Starting /dee2/code/volunteer_pipeline.sh ERR6133334 current disk space = 1548176408576 free memory = 1434276384 ERR6133334 SRAfilesize 6e9ab668b6c3062e303bb779455d7046 ERR6133334.sra ERR6133334.sra file validated ERR6133334 is single end ERR6133334 is conventional basespace ERR6133334 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133334_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 43 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.48075 37.0 37.0 37.0 37.0 37.0 2 36.628 37.0 37.0 37.0 37.0 37.0 3 36.418 37.0 37.0 37.0 37.0 37.0 4 36.377 37.0 37.0 37.0 37.0 37.0 5 36.431 37.0 37.0 37.0 37.0 37.0 6 36.47925 37.0 37.0 37.0 37.0 37.0 7 38.5895 40.0 37.0 40.0 37.0 40.0 8 38.68875 40.0 37.0 40.0 37.0 40.0 9 38.71475 40.0 37.0 40.0 37.0 40.0 10-11 38.70325 40.0 37.0 40.0 37.0 40.0 12-13 38.699 40.0 37.0 40.0 37.0 40.0 14-15 38.646 40.0 37.0 40.0 37.0 40.0 16-17 38.64725 40.0 37.0 40.0 37.0 40.0 18-19 38.70425 40.0 37.0 40.0 37.0 40.0 20-21 38.4865 40.0 37.0 40.0 37.0 40.0 22-23 38.581125 40.0 37.0 40.0 37.0 40.0 24-25 38.579625 40.0 37.0 40.0 37.0 40.0 26-27 38.473375 40.0 37.0 40.0 37.0 40.0 28-29 38.418125 40.0 37.0 40.0 37.0 40.0 30-31 38.418 40.0 37.0 40.0 37.0 40.0 32-33 38.441625 40.0 37.0 40.0 37.0 40.0 34-35 38.354 40.0 37.0 40.0 37.0 40.0 36-37 38.187875000000005 40.0 37.0 40.0 37.0 40.0 38-39 38.035125 40.0 37.0 40.0 37.0 40.0 40-41 37.896375 40.0 37.0 40.0 37.0 40.0 42-43 37.8955 37.0 37.0 40.0 37.0 40.0 44-45 37.658 37.0 37.0 40.0 35.0 40.0 46-47 37.479875 37.0 37.0 40.0 33.0 40.0 48-49 37.406375 37.0 37.0 40.0 33.0 40.0 50-51 37.17325 37.0 37.0 40.0 33.0 40.0 52-53 37.054875 37.0 37.0 40.0 33.0 40.0 54-55 36.843125 37.0 37.0 37.0 33.0 40.0 56-57 36.661249999999995 37.0 37.0 37.0 33.0 40.0 58-59 36.3395 37.0 37.0 37.0 33.0 40.0 60-61 36.139375 37.0 37.0 37.0 33.0 40.0 62-63 35.702875000000006 37.0 33.0 37.0 33.0 37.0 64-65 35.362875 37.0 33.0 37.0 33.0 37.0 66-67 35.232875 37.0 33.0 37.0 33.0 37.0 68-69 33.81325 35.0 33.0 37.0 30.0 37.0 70-71 33.6766455134659 33.0 33.0 37.0 30.0 37.0 72-73 34.19547649543243 33.0 33.0 37.0 33.0 37.0 74-75 34.1194435508209 33.0 33.0 37.0 33.0 37.0 76-77 33.760145640776145 33.0 33.0 37.0 30.0 37.0 78-79 33.477774765530896 33.0 33.0 37.0 27.0 37.0 80-81 33.125859467761984 33.0 33.0 37.0 27.0 37.0 82-83 33.02559140302044 33.0 33.0 37.0 27.0 37.0 84-85 32.47704854556895 33.0 33.0 35.0 27.0 37.0 86-87 32.07975372279496 33.0 33.0 33.0 27.0 37.0 88-89 32.13230240549828 33.0 33.0 33.0 27.0 37.0 90-91 31.590206185567013 33.0 30.0 33.0 27.0 37.0 92-93 30.654925544100802 33.0 27.0 33.0 24.5 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 1.0 21 2.0 22 3.0 23 3.0 24 7.0 25 6.0 26 10.0 27 9.0 28 14.0 29 17.0 30 28.0 31 43.0 32 64.0 33 90.0 34 197.0 35 626.0 36 1019.0 37 1508.0 38 333.0 39 20.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 69.0 7.825 6.575 16.6 2 49.375 26.150000000000002 14.875 9.6 3 30.85 37.65 18.425 13.075000000000001 4 33.025 25.95 22.425 18.6 5 24.5 26.0 29.099999999999998 20.4 6 19.400000000000002 31.924999999999997 30.275000000000002 18.4 7 30.7 27.275 24.675 17.349999999999998 8 27.175 27.425 28.15 17.25 9 26.025 27.075 28.95 17.95 10-11 24.075 27.0 30.125 18.8 12-13 24.337500000000002 27.237499999999997 30.45 17.974999999999998 14-15 21.3625 27.037499999999998 32.05 19.55 16-17 23.275000000000002 29.299999999999997 27.187499999999996 20.2375 18-19 23.724999999999998 25.424999999999997 30.575000000000003 20.275000000000002 20-21 23.525 25.275 30.012499999999996 21.1875 22-23 25.374999999999996 26.0 28.512500000000003 20.1125 24-25 23.724999999999998 26.650000000000002 29.25 20.375 26-27 22.975 25.7625 30.775000000000002 20.4875 28-29 24.3125 26.337500000000002 28.6625 20.6875 30-31 23.575 27.750000000000004 28.787499999999998 19.8875 32-33 23.4625 26.35 30.112499999999997 20.075000000000003 34-35 22.412499999999998 27.712500000000002 29.45 20.424999999999997 36-37 22.9375 27.175 28.487499999999997 21.4 38-39 23.325000000000003 26.087500000000002 29.7125 20.875 40-41 25.1 26.3625 27.725 20.8125 42-43 24.5625 28.275 28.1 19.0625 44-45 22.037499999999998 27.737499999999997 29.9 20.325 46-47 23.5125 27.200000000000003 29.1875 20.1 48-49 22.912499999999998 25.924999999999997 30.9375 20.225 50-51 21.55 27.712500000000002 31.837500000000002 18.9 52-53 24.099999999999998 28.575 28.0625 19.2625 54-55 23.549999999999997 28.025 30.1875 18.2375 56-57 23.525 27.0 29.062500000000004 20.4125 58-59 23.775 27.187499999999996 29.0875 19.950000000000003 60-61 25.324999999999996 27.950000000000003 28.237499999999997 18.4875 62-63 21.55 28.487499999999997 31.112499999999997 18.85 64-65 22.45 30.5125 28.812500000000004 18.224999999999998 66-67 23.962500000000002 27.2625 28.8875 19.8875 68-69 21.275 29.1625 29.575000000000003 19.9875 70-71 23.830427693465445 27.781261758434717 29.148375768217733 19.239934779882102 72-73 24.08423739629866 27.849393746011486 29.393746011486915 18.672622846202934 74-75 22.941252755803397 27.259758786149657 29.68486577616392 20.114122681883025 76-77 22.870309414088215 27.307439104674124 29.54575378538512 20.276497695852534 78-79 22.647058823529413 27.794117647058826 29.759358288770056 19.799465240641712 80-81 22.193565901995385 29.319940274195737 30.18867924528302 18.29781457852586 82-83 21.895787139689578 28.04878048780488 29.46230598669623 20.593126385809313 84-85 22.990627662595852 25.617722238000567 30.33229196251065 21.05935813689293 86-87 21.534936998854526 29.810996563573884 28.235967926689575 20.418098510882015 88-89 21.764032073310425 29.853951890034363 28.88029782359679 19.50171821305842 90-91 22.164948453608247 30.42668957617411 28.13573883161512 19.272623138602523 92-93 20.24627720504009 32.13058419243986 28.264604810996563 19.358533791523485 >>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 0.0 17 1.5 18 3.0 19 2.0 20 1.0 21 2.0 22 5.0 23 7.0 24 6.5 25 7.0 26 11.0 27 16.0 28 26.5 29 35.0 30 37.5 31 52.5 32 66.5 33 73.5 34 90.5 35 116.0 36 159.5 37 214.5 38 230.0 39 209.5 40 228.0 41 242.5 42 249.0 43 269.0 44 232.0 45 182.5 46 164.5 47 163.5 48 149.0 49 148.0 50 140.5 51 127.0 52 138.0 53 148.0 54 126.0 55 91.0 56 87.5 57 87.5 58 59.5 59 24.0 60 13.5 61 11.5 62 10.0 63 4.5 64 3.0 65 4.0 66 3.5 67 3.5 68 5.0 69 4.0 70 1.5 71 1.0 72 0.5 73 0.0 74 0.0 75 0.0 76 0.0 77 0.0 78 0.0 79 0.0 80 0.0 81 0.0 82 0.0 83 0.0 84 0.0 85 0.0 86 0.0 87 0.0 88 0.0 89 0.0 90 0.0 91 0.0 92 0.0 93 0.0 94 0.0 95 0.0 96 0.0 97 0.0 98 0.0 99 0.0 100 0.0 >>END_MODULE >>Per base N content pass #Base N-Count 1 0.0 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 0.0 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 27.0 71 37.0 72 37.0 73 26.0 74 35.0 75 27.0 76 27.0 77 28.0 78 32.0 79 27.0 80 27.0 81 41.0 82 42.0 83 37.0 84 58.0 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 3492.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 80.125 #Duplication Level Percentage of deduplicated Percentage of total 1 92.51170046801872 74.125 2 3.5257410296411855 5.65 3 1.341653666146646 3.225 4 0.8424336973478939 2.7 5 0.49921996879875197 2.0 6 0.187207488299532 0.8999999999999999 7 0.062402496099843996 0.35000000000000003 8 0.21840873634945399 1.4000000000000001 9 0.12480499219968799 0.8999999999999999 >10 0.6864274570982839 8.75 >50 0.0 0.0 >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 warn #Sequence Count Percentage Possible Source CAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCT 32 0.8 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 27 0.675 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 24 0.6 No Hit GGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGC 24 0.6 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 23 0.575 No Hit GGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAA 22 0.5499999999999999 No Hit CAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATAT 18 0.44999999999999996 No Hit GGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTCCT 17 0.42500000000000004 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 16 0.4 No Hit GGAGTTTGGCTGGGGCGGCACATCTGTTAAAAGATAACGCAGGTGTCCTA 13 0.325 No Hit GGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTT 13 0.325 No Hit GGGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTA 12 0.3 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 12 0.3 No Hit GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGC 12 0.3 No Hit CAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTG 12 0.3 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 11 0.27499999999999997 No Hit GGGGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCT 11 0.27499999999999997 No Hit GTACTATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTT 11 0.27499999999999997 No Hit GGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGCTAAATACAG 10 0.25 No Hit GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 10 0.25 No Hit GGGGCAGAGGGAATTTCCGGTGGAGCGGTGAAATGCATTGAGATCGGAAA 10 0.25 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 10 0.25 No Hit GGCCTGTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCG 9 0.22499999999999998 No Hit GTATTAGTACTATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATCT 9 0.22499999999999998 No Hit GTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTC 9 0.22499999999999998 No Hit TCAAAAGAGGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGGA 9 0.22499999999999998 No Hit GTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAA 8 0.2 No Hit GGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGC 8 0.2 No Hit GCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGGTATG 8 0.2 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 8 0.2 No Hit GTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAG 8 0.2 No Hit GGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAA 8 0.2 No Hit GGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGCT 8 0.2 No Hit AACGTAATGCTCACAACTTCCCTCTAGATCTAGCTGCTCTTGAAGTTCCC 7 0.17500000000000002 No Hit GTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGCTA 7 0.17500000000000002 No Hit GAAGTAATGCACGAACGTAATGCTCACAACTTCCCTCTAGATCTAGCTGC 6 0.15 No Hit GTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCT 6 0.15 No Hit GGTGGATACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAA 6 0.15 No Hit GCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATC 6 0.15 No Hit GGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGG 6 0.15 No Hit GAACGTAATGCTCACAACTTCCCTCTAGATCTAGCTGCTCTTGAAGTTCC 6 0.15 No Hit GGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAAGGCGATCAAATTC 5 0.125 No Hit AATGCACGAACGTAATGCTCACAACTTCCCTCTAGATCTAGCTGCTCTTG 5 0.125 No Hit CAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTT 5 0.125 No Hit GGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTT 5 0.125 No Hit CGAGTCGGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTC 5 0.125 No Hit GCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCT 5 0.125 No Hit GGAAGAGCCCGAGCTGCTGCAGCAGGTTTTGAAAAGGGAATCGATCGTGA 5 0.125 No Hit GGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAAA 5 0.125 No Hit CGGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGG 5 0.125 No Hit GCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATA 5 0.125 No Hit GAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGC 5 0.125 No Hit CAAATAGGTCAACCTTTTAAACTGCCTGCTGAATCCATGAGCAGGCAAGA 5 0.125 No Hit GGATACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATG 5 0.125 No Hit GTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGGT 5 0.125 No Hit CAACGAGTCGGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCC 5 0.125 No Hit GGGTGAGAGCCCCGTCCGGCCCGGACCCTGTCGCCCCACGAGGCGCCGTC 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 0.025 0.0 0.0 0.0 68-69 0.0 0.025 0.0 0.0 0.0 70-71 0.0 0.025 0.0 0.0 0.0 72-73 0.0 0.025 0.0 0.0 0.0 74-75 0.0 0.025 0.0 0.0 0.0 76-77 0.0 0.025 0.0 0.0 0.0 78-79 0.0 0.025 0.0 0.0 0.0 80-81 0.0 0.025 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position AAAAAAA 15 0.009421421 48.112675 86-87 >>END_MODULE Rejected 85456 READS because READLEN < 1 Read 85456 spots for ERR6133334.sra Written 85456 spots for ERR6133334.sra Rejected 85456 READS because READLEN < 1 Read 85456 spots for ERR6133334.sra Written 85456 spots for ERR6133334.sra Rejected 85456 READS because READLEN < 1 Read 85456 spots for ERR6133334.sra Written 85456 spots for ERR6133334.sra Rejected 85456 READS because READLEN < 1 Read 85456 spots for ERR6133334.sra Written 85456 spots for ERR6133334.sra Rejected 85456 READS because READLEN < 1 Read 85456 spots for ERR6133334.sra Written 85456 spots for ERR6133334.sra Rejected 85456 READS because READLEN < 1 Read 85456 spots for ERR6133334.sra Written 85456 spots for ERR6133334.sra Rejected 85456 READS because READLEN < 1 Read 85456 spots for ERR6133334.sra Written 85456 spots for ERR6133334.sra Rejected 85456 READS because READLEN < 1 Read 85456 spots for ERR6133334.sra Written 85456 spots for ERR6133334.sra Rejected 85456 READS because READLEN < 1 Read 85456 spots for ERR6133334.sra Written 85456 spots for ERR6133334.sra Rejected 85456 READS because READLEN < 1 Read 85456 spots for ERR6133334.sra Written 85456 spots for ERR6133334.sra Rejected 85456 READS because READLEN < 1 Read 85456 spots for ERR6133334.sra Written 85456 spots for ERR6133334.sra Rejected 85456 READS because READLEN < 1 Read 85456 spots for ERR6133334.sra Written 85456 spots for ERR6133334.sra Rejected 85464 READS because READLEN < 1 Read 85464 spots for ERR6133334.sra Written 85464 spots for ERR6133334.sra Rejected 85456 READS because READLEN < 1 Read 85456 spots for ERR6133334.sra Written 85456 spots for ERR6133334.sra Rejected 85456 READS because READLEN < 1 Read 85456 spots for ERR6133334.sra Written 85456 spots for ERR6133334.sra Rejected 85456 READS because READLEN < 1 Read 85456 spots for ERR6133334.sra Written 85456 spots for ERR6133334.sra Rejected 85456 READS because READLEN < 1 Read 85456 spots for ERR6133334.sra Written 85456 spots for ERR6133334.sra Rejected 85456 READS because READLEN < 1 Read 85456 spots for ERR6133334.sra Written 85456 spots for ERR6133334.sra Rejected 85456 READS because READLEN < 1 Read 85456 spots for ERR6133334.sra Written 85456 spots for ERR6133334.sra Rejected 85456 READS because READLEN < 1 Read 85456 spots for ERR6133334.sra Written 85456 spots for ERR6133334.sra SRR ids: ['ERR6133334.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_dtcae02n ERR6133334.sra spots: 1709128 blocks: [[1, 85456], [85457, 170912], [170913, 256368], [256369, 341824], [341825, 427280], [427281, 512736], [512737, 598192], [598193, 683648], [683649, 769104], [769105, 854560], [854561, 940016], [940017, 1025472], [1025473, 1110928], [1110929, 1196384], [1196385, 1281840], [1281841, 1367296], [1367297, 1452752], [1452753, 1538208], [1538209, 1623664], [1623665, 1709128]] ERR6133334 file size 372126 ERR6133334 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 ERR6133334 ERR6133334_1.fastq Input file: ERR6133334_1.fastq trimmed: ERR6133334-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 00:51:51 2024 >> started Sat Dec 7 00:51:52 2024 >> done (1.226s) 1709128 reads processed; of these: 307 ( 0.02%) short reads filtered out after trimming by size control 10 ( 0.00%) empty reads filtered out after trimming by size control 1708811 (99.98%) reads available; of these: 23859 ( 1.40%) trimmed reads available after processing 1684952 (98.60%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 20 0.00% 19 23 0.00% 20 16 0.00% 21 20 0.00% 22 23 0.00% 23 21 0.00% 24 13 0.00% 25 14 0.00% 26 14 0.00% 27 17 0.00% 28 59 0.00% 29 19 0.00% 30 14 0.00% 31 14 0.00% 32 24 0.00% 33 8 0.00% 34 18 0.00% 35 39 0.00% 36 16 0.00% 37 8 0.00% 38 15 0.00% 39 23 0.00% 40 35 0.00% 41 18 0.00% 42 8 0.00% 43 15 0.00% 44 15 0.00% 45 7 0.00% 46 10 0.00% 47 5 0.00% 48 7 0.00% 49 6 0.00% 50 8 0.00% 51 29 0.00% 52 11 0.00% 53 8 0.00% 54 11 0.00% 55 9 0.00% 56 7 0.00% 57 6 0.00% 58 3 0.00% 59 8 0.00% 60 13 0.00% 61 6 0.00% 62 1 0.00% 63 2 0.00% 64 1 0.00% 65 2 0.00% 66 3 0.00% 67 3 0.00% 68 17 0.00% 69 48 0.00% 70 12606 0.74% 71 12492 0.73% 72 13491 0.79% 73 12601 0.74% 74 12046 0.70% 75 11752 0.69% 76 11546 0.68% 77 12828 0.75% 78 12889 0.75% 79 13136 0.77% 80 12927 0.76% 81 16495 0.97% 82 17172 1.00% 83 14994 0.88% 84 19125 1.12% 85 13 0.00% 86 40 0.00% 87 67 0.00% 88 151 0.01% 89 327 0.02% 90 853 0.05% 91 2749 0.16% 92 17520 1.03% 93 1480231 86.62% 1708811 reads passed initial QC criterion=sequence-density sequence-density=4.75 sequence-density-rank=1 fanout-score=2.01 fanout-score-rank=32 prefix-density=4.78 prefix-fanout=2.0 sequence=CAAGGCTAAATAC criterion=fanout-score sequence-density=0.02 sequence-density-rank=25 fanout-score=63.68 fanout-score-rank=1 prefix-density=0.18 prefix-fanout=8.8 sequence=TTTCCTTTTTTCCTTAGAAAAATAACTCAATCAAAATCCAATTATTTACTCTACAAGAACGAAATGCTTGTTATGCCTAATATACTTAGTTTAACCTGTATCTGTTTTAATTGTGTTCTTTATCCGACTAGTTTTTTCTTTGCTAAACTACCCGAAGCTTATGCTATTTTCAACCCAATCGTGGATTTTATGCCTGTCATACCTCTATTCTTTTTTCTATTAGCCTTTGTTTGGCAAGCTGCTGTAAGTTTTCGATGAAATCTTTACTACTCCGTCTGCCAAATTGAATGGTCTATTCATTCCAAAACC 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 00:52:11 Started mapping on | Dec 07 00:52:11 Finished on | Dec 07 00:52:15 Mapping speed, Million of reads per hour | 1537.93 Number of input reads | 1708811 Average input read length | 91 UNIQUE READS: Uniquely mapped reads number | 1028271 Uniquely mapped reads % | 60.17% Average mapped length | 90.17 Number of splices: Total | 30151 Number of splices: Annotated (sjdb) | 23897 Number of splices: GT/AG | 28291 Number of splices: GC/AG | 737 Number of splices: AT/AC | 29 Number of splices: Non-canonical | 1094 Mismatch rate per base, % | 0.44% Deletion rate per base | 0.05% Deletion average length | 1.76 Insertion rate per base | 0.02% Insertion average length | 1.62 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 562345 % of reads mapped to multiple loci | 32.91% Number of reads mapped to too many loci | 79322 % of reads mapped to too many loci | 4.64% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 2.02% % of reads unmapped: other | 0.25% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 118195 118195 118195 N_multimapping 562345 562345 562345 N_noFeature 84326 93860 983576 N_ambiguous 40664 5458 182 UnstrandedReadsAssigned:903281 PositiveStrandReadsAssigned:928953 NegativeStrandReadsAssigned:44513 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=93 echo kmer=89 ERR6133334 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: ERR6133334-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 1,708,811 reads, 1,257,705 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,107 rounds 52973 ERR6133334.ke.tsv 35125 ERR6133334.se.tsv 88098 total ==> ERR6133334.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 20 15.7944 PNS24243 293 194 0 0 KQK14069 1603 1504 9 6.48368 KQK14071 474 375 0 0 ==> ERR6133334.se.tsv <== BRADI_1g14170v3 9 BRADI_1g53295v3 34 BRADI_1g59795v3 19 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 13 BRADI_1g74790v3 12 BRADI_1g09890v3 0 BRADI_1g77505v3 25 BRADI_1g48960v3 0 ERR6133334 completed mapping pipeline successfully