Starting /dee2/code/volunteer_pipeline.sh ERR6133357 current disk space = 1548258738176 free memory = 1395875796 ERR6133357 SRAfilesize 1c3fa104ad35327706c2588be156ed96 ERR6133357.sra ERR6133357.sra file validated ERR6133357 is single end ERR6133357 is conventional basespace ERR6133357 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133357_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 36.43275 37.0 37.0 37.0 33.0 37.0 2 36.748 37.0 37.0 37.0 37.0 37.0 3 36.6685 37.0 37.0 37.0 37.0 37.0 4 36.3905 37.0 37.0 37.0 37.0 37.0 5 36.36275 37.0 37.0 37.0 37.0 37.0 6 36.5215 37.0 37.0 37.0 37.0 37.0 7 38.69125 40.0 37.0 40.0 37.0 40.0 8 38.81125 40.0 37.0 40.0 37.0 40.0 9 38.79975 40.0 37.0 40.0 37.0 40.0 10-11 38.805375 40.0 37.0 40.0 37.0 40.0 12-13 38.75 40.0 37.0 40.0 37.0 40.0 14-15 38.74925 40.0 37.0 40.0 37.0 40.0 16-17 38.726875 40.0 37.0 40.0 37.0 40.0 18-19 38.656125 40.0 37.0 40.0 37.0 40.0 20-21 38.64475 40.0 37.0 40.0 37.0 40.0 22-23 38.588625 40.0 37.0 40.0 37.0 40.0 24-25 38.464625 40.0 37.0 40.0 37.0 40.0 26-27 38.500249999999994 40.0 37.0 40.0 37.0 40.0 28-29 38.518125 40.0 37.0 40.0 37.0 40.0 30-31 38.460375 40.0 37.0 40.0 37.0 40.0 32-33 38.341125000000005 40.0 37.0 40.0 37.0 40.0 34-35 38.264875 40.0 37.0 40.0 37.0 40.0 36-37 38.186499999999995 40.0 37.0 40.0 37.0 40.0 38-39 38.204 40.0 37.0 40.0 37.0 40.0 40-41 37.973625 40.0 37.0 40.0 37.0 40.0 42-43 37.853750000000005 37.0 37.0 40.0 37.0 40.0 44-45 37.729875 37.0 37.0 40.0 37.0 40.0 46-47 37.613749999999996 37.0 37.0 40.0 37.0 40.0 48-49 37.474500000000006 37.0 37.0 40.0 37.0 40.0 50-51 37.316500000000005 37.0 37.0 40.0 35.0 40.0 52-53 37.121375 37.0 37.0 40.0 33.0 40.0 54-55 36.958375000000004 37.0 37.0 37.0 33.0 40.0 56-57 36.709374999999994 37.0 37.0 37.0 33.0 40.0 58-59 36.557500000000005 37.0 37.0 37.0 33.0 40.0 60-61 36.448 37.0 37.0 37.0 33.0 38.5 62-63 36.295375 37.0 37.0 37.0 33.0 37.0 64-65 36.164375 37.0 37.0 37.0 33.0 37.0 66-67 36.1205 37.0 37.0 37.0 33.0 37.0 68-69 35.215625 35.0 35.0 37.0 33.0 37.0 70-71 35.433724265628925 37.0 35.0 37.0 33.0 37.0 72-73 35.861152160286935 37.0 37.0 37.0 33.0 37.0 74-75 35.794664445405566 37.0 37.0 37.0 33.0 37.0 76-77 35.77782807276613 37.0 37.0 37.0 33.0 37.0 78-79 35.82993565646066 37.0 37.0 37.0 33.0 37.0 80-81 35.81312610075177 37.0 37.0 37.0 33.0 37.0 82-83 35.721360584066105 37.0 37.0 37.0 33.0 37.0 84-85 35.65718443063644 37.0 37.0 37.0 33.0 37.0 86-87 35.62941970310391 37.0 37.0 37.0 33.0 37.0 88-89 35.688529014844804 37.0 37.0 37.0 33.0 37.0 90-91 35.57246963562753 37.0 37.0 37.0 33.0 37.0 92-93 35.37800269905533 37.0 33.0 37.0 33.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 1.0 21 3.0 22 1.0 23 3.0 24 2.0 25 5.0 26 7.0 27 13.0 28 11.0 29 25.0 30 28.0 31 34.0 32 44.0 33 58.0 34 81.0 35 173.0 36 793.0 37 1155.0 38 1497.0 39 66.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 67.125 8.325000000000001 8.025 16.525000000000002 2 50.05 26.224999999999998 14.025000000000002 9.700000000000001 3 29.625 38.35 17.375 14.649999999999999 4 31.8 26.200000000000003 20.05 21.95 5 26.825 27.1 26.8 19.275000000000002 6 21.425 34.55 26.424999999999997 17.599999999999998 7 34.575 27.625 20.7 17.1 8 28.999999999999996 28.075 25.874999999999996 17.05 9 23.724999999999998 27.150000000000002 28.749999999999996 20.375 10-11 24.474999999999998 28.212500000000002 28.4125 18.9 12-13 23.375 28.525 28.712500000000002 19.3875 14-15 20.9 29.1375 30.9625 19.0 16-17 24.6 30.6375 23.7 21.0625 18-19 23.1875 26.4125 30.162499999999998 20.2375 20-21 26.700000000000003 25.85 27.3 20.150000000000002 22-23 28.349999999999998 23.4375 27.0125 21.2 24-25 25.275 26.924999999999997 28.050000000000004 19.75 26-27 26.05 24.3 28.95 20.7 28-29 24.3625 28.1 27.325 20.2125 30-31 24.712500000000002 27.3 27.6875 20.3 32-33 24.224999999999998 25.2625 28.487499999999997 22.025 34-35 23.1125 29.862499999999997 26.8125 20.2125 36-37 24.8625 26.8625 24.575 23.7 38-39 26.637499999999996 25.0375 27.9125 20.4125 40-41 25.575 25.75 26.7625 21.912499999999998 42-43 25.05 29.312500000000004 26.424999999999997 19.2125 44-45 22.35 28.499999999999996 29.1375 20.0125 46-47 25.2625 26.337500000000002 27.175 21.224999999999998 48-49 24.25 25.3 29.425 21.025 50-51 22.650000000000002 27.400000000000002 29.0875 20.8625 52-53 25.6125 27.55 26.200000000000003 20.6375 54-55 25.9625 26.487500000000004 29.062500000000004 18.4875 56-57 24.9375 28.15 27.712500000000002 19.2 58-59 24.887500000000003 28.349999999999998 26.974999999999998 19.787499999999998 60-61 26.724999999999998 28.6375 26.187500000000004 18.45 62-63 21.9375 28.6875 30.0 19.375 64-65 22.277784723090384 32.054006750843854 28.003500437554695 17.664708088511063 66-67 24.95 29.325000000000003 26.025 19.7 68-69 21.95 29.1125 26.950000000000003 21.987499999999997 70-71 24.97807841663535 28.310159088062132 26.230740323186772 20.481022172115747 72-73 25.895003162555348 27.703984819734345 27.855787476280835 18.545224541429477 74-75 24.6360153256705 28.492975734355046 28.735632183908045 18.135376756066414 76-77 22.972972972972975 27.722007722007724 26.833976833976834 22.47104247104247 78-79 26.208058038606037 25.832361704884054 28.384505764995467 19.575074491514442 80-81 22.840314136125656 31.976439790575917 25.641361256544503 19.541884816753928 82-83 22.44438559322034 29.27701271186441 26.615466101694917 21.66313559322034 84-85 20.805910006715916 27.172599059771656 30.355943586299528 21.665547347212893 86-87 21.120107962213226 28.272604588394064 27.39541160593792 23.21187584345479 88-89 21.120107962213226 29.40620782726046 28.502024291497975 20.97165991902834 90-91 22.73954116059379 29.622132253711204 25.74898785425101 21.889338731443996 92-93 21.65991902834008 31.551956815114714 26.58569500674764 20.20242914979757 >>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 0.0 10 0.0 11 0.0 12 0.0 13 0.0 14 0.0 15 0.5 16 0.5 17 0.5 18 1.5 19 1.5 20 1.0 21 2.5 22 5.0 23 6.5 24 6.5 25 6.5 26 9.5 27 15.5 28 26.0 29 33.0 30 33.5 31 38.0 32 46.5 33 56.5 34 73.0 35 81.0 36 111.0 37 147.0 38 155.5 39 148.0 40 189.5 41 254.0 42 300.0 43 333.0 44 275.0 45 213.0 46 193.0 47 189.5 48 155.5 49 122.5 50 167.5 51 176.5 52 132.5 53 120.0 54 139.0 55 125.5 56 81.0 57 64.5 58 54.0 59 35.5 60 26.0 61 25.5 62 22.5 63 12.5 64 8.0 65 10.0 66 8.5 67 8.0 68 15.0 69 19.5 70 11.5 71 3.0 72 2.0 73 0.5 74 0.5 75 1.0 76 0.5 77 0.0 78 0.0 79 0.0 80 0.0 81 0.0 82 0.0 83 0.0 84 0.0 85 0.0 86 0.0 87 0.0 88 0.0 89 0.0 90 0.0 91 0.0 92 0.0 93 0.0 94 0.0 95 0.0 96 0.0 97 0.0 98 0.0 99 0.0 100 0.0 >>END_MODULE >>Per base N content pass #Base N-Count 1 0.0 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10-11 0.0 12-13 0.0 14-15 0.0 16-17 0.0 18-19 0.0 20-21 0.0 22-23 0.0 24-25 0.0 26-27 0.0 28-29 0.0 30-31 0.0 32-33 0.0 34-35 0.0 36-37 0.0 38-39 0.0 40-41 0.0 42-43 0.0 44-45 0.0 46-47 0.0 48-49 0.0 50-51 0.0 52-53 0.0 54-55 0.0 56-57 0.0 58-59 0.0 60-61 0.0 62-63 0.0 64-65 0.0125 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 17.0 71 22.0 72 17.0 73 15.0 74 28.0 75 9.0 76 14.0 77 10.0 78 17.0 79 21.0 80 20.0 81 26.0 82 16.0 83 28.0 84 35.0 85 0.0 86 0.0 87 0.0 88 0.0 89 0.0 90 0.0 91 0.0 92 0.0 93 3705.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 70.19999999999999 #Duplication Level Percentage of deduplicated Percentage of total 1 89.95726495726495 63.14999999999999 2 4.62962962962963 6.5 3 1.7806267806267806 3.75 4 1.2108262108262107 3.4000000000000004 5 0.5341880341880342 1.875 6 0.2136752136752137 0.8999999999999999 7 0.24928774928774927 1.225 8 0.17806267806267806 1.0 9 0.07122507122507123 0.44999999999999996 >10 1.0327635327635327 10.875 >50 0.14245014245014245 6.875000000000001 >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 GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 74 1.8499999999999999 No Hit CAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCT 70 1.7500000000000002 No Hit GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGC 67 1.675 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 64 1.6 No Hit CAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTG 27 0.675 No Hit CAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATAT 24 0.6 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 23 0.575 No Hit GGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTT 22 0.5499999999999999 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 22 0.5499999999999999 No Hit GGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGC 21 0.525 No Hit GTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAA 18 0.44999999999999996 No Hit GGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAA 16 0.4 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 16 0.4 No Hit TCAAAAGAGGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGGA 16 0.4 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 15 0.375 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 15 0.375 No Hit GAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGC 15 0.375 No Hit GCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATC 13 0.325 No Hit AGTCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAA 13 0.325 No Hit GGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGC 13 0.325 No Hit GGAAGGGCGTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAGCAT 12 0.3 No Hit GCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCT 12 0.3 No Hit GTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGGT 12 0.3 No Hit GGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAAA 12 0.3 No Hit CGAGGAAGGGCGTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAG 12 0.3 No Hit GGGTGAGAGCCCCGTCCGGCCCGGACCCTGTCGCCCCACGAGGCGCCGTC 12 0.3 No Hit GGAAAAGAAAGCAAAAGCGATTCCCGTAGTAGCGGCGAGCGAAATGGGAG 12 0.3 No Hit GGATACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATG 11 0.27499999999999997 No Hit GCAGCTTGCAAATGGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAA 11 0.27499999999999997 No Hit GAGGAAGGGCGTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAGC 10 0.25 No Hit GGAGGGTGAGAGCCCCGTCCGGCCCGGACCCTGTCGCCCCACGAGGCGCC 10 0.25 No Hit GGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTCCT 10 0.25 No Hit GTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTC 10 0.25 No Hit GCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGGTATG 9 0.22499999999999998 No Hit GGGGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCT 9 0.22499999999999998 No Hit GGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTG 8 0.2 No Hit GGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGG 8 0.2 No Hit AACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGA 8 0.2 No Hit GTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAG 8 0.2 No Hit GGGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTA 8 0.2 No Hit CGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGGTAT 7 0.17500000000000002 No Hit GGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGCTAAATACAG 7 0.17500000000000002 No Hit GTACTATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTT 7 0.17500000000000002 No Hit TGGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGA 7 0.17500000000000002 No Hit GTAATGCACGAACGTAATGCTCACAACTTCCCTCTAGATCTAGCTGCTCT 7 0.17500000000000002 No Hit GTCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAAT 7 0.17500000000000002 No Hit GAACGTAATGCTCACAACTTCCCTCTAGATCTAGCTGCTCTTGAAGTTCC 7 0.17500000000000002 No Hit GGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAAGGCGATCAAATTC 6 0.15 No Hit AACGTAATGCTCACAACTTCCCTCTAGATCTAGCTGCTCTTGAAGTTCCC 6 0.15 No Hit GTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAAGGCGATCAAATTCGAG 6 0.15 No Hit GGGCGGAAGACATTGTCAGGTGGGGAGTTTGGCTGGGGCGGCACATCTGT 6 0.15 No Hit GGCCCGGACCCTGTCGCCCCACGAGGCGCCGTCAACGAGTCGGGTTGTTT 6 0.15 No Hit CGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAA 6 0.15 No Hit GGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAAC 5 0.125 No Hit GTCAACGAGTCGGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACT 5 0.125 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 5 0.125 No Hit GTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAA 5 0.125 No Hit TCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATC 5 0.125 No Hit ATATTGGGTAGGTTGTGGTATTTCATTGCTACAAACATGGGTTATTGTAA 5 0.125 No Hit GGGCCGGGTATCTCTCTGCATGTACGTATGCCTGTAATGTACGTAGCTAC 5 0.125 No Hit GATACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGC 5 0.125 No Hit GTATTTAGCCTTGCAAGGTGGTCCTTGCTGATTCACACGGGATTCCACGT 5 0.125 No Hit GTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCG 5 0.125 No Hit GGGGTTGTGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTG 5 0.125 No Hit GATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAG 5 0.125 No Hit GGAAAAGAGGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTTG 5 0.125 No Hit TCTCATGGAGAGTTCGATCCTGGCTCAGGATGAACGCTGGCGGCATGCTT 5 0.125 No Hit AAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCC 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 0.025 0.0 0.0 0.0 0.0 26-27 0.025 0.0 0.0 0.0 0.0 28-29 0.025 0.0 0.0 0.0 0.0 30-31 0.025 0.0 0.0 0.0 0.0 32-33 0.025 0.0 0.0 0.0 0.0 34-35 0.025 0.0 0.0 0.0 0.0 36-37 0.025 0.0 0.0 0.0 0.0 38-39 0.025 0.0 0.0 0.0 0.0 40-41 0.025 0.0 0.0 0.0 0.0 42-43 0.025 0.0 0.0 0.0 0.0 44-45 0.025 0.0 0.0 0.0 0.0 46-47 0.025 0.0 0.0 0.0 0.0 48-49 0.025 0.0 0.0 0.0 0.0 50-51 0.025 0.0 0.0 0.0 0.0 52-53 0.05 0.0 0.0 0.0 0.0 54-55 0.05 0.0 0.0 0.0 0.0 56-57 0.05 0.0 0.0 0.0 0.0 58-59 0.05 0.0 0.0 0.0 0.0 60-61 0.05 0.0 0.0 0.0 0.0 62-63 0.05 0.0 0.0 0.0 0.0 64-65 0.05 0.0 0.0 0.0 0.0 66-67 0.05 0.0 0.0 0.0 0.0 68-69 0.05 0.0 0.0 0.0 0.0 70-71 0.05 0.0 0.0 0.0 0.0 72-73 0.0625 0.0 0.0 0.0 0.0 74-75 0.0875 0.0 0.0 0.0 0.0 76-77 0.1 0.0 0.0 0.0 0.0 78-79 0.1 0.0 0.0 0.0 0.0 80-81 0.1 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GGAGAGC 30 1.9212287E-4 57.091667 2 GCAATAC 30 1.9212287E-4 57.091667 7 GGGAGAG 30 1.9212287E-4 57.091667 1 CAATACA 30 1.9212287E-4 57.091667 8 GAGCAAT 30 1.9212287E-4 57.091667 5 AGAGCAA 30 1.9212287E-4 57.091667 4 GAGAGCA 30 1.9212287E-4 57.091667 3 AATACAA 30 1.9212287E-4 57.091667 9 AGCAATA 30 1.9212287E-4 57.091667 6 CATCACT 20 5.354322E-4 46.924656 82-83 ATCACTA 20 5.354322E-4 46.924656 84-85 AGCATCA 20 5.354322E-4 46.924656 80-81 CACTAGC 20 5.354322E-4 46.924656 86-87 TCACTAG 20 5.354322E-4 46.924656 84-85 ACTAGCT 20 5.354322E-4 46.924656 86-87 GCATCAC 20 5.354322E-4 46.924656 82-83 AAGCATC 20 5.354322E-4 46.924656 80-81 AGCCGAA 20 6.1286165E-4 45.673336 74-75 GCCGAAA 20 6.1286165E-4 45.673336 74-75 CCGAAAG 20 6.1286165E-4 45.673336 76-77 >>END_MODULE Rejected 344062 READS because READLEN < 1 Read 344062 spots for ERR6133357.sra Written 344062 spots for ERR6133357.sra Rejected 344062 READS because READLEN < 1 Read 344062 spots for ERR6133357.sra Written 344062 spots for ERR6133357.sra Rejected 344062 READS because READLEN < 1 Read 344062 spots for ERR6133357.sra Written 344062 spots for ERR6133357.sra Rejected 344062 READS because READLEN < 1 Read 344062 spots for ERR6133357.sra Written 344062 spots for ERR6133357.sra Rejected 344062 READS because READLEN < 1 Read 344062 spots for ERR6133357.sra Written 344062 spots for ERR6133357.sra Rejected 344062 READS because READLEN < 1 Read 344062 spots for ERR6133357.sra Written 344062 spots for ERR6133357.sra Rejected 344062 READS because READLEN < 1 Read 344062 spots for ERR6133357.sra Written 344062 spots for ERR6133357.sra Rejected 344062 READS because READLEN < 1 Read 344062 spots for ERR6133357.sra Written 344062 spots for ERR6133357.sra Rejected 344062 READS because READLEN < 1 Read 344062 spots for ERR6133357.sra Written 344062 spots for ERR6133357.sra Rejected 344062 READS because READLEN < 1 Read 344062 spots for ERR6133357.sra Written 344062 spots for ERR6133357.sra Rejected 344062 READS because READLEN < 1 Read 344062 spots for ERR6133357.sra Written 344062 spots for ERR6133357.sra Rejected 344062 READS because READLEN < 1 Read 344062 spots for ERR6133357.sra Written 344062 spots for ERR6133357.sra Rejected 344062 READS because READLEN < 1 Read 344062 spots for ERR6133357.sra Written 344062 spots for ERR6133357.sra Rejected 344062 READS because READLEN < 1 Read 344062 spots for ERR6133357.sra Written 344062 spots for ERR6133357.sra Rejected 344062 READS because READLEN < 1 Read 344062 spots for ERR6133357.sra Written 344062 spots for ERR6133357.sra Rejected 344081 READS because READLEN < 1 Read 344081 spots for ERR6133357.sra Written 344081 spots for ERR6133357.sra Rejected 344062 READS because READLEN < 1 Read 344062 spots for ERR6133357.sra Written 344062 spots for ERR6133357.sra Rejected 344062 READS because READLEN < 1 Read 344062 spots for ERR6133357.sra Written 344062 spots for ERR6133357.sra Rejected 344062 READS because READLEN < 1 Read 344062 spots for ERR6133357.sra Written 344062 spots for ERR6133357.sra Rejected 344062 READS because READLEN < 1 Read 344062 spots for ERR6133357.sra Written 344062 spots for ERR6133357.sra SRR ids: ['ERR6133357.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_xlhnl46b ERR6133357.sra spots: 6881259 blocks: [[1, 344062], [344063, 688124], [688125, 1032186], [1032187, 1376248], [1376249, 1720310], [1720311, 2064372], [2064373, 2408434], [2408435, 2752496], [2752497, 3096558], [3096559, 3440620], [3440621, 3784682], [3784683, 4128744], [4128745, 4472806], [4472807, 4816868], [4816869, 5160930], [5160931, 5504992], [5504993, 5849054], [5849055, 6193116], [6193117, 6537178], [6537179, 6881259]] ERR6133357 file size 1516235 ERR6133357 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 ERR6133357 ERR6133357_1.fastq Input file: ERR6133357_1.fastq trimmed: ERR6133357-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 01:21:22 2024 >> started Sat Dec 7 01:21:27 2024 >> done (4.524s) 6881259 reads processed; of these: 679 ( 0.01%) short reads filtered out after trimming by size control 12 ( 0.00%) empty reads filtered out after trimming by size control 6880568 (99.99%) reads available; of these: 42319 ( 0.62%) trimmed reads available after processing 6838249 (99.38%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 52 0.00% 19 124 0.00% 20 78 0.00% 21 46 0.00% 22 58 0.00% 23 43 0.00% 24 26 0.00% 25 41 0.00% 26 52 0.00% 27 44 0.00% 28 66 0.00% 29 248 0.00% 30 33 0.00% 31 48 0.00% 32 88 0.00% 33 62 0.00% 34 35 0.00% 35 141 0.00% 36 30 0.00% 37 37 0.00% 38 77 0.00% 39 137 0.00% 40 189 0.00% 41 57 0.00% 42 32 0.00% 43 61 0.00% 44 62 0.00% 45 30 0.00% 46 29 0.00% 47 21 0.00% 48 27 0.00% 49 25 0.00% 50 27 0.00% 51 185 0.00% 52 46 0.00% 53 24 0.00% 54 26 0.00% 55 31 0.00% 56 26 0.00% 57 58 0.00% 58 32 0.00% 59 37 0.00% 60 47 0.00% 61 50 0.00% 62 15 0.00% 63 18 0.00% 64 30 0.00% 65 30 0.00% 66 41 0.00% 67 71 0.00% 68 129 0.00% 69 217 0.00% 70 28933 0.42% 71 27301 0.40% 72 28595 0.42% 73 27023 0.39% 74 25996 0.38% 75 25337 0.37% 76 24480 0.36% 77 26889 0.39% 78 27543 0.40% 79 30083 0.44% 80 29280 0.43% 81 38601 0.56% 82 40439 0.59% 83 34342 0.50% 84 40384 0.59% 85 252 0.00% 86 417 0.01% 87 589 0.01% 88 966 0.01% 89 1579 0.02% 90 2927 0.04% 91 6550 0.10% 92 21927 0.32% 93 6386896 92.83% 6880568 reads passed initial QC criterion=sequence-density sequence-density=3.12 sequence-density-rank=1 fanout-score=2.03 fanout-score-rank=24 prefix-density=3.17 prefix-fanout=2.0 sequence=CAAGGCTAAATAC criterion=fanout-score sequence-density=0.02 sequence-density-rank=21 fanout-score=16.81 fanout-score-rank=1 prefix-density=0.15 prefix-fanout=2.2 sequence=TGCTGCAGCAGCTTAATTTGCATGCCAGGGACGCATGCAACGACCATCTACATATAGCTACTCGATCTACCGCTACCATGAACCGATCCAAGGCTAGCTGCACAAGCTAGGCCCTTATTTCCCTTTGTACGGGTGCATGCATGCCATCCCATGCCATGCTTGTAACCCCCCATAAATAAAATCGCCCTGGTTTAACTA Potential 3prime adapter identified. Now checking if in reference sequence Warning: gzbuffer added in zlib v1.2.3.5. Unable to change buffer size from default of 8192. 1 reads; of these: 1 (100.00%) were unpaired; of these: 0 (0.00%) aligned 0 times 0 (0.00%) aligned exactly 1 time 1 (100.00%) aligned >1 times 100.00% overall alignment rate Potential adapter found in reference sequence. Continuing without clipping. Started job on | Dec 07 01:21:44 Started mapping on | Dec 07 01:21:44 Finished on | Dec 07 01:21:56 Mapping speed, Million of reads per hour | 2064.17 Number of input reads | 6880568 Average input read length | 91 UNIQUE READS: Uniquely mapped reads number | 3219719 Uniquely mapped reads % | 46.79% Average mapped length | 91.00 Number of splices: Total | 133738 Number of splices: Annotated (sjdb) | 112834 Number of splices: GT/AG | 128600 Number of splices: GC/AG | 2274 Number of splices: AT/AC | 162 Number of splices: Non-canonical | 2702 Mismatch rate per base, % | 0.42% Deletion rate per base | 0.05% Deletion average length | 1.73 Insertion rate per base | 0.02% Insertion average length | 1.75 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 3177062 % of reads mapped to multiple loci | 46.17% Number of reads mapped to too many loci | 291219 % of reads mapped to too many loci | 4.23% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 2.55% % of reads unmapped: other | 0.25% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 483787 483787 483787 N_multimapping 3177062 3177062 3177062 N_noFeature 263107 296077 3087784 N_ambiguous 116124 17156 565 UnstrandedReadsAssigned:2840488 PositiveStrandReadsAssigned:2906486 NegativeStrandReadsAssigned:131370 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=93 echo kmer=89 ERR6133357 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: ERR6133357-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 6,880,568 reads, 4,714,998 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 994 rounds 52973 ERR6133357.ke.tsv 35125 ERR6133357.se.tsv 88098 total ==> ERR6133357.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 78 16.0249 PNS24243 293 194 0 0 KQK14069 1603 1504 149 27.925 KQK14071 474 375 0 0 ==> ERR6133357.se.tsv <== BRADI_1g14170v3 147 BRADI_1g53295v3 69 BRADI_1g59795v3 37 BRADI_1g07683v3 0 BRADI_1g00485v3 5 BRADI_1g20270v3 22 BRADI_1g74790v3 38 BRADI_1g09890v3 0 BRADI_1g77505v3 46 BRADI_1g48960v3 0 ERR6133357 completed mapping pipeline successfully