Starting /dee2/code/volunteer_pipeline.sh ERR6133485 current disk space = 1544809775104 free memory = 1600136568 ERR6133485 SRAfilesize 42163321a00f194396ac8167a1d97de7 ERR6133485.sra ERR6133485.sra file validated ERR6133485 is single end ERR6133485 is conventional basespace ERR6133485 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133485_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 35.0735 37.0 33.0 37.0 33.0 37.0 2 36.27125 37.0 37.0 37.0 33.0 37.0 3 35.6635 37.0 37.0 37.0 33.0 37.0 4 35.22675 37.0 37.0 37.0 33.0 37.0 5 35.33875 37.0 37.0 37.0 33.0 37.0 6 35.4915 37.0 37.0 37.0 33.0 37.0 7 37.30275 37.0 37.0 40.0 33.0 40.0 8 37.287 37.0 37.0 40.0 33.0 40.0 9 37.365 37.0 37.0 40.0 33.0 40.0 10-11 37.349625 37.0 37.0 40.0 33.0 40.0 12-13 37.254875 37.0 37.0 40.0 33.0 40.0 14-15 37.246875 37.0 37.0 40.0 33.0 40.0 16-17 37.054125 37.0 37.0 40.0 33.0 40.0 18-19 36.813874999999996 37.0 37.0 40.0 33.0 40.0 20-21 36.531375 37.0 37.0 40.0 33.0 40.0 22-23 36.504125 37.0 37.0 40.0 33.0 40.0 24-25 36.308 37.0 37.0 40.0 33.0 40.0 26-27 36.6865 37.0 37.0 40.0 33.0 40.0 28-29 36.85375 37.0 37.0 40.0 33.0 40.0 30-31 36.68875 37.0 37.0 40.0 33.0 40.0 32-33 36.547375 37.0 37.0 40.0 33.0 40.0 34-35 36.419 37.0 37.0 40.0 33.0 40.0 36-37 36.340375 37.0 37.0 40.0 33.0 40.0 38-39 36.266875 37.0 37.0 40.0 33.0 40.0 40-41 35.906625 37.0 35.0 40.0 33.0 40.0 42-43 35.933499999999995 37.0 35.0 40.0 33.0 40.0 44-45 35.89275000000001 37.0 35.0 40.0 33.0 40.0 46-47 35.855625 37.0 33.0 40.0 33.0 40.0 48-49 35.867999999999995 37.0 33.0 37.0 33.0 40.0 50-51 35.72775 37.0 33.0 37.0 33.0 40.0 52-53 35.445625 37.0 33.0 37.0 33.0 40.0 54-55 35.277375 37.0 33.0 37.0 33.0 40.0 56-57 34.995625000000004 37.0 33.0 37.0 33.0 40.0 58-59 33.850875 37.0 33.0 37.0 27.0 37.0 60-61 34.527249999999995 37.0 33.0 37.0 27.0 37.0 62-63 34.546125 37.0 33.0 37.0 30.0 37.0 64-65 34.408 37.0 33.0 37.0 27.0 37.0 66-67 34.3165 37.0 33.0 37.0 30.0 37.0 68-69 33.461625 35.0 33.0 37.0 27.0 37.0 70-71 33.62506573980876 35.0 33.0 37.0 27.0 37.0 72-73 34.051170924535 37.0 33.0 37.0 27.0 37.0 74-75 34.02723293077121 37.0 33.0 37.0 27.0 37.0 76-77 33.76083367395516 37.0 33.0 37.0 27.0 37.0 78-79 33.54315523368973 37.0 33.0 37.0 27.0 37.0 80-81 33.51089977728221 37.0 33.0 37.0 27.0 37.0 82-83 33.28838141839524 35.0 33.0 37.0 27.0 37.0 84-85 33.15057174894274 33.0 33.0 37.0 27.0 37.0 86-87 33.32295988934993 33.0 33.0 37.0 27.0 37.0 88-89 33.397510373443986 33.0 33.0 37.0 27.0 37.0 90-91 33.224619640387274 33.0 33.0 37.0 27.0 37.0 92-93 33.03582295988935 33.0 33.0 37.0 27.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 7.0 21 11.0 22 12.0 23 19.0 24 23.0 25 37.0 26 39.0 27 56.0 28 48.0 29 70.0 30 115.0 31 127.0 32 156.0 33 198.0 34 278.0 35 477.0 36 812.0 37 924.0 38 557.0 39 34.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 75.125 6.950000000000001 9.475 8.450000000000001 2 57.62500000000001 23.175 11.95 7.249999999999999 3 31.8 33.300000000000004 16.775000000000002 18.125 4 28.249999999999996 29.925 18.475 23.35 5 29.125 23.7 29.075 18.099999999999998 6 17.95 40.225 24.5 17.325 7 39.85 27.675 18.0 14.475 8 29.625 27.400000000000002 22.05 20.925 9 22.825 31.15 25.95 20.075000000000003 10-11 22.237499999999997 30.275000000000002 28.525 18.9625 12-13 23.8625 27.800000000000004 25.4625 22.875 14-15 21.8 34.362500000000004 26.400000000000002 17.4375 16-17 25.650000000000002 30.412499999999998 22.6125 21.325 18-19 25.203150393799223 26.140767595949495 28.066008251031377 20.5900737592199 20-21 27.938969484742373 25.312656328164078 28.501750875437722 18.246623311655828 22-23 31.624999999999996 21.512500000000003 27.325 19.537499999999998 24-25 23.6875 27.5625 27.462500000000002 21.2875 26-27 29.6625 23.45 26.6125 20.275000000000002 28-29 24.587500000000002 28.537499999999998 27.325 19.55 30-31 30.4625 24.725 25.900000000000002 18.912499999999998 32-33 26.487500000000004 27.0125 25.3 21.2 34-35 23.025000000000002 32.75 24.6 19.625 36-37 27.28182045511378 25.95648912228057 23.63090772693173 23.13078269567392 38-39 31.874999999999996 23.8875 26.2625 17.974999999999998 40-41 23.418354588647162 24.731182795698924 29.744936234058517 22.1055263815954 42-43 27.3375 32.0125 23.5125 17.1375 44-45 22.1875 29.6625 30.025000000000002 18.125 46-47 27.212500000000002 24.825 25.7625 22.2 48-49 24.7875 25.1875 26.937499999999996 23.0875 50-51 21.4875 27.925 26.700000000000003 23.8875 52-53 26.01626016260163 24.102564102564102 24.690431519699814 25.19074421513446 54-55 26.0625 25.4375 28.8625 19.6375 56-57 27.1375 29.4875 25.25 18.125 58-59 21.525 27.900000000000002 31.2375 19.3375 60-61 30.099999999999998 27.1375 25.2375 17.525 62-63 20.2875 31.887500000000003 28.475 19.35 64-65 21.075 34.1625 27.425 17.3375 66-67 24.337500000000002 33.862500000000004 24.212500000000002 17.5875 68-69 21.912499999999998 26.087500000000002 28.1 23.9 70-71 22.134436919989966 29.408076247805365 25.909204915976925 22.54828191622774 72-73 27.60853008377761 26.68189895912668 27.900482355927902 17.809088601167808 74-75 24.064789818742767 29.10399794318036 28.35840082272786 18.472811415349017 76-77 21.60718937223235 24.602761135712427 24.811148736650168 28.97890075540505 78-79 28.82159315339039 26.899275839368002 26.214614878209346 18.064516129032256 80-81 22.685370741482966 36.00534402137608 24.141616566466265 17.167668670674683 82-83 23.087357569180682 27.807921866521973 27.794357026587086 21.310363537710256 84-85 20.96418732782369 25.6198347107438 33.388429752066116 20.02754820936639 86-87 19.723374827109268 29.05947441217151 25.988934993084374 25.228215767634854 88-89 17.7731673582296 33.11203319502074 28.561549100968186 20.553250345781464 90-91 25.089903181189488 31.507607192254493 25.76763485477178 17.634854771784234 92-93 21.82572614107884 30.843706777316736 27.39972337482711 19.930843706777317 >>END_MODULE >>Per sequence GC content fail #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 0.5 10 0.5 11 0.0 12 0.0 13 0.0 14 0.0 15 0.5 16 1.5 17 8.5 18 10.0 19 3.0 20 0.5 21 0.0 22 3.0 23 9.0 24 9.5 25 11.5 26 14.5 27 16.0 28 22.0 29 24.5 30 29.0 31 40.5 32 39.0 33 42.5 34 67.0 35 94.0 36 129.0 37 147.5 38 178.5 39 185.5 40 177.5 41 189.0 42 202.0 43 222.0 44 188.0 45 168.0 46 175.0 47 166.0 48 149.5 49 145.5 50 214.0 51 221.0 52 147.0 53 133.5 54 222.5 55 190.5 56 68.5 57 59.5 58 44.0 59 29.5 60 25.5 61 21.0 62 22.5 63 18.0 64 19.0 65 17.5 66 13.5 67 14.0 68 10.5 69 9.0 70 6.5 71 4.0 72 2.5 73 2.0 74 2.5 75 4.0 76 3.5 77 1.0 78 0.5 79 0.0 80 0.0 81 0.0 82 0.5 83 0.5 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 0.0125 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 0.025 38-39 0.0 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 0.0625 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 26.0 71 18.0 72 34.0 73 22.0 74 21.0 75 27.0 76 26.0 77 19.0 78 19.0 79 30.0 80 31.0 81 25.0 82 32.0 83 25.0 84 30.0 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 3615.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 70.6 #Duplication Level Percentage of deduplicated Percentage of total 1 91.39518413597733 64.525 2 4.674220963172805 6.6000000000000005 3 1.3810198300283285 2.9250000000000003 4 0.6728045325779036 1.9 5 0.3186968838526912 1.125 6 0.17705382436260625 0.75 7 0.17705382436260625 0.8750000000000001 8 0.17705382436260625 1.0 9 0.10623229461756376 0.675 >10 0.84985835694051 9.8 >50 0.0 0.0 >100 0.0708215297450425 9.825000000000001 >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 247 6.175 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 146 3.65 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 38 0.95 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 32 0.8 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 29 0.7250000000000001 No Hit GAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGC 28 0.7000000000000001 No Hit GGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAAGGCGATCAAATTC 20 0.5 No Hit GGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGG 18 0.44999999999999996 No Hit GTATTTAGCCTTGCAAGGTGGTCCTTGCTGATTCACACGGGATTCCACGT 17 0.42500000000000004 No Hit GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 17 0.42500000000000004 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 16 0.4 No Hit GGAGTATCCTTGATATATAAATATATAGATAAATAGATTTAAATGGAAAA 16 0.4 No Hit GGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGC 14 0.35000000000000003 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 13 0.325 No Hit GGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAAA 13 0.325 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 12 0.3 No Hit GGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGGG 12 0.3 No Hit GTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAAGGCGATCAAATTCGAG 12 0.3 No Hit GGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTCCT 11 0.27499999999999997 No Hit CGAGGAAGGGCGTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAG 11 0.27499999999999997 No Hit GTACAAGCTCGTAACGAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAAT 11 0.27499999999999997 No Hit TCTCATGGAGAGTTCGATCCTGGCTCAGGATGAACGCTGGCGGCATGCTT 11 0.27499999999999997 No Hit TCAAAAGAGGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGGA 11 0.27499999999999997 No Hit GTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAA 10 0.25 No Hit GTATGGAAGGCGATCAAATTCGAGTTCGCGCCGGTAGATACTATCGATTA 10 0.25 No Hit GGGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTG 10 0.25 No Hit GGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTT 9 0.22499999999999998 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 9 0.22499999999999998 No Hit GGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAA 9 0.22499999999999998 No Hit GTAACGAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCA 8 0.2 No Hit GGCCTGTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCG 8 0.2 No Hit GGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTT 8 0.2 No Hit GCAGCTTGCAAATGGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAA 8 0.2 No Hit GAAGTATGGAAGGCGATCAAATTCGAGTTCGCGCCGGTAGATACTATCGA 8 0.2 No Hit GGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAA 7 0.17500000000000002 No Hit CACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTTCGGGGAGT 7 0.17500000000000002 No Hit GGAAGGCGATCAAATTCGAGTTCGCGCCGGTAGATACTATCGATTAATAG 7 0.17500000000000002 No Hit AACAGTAAAGCTTCATAGGGTCTTTCTGTCCAGGTGCAGGTAGTCCGCAT 7 0.17500000000000002 No Hit GATACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGC 7 0.17500000000000002 No Hit GGGGGTCGCAGTGACCAGGCCCGGGCGACTGTTTACCAAAAACACAGGTC 6 0.15 No Hit CAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCT 6 0.15 No Hit GGGAGTATTATGAAAGGAGATTAATCATAGATTATCAAAAACCCTAGAAA 6 0.15 No Hit GGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGCA 6 0.15 No Hit GCTTGTGAAGTATGGAAGGCGATCAAATTCGAGTTCGCGCCGGTAGATAC 6 0.15 No Hit GGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCG 5 0.125 No Hit GCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCT 5 0.125 No Hit GGATACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATG 5 0.125 No Hit GGTGGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGC 5 0.125 No Hit GGTTTCAGTATATTGAAATAGAAAGATAAAATAGAAGAGAGAGGATAGGC 5 0.125 No Hit GGGCCGGGTATCTCTCTGCATGTACGTATGCCTGTAATGTACGTAGCTAC 5 0.125 No Hit AGTATGGCATCGGTTACATACTTCAGTGCCGTAGCGCCTGGTATGAGCCT 5 0.125 No Hit CAACATAGGTCATCGAAAAGATCTCGGACGACTCACCAAAGCACGAAAGC 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 0.025 0.0 0.0 0.0 0.0 12-13 0.025 0.0 0.0 0.0 0.0 14-15 0.075 0.0 0.0 0.0 0.0 16-17 0.075 0.0 0.0 0.0 0.0 18-19 0.075 0.0 0.0 0.0 0.0 20-21 0.075 0.0 0.0 0.0 0.0 22-23 0.075 0.0 0.0 0.0 0.0 24-25 0.075 0.0 0.0 0.0 0.0 26-27 0.075 0.0 0.0 0.0 0.0 28-29 0.11249999999999999 0.0 0.0 0.0 0.0 30-31 0.175 0.0 0.0 0.0 0.0 32-33 0.175 0.0 0.0 0.0 0.0 34-35 0.2 0.0 0.0 0.0 0.0 36-37 0.21250000000000002 0.0 0.0 0.0 0.0 38-39 0.225 0.0 0.0 0.0 0.0 40-41 0.25 0.0 0.0 0.0 0.0 42-43 0.25 0.0 0.0 0.0 0.0 44-45 0.25 0.0 0.0 0.0 0.0 46-47 0.275 0.0 0.0 0.0 0.0 48-49 0.275 0.0 0.0 0.0 0.0 50-51 0.275 0.0 0.0 0.0 0.0 52-53 0.275 0.0 0.0 0.0 0.0 54-55 0.275 0.0 0.0 0.0 0.0 56-57 0.3 0.0 0.0 0.0 0.0 58-59 0.3 0.0 0.0 0.0 0.0 60-61 0.3 0.0 0.0 0.0 0.0 62-63 0.3 0.0 0.0 0.0 0.0 64-65 0.3 0.0 0.0 0.0 0.0 66-67 0.3 0.0 0.0 0.0 0.0 68-69 0.3 0.0 0.0 0.0 0.0 70-71 0.325 0.0 0.0 0.0 0.0 72-73 0.4 0.0 0.0 0.0 0.0 74-75 0.4125 0.0 0.0 0.0 0.0 76-77 0.425 0.0 0.0 0.0 0.0 78-79 0.425 0.0 0.0 0.0 0.0 80-81 0.4375 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GGCACCC 15 9.4021007E-4 85.35 7 AGGCACC 15 9.4021007E-4 85.35 6 GCACCCA 15 9.4021007E-4 85.35 8 TACCTAG 15 9.4021007E-4 85.35 1 ACCTAGG 15 9.4021007E-4 85.35 2 CCTAGGC 15 9.4021007E-4 85.35 3 TAGGCAC 15 9.4021007E-4 85.35 5 CTAGGCA 20 0.0029452087 64.0125 4 CACCCAG 20 0.0029452087 64.0125 9 >>END_MODULE Rejected 22357 READS because READLEN < 1 Read 22357 spots for ERR6133485.sra Written 22357 spots for ERR6133485.sra Rejected 22357 READS because READLEN < 1 Read 22357 spots for ERR6133485.sra Written 22357 spots for ERR6133485.sra Rejected 22357 READS because READLEN < 1 Read 22357 spots for ERR6133485.sra Written 22357 spots for ERR6133485.sra Rejected 22357 READS because READLEN < 1 Read 22357 spots for ERR6133485.sra Written 22357 spots for ERR6133485.sra Rejected 22357 READS because READLEN < 1 Read 22357 spots for ERR6133485.sra Written 22357 spots for ERR6133485.sra Rejected 22357 READS because READLEN < 1 Read 22357 spots for ERR6133485.sra Written 22357 spots for ERR6133485.sra Rejected 22357 READS because READLEN < 1 Read 22357 spots for ERR6133485.sra Written 22357 spots for ERR6133485.sra Rejected 22357 READS because READLEN < 1 Read 22357 spots for ERR6133485.sra Written 22357 spots for ERR6133485.sra Rejected 22357 READS because READLEN < 1 Read 22357 spots for ERR6133485.sra Written 22357 spots for ERR6133485.sra Rejected 22357 READS because READLEN < 1 Read 22357 spots for ERR6133485.sra Written 22357 spots for ERR6133485.sra Rejected 22357 READS because READLEN < 1 Read 22357 spots for ERR6133485.sra Written 22357 spots for ERR6133485.sra Rejected 22357 READS because READLEN < 1 Read 22357 spots for ERR6133485.sra Written 22357 spots for ERR6133485.sra Rejected 22357 READS because READLEN < 1 Read 22357 spots for ERR6133485.sra Written 22357 spots for ERR6133485.sra Rejected 22357 READS because READLEN < 1 Read 22357 spots for ERR6133485.sra Written 22357 spots for ERR6133485.sra Rejected 22357 READS because READLEN < 1 Read 22357 spots for ERR6133485.sra Written 22357 spots for ERR6133485.sra Rejected 22371 READS because READLEN < 1 Read 22371 spots for ERR6133485.sra Written 22371 spots for ERR6133485.sra Rejected 22357 READS because READLEN < 1 Read 22357 spots for ERR6133485.sra Written 22357 spots for ERR6133485.sra Rejected 22357 READS because READLEN < 1 Read 22357 spots for ERR6133485.sra Written 22357 spots for ERR6133485.sra Rejected 22357 READS because READLEN < 1 Read 22357 spots for ERR6133485.sra Written 22357 spots for ERR6133485.sra Rejected 22357 READS because READLEN < 1 Read 22357 spots for ERR6133485.sra Written 22357 spots for ERR6133485.sra SRR ids: ['ERR6133485.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_5ooul8aa ERR6133485.sra spots: 447154 blocks: [[1, 22357], [22358, 44714], [44715, 67071], [67072, 89428], [89429, 111785], [111786, 134142], [134143, 156499], [156500, 178856], [178857, 201213], [201214, 223570], [223571, 245927], [245928, 268284], [268285, 290641], [290642, 312998], [312999, 335355], [335356, 357712], [357713, 380069], [380070, 402426], [402427, 424783], [424784, 447154]] ERR6133485 file size 96936 ERR6133485 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 ERR6133485 ERR6133485_1.fastq Input file: ERR6133485_1.fastq trimmed: ERR6133485-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 07:02:28 2024 >> started Sat Dec 7 07:02:28 2024 >> done (0.351s) 447154 reads processed; of these: 239 ( 0.05%) short reads filtered out after trimming by size control 49 ( 0.01%) empty reads filtered out after trimming by size control 446866 (99.94%) reads available; of these: 9291 ( 2.08%) trimmed reads available after processing 437575 (97.92%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 34 0.01% 19 49 0.01% 20 28 0.01% 21 13 0.00% 22 33 0.01% 23 16 0.00% 24 9 0.00% 25 16 0.00% 26 11 0.00% 27 24 0.01% 28 172 0.04% 29 70 0.02% 30 23 0.01% 31 37 0.01% 32 39 0.01% 33 47 0.01% 34 42 0.01% 35 222 0.05% 36 434 0.10% 37 20 0.00% 38 29 0.01% 39 92 0.02% 40 40 0.01% 41 37 0.01% 42 15 0.00% 43 17 0.00% 44 10 0.00% 45 17 0.00% 46 16 0.00% 47 16 0.00% 48 7 0.00% 49 7 0.00% 50 14 0.00% 51 33 0.01% 52 9 0.00% 53 9 0.00% 54 5 0.00% 55 11 0.00% 56 15 0.00% 57 11 0.00% 58 12 0.00% 59 8 0.00% 60 14 0.00% 61 6 0.00% 62 0 0.00% 63 1 0.00% 64 0 0.00% 65 3 0.00% 66 3 0.00% 67 1 0.00% 68 8 0.00% 69 32 0.01% 70 3486 0.78% 71 3106 0.70% 72 3590 0.80% 73 3039 0.68% 74 3025 0.68% 75 3261 0.73% 76 2638 0.59% 77 2766 0.62% 78 3260 0.73% 79 3617 0.81% 80 3127 0.70% 81 3385 0.76% 82 4014 0.90% 83 4125 0.92% 84 3076 0.69% 85 17 0.00% 86 37 0.01% 87 56 0.01% 88 83 0.02% 89 190 0.04% 90 337 0.08% 91 968 0.22% 92 4932 1.10% 93 388894 87.03% 446866 reads passed initial QC criterion=sequence-density sequence-density=6.91 sequence-density-rank=1 fanout-score=1.42 fanout-score-rank=18 prefix-density=0.32 prefix-fanout=1.4 sequence=GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGCACCCTAGATGGCTAAAGTCCAGTAGCCGAAAGCATCACTAGCTTACGCTCTGACCCGAGTAGCATGGGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTCCTGGGTGACCGATAGCGAAGTAGTACCGTGAGGGAAA criterion=fanout-score sequence-density=0.10 sequence-density-rank=21 fanout-score=63.77 fanout-score-rank=1 prefix-density=6.29 prefix-fanout=1.0 sequence=AAGCATAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGCACCCATCTCGTATGCCG 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: 1 (100.00%) aligned 0 times 0 (0.00%) aligned exactly 1 time 0 (0.00%) aligned >1 times 0.00% overall alignment rate Adapter seq not found in reference. Now shuffling file before clipping skewer v0.2.2 [April 4, 2016] COMMAND LINE: skewer -f sanger -l 18 -t 20 -x GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGCACCCTAGATGGCTAAAGTCCAGTAGCCGAAAGCATCACTAGCTTACGCTCTGACCCGAGTAGCATGGGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTCCTGGGTGACCGATAGCGAAGTAGTACCGTGAGGGAAA -o ERR6133485 - Input file: STDIN trimmed: ERR6133485-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGCACCCTAGATGGCTA -- maximum error ratio allowed (-r): 0.100 -- maximum indel error ratio allowed (-d): 0.030 -- minimum read length allowed after trimming (-l): 18 -- file format (-f): Sanger/Illumina 1.8+ FASTQ -- minimum overlap length for adapter detection (-k): 3 -- number of concurrent threads (-t): 20 Sat Dec 7 07:02:30 2024 >> started Sat Dec 7 07:02:31 2024 >> done (0.400s) 319190 reads processed; of these: 1028 ( 0.32%) short reads filtered out after trimming by size control 21362 ( 6.69%) empty reads filtered out after trimming by size control 296800 (92.99%) reads available; of these: 4715 ( 1.59%) trimmed reads available after processing 292085 (98.41%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 28 0.01% 19 36 0.01% 20 21 0.01% 21 10 0.00% 22 23 0.01% 23 11 0.00% 24 8 0.00% 25 13 0.00% 26 11 0.00% 27 14 0.00% 28 128 0.04% 29 51 0.02% 30 16 0.01% 31 115 0.04% 32 41 0.01% 33 38 0.01% 34 32 0.01% 35 169 0.06% 36 320 0.11% 37 34 0.01% 38 21 0.01% 39 66 0.02% 40 28 0.01% 41 27 0.01% 42 17 0.01% 43 15 0.01% 44 15 0.01% 45 17 0.01% 46 16 0.01% 47 12 0.00% 48 6 0.00% 49 9 0.00% 50 13 0.00% 51 25 0.01% 52 16 0.01% 53 11 0.00% 54 2 0.00% 55 5 0.00% 56 10 0.00% 57 8 0.00% 58 9 0.00% 59 8 0.00% 60 10 0.00% 61 5 0.00% 62 0 0.00% 63 1 0.00% 64 0 0.00% 65 2 0.00% 66 5 0.00% 67 44 0.01% 68 63 0.02% 69 75 0.03% 70 2535 0.85% 71 2198 0.74% 72 2535 0.85% 73 2185 0.74% 74 2151 0.72% 75 2312 0.78% 76 1888 0.64% 77 2318 0.78% 78 2388 0.80% 79 2961 1.00% 80 2204 0.74% 81 2491 0.84% 82 2505 0.84% 83 2873 0.97% 84 2043 0.69% 85 26 0.01% 86 97 0.03% 87 101 0.03% 88 190 0.06% 89 639 0.22% 90 2354 0.79% 91 658 0.22% 92 3248 1.09% 93 252220 84.98% criterion=sequence-density sequence-density=2.06 sequence-density-rank=1 fanout-score=1.97 fanout-score-rank=18 prefix-density=0.14 prefix-fanout=2.0 sequence=GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGCACCCTAGATGGCTAAAGTCCAGTAGCCGAAAGCATCACTAGCTTACGCTCTGACCCGAGTAGCATGGGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTCCTGGGTGACCGATAGCGAAGTAGTACCGTGAGGGAAA criterion=fanout-score sequence-density=0.10 sequence-density-rank=22 fanout-score=63.77 fanout-score-rank=1 prefix-density=6.63 prefix-fanout=1.0 sequence=AAGCATAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGCACCCATCTCGTATGCCG Started job on | Dec 07 07:02:42 Started mapping on | Dec 07 07:02:42 Finished on | Dec 07 07:02:46 Mapping speed, Million of reads per hour | 382.03 Number of input reads | 424476 Average input read length | 90 UNIQUE READS: Uniquely mapped reads number | 225229 Uniquely mapped reads % | 53.06% Average mapped length | 90.11 Number of splices: Total | 7220 Number of splices: Annotated (sjdb) | 5635 Number of splices: GT/AG | 6758 Number of splices: GC/AG | 148 Number of splices: AT/AC | 3 Number of splices: Non-canonical | 311 Mismatch rate per base, % | 0.50% Deletion rate per base | 0.04% Deletion average length | 1.79 Insertion rate per base | 0.02% Insertion average length | 1.92 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 165889 % of reads mapped to multiple loci | 39.08% Number of reads mapped to too many loci | 4106 % of reads mapped to too many loci | 0.97% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 6.82% % of reads unmapped: other | 0.07% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 33358 33358 33358 N_multimapping 165889 165889 165889 N_noFeature 17119 20025 214683 N_ambiguous 8702 1053 41 UnstrandedReadsAssigned:199408 PositiveStrandReadsAssigned:204151 NegativeStrandReadsAssigned:10505 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=93 echo kmer=89 ERR6133485 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: ERR6133485-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 424,476 reads, 299,052 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 756 rounds 52973 ERR6133485.ke.tsv 35125 ERR6133485.se.tsv 88098 total ==> ERR6133485.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 9 30.8644 PNS24243 293 194 0 0 KQK14069 1603 1504 6 18.7704 KQK14071 474 375 0 0 ==> ERR6133485.se.tsv <== BRADI_1g14170v3 6 BRADI_1g53295v3 2 BRADI_1g59795v3 1 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 3 BRADI_1g74790v3 4 BRADI_1g09890v3 0 BRADI_1g77505v3 5 BRADI_1g48960v3 0 ERR6133485 completed mapping pipeline successfully