Starting /dee2/code/volunteer_pipeline.sh ERR6133308 current disk space = 1548417671168 free memory = 1602848548 ERR6133308 SRAfilesize 234a83ce57f5f17c45b229742b235082 ERR6133308.sra ERR6133308.sra file validated ERR6133308 is single end ERR6133308 is conventional basespace ERR6133308 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133308_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 35.186 37.0 33.0 37.0 33.0 37.0 2 36.49975 37.0 37.0 37.0 37.0 37.0 3 36.1195 37.0 37.0 37.0 33.0 37.0 4 35.68525 37.0 37.0 37.0 33.0 37.0 5 35.63425 37.0 37.0 37.0 33.0 37.0 6 35.9185 37.0 37.0 37.0 33.0 37.0 7 37.7475 40.0 37.0 40.0 33.0 40.0 8 37.71725 40.0 37.0 40.0 33.0 40.0 9 37.86 40.0 37.0 40.0 33.0 40.0 10-11 37.661 40.0 37.0 40.0 33.0 40.0 12-13 37.605125 38.5 37.0 40.0 33.0 40.0 14-15 37.646625 40.0 37.0 40.0 33.0 40.0 16-17 37.536375 40.0 37.0 40.0 33.0 40.0 18-19 37.4915 40.0 37.0 40.0 33.0 40.0 20-21 37.255375 37.0 37.0 40.0 33.0 40.0 22-23 37.173874999999995 37.0 37.0 40.0 33.0 40.0 24-25 37.409625 37.0 37.0 40.0 33.0 40.0 26-27 37.307625 37.0 37.0 40.0 33.0 40.0 28-29 37.274375 37.0 37.0 40.0 33.0 40.0 30-31 37.192125000000004 37.0 37.0 40.0 33.0 40.0 32-33 37.019625 37.0 37.0 40.0 33.0 40.0 34-35 36.80975 37.0 37.0 40.0 33.0 40.0 36-37 36.732124999999996 37.0 37.0 40.0 33.0 40.0 38-39 36.357875 37.0 37.0 40.0 33.0 40.0 40-41 36.242000000000004 37.0 37.0 40.0 33.0 40.0 42-43 36.0225 37.0 37.0 40.0 33.0 40.0 44-45 35.733999999999995 37.0 35.0 40.0 33.0 40.0 46-47 35.396874999999994 37.0 33.0 37.0 30.0 40.0 48-49 35.253375000000005 37.0 33.0 37.0 30.0 40.0 50-51 35.072625 37.0 33.0 37.0 27.0 40.0 52-53 34.857749999999996 37.0 33.0 37.0 27.0 40.0 54-55 34.755 37.0 33.0 37.0 27.0 40.0 56-57 34.32875 37.0 33.0 37.0 27.0 38.5 58-59 32.031875 33.0 30.0 37.0 24.5 37.0 60-61 33.538375 37.0 33.0 37.0 27.0 37.0 62-63 33.786500000000004 37.0 33.0 37.0 27.0 37.0 64-65 33.760625000000005 37.0 33.0 37.0 27.0 37.0 66-67 33.47775 37.0 33.0 37.0 27.0 37.0 68-69 32.933499999999995 35.0 33.0 37.0 27.0 37.0 70-71 32.93618706118355 35.0 33.0 37.0 27.0 37.0 72-73 33.35354655055532 37.0 33.0 37.0 27.0 37.0 74-75 33.26621436639108 37.0 33.0 37.0 27.0 37.0 76-77 33.40135246737185 37.0 33.0 37.0 27.0 37.0 78-79 33.40050480521583 37.0 33.0 37.0 27.0 37.0 80-81 33.35311983934147 37.0 33.0 37.0 27.0 37.0 82-83 33.2372958353519 37.0 33.0 37.0 27.0 37.0 84-85 32.926622672104 33.0 33.0 37.0 27.0 37.0 86-87 32.892568448500654 33.0 33.0 37.0 27.0 37.0 88-89 33.065840938722296 37.0 33.0 37.0 27.0 37.0 90-91 32.796219035202085 33.0 33.0 37.0 27.0 37.0 92-93 32.65541069100391 33.0 33.0 37.0 27.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 14.0 21 23.0 22 18.0 23 34.0 24 29.0 25 33.0 26 36.0 27 52.0 28 52.0 29 78.0 30 91.0 31 122.0 32 159.0 33 196.0 34 265.0 35 471.0 36 807.0 37 955.0 38 555.0 39 10.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 82.8 3.4750000000000005 4.9 8.825 2 62.675000000000004 23.175 9.049999999999999 5.1 3 30.4 39.625 17.05 12.925 4 29.975 25.95 20.474999999999998 23.599999999999998 5 22.25 29.325000000000003 32.05 16.375 6 17.8 38.0 25.6 18.6 7 34.9 29.9 19.675 15.525 8 28.799999999999997 30.475 25.7 15.024999999999999 9 22.925 26.625 30.825000000000003 19.625 10-11 23.3125 27.5625 30.7625 18.3625 12-13 24.9 27.187499999999996 28.262500000000003 19.650000000000002 14-15 19.75 30.6375 30.5 19.112499999999997 16-17 22.0625 33.2125 24.462500000000002 20.2625 18-19 21.5375 28.537499999999998 30.7625 19.162499999999998 20-21 24.925 25.387500000000003 29.9 19.787499999999998 22-23 28.050000000000004 22.4375 27.975 21.5375 24-25 25.5375 27.150000000000002 27.925 19.3875 26-27 24.525 25.650000000000002 32.05 17.775 28-29 24.2625 27.6 29.299999999999997 18.8375 30-31 25.112499999999997 26.187500000000004 28.325 20.375 32-33 24.0 26.337500000000002 29.6375 20.025000000000002 34-35 21.85 30.3 26.6125 21.2375 36-37 24.478059757469683 26.665833229153645 26.778347293411674 22.077759719964995 38-39 26.39409852463116 25.331332833208304 30.795198799699925 17.479369842460617 40-41 26.0375 25.5 26.0125 22.45 42-43 24.965620702587824 27.990998874859358 28.416052006500813 18.627328416052006 44-45 21.502687835979497 27.415926990873857 31.603950493811727 19.47743467933492 46-47 23.1125 25.85 29.95 21.087500000000002 48-49 23.9375 25.587500000000002 30.55 19.925 50-51 22.814258911819888 26.691682301438398 30.268918073796126 20.225140712945592 52-53 24.265165728580364 28.230143839899934 25.853658536585368 21.651031894934334 54-55 25.5375 26.5125 30.425 17.525 56-57 26.9625 27.325 27.237499999999997 18.475 58-59 22.8625 25.0 31.4375 20.7 60-61 24.7875 27.037499999999998 29.562500000000004 18.6125 62-63 21.775 29.462500000000002 31.424999999999997 17.3375 64-65 21.5375 29.6875 30.662499999999998 18.1125 66-67 23.925 28.999999999999996 28.1375 18.9375 68-69 20.925 28.037499999999998 28.0875 22.95 70-71 22.646469704556836 28.44266399599399 28.65548322483726 20.255383074611917 72-73 24.75770925110132 25.37444933920705 29.074889867841406 20.792951541850222 74-75 22.991269138301913 28.141212197899534 30.342907756548147 18.52461090725041 76-77 21.224074309708616 27.382618653772745 27.866140730372823 23.52716630614582 78-79 23.644501278772378 25.498721227621484 30.818414322250636 20.0383631713555 80-81 21.44141829393628 30.716855087358685 29.14953751284687 18.69218910585817 82-83 21.287320666925165 27.413726250484682 30.632027917797593 20.666925164792556 84-85 22.058823529411764 22.813638729828213 33.68037480478917 21.447162935970848 86-87 20.78226857887875 26.584093872229463 30.834419817470664 21.799217731421123 88-89 19.126466753585397 29.308996088657107 31.290743155149936 20.273794002607563 90-91 23.833116036505867 28.26597131681877 29.26988265971317 18.63102998696219 92-93 21.760104302477185 31.095176010430247 28.878748370273794 18.265971316818774 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 0.0 1 0.0 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10 0.0 11 0.0 12 0.0 13 0.0 14 0.0 15 0.0 16 0.5 17 9.5 18 10.5 19 2.5 20 2.5 21 2.5 22 3.5 23 10.0 24 10.5 25 10.0 26 17.0 27 19.5 28 24.5 29 28.5 30 34.0 31 46.0 32 61.5 33 82.5 34 93.0 35 100.5 36 130.0 37 184.0 38 245.5 39 224.5 40 194.0 41 194.0 42 231.5 43 287.5 44 223.5 45 170.5 46 184.0 47 173.0 48 157.0 49 152.0 50 174.0 51 162.0 52 115.5 53 124.0 54 111.0 55 71.5 56 53.5 57 45.5 58 38.5 59 30.0 60 26.5 61 21.5 62 16.0 63 13.5 64 15.0 65 10.0 66 4.0 67 4.5 68 7.0 69 8.5 70 7.0 71 6.0 72 7.5 73 8.5 74 5.5 75 2.5 76 2.0 77 1.5 78 1.0 79 0.5 80 0.0 81 0.0 82 0.0 83 0.0 84 0.0 85 0.0 86 0.0 87 0.0 88 0.0 89 0.0 90 0.0 91 0.0 92 0.0 93 0.0 94 0.0 95 0.0 96 0.0 97 0.0 98 0.0 99 0.0 100 0.0 >>END_MODULE >>Per base N content pass #Base N-Count 1 0.0 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10-11 0.0 12-13 0.0 14-15 0.0 16-17 0.0 18-19 0.0 20-21 0.0 22-23 0.0 24-25 0.0 26-27 0.0 28-29 0.0 30-31 0.0 32-33 0.0 34-35 0.0 36-37 0.0125 38-39 0.025 40-41 0.0 42-43 0.0125 44-45 0.0125 46-47 0.0 48-49 0.0 50-51 0.0625 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 12.0 71 9.0 72 13.0 73 10.0 74 9.0 75 15.0 76 5.0 77 12.0 78 10.0 79 10.0 80 6.0 81 14.0 82 13.0 83 13.0 84 14.0 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 3835.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 70.89999999999999 #Duplication Level Percentage of deduplicated Percentage of total 1 90.30324400564174 64.025 2 5.04231311706629 7.1499999999999995 3 1.4809590973201692 3.15 4 0.9167842031029618 2.6 5 0.5641748942172073 2.0 6 0.4231311706629055 1.7999999999999998 7 0.07052186177715092 0.35000000000000003 8 0.10578279266572638 0.6 9 0.07052186177715092 0.44999999999999996 >10 0.9167842031029618 11.875 >50 0.10578279266572638 6.0 >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 fail #Sequence Count Percentage Possible Source GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 85 2.125 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 78 1.95 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 77 1.925 No Hit GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGC 40 1.0 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 34 0.8500000000000001 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 31 0.775 No Hit GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 31 0.775 No Hit CAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCT 29 0.7250000000000001 No Hit GGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGG 26 0.65 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 22 0.5499999999999999 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 20 0.5 No Hit GGGCATTCGTATTTCATAGTCAGAGGTGAAATTCTTGGATTTATGAAAGA 19 0.475 No Hit GTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCT 18 0.44999999999999996 No Hit GGCCTGTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCG 17 0.42500000000000004 No Hit GGAGTATCCTTGATATATAAATATATAGATAAATAGATTTAAATGGAAAA 16 0.4 No Hit GGGATGGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACGA 15 0.375 No Hit GGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGGG 14 0.35000000000000003 No Hit GGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTT 14 0.35000000000000003 No Hit GGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAACCCTCTTAACT 13 0.325 No Hit GGAAAAGAGGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTTG 13 0.325 No Hit GAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGC 13 0.325 No Hit GGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGC 13 0.325 No Hit GGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGC 12 0.3 No Hit GTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAA 12 0.3 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 11 0.27499999999999997 No Hit GATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAAT 11 0.27499999999999997 No Hit GGGGATGGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACG 11 0.27499999999999997 No Hit GGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTT 10 0.25 No Hit GGTTTTGAAAAGGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAA 10 0.25 No Hit GGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAA 9 0.22499999999999998 No Hit GTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAG 9 0.22499999999999998 No Hit GGGCCGGGTATCTCTCTGCATGTACGTATGCCTGTAATGTACGTAGCTAC 8 0.2 No Hit GATACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGC 8 0.2 No Hit GGGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTG 8 0.2 No Hit GGGAGTATTATGAAAGGAGATTAATCATAGATTATCAAAAACCCTAGAAA 7 0.17500000000000002 No Hit GGAAGAGCCCGAGCTGCTGCAGCAGGTTTTGAAAAGGGAATCGATCGTGA 7 0.17500000000000002 No Hit GGGAAAAGAGGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTT 6 0.15 No Hit GGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAAGGCGATCAAATTC 6 0.15 No Hit GGAGGGTGAGAGCCCCGTCCGGCCCGGACCCTGTCGCCCCACGAGGCGCC 6 0.15 No Hit GGACATTTCTTCGAAAAAATTCGAATAGTGAGACGCATTAAAACGCAATT 6 0.15 No Hit GGATACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATG 6 0.15 No Hit GGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAACCCTCTTAACTA 6 0.15 No Hit GTATTTAGCCTTGCAAGGTGGTCCTTGCTGATTCACACGGGATTCCACGT 6 0.15 No Hit GAAGTAATGCACGAACGTAATGCTCACAACTTCCCTCTAGATCTAGCTGC 6 0.15 No Hit GGAATAAGAATAAATCGCAACTCCTTTCCACTACACATAAAAATTGATTT 6 0.15 No Hit GTACAAGCTCGTAACGAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAAT 6 0.15 No Hit GGCATATGCCAGCTCTGACCGAAATCTTTGGGGATGATTCTGTATTACAA 6 0.15 No Hit GGGTGAGAGCCCCGTCCGGCCCGGACCCTGTCGCCCCACGAGGCGCCGTC 6 0.15 No Hit GGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAA 5 0.125 No Hit GGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGGAAGGGCGTA 5 0.125 No Hit GTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGCA 5 0.125 No Hit GGCTGCTTGGCCTGTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTA 5 0.125 No Hit GTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAGCATAGATCCGG 5 0.125 No Hit GGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAAA 5 0.125 No Hit GGATATCGTGTGTGTACATTTGAATGTACCGACATGGGCTCGAGGAGCAT 5 0.125 No Hit GGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTCCT 5 0.125 No Hit GGATTTGAAGAAAAAAAAGACTTCGATTCATTTTCTATTTATTTCGTTAG 5 0.125 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTTTTAA 5 0.125 No Hit GGGGTACTCTTTCTACACCTATATTAGTATTAGTACCGAAATGCTTTAAA 5 0.125 No Hit GGGACAGTCGGGGGCATTCGTATTTCATAGTCAGAGGTGAAATTCTTGGA 5 0.125 No Hit GGGGCATTCGTATTTCATAGTCAGAGGTGAAATTCTTGGATTTATGAAAG 5 0.125 No Hit AATCTCCGGATCTATGCTTATTTTCAACTCCCCGAAGCATTTCGTCGCTT 5 0.125 No Hit CCATGAACCGATCCAAGGCTAGCTGCACAAGCTAGGCCCTTATTTCCCTT 5 0.125 No Hit CAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTG 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 0.0125 0.0 0.0 0.0 0.0 20-21 0.025 0.0 0.0 0.0 0.0 22-23 0.025 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 0.037500000000000006 0.0 0.0 0.0 0.0 46-47 0.05 0.0 0.0 0.0 0.0 48-49 0.05 0.0 0.0 0.0 0.0 50-51 0.05 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 0.05 0.0 0.0 0.0 0.0 74-75 0.05 0.0 0.0 0.0 0.0 76-77 0.075 0.0 0.0 0.0 0.0 78-79 0.075 0.0 0.0 0.0 0.0 80-81 0.075 0.0 0.0 0.025 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GCAATAC 15 9.018277E-4 86.24999 7 CAATACA 15 9.018277E-4 86.24999 8 GAGCAAT 15 9.018277E-4 86.24999 5 AGAGCAA 15 9.018277E-4 86.24999 4 AGCAATA 15 9.018277E-4 86.24999 6 GGAGAGC 20 0.002825237 64.6875 2 AATACAA 20 0.002825237 64.6875 9 GGGAGAG 25 0.0068371096 51.75 1 GAGAGCA 25 0.0068371096 51.75 3 AGTAGCC 20 7.1969756E-4 44.230774 70-71 >>END_MODULE Rejected 276040 READS because READLEN < 1 Read 276040 spots for ERR6133308.sra Written 276040 spots for ERR6133308.sra Rejected 276040 READS because READLEN < 1 Read 276040 spots for ERR6133308.sra Written 276040 spots for ERR6133308.sra Rejected 276040 READS because READLEN < 1 Read 276040 spots for ERR6133308.sra Written 276040 spots for ERR6133308.sra Rejected 276040 READS because READLEN < 1 Read 276040 spots for ERR6133308.sra Written 276040 spots for ERR6133308.sra Rejected 276040 READS because READLEN < 1 Read 276040 spots for ERR6133308.sra Written 276040 spots for ERR6133308.sra Rejected 276040 READS because READLEN < 1 Read 276040 spots for ERR6133308.sra Written 276040 spots for ERR6133308.sra Rejected 276040 READS because READLEN < 1 Read 276040 spots for ERR6133308.sra Written 276040 spots for ERR6133308.sra Rejected 276040 READS because READLEN < 1 Read 276040 spots for ERR6133308.sra Written 276040 spots for ERR6133308.sra Rejected 276040 READS because READLEN < 1 Read 276040 spots for ERR6133308.sra Written 276040 spots for ERR6133308.sra Rejected 276040 READS because READLEN < 1 Read 276040 spots for ERR6133308.sra Written 276040 spots for ERR6133308.sra Rejected 276040 READS because READLEN < 1 Read 276040 spots for ERR6133308.sra Written 276040 spots for ERR6133308.sra Rejected 276040 READS because READLEN < 1 Read 276040 spots for ERR6133308.sra Written 276040 spots for ERR6133308.sra Rejected 276040 READS because READLEN < 1 Read 276040 spots for ERR6133308.sra Written 276040 spots for ERR6133308.sra Rejected 276040 READS because READLEN < 1 Read 276040 spots for ERR6133308.sra Written 276040 spots for ERR6133308.sra Rejected 276040 READS because READLEN < 1 Read 276040 spots for ERR6133308.sra Written 276040 spots for ERR6133308.sra Rejected 276054 READS because READLEN < 1 Read 276054 spots for ERR6133308.sra Written 276054 spots for ERR6133308.sra Rejected 276040 READS because READLEN < 1 Read 276040 spots for ERR6133308.sra Written 276040 spots for ERR6133308.sra Rejected 276040 READS because READLEN < 1 Read 276040 spots for ERR6133308.sra Written 276040 spots for ERR6133308.sra Rejected 276040 READS because READLEN < 1 Read 276040 spots for ERR6133308.sra Written 276040 spots for ERR6133308.sra Rejected 276040 READS because READLEN < 1 Read 276040 spots for ERR6133308.sra Written 276040 spots for ERR6133308.sra SRR ids: ['ERR6133308.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_4ywej5u_ ERR6133308.sra spots: 5520814 blocks: [[1, 276040], [276041, 552080], [552081, 828120], [828121, 1104160], [1104161, 1380200], [1380201, 1656240], [1656241, 1932280], [1932281, 2208320], [2208321, 2484360], [2484361, 2760400], [2760401, 3036440], [3036441, 3312480], [3312481, 3588520], [3588521, 3864560], [3864561, 4140600], [4140601, 4416640], [4416641, 4692680], [4692681, 4968720], [4968721, 5244760], [5244761, 5520814]] ERR6133308 file size 1219188 ERR6133308 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 ERR6133308 ERR6133308_1.fastq Input file: ERR6133308_1.fastq trimmed: ERR6133308-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 00:21:49 2024 >> started Sat Dec 7 00:21:57 2024 >> done (7.927s) 5520814 reads processed; of these: 329 ( 0.01%) short reads filtered out after trimming by size control 36 ( 0.00%) empty reads filtered out after trimming by size control 5520449 (99.99%) reads available; of these: 80459 ( 1.46%) trimmed reads available after processing 5439990 (98.54%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 62 0.00% 19 109 0.00% 20 82 0.00% 21 99 0.00% 22 129 0.00% 23 14 0.00% 24 38 0.00% 25 14 0.00% 26 23 0.00% 27 37 0.00% 28 76 0.00% 29 80 0.00% 30 64 0.00% 31 83 0.00% 32 55 0.00% 33 38 0.00% 34 35 0.00% 35 252 0.00% 36 600 0.01% 37 89 0.00% 38 98 0.00% 39 419 0.01% 40 167 0.00% 41 132 0.00% 42 27 0.00% 43 24 0.00% 44 22 0.00% 45 13 0.00% 46 17 0.00% 47 16 0.00% 48 17 0.00% 49 28 0.00% 50 29 0.00% 51 59 0.00% 52 21 0.00% 53 14 0.00% 54 11 0.00% 55 20 0.00% 56 19 0.00% 57 22 0.00% 58 40 0.00% 59 16 0.00% 60 26 0.00% 61 28 0.00% 62 2 0.00% 63 5 0.00% 64 5 0.00% 65 6 0.00% 66 10 0.00% 67 11 0.00% 68 43 0.00% 69 151 0.00% 70 17661 0.32% 71 15259 0.28% 72 17558 0.32% 73 14394 0.26% 74 15400 0.28% 75 15765 0.29% 76 13524 0.24% 77 13753 0.25% 78 16051 0.29% 79 17453 0.32% 80 16930 0.31% 81 20603 0.37% 82 23982 0.43% 83 21456 0.39% 84 20200 0.37% 85 240 0.00% 86 491 0.01% 87 668 0.01% 88 1284 0.02% 89 2309 0.04% 90 4668 0.08% 91 14194 0.26% 92 50528 0.92% 93 5182581 93.88% 5520449 reads passed initial QC criterion=sequence-density sequence-density=0.65 sequence-density-rank=1 fanout-score=2.30 fanout-score-rank=29 prefix-density=0.73 prefix-fanout=2.0 sequence=TGTACATTTGAACCCTGACTACACATATACACACATATACATGTAATATTATACAATCTGTCGAGTATGTGTTGGTTCATACT criterion=fanout-score sequence-density=0.01 sequence-density-rank=36 fanout-score=84.13 fanout-score-rank=1 prefix-density=0.09 prefix-fanout=6.4 sequence=AAAAGAAGGGGTGTTCCATCTCCGGACGACGATCCTGCCTGCGGAGGAAGACATGCCGGCGATCATGTCGAGCTTCAAGAAGTTCAACGACTCATTCATGGAGCAATACCAAGACTACTCCAGGCTGTGATGTGAAGAGGGAAACAACGACGTCATCATCGACATGATATATTGCTGCTATTTTCCACCAGCGATTAAAAGTTAAAAAATTTAGCTGTAAGCTGTAACTATCTTGAAGAAACTAAACTGGTTGCTGTGCTTGATATGTATAGGGAAAACATAATTTATGAGACAATCATACTGTGCAACTCTTGGCTCCATCGATTAATTAATACTCCTTGTTATTGCTTGCATGGTGG Started job on | Dec 07 00:22:33 Started mapping on | Dec 07 00:22:37 Finished on | Dec 07 00:22:44 Mapping speed, Million of reads per hour | 2839.09 Number of input reads | 5520449 Average input read length | 92 UNIQUE READS: Uniquely mapped reads number | 3111503 Uniquely mapped reads % | 56.36% Average mapped length | 91.67 Number of splices: Total | 109572 Number of splices: Annotated (sjdb) | 88809 Number of splices: GT/AG | 104682 Number of splices: GC/AG | 2745 Number of splices: AT/AC | 106 Number of splices: Non-canonical | 2039 Mismatch rate per base, % | 0.39% Deletion rate per base | 0.04% Deletion average length | 1.73 Insertion rate per base | 0.02% Insertion average length | 1.89 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 2182446 % of reads mapped to multiple loci | 39.53% Number of reads mapped to too many loci | 145420 % of reads mapped to too many loci | 2.63% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.30% % of reads unmapped: other | 0.17% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 226500 226500 226500 N_multimapping 2182446 2182446 2182446 N_noFeature 293566 324917 2973363 N_ambiguous 122573 15473 718 UnstrandedReadsAssigned:2695364 PositiveStrandReadsAssigned:2771113 NegativeStrandReadsAssigned:137422 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=93 echo kmer=89 ERR6133308 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: ERR6133308-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 5,520,449 reads, 4,288,431 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 994 rounds 52973 ERR6133308.ke.tsv 35125 ERR6133308.se.tsv 88098 total ==> ERR6133308.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 70 15.7226 PNS24243 293 194 0 0 KQK14069 1603 1504 31 6.35178 KQK14071 474 375 0 0 ==> ERR6133308.se.tsv <== BRADI_1g14170v3 31 BRADI_1g53295v3 10 BRADI_1g59795v3 28 BRADI_1g07683v3 0 BRADI_1g00485v3 1 BRADI_1g20270v3 43 BRADI_1g74790v3 28 BRADI_1g09890v3 0 BRADI_1g77505v3 79 BRADI_1g48960v3 0 ERR6133308 completed mapping pipeline successfully