Starting /dee2/code/volunteer_pipeline.sh ERR6133309 current disk space = 1548412456960 free memory = 1420897320 ERR6133309 SRAfilesize ae4dcd07db459dd5355826c78f26c19f ERR6133309.sra ERR6133309.sra file validated ERR6133309 is single end ERR6133309 is conventional basespace ERR6133309 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133309_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 44 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 34.962 37.0 33.0 37.0 33.0 37.0 2 36.284 37.0 37.0 37.0 33.0 37.0 3 35.93225 37.0 37.0 37.0 33.0 37.0 4 35.55475 37.0 37.0 37.0 33.0 37.0 5 35.4125 37.0 37.0 37.0 33.0 37.0 6 35.7795 37.0 37.0 37.0 33.0 37.0 7 37.49375 40.0 37.0 40.0 33.0 40.0 8 37.5095 40.0 37.0 40.0 33.0 40.0 9 37.59525 40.0 37.0 40.0 33.0 40.0 10-11 37.479625 40.0 37.0 40.0 33.0 40.0 12-13 37.473625 38.5 37.0 40.0 33.0 40.0 14-15 37.392624999999995 37.0 37.0 40.0 33.0 40.0 16-17 37.249625 37.0 37.0 40.0 33.0 40.0 18-19 37.237375 37.0 37.0 40.0 33.0 40.0 20-21 36.924875 37.0 37.0 40.0 33.0 40.0 22-23 36.958 37.0 37.0 40.0 33.0 40.0 24-25 37.06762500000001 37.0 37.0 40.0 33.0 40.0 26-27 37.05875 37.0 37.0 40.0 33.0 40.0 28-29 37.003625 37.0 37.0 40.0 33.0 40.0 30-31 36.870125 37.0 37.0 40.0 33.0 40.0 32-33 36.743 37.0 37.0 40.0 33.0 40.0 34-35 36.62025 37.0 37.0 40.0 33.0 40.0 36-37 36.535375 37.0 37.0 40.0 33.0 40.0 38-39 36.192 37.0 37.0 40.0 33.0 40.0 40-41 36.00475 37.0 37.0 40.0 33.0 40.0 42-43 35.702625 37.0 33.0 40.0 30.0 40.0 44-45 35.344125000000005 37.0 33.0 40.0 27.0 40.0 46-47 35.02425 37.0 33.0 37.0 27.0 40.0 48-49 35.021875 37.0 33.0 37.0 27.0 40.0 50-51 34.84125 37.0 33.0 37.0 27.0 40.0 52-53 34.58725 37.0 33.0 37.0 27.0 40.0 54-55 34.5445 37.0 33.0 37.0 27.0 40.0 56-57 34.105000000000004 37.0 33.0 37.0 27.0 38.5 58-59 31.92175 33.0 30.0 37.0 22.0 37.0 60-61 33.441625 35.0 33.0 37.0 27.0 37.0 62-63 33.670249999999996 37.0 33.0 37.0 27.0 37.0 64-65 33.588625 37.0 33.0 37.0 27.0 37.0 66-67 33.277875 37.0 33.0 37.0 27.0 37.0 68-69 32.7005 35.0 33.0 37.0 27.0 37.0 70-71 32.725626003009026 33.0 33.0 37.0 27.0 37.0 72-73 33.12090424704497 37.0 33.0 37.0 27.0 37.0 74-75 33.06353497718923 37.0 33.0 37.0 27.0 37.0 76-77 33.2188646126794 37.0 33.0 37.0 27.0 37.0 78-79 33.08946273164374 37.0 33.0 37.0 27.0 37.0 80-81 33.143878370533585 37.0 33.0 37.0 27.0 37.0 82-83 32.92307790591155 33.0 33.0 37.0 27.0 37.0 84-85 32.66940127248492 33.0 33.0 37.0 24.5 37.0 86-87 32.58241469816273 33.0 33.0 37.0 24.5 37.0 88-89 32.83031496062992 33.0 33.0 37.0 27.0 37.0 90-91 32.530183727034114 33.0 33.0 37.0 27.0 37.0 92-93 32.43976377952756 33.0 33.0 37.0 27.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 19.0 21 19.0 22 35.0 23 23.0 24 38.0 25 49.0 26 36.0 27 62.0 28 71.0 29 85.0 30 116.0 31 130.0 32 154.0 33 189.0 34 295.0 35 442.0 36 784.0 37 912.0 38 530.0 39 11.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 82.95 3.8249999999999997 4.8500000000000005 8.375 2 63.87500000000001 20.625 10.5 5.0 3 30.7 39.825 16.35 13.125 4 32.05 26.05 19.725 22.175 5 22.475 28.549999999999997 32.75 16.225 6 17.849999999999998 40.225 24.25 17.675 7 34.150000000000006 29.875 20.525 15.45 8 26.724999999999998 29.575000000000003 27.150000000000002 16.55 9 23.400000000000002 27.575 29.275000000000002 19.75 10-11 22.375 28.012500000000003 30.4625 19.15 12-13 23.5375 26.787499999999998 28.012500000000003 21.6625 14-15 21.1875 31.7875 29.012500000000003 18.0125 16-17 22.775000000000002 31.7375 23.8625 21.625 18-19 22.0625 27.437499999999996 28.975 21.525 20-21 25.378172271533945 25.87823477934742 28.691086385798226 20.052506563320417 22-23 27.700000000000003 22.662499999999998 28.3875 21.25 24-25 25.15 26.4625 28.65 19.7375 26-27 24.575 26.087500000000002 32.425 16.9125 28-29 24.337500000000002 29.075 27.212500000000002 19.375 30-31 26.237500000000004 26.9125 27.8625 18.987499999999997 32-33 24.125 26.3125 29.975 19.5875 34-35 23.177897237154642 29.428678584823103 26.26578322290286 21.12764095511939 36-37 25.51887971992998 25.731432858214554 26.9567391847962 21.792948237059264 38-39 27.683262446835126 22.9672254190643 31.986489867400554 17.363022266700025 40-41 27.4125 25.900000000000002 25.387500000000003 21.3 42-43 25.146930098787045 30.036263598849565 26.885081905714642 17.931724396648743 44-45 22.748874437218607 27.051025512756375 30.1775887943972 20.022511255627816 46-47 23.42128298111792 24.946855070651495 30.16131049143429 21.4705514567963 48-49 24.3625 24.6875 31.075000000000003 19.875 50-51 24.390243902439025 26.25390869293308 29.40587867417136 19.949968730456536 52-53 24.76214321482223 28.380070105157735 26.189283925888834 20.668502754131197 54-55 25.0625 28.1125 29.575000000000003 17.25 56-57 26.7125 26.8125 27.5125 18.9625 58-59 22.9875 25.6125 30.8125 20.5875 60-61 25.7375 26.275 28.7375 19.25 62-63 20.200000000000003 30.875000000000004 31.874999999999996 17.05 64-65 21.087500000000002 29.812499999999996 29.8375 19.2625 66-67 24.675 29.3875 28.0625 17.875 68-69 20.7125 28.349999999999998 26.637499999999996 24.3 70-71 23.823234852278418 27.854281422133198 27.478718077115673 20.843765648472708 72-73 25.72039763432742 25.3554800553668 28.61457153642884 20.309550773876936 74-75 23.089574898785425 29.023279352226723 29.07388663967611 18.81325910931174 76-77 22.786906126608073 25.882053241625268 27.90727295885874 23.42376767290791 78-79 25.04481434058899 25.403329065300895 29.82074263764405 19.73111395646607 80-81 22.473215438234156 31.30243965405964 29.133858267716533 17.090486639989674 82-83 21.76516532153085 26.594636813329863 29.835980213486074 21.804217651653214 84-85 22.752293577981654 23.787680209698557 33.5124508519004 19.947575360419396 86-87 21.325459317585302 26.876640419947506 30.997375328083987 20.8005249343832 88-89 19.27821522309711 31.128608923884514 29.58005249343832 20.01312335958005 90-91 26.246719160104988 26.797900262467188 29.107611548556427 17.84776902887139 92-93 22.020997375328083 33.22834645669291 26.154855643044623 18.595800524934383 >>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 0.5 16 0.5 17 11.5 18 15.0 19 5.0 20 3.0 21 4.5 22 4.5 23 8.0 24 11.5 25 9.0 26 11.0 27 19.0 28 30.0 29 35.5 30 37.5 31 42.0 32 54.0 33 67.0 34 75.5 35 88.5 36 126.5 37 198.0 38 234.0 39 204.0 40 184.0 41 189.5 42 216.0 43 243.0 44 213.5 45 160.0 46 169.5 47 164.5 48 144.0 49 165.0 50 178.5 51 164.0 52 140.5 53 150.0 54 156.0 55 101.0 56 50.0 57 50.0 58 42.5 59 27.0 60 21.0 61 22.5 62 18.5 63 14.5 64 13.5 65 12.5 66 13.5 67 11.5 68 5.5 69 7.0 70 9.5 71 9.0 72 6.0 73 3.5 74 3.0 75 1.5 76 0.5 77 0.5 78 0.5 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 0.0125 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 0.0125 36-37 0.025 38-39 0.075 40-41 0.0 42-43 0.0375 44-45 0.05 46-47 0.0375 48-49 0.0 50-51 0.0625 52-53 0.15 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 12.0 71 9.0 72 11.0 73 11.0 74 10.0 75 15.0 76 13.0 77 10.0 78 8.0 79 19.0 80 17.0 81 18.0 82 12.0 83 15.0 84 10.0 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 3810.0 >>END_MODULE >>Sequence Duplication Levels warn #Total Deduplicated Percentage 66.625 #Duplication Level Percentage of deduplicated Percentage of total 1 89.41838649155723 59.575 2 5.628517823639775 7.5 3 1.5384615384615385 3.075 4 0.6378986866791745 1.7000000000000002 5 0.5628517823639775 1.875 6 0.450281425891182 1.7999999999999998 7 0.300187617260788 1.4000000000000001 8 0.18761726078799248 1.0 9 0.18761726078799248 1.125 >10 0.900562851782364 12.675 >50 0.18761726078799248 8.275 >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 TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 73 1.825 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 70 1.7500000000000002 No Hit GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGC 67 1.675 No Hit GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 61 1.525 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 60 1.5 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 42 1.05 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 38 0.95 No Hit GTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAA 35 0.8750000000000001 No Hit GGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGG 34 0.8500000000000001 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 30 0.75 No Hit GGCCTGTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCG 29 0.7250000000000001 No Hit GGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAA 27 0.675 No Hit GTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCT 27 0.675 No Hit GGAGTATCCTTGATATATAAATATATAGATAAATAGATTTAAATGGAAAA 25 0.625 No Hit GGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGGG 21 0.525 No Hit GTACTATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTT 20 0.5 No Hit GGGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTG 19 0.475 No Hit GGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAA 18 0.44999999999999996 No Hit GGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTT 16 0.4 No Hit GGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGC 16 0.4 No Hit GTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAG 15 0.375 No Hit GGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCG 14 0.35000000000000003 No Hit GGGATGGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACGA 14 0.35000000000000003 No Hit GGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAAGGCGATCAAATTC 13 0.325 No Hit GGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGC 11 0.27499999999999997 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 11 0.27499999999999997 No Hit GGGGATGGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACG 11 0.27499999999999997 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 11 0.27499999999999997 No Hit GAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGC 10 0.25 No Hit GGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAAA 9 0.22499999999999998 No Hit GGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTT 9 0.22499999999999998 No Hit GGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTCCT 9 0.22499999999999998 No Hit GGAGTCCCATATATATATGTATAAGATGCCAGCCCGGTTTCGTCAACCAT 9 0.22499999999999998 No Hit GAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAAT 9 0.22499999999999998 No Hit GGTGGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGC 8 0.2 No Hit GCAGCTTGCAAATGGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAA 8 0.2 No Hit CAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCT 8 0.2 No Hit GTACAAGCTCGTAACGAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAAT 8 0.2 No Hit GGGGTACTCTTTCTACACCTATATTAGTATTAGTACCGAAATGCTTTAAA 8 0.2 No Hit GGAGTGACGACGGCAGCTGCCTTTACACCTTTTAAGCATGCCACTTTAAT 7 0.17500000000000002 No Hit GGCTGCTTGGCCTGTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTA 7 0.17500000000000002 No Hit GATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAAT 7 0.17500000000000002 No Hit GGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAAA 7 0.17500000000000002 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTTTTAA 7 0.17500000000000002 No Hit GGGCTTGGCTACAATTCCGAATACGCTATTACATGTTTGCGCTAGTTTTT 7 0.17500000000000002 No Hit CACGAACGTAATGCTCACAACTTCCCTCTAGATCTAGCTGCTCTTGAAGT 7 0.17500000000000002 No Hit GGTTTTGAAAAGGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAA 7 0.17500000000000002 No Hit GTATGGAAGGCGATCAAATTCGAGTTCGCGCCGGTAGATACTATCGATTA 6 0.15 No Hit GGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTA 6 0.15 No Hit GGATATCGTGTGTGTACATTTGAATGTACCGACATGGGCTCGAGGAGCAT 6 0.15 No Hit GTATTTAGCCTTGCAAGGTGGTCCTTGCTGATTCACACGGGATTCCACGT 6 0.15 No Hit AGTATGGCATCGGTTACATACTTCAGTGCCGTAGCGCCTGGTATGAGCCT 6 0.15 No Hit GGGAGTATTATGAAAGGAGATTAATCATAGATTATCAAAAACCCTAGAAA 6 0.15 No Hit GGAATAAGAATAAATCGCAACTCCTTTCCACTACACATAAAAATTGATTT 6 0.15 No Hit GAAATCTTTGGGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGG 6 0.15 No Hit GGGCAAGGAGAAGTACAAGTGCGGATCCAACGTCTTCTGGAAATGGTGAA 6 0.15 No Hit GGAAAAGAGGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTTG 6 0.15 No Hit GAACGTAATGCTCACAACTTCCCTCTAGATCTAGCTGCTCTTGAAGTTCC 6 0.15 No Hit TCAAAAGAGGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGGA 6 0.15 No Hit GGTATTAGTACTATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATC 5 0.125 No Hit GGCTTTAGAAGCCTGTGTACAAGCTCGTAACGAAGGGCGCGATCTTGCTC 5 0.125 No Hit GGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTG 5 0.125 No Hit GGGGTGTTGTAGGTCACCGAGGCTGTTCTGAGATTGCGACCAAGCACGTA 5 0.125 No Hit GGGAGGGGCTTGGCTACAATTCCGAATACGCTATTACATGTTTGCGCTAG 5 0.125 No Hit GAAGTATGGAAGGCGATCAAATTCGAGTTCGCGCCGGTAGATACTATCGA 5 0.125 No Hit GAAGTAATGCACGAACGTAATGCTCACAACTTCCCTCTAGATCTAGCTGC 5 0.125 No Hit GTATTAGTACTATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATCT 5 0.125 No Hit CACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCT 5 0.125 No Hit GGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAACCCTCTTAACT 5 0.125 No Hit GGGGAAGTACACCAGCGACGGCGAGGCCGCCGCCGCCAAGGAAGGCATGT 5 0.125 No Hit GGGAAACAACGAGGTCATCATCGACATGATATATTGCTGCTATTTTCCAC 5 0.125 No Hit GGGACAGTCGGGGGCATTCGTATTTCATAGTCAGAGGTGAAATTCTTGGA 5 0.125 No Hit GGGCCATTTGTGGCATGCAGGAAGAGCCCGAGCTGCTGCAGCAGGTTTTG 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 0.0 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 0.0 0.0 0.0 0.0 0.0 40-41 0.0 0.0 0.0 0.0 0.0 42-43 0.0 0.0 0.0 0.0 0.0 44-45 0.0 0.0 0.0 0.0 0.0 46-47 0.0 0.0 0.0 0.0 0.0 48-49 0.0 0.0 0.0 0.0 0.0 50-51 0.0 0.0 0.0 0.0 0.0 52-53 0.0 0.0 0.0 0.0 0.0 54-55 0.0 0.0 0.0 0.0 0.0 56-57 0.0 0.0 0.0 0.0 0.0 58-59 0.0 0.0 0.0 0.0 0.0 60-61 0.0 0.0 0.0 0.0 0.0 62-63 0.0 0.0 0.0 0.0 0.0 64-65 0.0 0.0 0.0 0.0 0.0 66-67 0.0 0.0 0.0 0.0 0.0 68-69 0.0 0.0 0.0 0.0 0.0 70-71 0.0 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 warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GGCACCC 20 2.4745274E-5 86.3375 7 CTAGGCA 20 2.4745274E-5 86.3375 4 CACCCAG 20 2.4745274E-5 86.3375 9 AGGCACC 20 2.4745274E-5 86.3375 6 GCACCCA 20 2.4745274E-5 86.3375 8 TACCTAG 20 2.4745274E-5 86.3375 1 ACCTAGG 20 2.4745274E-5 86.3375 2 CCTAGGC 20 2.4745274E-5 86.3375 3 TAGGCAC 20 2.4745274E-5 86.3375 5 CGGAGAT 20 6.714454E-4 44.850647 76-77 TCCGGAG 20 6.714454E-4 44.850647 74-75 GAGATTC 20 6.714454E-4 44.850647 78-79 TAGATCC 20 7.393111E-4 43.99363 70-71 GTTGAAA 20 8.1251236E-4 43.16875 56-57 CCCAGAG 20 8.1251236E-4 43.16875 10-11 GCGACGA 20 8.1251236E-4 43.16875 36-37 GGCGTAG 20 8.1251236E-4 43.16875 26-27 AGGGCGT 25 4.5418237E-5 43.16875 24-25 CCAGAGA 20 8.1251236E-4 43.16875 12-13 CGTAGCA 20 8.1251236E-4 43.16875 28-29 >>END_MODULE Rejected 235705 READS because READLEN < 1 Read 235705 spots for ERR6133309.sra Written 235705 spots for ERR6133309.sra Rejected 235705 READS because READLEN < 1 Read 235705 spots for ERR6133309.sra Written 235705 spots for ERR6133309.sra Rejected 235705 READS because READLEN < 1 Read 235705 spots for ERR6133309.sra Written 235705 spots for ERR6133309.sra Rejected 235705 READS because READLEN < 1 Read 235705 spots for ERR6133309.sra Written 235705 spots for ERR6133309.sra Rejected 235705 READS because READLEN < 1 Read 235705 spots for ERR6133309.sra Written 235705 spots for ERR6133309.sra Rejected 235705 READS because READLEN < 1 Read 235705 spots for ERR6133309.sra Written 235705 spots for ERR6133309.sra Rejected 235705 READS because READLEN < 1 Read 235705 spots for ERR6133309.sra Written 235705 spots for ERR6133309.sra Rejected 235705 READS because READLEN < 1 Read 235705 spots for ERR6133309.sra Written 235705 spots for ERR6133309.sra Rejected 235705 READS because READLEN < 1 Read 235705 spots for ERR6133309.sra Written 235705 spots for ERR6133309.sra Rejected 235705 READS because READLEN < 1 Read 235705 spots for ERR6133309.sra Written 235705 spots for ERR6133309.sra Rejected 235705 READS because READLEN < 1 Read 235705 spots for ERR6133309.sra Written 235705 spots for ERR6133309.sra Rejected 235705 READS because READLEN < 1 Read 235705 spots for ERR6133309.sra Written 235705 spots for ERR6133309.sra Rejected 235715 READS because READLEN < 1 Read 235715 spots for ERR6133309.sra Written 235715 spots for ERR6133309.sra Rejected 235705 READS because READLEN < 1 Read 235705 spots for ERR6133309.sra Written 235705 spots for ERR6133309.sra Rejected 235705 READS because READLEN < 1 Read 235705 spots for ERR6133309.sra Written 235705 spots for ERR6133309.sra Rejected 235705 READS because READLEN < 1 Read 235705 spots for ERR6133309.sra Written 235705 spots for ERR6133309.sra Rejected 235705 READS because READLEN < 1 Read 235705 spots for ERR6133309.sra Written 235705 spots for ERR6133309.sra Rejected 235705 READS because READLEN < 1 Read 235705 spots for ERR6133309.sra Written 235705 spots for ERR6133309.sra Rejected 235705 READS because READLEN < 1 Read 235705 spots for ERR6133309.sra Written 235705 spots for ERR6133309.sra Rejected 235705 READS because READLEN < 1 Read 235705 spots for ERR6133309.sra Written 235705 spots for ERR6133309.sra SRR ids: ['ERR6133309.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_kmw_cn70 ERR6133309.sra spots: 4714110 blocks: [[1, 235705], [235706, 471410], [471411, 707115], [707116, 942820], [942821, 1178525], [1178526, 1414230], [1414231, 1649935], [1649936, 1885640], [1885641, 2121345], [2121346, 2357050], [2357051, 2592755], [2592756, 2828460], [2828461, 3064165], [3064166, 3299870], [3299871, 3535575], [3535576, 3771280], [3771281, 4006985], [4006986, 4242690], [4242691, 4478395], [4478396, 4714110]] ERR6133309 file size 1040510 ERR6133309 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 ERR6133309 ERR6133309_1.fastq Input file: ERR6133309_1.fastq trimmed: ERR6133309-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 00:22:27 2024 >> started Sat Dec 7 00:22:30 2024 >> done (2.793s) 4714110 reads processed; of these: 426 ( 0.01%) short reads filtered out after trimming by size control 47 ( 0.00%) empty reads filtered out after trimming by size control 4713637 (99.99%) reads available; of these: 85330 ( 1.81%) trimmed reads available after processing 4628307 (98.19%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 80 0.00% 19 181 0.00% 20 82 0.00% 21 96 0.00% 22 110 0.00% 23 21 0.00% 24 27 0.00% 25 17 0.00% 26 22 0.00% 27 49 0.00% 28 64 0.00% 29 64 0.00% 30 36 0.00% 31 83 0.00% 32 86 0.00% 33 43 0.00% 34 38 0.00% 35 250 0.01% 36 865 0.02% 37 61 0.00% 38 106 0.00% 39 376 0.01% 40 240 0.01% 41 110 0.00% 42 37 0.00% 43 51 0.00% 44 38 0.00% 45 37 0.00% 46 28 0.00% 47 33 0.00% 48 24 0.00% 49 29 0.00% 50 27 0.00% 51 138 0.00% 52 40 0.00% 53 22 0.00% 54 20 0.00% 55 23 0.00% 56 32 0.00% 57 30 0.00% 58 45 0.00% 59 19 0.00% 60 37 0.00% 61 30 0.00% 62 0 0.00% 63 3 0.00% 64 2 0.00% 65 10 0.00% 66 13 0.00% 67 25 0.00% 68 35 0.00% 69 189 0.00% 70 15311 0.32% 71 13575 0.29% 72 15845 0.34% 73 12573 0.27% 74 13576 0.29% 75 14366 0.30% 76 11461 0.24% 77 11731 0.25% 78 14280 0.30% 79 16377 0.35% 80 14597 0.31% 81 18543 0.39% 82 20203 0.43% 83 19056 0.40% 84 16839 0.36% 85 252 0.01% 86 449 0.01% 87 689 0.01% 88 1198 0.03% 89 2400 0.05% 90 4981 0.11% 91 14779 0.31% 92 53634 1.14% 93 4402798 93.41% 4713637 reads passed initial QC criterion=sequence-density sequence-density=0.93 sequence-density-rank=1 fanout-score=1.99 fanout-score-rank=29 prefix-density=0.94 prefix-fanout=2.0 sequence=CAAGGCTAAATAC criterion=fanout-score sequence-density=0.01 sequence-density-rank=44 fanout-score=86.21 fanout-score-rank=1 prefix-density=0.44 prefix-fanout=1.0 sequence=GGCATTTTGGATTTCAGGGCTTTTAGCCCCGATTAGTGAAGGACCCGAAAAGCTTTCTAGTTATGAATCGGGTATAGAACCCATGGGAGGGGCTTGGCTACAATTCCGAATACGCTATTACATGTTTGCGCTAGTTTTTGTTGTTTTTGATGTGGAAACCGTCTTTCTCTACCCTTGGGCAATGAGTTTCGACGTATTGGGTGTATCCGTTTTTATCGAAGCTTTCATTTTCGTGCTTATCCTAGTTGTTGGTTTAGTTTATGCATGGCGAAAAGGAGCCTTGGAATGGTCTTAACTGAATATTT Started job on | Dec 07 00:22:48 Started mapping on | Dec 07 00:22:48 Finished on | Dec 07 00:22:55 Mapping speed, Million of reads per hour | 2424.16 Number of input reads | 4713637 Average input read length | 92 UNIQUE READS: Uniquely mapped reads number | 2465743 Uniquely mapped reads % | 52.31% Average mapped length | 91.53 Number of splices: Total | 96800 Number of splices: Annotated (sjdb) | 75836 Number of splices: GT/AG | 91350 Number of splices: GC/AG | 2113 Number of splices: AT/AC | 97 Number of splices: Non-canonical | 3240 Mismatch rate per base, % | 0.51% Deletion rate per base | 0.05% Deletion average length | 1.82 Insertion rate per base | 0.03% Insertion average length | 1.83 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 2077145 % of reads mapped to multiple loci | 44.07% Number of reads mapped to too many loci | 84846 % of reads mapped to too many loci | 1.80% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.69% % of reads unmapped: other | 0.13% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 170749 170749 170749 N_multimapping 2077145 2077145 2077145 N_noFeature 245168 267851 2362961 N_ambiguous 92499 12175 620 UnstrandedReadsAssigned:2128076 PositiveStrandReadsAssigned:2185717 NegativeStrandReadsAssigned:102162 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=93 echo kmer=89 ERR6133309 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: ERR6133309-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 4,713,637 reads, 3,729,893 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 969 rounds 52973 ERR6133309.ke.tsv 35125 ERR6133309.se.tsv 88098 total ==> ERR6133309.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 69 17.8184 PNS24243 293 194 0 0 KQK14069 1603 1504 29 6.83164 KQK14071 474 375 0 0 ==> ERR6133309.se.tsv <== BRADI_1g14170v3 29 BRADI_1g53295v3 26 BRADI_1g59795v3 13 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 32 BRADI_1g74790v3 30 BRADI_1g09890v3 0 BRADI_1g77505v3 81 BRADI_1g48960v3 0 ERR6133309 completed mapping pipeline successfully