Starting /dee2/code/volunteer_pipeline.sh ERR6133401 current disk space = 1547691462656 free memory = 1601606168 ERR6133401 SRAfilesize b7c936fe3e5457c02f1734f399ccc56b ERR6133401.sra ERR6133401.sra file validated ERR6133401 is single end ERR6133401 is conventional basespace ERR6133401 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133401_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 fail #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 28.55325 33.0 27.0 33.0 15.0 37.0 2 33.1945 33.0 33.0 37.0 27.0 37.0 3 33.722 37.0 33.0 37.0 27.0 37.0 4 34.072 37.0 33.0 37.0 27.0 37.0 5 34.1855 37.0 33.0 37.0 27.0 37.0 6 34.68 37.0 33.0 37.0 33.0 37.0 7 35.33525 37.0 33.0 40.0 27.0 40.0 8 35.5445 37.0 33.0 40.0 33.0 40.0 9 35.746 37.0 33.0 40.0 33.0 40.0 10-11 35.623000000000005 37.0 33.0 40.0 33.0 40.0 12-13 35.291375 37.0 33.0 40.0 27.0 40.0 14-15 35.192125000000004 37.0 33.0 40.0 27.0 40.0 16-17 35.155 37.0 33.0 40.0 27.0 40.0 18-19 35.011750000000006 37.0 33.0 37.0 27.0 40.0 20-21 34.363625 37.0 33.0 37.0 27.0 40.0 22-23 34.107625 37.0 33.0 37.0 27.0 40.0 24-25 33.573499999999996 37.0 33.0 37.0 24.5 40.0 26-27 33.0955 37.0 33.0 37.0 22.0 40.0 28-29 32.878125 37.0 33.0 37.0 22.0 40.0 30-31 32.62675 37.0 33.0 37.0 22.0 40.0 32-33 32.3375 35.0 33.0 37.0 22.0 40.0 34-35 31.485375 33.0 27.0 37.0 18.5 40.0 36-37 31.18625 33.0 27.0 37.0 15.0 40.0 38-39 30.994875 33.0 27.0 37.0 15.0 40.0 40-41 31.588625 33.0 27.0 37.0 22.0 40.0 42-43 31.193624999999997 33.0 27.0 37.0 15.0 40.0 44-45 31.054125 33.0 27.0 37.0 15.0 40.0 46-47 30.329625 33.0 27.0 37.0 15.0 37.0 48-49 29.888875 33.0 27.0 37.0 15.0 37.0 50-51 29.67375 33.0 27.0 37.0 15.0 37.0 52-53 29.605249999999998 33.0 27.0 37.0 15.0 37.0 54-55 29.19525 33.0 27.0 37.0 15.0 37.0 56-57 28.3765 33.0 27.0 35.0 15.0 37.0 58-59 28.335500000000003 33.0 27.0 33.0 15.0 37.0 60-61 27.82575 33.0 22.0 33.0 15.0 37.0 62-63 27.434625 33.0 22.0 33.0 15.0 37.0 64-65 27.11125 33.0 22.0 33.0 15.0 37.0 66-67 26.770875 30.0 22.0 33.0 6.0 37.0 68-69 26.28325 27.0 22.0 33.0 10.5 35.0 70-71 27.92232556675063 33.0 27.0 33.0 15.0 37.0 72-73 28.63724793111449 33.0 27.0 33.0 15.0 37.0 74-75 28.418541121425235 33.0 27.0 33.0 15.0 37.0 76-77 27.882975910398216 33.0 27.0 33.0 15.0 37.0 78-79 27.52252905048544 33.0 27.0 33.0 10.5 37.0 80-81 26.928891263676835 33.0 24.5 33.0 6.0 37.0 82-83 26.16251857344043 33.0 22.0 33.0 2.0 37.0 84-85 25.617664901463282 33.0 22.0 33.0 2.0 37.0 86-87 24.492827004219407 33.0 15.0 33.0 2.0 37.0 88-89 23.469198312236287 30.0 10.5 33.0 2.0 37.0 90-91 22.329395218002812 27.0 2.0 33.0 2.0 37.0 92-93 20.8971870604782 27.0 2.0 33.0 2.0 33.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 90.0 21 107.0 22 123.0 23 155.0 24 181.0 25 230.0 26 236.0 27 225.0 28 235.0 29 288.0 30 242.0 31 263.0 32 252.0 33 302.0 34 262.0 35 309.0 36 282.0 37 177.0 38 41.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 66.75 8.725 7.825 16.7 2 48.175000000000004 26.275 15.775 9.775 3 28.799999999999997 38.35 17.575 15.275 4 29.299999999999997 26.224999999999998 23.45 21.025 5 23.549999999999997 26.6 28.475 21.375 6 19.8 34.599999999999994 27.55 18.05 7 32.025 28.000000000000004 22.925 17.05 8 25.124999999999996 28.999999999999996 28.325 17.549999999999997 9 23.125 26.625 29.549999999999997 20.7 10-11 23.45 27.8625 28.65 20.0375 12-13 22.662499999999998 29.5375 29.3375 18.462500000000002 14-15 20.6125 29.5 29.5875 20.3 16-17 23.1625 30.0375 25.15 21.65 18-19 23.025000000000002 25.900000000000002 30.5125 20.5625 20-21 24.85 25.2125 27.800000000000004 22.1375 22-23 27.1375 23.9 27.712500000000002 21.25 24-25 24.7375 26.525 28.462500000000002 20.275000000000002 26-27 23.5625 25.1 29.375 21.9625 28-29 24.0625 28.4375 27.425 20.075000000000003 30-31 25.174999999999997 27.0875 27.725 20.0125 32-33 24.2625 25.224999999999998 29.1875 21.325 34-35 23.025000000000002 29.8875 26.6625 20.424999999999997 36-37 24.375 27.275 25.4875 22.8625 38-39 25.687500000000004 25.637500000000003 27.650000000000002 21.025 40-41 25.0625 26.6 27.425 20.9125 42-43 26.174999999999997 27.800000000000004 26.85 19.175 44-45 21.587500000000002 29.125 28.725 20.5625 46-47 23.9375 27.875 27.025 21.1625 48-49 23.3375 27.025 29.1875 20.45 50-51 20.7375 29.362500000000004 28.449999999999996 21.45 52-53 24.025 27.987499999999997 27.400000000000002 20.5875 54-55 23.2625 28.95 28.849999999999998 18.9375 56-57 24.525 28.1125 27.224999999999998 20.1375 58-59 24.0375 28.325 26.5375 21.099999999999998 60-61 24.575 27.762500000000003 27.737499999999997 19.925 62-63 22.662499999999998 28.849999999999998 29.4375 19.05 64-65 22.650000000000002 31.275 27.750000000000004 18.325 66-67 23.2625 28.762500000000003 27.187499999999996 20.7875 68-69 20.925 29.5875 27.4125 22.075 70-71 24.341279799247175 28.732747804265994 26.612296110414054 20.313676286072774 72-73 23.305407463823304 28.293983244478294 29.220614369129223 19.17999492256918 74-75 24.652061855670105 28.20876288659794 27.538659793814436 19.600515463917525 76-77 23.58994398853719 27.35443532629934 27.601927836394424 21.45369284876905 78-79 22.843176113092877 28.92059717267803 27.929713304267406 20.306513409961685 80-81 22.17898832684825 31.946867033409365 26.365222058231584 19.508922581510802 82-83 22.02649187491465 29.45514133551823 27.420456097227913 21.097910692339205 84-85 21.781625244345154 27.199106394861772 29.516894722144656 21.50237363864842 86-87 22.180028129395218 30.492264416315052 25.49929676511955 21.828410689170184 88-89 20.829817158931082 30.857946554149084 27.17299578059072 21.139240506329113 90-91 24.0084388185654 30.604781997187057 25.42897327707454 19.957805907172997 92-93 21.434599156118146 33.9521800281294 25.766526019690577 18.846694796061886 >>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 1.0 17 1.5 18 3.0 19 3.0 20 2.0 21 1.5 22 4.0 23 6.0 24 8.5 25 11.5 26 13.0 27 22.5 28 28.5 29 28.0 30 37.0 31 54.5 32 64.0 33 70.5 34 80.0 35 100.0 36 121.5 37 150.5 38 188.0 39 199.5 40 232.0 41 253.5 42 265.0 43 285.5 44 246.5 45 212.0 46 197.5 47 157.0 48 124.5 49 125.0 50 129.0 51 122.0 52 114.5 53 126.5 54 137.0 55 108.5 56 90.5 57 97.0 58 78.5 59 45.5 60 24.5 61 15.0 62 12.0 63 6.5 64 7.0 65 13.0 66 12.0 67 8.5 68 13.0 69 23.5 70 20.0 71 11.0 72 8.0 73 2.5 74 1.0 75 1.0 76 0.0 77 0.0 78 0.5 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 0.0 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 30.0 71 20.0 72 22.0 73 31.0 74 34.0 75 15.0 76 19.0 77 33.0 78 23.0 79 33.0 80 27.0 81 33.0 82 37.0 83 36.0 84 52.0 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 3555.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 76.3 #Duplication Level Percentage of deduplicated Percentage of total 1 92.00524246395806 70.19999999999999 2 3.800786369593709 5.800000000000001 3 1.0812581913499346 2.475 4 0.8519003931847969 2.6 5 0.42595019659239847 1.625 6 0.49148099606815204 2.25 7 0.1310615989515072 0.7000000000000001 8 0.2621231979030144 1.6 9 0.163826998689384 1.125 >10 0.7863695937090431 11.625 >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 fail #Sequence Count Percentage Possible Source GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 42 1.05 No Hit GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGC 41 1.0250000000000001 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 38 0.95 No Hit GGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGC 30 0.75 No Hit CAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCT 27 0.675 No Hit CAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTG 26 0.65 No Hit CAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATAT 22 0.5499999999999999 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 20 0.5 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 19 0.475 No Hit GGGTGAGAGCCCCGTCCGGCCCGGACCCTGTCGCCCCACGAGGCGCCGTC 19 0.475 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 18 0.44999999999999996 No Hit GGGGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCT 18 0.44999999999999996 No Hit GGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTT 14 0.35000000000000003 No Hit GGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTCCT 14 0.35000000000000003 No Hit GGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGC 14 0.35000000000000003 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 13 0.325 No Hit GTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTC 13 0.325 No Hit GGGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTA 13 0.325 No Hit GGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAA 12 0.3 No Hit GGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAAGGCGATCAAATTC 11 0.27499999999999997 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 11 0.27499999999999997 No Hit GGAGGGTGAGAGCCCCGTCCGGCCCGGACCCTGTCGCCCCACGAGGCGCC 10 0.25 No Hit GGATTTGTTAAATCAAATCCTTGGTTTAATAACGAACGGTGTTAACTTAC 10 0.25 No Hit TCAAAAGAGGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGGA 10 0.25 No Hit GGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGCTAAATACAG 9 0.22499999999999998 No Hit GATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAAT 9 0.22499999999999998 No Hit GGGAGGGTGAGAGCCCCGTCCGGCCCGGACCCTGTCGCCCCACGAGGCGC 9 0.22499999999999998 No Hit GTCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAAT 9 0.22499999999999998 No Hit GAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGC 9 0.22499999999999998 No Hit GGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAAATGGATTC 8 0.2 No Hit GGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGGG 8 0.2 No Hit GCCGCAGCTTGTGAAGTATGGAAGGCGATCAAATTCGAGTTCGCGCCGGT 8 0.2 No Hit GTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAA 8 0.2 No Hit GGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAAA 8 0.2 No Hit GTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAA 8 0.2 No Hit CACGAACGTAATGCTCACAACTTCCCTCTAGATCTAGCTGCTCTTGAAGT 8 0.2 No Hit AACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGA 8 0.2 No Hit CAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTT 7 0.17500000000000002 No Hit GTATGGAAGGCGATCAAATTCGAGTTCGCGCCGGTAGATACTATCGATTA 7 0.17500000000000002 No Hit GTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGGT 7 0.17500000000000002 No Hit GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 7 0.17500000000000002 No Hit GCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGGTATG 6 0.15 No Hit CGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGGTAT 6 0.15 No Hit GAGGAAGGGCGTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAGC 6 0.15 No Hit GGGGCAGAGGGAATTTCCGGTGGAGCGGTGAAATGCATTGAGATCGGAAA 6 0.15 No Hit GCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCT 6 0.15 No Hit GGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAAA 6 0.15 No Hit CTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGT 6 0.15 No Hit GATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAACGTAA 6 0.15 No Hit GAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTG 6 0.15 No Hit GTATTAGTACTATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATCT 6 0.15 No Hit GGCCCGGACCCTGTCGCCCCACGAGGCGCCGTCAACGAGTCGGGTTGTTT 6 0.15 No Hit GAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTCCTG 6 0.15 No Hit GGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAA 6 0.15 No Hit GTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAG 6 0.15 No Hit CGCTCTGACCCGAGTAGCATGGGGCACGTGGAATCCCGTGTGAATCAGCA 6 0.15 No Hit GGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAAC 5 0.125 No Hit GCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATC 5 0.125 No Hit CAAGCTCGTAACGAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAATTAT 5 0.125 No Hit TCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATC 5 0.125 No Hit AACGTAATGCTCACAACTTCCCTCTAGATCTAGCTGCTCTTGAAGTTCCC 5 0.125 No Hit GGGAATTTCCGGTGGAGCGGTGAAATGCATTGAGATCGGAAAGAACACCA 5 0.125 No Hit CAACGAGTCGGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCC 5 0.125 No Hit GTACAAGCTCGTAACGAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAAT 5 0.125 No Hit GTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGCTA 5 0.125 No Hit TATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAG 5 0.125 No Hit GAGTCGGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCC 5 0.125 No Hit GAACGTAATGCTCACAACTTCCCTCTAGATCTAGCTGCTCTTGAAGTTCC 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 0.0125 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 0.025 0.0 0.0 0.0 0.0 54-55 0.025 0.0 0.0 0.0 0.0 56-57 0.025 0.0 0.0 0.0 0.0 58-59 0.025 0.0 0.0 0.0 0.0 60-61 0.025 0.0 0.0 0.0 0.0 62-63 0.025 0.0 0.0 0.0 0.0 64-65 0.025 0.0 0.0 0.0 0.0 66-67 0.025 0.0 0.0 0.0 0.0 68-69 0.025 0.0 0.0 0.0 0.0 70-71 0.025 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 AAAAAAA 45 2.9038152E-5 30.232454 86-87 CCAAGGC 30 0.006003216 28.72083 44-45 >>END_MODULE Rejected 36305 READS because READLEN < 1 Read 36305 spots for ERR6133401.sra Written 36305 spots for ERR6133401.sra Rejected 36305 READS because READLEN < 1 Read 36305 spots for ERR6133401.sra Written 36305 spots for ERR6133401.sra Rejected 36305 READS because READLEN < 1 Read 36305 spots for ERR6133401.sra Written 36305 spots for ERR6133401.sra Rejected 36305 READS because READLEN < 1 Read 36305 spots for ERR6133401.sra Written 36305 spots for ERR6133401.sra Rejected 36305 READS because READLEN < 1 Read 36305 spots for ERR6133401.sra Written 36305 spots for ERR6133401.sra Rejected 36305 READS because READLEN < 1 Read 36305 spots for ERR6133401.sra Written 36305 spots for ERR6133401.sra Rejected 36305 READS because READLEN < 1 Read 36305 spots for ERR6133401.sra Written 36305 spots for ERR6133401.sra Rejected 36305 READS because READLEN < 1 Read 36305 spots for ERR6133401.sra Rejected 36305 READS because READLEN < 1 Written 36305 spots for ERR6133401.sra Read 36305 spots for ERR6133401.sra Written 36305 spots for ERR6133401.sra Rejected 36311 READS because READLEN < 1 Read 36311 spots for ERR6133401.sra Written 36311 spots for ERR6133401.sra Rejected 36305 READS because READLEN < 1 Read 36305 spots for ERR6133401.sra Written 36305 spots for ERR6133401.sra Rejected 36305 READS because READLEN < 1 Read 36305 spots for ERR6133401.sra Written 36305 spots for ERR6133401.sra Rejected 36305 READS because READLEN < 1 Read 36305 spots for ERR6133401.sra Written 36305 spots for ERR6133401.sra Rejected 36305 READS because READLEN < 1 Read 36305 spots for ERR6133401.sra Written 36305 spots for ERR6133401.sra Rejected 36305 READS because READLEN < 1 Read 36305 spots for ERR6133401.sra Written 36305 spots for ERR6133401.sra Rejected 36305 READS because READLEN < 1 Read 36305 spots for ERR6133401.sra Written 36305 spots for ERR6133401.sra Rejected 36305 READS because READLEN < 1 Read 36305 spots for ERR6133401.sra Written 36305 spots for ERR6133401.sra Rejected 36305 READS because READLEN < 1 Read 36305 spots for ERR6133401.sra Written 36305 spots for ERR6133401.sra Rejected 36305 READS because READLEN < 1 Read 36305 spots for ERR6133401.sra Written 36305 spots for ERR6133401.sra Rejected 36305 READS because READLEN < 1 Read 36305 spots for ERR6133401.sra Written 36305 spots for ERR6133401.sra SRR ids: ['ERR6133401.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_9i2akcn7 ERR6133401.sra spots: 726106 blocks: [[1, 36305], [36306, 72610], [72611, 108915], [108916, 145220], [145221, 181525], [181526, 217830], [217831, 254135], [254136, 290440], [290441, 326745], [326746, 363050], [363051, 399355], [399356, 435660], [435661, 471965], [471966, 508270], [508271, 544575], [544576, 580880], [580881, 617185], [617186, 653490], [653491, 689795], [689796, 726106]] ERR6133401 file size 157664 ERR6133401 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 ERR6133401 ERR6133401_1.fastq Input file: ERR6133401_1.fastq trimmed: ERR6133401-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 03:10:11 2024 >> started Sat Dec 7 03:10:12 2024 >> done (1.598s) 726106 reads processed; of these: 20 ( 0.00%) short reads filtered out after trimming by size control 3 ( 0.00%) empty reads filtered out after trimming by size control 726083 (100.00%) reads available; of these: 182838 (25.18%) trimmed reads available after processing 543245 (74.82%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 4 0.00% 19 9 0.00% 20 3 0.00% 21 5 0.00% 22 3 0.00% 23 0 0.00% 24 3 0.00% 25 0 0.00% 26 2 0.00% 27 1 0.00% 28 10 0.00% 29 11 0.00% 30 2 0.00% 31 2 0.00% 32 4 0.00% 33 0 0.00% 34 2 0.00% 35 1 0.00% 36 4 0.00% 37 5 0.00% 38 10 0.00% 39 10 0.00% 40 18 0.00% 41 9 0.00% 42 14 0.00% 43 16 0.00% 44 16 0.00% 45 22 0.00% 46 37 0.01% 47 58 0.01% 48 63 0.01% 49 80 0.01% 50 99 0.01% 51 148 0.02% 52 173 0.02% 53 220 0.03% 54 330 0.05% 55 410 0.06% 56 562 0.08% 57 854 0.12% 58 542 0.07% 59 709 0.10% 60 878 0.12% 61 994 0.14% 62 1097 0.15% 63 1059 0.15% 64 1257 0.17% 65 1286 0.18% 66 1332 0.18% 67 1314 0.18% 68 1311 0.18% 69 1408 0.19% 70 6066 0.84% 71 5995 0.83% 72 7011 0.97% 73 7318 1.01% 74 7299 1.01% 75 7789 1.07% 76 7814 1.08% 77 8503 1.17% 78 9300 1.28% 79 9843 1.36% 80 10262 1.41% 81 12256 1.69% 82 12997 1.79% 83 13014 1.79% 84 14464 1.99% 85 9065 1.25% 86 9822 1.35% 87 10514 1.45% 88 11877 1.64% 89 13106 1.81% 90 14178 1.95% 91 15327 2.11% 92 12994 1.79% 93 472862 65.13% 726083 reads passed initial QC criterion=sequence-density sequence-density=5.20 sequence-density-rank=1 fanout-score=2.07 fanout-score-rank=24 prefix-density=5.32 prefix-fanout=2.0 sequence=CAAGGCTAAATAC criterion=fanout-score sequence-density=0.05 sequence-density-rank=17 fanout-score=15.05 fanout-score-rank=1 prefix-density=0.27 prefix-fanout=3.0 sequence=TTTTTTCTATTTATTTTTCCATCTAGGATTAGAACTGTATATTTGTGAATAATAGTAACAGGACATTATGGCAAAAAAAAGTTTGATTCAGAGGGAAAAGAAGCGGCAGAAATTAGAACAAAAATATCATTTGATTCGCCAATCTT 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 03:10:28 Started mapping on | Dec 07 03:10:29 Finished on | Dec 07 03:10:36 Mapping speed, Million of reads per hour | 373.41 Number of input reads | 726083 Average input read length | 88 UNIQUE READS: Uniquely mapped reads number | 295675 Uniquely mapped reads % | 40.72% Average mapped length | 87.91 Number of splices: Total | 9031 Number of splices: Annotated (sjdb) | 7100 Number of splices: GT/AG | 8557 Number of splices: GC/AG | 177 Number of splices: AT/AC | 12 Number of splices: Non-canonical | 285 Mismatch rate per base, % | 0.91% Deletion rate per base | 0.04% Deletion average length | 1.80 Insertion rate per base | 0.02% Insertion average length | 1.73 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 340186 % of reads mapped to multiple loci | 46.85% Number of reads mapped to too many loci | 43728 % of reads mapped to too many loci | 6.02% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 5.41% % of reads unmapped: other | 0.99% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 90222 90222 90222 N_multimapping 340186 340186 340186 N_noFeature 28491 31917 282390 N_ambiguous 12338 2469 81 UnstrandedReadsAssigned:254846 PositiveStrandReadsAssigned:261289 NegativeStrandReadsAssigned:13204 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=84 echo kmer=79 ERR6133401 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: ERR6133401-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 726,083 reads, 472,396 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 778 rounds 52973 ERR6133401.ke.tsv 35125 ERR6133401.se.tsv 88098 total ==> ERR6133401.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 2 4.11747 PNS24243 293 194 0 0 KQK14069 1603 1504 13 24.4146 KQK14071 474 375 0 0 ==> ERR6133401.se.tsv <== BRADI_1g14170v3 13 BRADI_1g53295v3 2 BRADI_1g59795v3 7 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 2 BRADI_1g74790v3 3 BRADI_1g09890v3 0 BRADI_1g77505v3 2 BRADI_1g48960v3 0 ERR6133401 completed mapping pipeline successfully