83 33.935146622319984 37.0 33.0 37.0 27.0 37.0 84-85 33.86770448145158 37.0 33.0 37.0 27.0 37.0 86-87 33.66848249027237 37.0 33.0 37.0 27.0 37.0 88-89 33.80220492866407 37.0 33.0 37.0 27.0 37.0 90-91 33.54630350194553 37.0 33.0 37.0 27.0 37.0 92-93 33.391569390402076 37.0 33.0 37.0 27.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 10.0 21 13.0 22 13.0 23 23.0 24 26.0 25 26.0 26 31.0 27 52.0 28 42.0 29 64.0 30 80.0 31 111.0 32 137.0 33 164.0 34 253.0 35 458.0 36 914.0 37 948.0 38 622.0 39 13.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 86.725 2.675 3.5749999999999997 7.025 2 69.69999999999999 17.25 7.875 5.175 3 36.95 36.925000000000004 14.499999999999998 11.625 4 34.8 26.674999999999997 19.025 19.5 5 26.174999999999997 31.55 25.275 17.0 6 19.8 37.325 26.424999999999997 16.45 7 36.0 27.775 21.45 14.774999999999999 8 30.9 28.95 23.549999999999997 16.6 9 26.674999999999997 27.825 27.900000000000002 17.599999999999998 10-11 24.975 27.962500000000002 27.950000000000003 19.112499999999997 12-13 26.900000000000002 25.924999999999997 27.700000000000003 19.475 14-15 21.75 29.3875 29.4375 19.425 16-17 25.2 30.362499999999997 25.374999999999996 19.0625 18-19 24.4375 26.650000000000002 27.825 21.087500000000002 20-21 25.412499999999998 26.5 28.4375 19.650000000000002 22-23 27.0125 23.6875 27.8125 21.4875 24-25 24.74059257407176 25.828228528566072 28.27853481685211 21.152644080510065 26-27 24.962500000000002 25.2625 31.087500000000002 18.6875 28-29 25.337500000000002 26.8375 28.3375 19.4875 30-31 25.95 26.275 27.2625 20.5125 32-33 24.6875 25.2875 29.212500000000002 20.8125 34-35 23.8625 28.075 27.987499999999997 20.075000000000003 36-37 23.9 25.074999999999996 28.475 22.55 38-39 24.978122265283158 24.228028503562946 31.241405175646957 19.55244405550694 40-41 26.16904226056514 24.90622655663916 28.14453613403351 20.78019504876219 42-43 24.975 28.599999999999998 27.125 19.3 44-45 23.625 26.075 30.2875 20.0125 46-47 24.2625 24.637500000000003 27.712500000000002 23.3875 48-49 24.3125 25.2625 30.075000000000003 20.349999999999998 50-51 24.0375 26.224999999999998 29.725 20.0125 52-53 24.401253918495296 26.846394984326018 27.74921630094044 21.003134796238246 54-55 24.425 26.5625 29.7375 19.275000000000002 56-57 26.650000000000002 26.737499999999997 28.050000000000004 18.5625 58-59 24.962500000000002 24.6 29.3375 21.099999999999998 60-61 25.724999999999998 26.025 29.6625 18.587500000000002 62-63 22.162499999999998 28.050000000000004 32.0 17.7875 64-65 23.150000000000002 28.025 28.999999999999996 19.825 66-67 24.9 26.924999999999997 29.475 18.7 68-69 22.0 28.225 28.237499999999997 21.5375 70-71 24.896784686600775 25.2596021518829 28.962842487176278 20.880770674340045 72-73 25.85427135678392 26.118090452261306 28.165829145728644 19.86180904522613 74-75 24.192327107521454 26.89298334174659 29.618879353861686 19.295810196870267 76-77 22.798124445570902 26.23241667722722 29.172474971486505 21.796983905715372 78-79 23.949579831932773 25.00636618283677 31.62719633307869 19.41685765215177 80-81 22.812180143295805 30.01535312180143 29.311668372569088 17.860798362333675 82-83 22.844272844272844 26.615186615186616 29.11196911196911 21.428571428571427 84-85 22.704312912835125 24.413936018650435 31.78344773993006 21.098303328584382 86-87 21.47859922178988 26.316472114137486 32.26977950713359 19.93514915693904 88-89 21.802853437094683 28.92347600518807 30.440985732814525 18.832684824902724 90-91 25.629053177691308 25.94033722438392 29.80544747081712 18.625162127107654 92-93 23.11284046692607 28.573281452658883 29.701686121919586 18.612191958495462 >>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 13.5 18 15.5 19 3.0 20 1.0 21 1.0 22 2.5 23 4.5 24 5.0 25 5.0 26 7.5 27 13.5 28 20.5 29 23.5 30 27.0 31 33.5 32 46.5 33 64.5 34 72.5 35 84.0 36 105.5 37 130.0 38 170.0 39 182.5 40 197.5 41 216.0 42 230.5 43 253.0 44 226.0 45 205.0 46 214.5 47 196.0 48 163.5 49 156.5 50 159.5 51 156.5 52 142.0 53 139.5 54 136.0 55 92.5 56 58.0 57 56.0 58 53.5 59 40.5 60 34.0 61 34.0 62 29.0 63 25.0 64 17.0 65 15.0 66 14.5 67 13.0 68 14.0 69 11.0 70 9.5 71 10.0 72 7.5 73 3.5 74 1.5 75 1.5 76 1.0 77 0.0 78 0.5 79 0.5 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 0.0125 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 0.025 42-43 0.0 44-45 0.0 46-47 0.0 48-49 0.0 50-51 0.0 52-53 0.3125 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 7.0 71 8.0 72 10.0 73 9.0 74 8.0 75 7.0 76 11.0 77 10.0 78 6.0 79 12.0 80 8.0 81 14.0 82 10.0 83 14.0 84 11.0 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 3855.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 78.85 #Duplication Level Percentage of deduplicated Percentage of total 1 92.35890932149651 72.82499999999999 2 4.216867469879518 6.65 3 1.2999365884590994 3.075 4 0.6024096385542169 1.9 5 0.3487634749524413 1.375 6 0.22194039315155356 1.05 7 0.19023462270133165 1.05 8 0.12682308180088775 0.8 9 0.03170577045022194 0.22499999999999998 >10 0.538998097653773 8.450000000000001 >50 0.06341154090044387 2.6 >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 GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 53 1.325 No Hit GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGC 51 1.275 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 40 1.0 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 38 0.95 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 30 0.75 No Hit GGAGTATCCTTGATATATAAATATATAGATAAATAGATTTAAATGGAAAA 27 0.675 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 27 0.675 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 26 0.65 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 22 0.5499999999999999 No Hit GGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGC 15 0.375 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 15 0.375 No Hit GGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTT 14 0.35000000000000003 No Hit GGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGG 14 0.35000000000000003 No Hit GGGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTG 14 0.35000000000000003 No Hit GGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAA 13 0.325 No Hit GTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAA 12 0.3 No Hit GTATTTAGCCTTGCAAGGTGGTCCTTGCTGATTCACACGGGATTCCACGT 11 0.27499999999999997 No Hit GGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGGG 10 0.25 No Hit GGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTT 10 0.25 No Hit CAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCT 9 0.22499999999999998 No Hit GGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAAGGCGATCAAATTC 8 0.2 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 8 0.2 No Hit GAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGC 8 0.2 No Hit GGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAA 8 0.2 No Hit GGGAAAAGAGGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTT 7 0.17500000000000002 No Hit CAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATAT 7 0.17500000000000002 No Hit GGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGGAAGGGCGTA 7 0.17500000000000002 No Hit GGCCTGTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCG 7 0.17500000000000002 No Hit GAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTG 7 0.17500000000000002 No Hit GGGCCGGGTATCTCTCTGCATGTACGTATGCCTGTAATGTACGTAGCTAC 7 0.17500000000000002 No Hit GGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAAA 6 0.15 No Hit GGGGATGGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACG 6 0.15 No Hit GGAAGAGCCCGAGCTGCTGCAGCAGGTTTTGAAAAGGGAATCGATCGTGA 6 0.15 No Hit GGGAGTGGGGGTGCCATACGCAAAAAGGAAGCGACTCATAGAATGGCAGA 6 0.15 No Hit GCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATC 6 0.15 No Hit GGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAACCCTCTTAACT 6 0.15 No Hit GGAAAAGAGGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTTG 6 0.15 No Hit GGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTA 5 0.125 No Hit GCAGCTTGCAAATGGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAA 5 0.125 No Hit GGGAGTATTATGAAAGGAGATTAATCATAGATTATCAAAAACCCTAGAAA 5 0.125 No Hit GGAATAAGAATAAATCGCAACTCCTTTCCACTACACATAAAAATTGATTT 5 0.125 No Hit CTGAGCCGTGCTCTCTTCTGTGTACATCTTCATGTCATTTTAGCGATTCT 5 0.125 No Hit CGGGGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACC 5 0.125 No Hit GGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTTGAAATCGGA 5 0.125 No Hit GGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGT 5 0.125 No Hit GGAGGTGGAAGGCCTACGGGTCGTCAACTTCTTTTCTCGGAGAAGAAACA 5 0.125 No Hit GTACAAGCTCGTAACGAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAAT 5 0.125 No Hit GGAAATTAACAGTTGGAAAGGGCGATCGGTCTTGATCCCTCTGTGTTTCC 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 0.0125 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 0.05 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 0.05 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GCAATAC 15 8.8794064E-4 86.5875 7 CAATACA 15 8.8794064E-4 86.5875 8 GAGCAAT 15 8.8794064E-4 86.5875 5 AATACAA 15 8.8794064E-4 86.5875 9 AGCAATA 15 8.8794064E-4 86.5875 6 AGAGCAA 20 0.0027818275 64.94063 4 GAGAGCA 20 0.0027818275 64.94063 3 >>END_MODULE Rejected 186507 READS because READLEN < 1 Read 186507 spots for ERR6133573.sra Written 186507 spots for ERR6133573.sra Rejected 186507 READS because READLEN < 1 Read 186507 spots for ERR6133573.sra Written 186507 spots for ERR6133573.sra Rejected 186507 READS because READLEN < 1 Read 186507 spots for ERR6133573.sra Written 186507 spots for ERR6133573.sra Rejected 186507 READS because READLEN < 1 Read 186507 spots for ERR6133573.sra Written 186507 spots for ERR6133573.sra Rejected 186507 READS because READLEN < 1 Read 186507 spots for ERR6133573.sra Written 186507 spots for ERR6133573.sra Rejected 186507 READS because READLEN < 1 Read 186507 spots for ERR6133573.sra Written 186507 spots for ERR6133573.sra Rejected 186507 READS because READLEN < 1 Read 186507 spots for ERR6133573.sra Written 186507 spots for ERR6133573.sra Rejected 186507 READS because READLEN < 1 Read 186507 spots for ERR6133573.sra Written 186507 spots for ERR6133573.sra Rejected 186507 READS because READLEN < 1 Read 186507 spots for ERR6133573.sra Written 186507 spots for ERR6133573.sra Rejected 186507 READS because READLEN < 1 Read 186507 spots for ERR6133573.sra Written 186507 spots for ERR6133573.sra Rejected 186507 READS because READLEN < 1 Read 186507 spots for ERR6133573.sra Written 186507 spots for ERR6133573.sra Rejected 186507 READS because READLEN < 1 Read 186507 spots for ERR6133573.sra Written 186507 spots for ERR6133573.sra Rejected 186507 READS because READLEN < 1 Read 186507 spots for ERR6133573.sra Written 186507 spots for ERR6133573.sra Rejected 186507 READS because READLEN < 1 Read 186507 spots for ERR6133573.sra Written 186507 spots for ERR6133573.sra Rejected 186507 READS because READLEN < 1 Read 186507 spots for ERR6133573.sra Written 186507 spots for ERR6133573.sra Rejected 186507 READS because READLEN < 1 Read 186507 spots for ERR6133573.sra Written 186507 spots for ERR6133573.sra Rejected 186507 READS because READLEN < 1 Read 186507 spots for ERR6133573.sra Written 186507 spots for ERR6133573.sra Rejected 186509 READS because READLEN < 1 Read 186509 spots for ERR6133573.sra Written 186509 spots for ERR6133573.sra Rejected 186507 READS because READLEN < 1 Read 186507 spots for ERR6133573.sra Written 186507 spots for ERR6133573.sra Rejected 186507 READS because READLEN < 1 Read 186507 spots for ERR6133573.sra Written 186507 spots for ERR6133573.sra SRR ids: ['ERR6133573.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_ysqb09_y ERR6133573.sra spots: 3730142 blocks: [[1, 186507], [186508, 373014], [373015, 559521], [559522, 746028], [746029, 932535], [932536, 1119042], [1119043, 1305549], [1305550, 1492056], [1492057, 1678563], [1678564, 1865070], [1865071, 2051577], [2051578, 2238084], [2238085, 2424591], [2424592, 2611098], [2611099, 2797605], [2797606, 2984112], [2984113, 3170619], [3170620, 3357126], [3357127, 3543633], [3543634, 3730142]] ERR6133573 file size 823764 ERR6133573 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 ERR6133573 ERR6133573_1.fastq Input file: ERR6133573_1.fastq trimmed: ERR6133573-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 08:56:04 2024 >> started Sat Dec 7 08:56:07 2024 >> done (2.945s) 3730142 reads processed; of these: 383 ( 0.01%) short reads filtered out after trimming by size control 60 ( 0.00%) empty reads filtered out after trimming by size control 3729699 (99.99%) reads available; of these: 76148 ( 2.04%) trimmed reads available after processing 3653551 (97.96%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 100 0.00% 19 157 0.00% 20 67 0.00% 21 66 0.00% 22 74 0.00% 23 24 0.00% 24 34 0.00% 25 12 0.00% 26 9 0.00% 27 37 0.00% 28 62 0.00% 29 55 0.00% 30 31 0.00% 31 54 0.00% 32 74 0.00% 33 46 0.00% 34 36 0.00% 35 460 0.01% 36 588 0.02% 37 43 0.00% 38 98 0.00% 39 218 0.01% 40 204 0.01% 41 71 0.00% 42 18 0.00% 43 22 0.00% 44 22 0.00% 45 13 0.00% 46 18 0.00% 47 12 0.00% 48 13 0.00% 49 11 0.00% 50 15 0.00% 51 63 0.00% 52 29 0.00% 53 10 0.00% 54 12 0.00% 55 6 0.00% 56 9 0.00% 57 16 0.00% 58 16 0.00% 59 14 0.00% 60 27 0.00% 61 11 0.00% 62 2 0.00% 63 5 0.00% 64 4 0.00% 65 4 0.00% 66 7 0.00% 67 19 0.00% 68 28 0.00% 69 109 0.00% 70 9585 0.26% 71 9230 0.25% 72 10421 0.28% 73 9137 0.24% 74 9528 0.26% 75 9540 0.26% 76 8236 0.22% 77 8585 0.23% 78 9661 0.26% 79 11071 0.30% 80 9801 0.26% 81 10254 0.27% 82 11697 0.31% 83 12515 0.34% 84 10547 0.28% 85 126 0.00% 86 302 0.01% 87 442 0.01% 88 810 0.02% 89 1545 0.04% 90 3466 0.09% 91 10187 0.27% 92 54319 1.46% 93 3505539 93.99% 3729699 reads passed initial QC criterion=sequence-density sequence-density=0.40 sequence-density-rank=1 fanout-score=1.94 fanout-score-rank=32 prefix-density=0.40 prefix-fanout=1.9 sequence=CAAGGCTAAATAC criterion=fanout-score sequence-density=0.02 sequence-density-rank=25 fanout-score=287.59 fanout-score-rank=1 prefix-density=0.62 prefix-fanout=7.2 sequence=GAAGAAGAAAAGTTTTCTCAACATGGGGAGGAAGTCCCTCCGAAATTTGATTTGTTATTGTATTGTAAGGGGCTTTTTTAGTATTTATCTAAAGGAAGGAACAAACGAGGATAAGATAAAATTTCTTTAAATTTATTTTGCCCAAGTGGGATATATGGCATACTATTCTTTCCATTTTCATCTTTTTTTCTATTCCACTCCATCTAGATATAAGAAAGAACCCAATGCAATGAAATTCCACTAATATACAATACAAAAAAGAAGAATAGATACAGGGTCTCAAACCTTGCTATAGAGTTTTTGC Started job on | Dec 07 08:56:19 Started mapping on | Dec 07 08:56:19 Finished on | Dec 07 08:56:30 Mapping speed, Million of reads per hour | 1220.63 Number of input reads | 3729699 Average input read length | 92 UNIQUE READS: Uniquely mapped reads number | 2561823 Uniquely mapped reads % | 68.69% Average mapped length | 91.87 Number of splices: Total | 99930 Number of splices: Annotated (sjdb) | 82941 Number of splices: GT/AG | 95970 Number of splices: GC/AG | 2697 Number of splices: AT/AC | 41 Number of splices: Non-canonical | 1222 Mismatch rate per base, % | 0.42% Deletion rate per base | 0.04% Deletion average length | 1.83 Insertion rate per base | 0.02% Insertion average length | 1.82 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 1064646 % of reads mapped to multiple loci | 28.55% Number of reads mapped to too many loci | 35584 % of reads mapped to too many loci | 0.95% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.75% % of reads unmapped: other | 0.06% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 103230 103230 103230 N_multimapping 1064646 1064646 1064646 N_noFeature 173729 197293 2443402 N_ambiguous 106597 11698 348 UnstrandedReadsAssigned:2281497 PositiveStrandReadsAssigned:2352832 NegativeStrandReadsAssigned:118073 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=93 echo kmer=89 ERR6133573 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: ERR6133573-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 3,729,699 reads, 3,076,004 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,062 rounds 52973 ERR6133573.ke.tsv 35125 ERR6133573.se.tsv 88098 total ==> ERR6133573.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 104 32.6982 PNS24243 293 194 0 0 KQK14069 1603 1504 50 14.3406 KQK14071 474 375 0 0 ==> ERR6133573.se.tsv <== BRADI_1g14170v3 50 BRADI_1g53295v3 69 BRADI_1g59795v3 19 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 21 BRADI_1g74790v3 14 BRADI_1g09890v3 1 BRADI_1g77505v3 76 BRADI_1g48960v3 0 ERR6133573 completed mapping pipeline successfully