Starting /dee2/code/volunteer_pipeline.sh ERR6133336 current disk space = 1548160245760 free memory = 1598265008 ERR6133336 SRAfilesize 19add97d5b5448df881908741ea0eaa1 ERR6133336.sra ERR6133336.sra file validated ERR6133336 is single end ERR6133336 is conventional basespace ERR6133336 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133336_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 36.26375 37.0 37.0 37.0 33.0 37.0 2 36.349 37.0 37.0 37.0 37.0 37.0 3 36.31075 37.0 37.0 37.0 37.0 37.0 4 36.42425 37.0 37.0 37.0 37.0 37.0 5 36.5445 37.0 37.0 37.0 37.0 37.0 6 36.56025 37.0 37.0 37.0 37.0 37.0 7 38.72975 40.0 37.0 40.0 37.0 40.0 8 38.80225 40.0 37.0 40.0 37.0 40.0 9 38.8115 40.0 37.0 40.0 37.0 40.0 10-11 38.87287499999999 40.0 37.0 40.0 37.0 40.0 12-13 38.873000000000005 40.0 37.0 40.0 37.0 40.0 14-15 38.800875000000005 40.0 37.0 40.0 37.0 40.0 16-17 38.776375 40.0 37.0 40.0 37.0 40.0 18-19 38.855999999999995 40.0 37.0 40.0 37.0 40.0 20-21 38.667 40.0 37.0 40.0 37.0 40.0 22-23 38.707375 40.0 37.0 40.0 37.0 40.0 24-25 38.632875 40.0 37.0 40.0 37.0 40.0 26-27 38.53475 40.0 37.0 40.0 37.0 40.0 28-29 38.567875 40.0 37.0 40.0 37.0 40.0 30-31 38.503625 40.0 37.0 40.0 37.0 40.0 32-33 38.48625 40.0 37.0 40.0 37.0 40.0 34-35 38.427125000000004 40.0 37.0 40.0 37.0 40.0 36-37 38.32225 40.0 37.0 40.0 37.0 40.0 38-39 38.15412499999999 40.0 37.0 40.0 37.0 40.0 40-41 38.049499999999995 40.0 37.0 40.0 37.0 40.0 42-43 37.925250000000005 40.0 37.0 40.0 37.0 40.0 44-45 37.704750000000004 37.0 37.0 40.0 33.0 40.0 46-47 37.5355 37.0 37.0 40.0 33.0 40.0 48-49 37.344625 37.0 37.0 40.0 33.0 40.0 50-51 37.113375000000005 37.0 37.0 40.0 33.0 40.0 52-53 36.912 37.0 37.0 40.0 33.0 40.0 54-55 36.725125000000006 37.0 37.0 37.0 33.0 40.0 56-57 36.504999999999995 37.0 37.0 37.0 33.0 40.0 58-59 36.16225 37.0 37.0 37.0 33.0 40.0 60-61 36.07525 37.0 37.0 37.0 33.0 38.5 62-63 35.677625 37.0 33.0 37.0 33.0 37.0 64-65 35.301 37.0 33.0 37.0 33.0 37.0 66-67 35.094625 37.0 33.0 37.0 33.0 37.0 68-69 33.679 35.0 33.0 37.0 30.0 37.0 70-71 33.425057728410515 33.0 33.0 37.0 30.0 37.0 72-73 33.91854327114362 33.0 33.0 37.0 33.0 37.0 74-75 33.79577486445909 33.0 33.0 37.0 30.0 37.0 76-77 33.64898894750063 33.0 33.0 37.0 27.0 37.0 78-79 32.94819457339626 33.0 33.0 37.0 27.0 37.0 80-81 32.603089001328286 33.0 33.0 37.0 27.0 37.0 82-83 32.70725765473301 33.0 33.0 37.0 27.0 37.0 84-85 32.16417505744019 33.0 33.0 35.0 27.0 37.0 86-87 32.12308673469388 33.0 33.0 33.0 27.0 37.0 88-89 32.18303571428571 33.0 33.0 35.0 27.0 37.0 90-91 31.31377551020408 33.0 30.0 33.0 27.0 37.0 92-93 30.403316326530614 33.0 27.0 33.0 22.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 2.0 21 3.0 22 5.0 23 5.0 24 2.0 25 7.0 26 11.0 27 14.0 28 22.0 29 15.0 30 48.0 31 57.0 32 57.0 33 85.0 34 188.0 35 568.0 36 1189.0 37 1525.0 38 190.0 39 7.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 59.5 12.375 13.875000000000002 14.249999999999998 2 38.475 27.474999999999998 19.6 14.45 3 24.975 35.0 21.325 18.7 4 28.299999999999997 26.900000000000002 21.5 23.3 5 21.675 29.349999999999998 28.7 20.275000000000002 6 18.15 37.525 27.625 16.7 7 34.55 25.324999999999996 22.7 17.424999999999997 8 27.425 31.2 23.724999999999998 17.65 9 25.25 26.025 28.9 19.825 10-11 24.762500000000003 27.5625 27.3125 20.3625 12-13 24.5 29.012500000000003 27.150000000000002 19.3375 14-15 25.674999999999997 26.875 28.787499999999998 18.6625 16-17 24.775 27.987499999999997 27.0125 20.225 18-19 23.150000000000002 25.2 30.625000000000004 21.025 20-21 25.0375 25.95 27.787499999999998 21.224999999999998 22-23 27.8875 24.075 27.55 20.4875 24-25 27.525 25.9875 27.9375 18.55 26-27 24.275 27.250000000000004 30.662499999999998 17.8125 28-29 23.8625 26.075 27.625 22.4375 30-31 24.2 25.087500000000002 28.237499999999997 22.475 32-33 24.6875 28.287499999999998 27.775 19.25 34-35 24.7875 27.037499999999998 26.5375 21.637500000000003 36-37 23.2125 27.925 27.150000000000002 21.712500000000002 38-39 23.0875 23.8625 29.849999999999998 23.200000000000003 40-41 25.162499999999998 28.175 26.3625 20.3 42-43 25.387500000000003 29.225 26.974999999999998 18.4125 44-45 22.875 28.1125 27.150000000000002 21.8625 46-47 26.700000000000003 26.325 27.950000000000003 19.025 48-49 26.35 24.1125 30.175 19.3625 50-51 22.225 28.449999999999996 29.612500000000004 19.7125 52-53 28.299999999999997 26.525 26.900000000000002 18.275 54-55 26.9625 26.2125 27.1625 19.662499999999998 56-57 25.924999999999997 25.837500000000002 29.099999999999998 19.1375 58-59 24.224999999999998 27.0125 28.975 19.787499999999998 60-61 24.3875 28.3625 28.000000000000004 19.25 62-63 22.2125 30.575000000000003 29.325000000000003 17.8875 64-65 22.8875 27.775 29.375 19.9625 66-67 23.1625 30.025000000000002 27.0125 19.8 68-69 24.6125 27.125 27.3625 20.9 70-71 23.20200125078174 28.955597248280174 28.717948717948715 19.12445278298937 72-73 26.53547254951116 26.222110804712962 29.280521433943345 17.96189521183254 74-75 22.131559126286717 26.65076575445644 31.044438865177003 20.17323625407984 76-77 21.368381335681047 24.21079109545969 31.228776254559175 23.192051314300087 78-79 28.618296529968458 24.441640378548897 28.37854889589905 18.561514195583594 80-81 26.588205517590485 27.62591748924323 29.10655530245507 16.679321690711213 82-83 23.14826578579596 27.023249904713502 29.284716046245713 20.54376826324482 84-85 21.781799643130256 24.050471577874074 34.34871271985725 19.819016059138413 86-87 23.112244897959183 27.971938775510203 28.68622448979592 20.229591836734695 88-89 19.387755102040817 32.46173469387755 28.482142857142854 19.668367346938776 90-91 21.721938775510203 27.895408163265305 32.130102040816325 18.252551020408163 92-93 21.607142857142858 30.994897959183675 28.418367346938776 18.979591836734695 >>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 0.0 16 0.0 17 1.5 18 3.0 19 3.0 20 2.0 21 2.5 22 4.5 23 7.5 24 7.5 25 6.0 26 7.5 27 8.5 28 13.0 29 17.5 30 22.0 31 28.5 32 44.0 33 55.0 34 55.5 35 68.5 36 119.5 37 194.0 38 210.5 39 197.5 40 235.5 41 246.5 42 230.0 43 236.5 44 200.5 45 161.5 46 171.5 47 180.0 48 169.0 49 171.0 50 206.0 51 261.0 52 207.0 53 140.5 54 117.5 55 64.5 56 45.0 57 40.0 58 36.5 59 25.0 60 20.0 61 17.5 62 8.5 63 7.0 64 9.5 65 8.0 66 7.0 67 4.0 68 1.5 69 1.0 70 0.0 71 0.0 72 0.0 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 0.012551776076314799 76-77 0.02514774299006664 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 5.0 71 4.0 72 4.0 73 3.0 74 1.0 75 2.0 76 9.0 77 5.0 78 9.0 79 3.0 80 8.0 81 6.0 82 11.0 83 4.0 84 6.0 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 3920.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 73.7 #Duplication Level Percentage of deduplicated Percentage of total 1 91.89280868385346 67.72500000000001 2 3.8670284938941655 5.7 3 1.1533242876526457 2.55 4 0.8141112618724559 2.4 5 0.5427408412483039 2.0 6 0.33921302578018997 1.5 7 0.33921302578018997 1.7500000000000002 8 0.20352781546811397 1.2 9 0.10176390773405698 0.675 >10 0.6784260515603799 8.774999999999999 >50 0.033921302578018994 2.225 >100 0.033921302578018994 3.5000000000000004 >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 TCAAAAGAGGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGGA 140 3.5000000000000004 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 89 2.225 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 38 0.95 No Hit GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 31 0.775 No Hit GTATTAGTACTATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATCT 24 0.6 No Hit GTACTATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTT 22 0.5499999999999999 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 22 0.5499999999999999 No Hit GGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTT 21 0.525 No Hit GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGC 20 0.5 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 17 0.42500000000000004 No Hit AACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGA 16 0.4 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 15 0.375 No Hit CAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTG 15 0.375 No Hit GTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAA 14 0.35000000000000003 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 14 0.35000000000000003 No Hit GTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAG 14 0.35000000000000003 No Hit CAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCT 13 0.325 No Hit CAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATAT 12 0.3 No Hit GGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAA 11 0.27499999999999997 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 11 0.27499999999999997 No Hit GTCAAAAGAGGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGG 11 0.27499999999999997 No Hit TCTCATGGAGAGTTCGATCCTGGCTCAGGATGAACGCTGGCGGCATGCTT 10 0.25 No Hit GGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGT 9 0.22499999999999998 No Hit GAAGCCTGTGTACAAGCTCGTAACGAAGGGCGCGATCTTGCTCGTGAAGG 9 0.22499999999999998 No Hit ATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAG 9 0.22499999999999998 No Hit GGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAAATGGATTC 8 0.2 No Hit GGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGG 8 0.2 No Hit GCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCT 8 0.2 No Hit CTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGT 8 0.2 No Hit GGGAGTATTATGAAAGGAGATTAATCATAGATTATCAAAAACCCTAGAAA 8 0.2 No Hit GTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCT 8 0.2 No Hit GTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGGT 7 0.17500000000000002 No Hit GGCCTGTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCG 7 0.17500000000000002 No Hit GATACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGC 7 0.17500000000000002 No Hit GGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAAA 7 0.17500000000000002 No Hit AGTCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAA 7 0.17500000000000002 No Hit GAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTG 7 0.17500000000000002 No Hit CTATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGAT 7 0.17500000000000002 No Hit GCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCA 7 0.17500000000000002 No Hit GTCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAAT 7 0.17500000000000002 No Hit TCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCT 7 0.17500000000000002 No Hit GCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGGTATG 6 0.15 No Hit TCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATC 6 0.15 No Hit AACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCG 6 0.15 No Hit CGAGGAAGGGCGTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAG 6 0.15 No Hit CACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCT 6 0.15 No Hit GGGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTG 6 0.15 No Hit GGGACGCATGCAACGACCATCTACATATAGCTACTCGATCTACCGCTACC 6 0.15 No Hit GAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGC 6 0.15 No Hit GGTTTTGAAAAGGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAA 6 0.15 No Hit CTGTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTC 6 0.15 No Hit GATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGGGGAAA 5 0.125 No Hit GGGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGT 5 0.125 No Hit GTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAAATGGATTCA 5 0.125 No Hit GGTATTAGTACTATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATC 5 0.125 No Hit GGCTTTAGAAGCCTGTGTACAAGCTCGTAACGAAGGGCGCGATCTTGCTC 5 0.125 No Hit ATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGG 5 0.125 No Hit GGGCGTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAGCATAGAT 5 0.125 No Hit AATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTAT 5 0.125 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 5 0.125 No Hit GCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAACGAAGGGCG 5 0.125 No Hit GTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAA 5 0.125 No Hit GGTACTATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGT 5 0.125 No Hit TATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAG 5 0.125 No Hit AGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTG 5 0.125 No Hit GGGCCATTTGTGGCATGCAGGAAGAGCCCGAGCTGCTGCAGCAGGTTTTG 5 0.125 No Hit GTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAAC 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 0.025 0.0 0.0 0.0 0.0 2 0.025 0.0 0.0 0.0 0.0 3 0.025 0.0 0.0 0.0 0.0 4 0.025 0.0 0.0 0.0 0.0 5 0.025 0.0 0.0 0.0 0.0 6 0.025 0.0 0.0 0.0 0.0 7 0.025 0.0 0.0 0.0 0.0 8 0.025 0.0 0.0 0.0 0.0 9 0.025 0.0 0.0 0.0 0.0 10-11 0.025 0.0 0.0 0.0 0.0 12-13 0.025 0.0 0.0 0.0 0.0 14-15 0.025 0.0 0.0 0.0 0.0 16-17 0.025 0.0 0.0 0.0 0.0 18-19 0.025 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 0.037500000000000006 0.0 0.0 0.0 0.0 36-37 0.05 0.0 0.0 0.0 0.0 38-39 0.05 0.0 0.0 0.0 0.0 40-41 0.05 0.0 0.0 0.0 0.0 42-43 0.05 0.0 0.0 0.0 0.0 44-45 0.05 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 0.05 0.0 0.0 0.0 0.0 78-79 0.05 0.0 0.0 0.0 0.0 80-81 0.05 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TCCTTGG 15 8.8387734E-4 86.68749 6 CATCCTT 15 8.8387734E-4 86.68749 4 GGACATC 15 8.8387734E-4 86.68749 1 CCTTGGG 15 8.8387734E-4 86.68749 7 ACATCCT 15 8.8387734E-4 86.68749 3 GACATCC 15 8.8387734E-4 86.68749 2 TTGGGGA 15 8.8387734E-4 86.68749 9 ATCCTTG 20 0.0027691256 65.015625 5 CGTTCAA 25 0.006701614 52.0125 3 GGCGTTC 25 0.006701614 52.0125 1 TCAACCT 25 0.006701614 52.0125 6 CTTGGGG 25 0.006701614 52.0125 8 GCGTTCA 25 0.006701614 52.0125 2 >>END_MODULE Rejected 48803 READS because READLEN < 1 Read 48803 spots for ERR6133336.sra Written 48803 spots for ERR6133336.sra Rejected 48803 READS because READLEN < 1 Read 48803 spots for ERR6133336.sra Written 48803 spots for ERR6133336.sra Rejected 48803 READS because READLEN < 1 Read 48803 spots for ERR6133336.sra Written 48803 spots for ERR6133336.sra Rejected 48803 READS because READLEN < 1 Read 48803 spots for ERR6133336.sra Written 48803 spots for ERR6133336.sra Rejected 48803 READS because READLEN < 1 Read 48803 spots for ERR6133336.sra Written 48803 spots for ERR6133336.sra Rejected 48803 READS because READLEN < 1 Read 48803 spots for ERR6133336.sra Written 48803 spots for ERR6133336.sra Rejected 48803 READS because READLEN < 1 Read 48803 spots for ERR6133336.sra Written 48803 spots for ERR6133336.sra Rejected 48803 READS because READLEN < 1 Read 48803 spots for ERR6133336.sra Written 48803 spots for ERR6133336.sra Rejected 48803 READS because READLEN < 1 Read 48803 spots for ERR6133336.sra Written 48803 spots for ERR6133336.sra Rejected 48803 READS because READLEN < 1 Read 48803 spots for ERR6133336.sra Written 48803 spots for ERR6133336.sra Rejected 48803 READS because READLEN < 1 Read 48803 spots for ERR6133336.sra Written 48803 spots for ERR6133336.sra Rejected 48803 READS because READLEN < 1 Read 48803 spots for ERR6133336.sra Written 48803 spots for ERR6133336.sra Rejected 48803 READS because READLEN < 1 Read 48803 spots for ERR6133336.sra Written 48803 spots for ERR6133336.sra Rejected 48803 READS because READLEN < 1 Read 48803 spots for ERR6133336.sra Written 48803 spots for ERR6133336.sra Rejected 48807 READS because READLEN < 1 Read 48807 spots for ERR6133336.sra Written 48807 spots for ERR6133336.sra Rejected 48803 READS because READLEN < 1 Read 48803 spots for ERR6133336.sra Written 48803 spots for ERR6133336.sra Rejected 48803 READS because READLEN < 1 Read 48803 spots for ERR6133336.sra Written 48803 spots for ERR6133336.sra Rejected 48803 READS because READLEN < 1 Read 48803 spots for ERR6133336.sra Written 48803 spots for ERR6133336.sra Rejected 48803 READS because READLEN < 1 Read 48803 spots for ERR6133336.sra Written 48803 spots for ERR6133336.sra Rejected 48803 READS because READLEN < 1 Read 48803 spots for ERR6133336.sra Written 48803 spots for ERR6133336.sra SRR ids: ['ERR6133336.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_t7g5qymr ERR6133336.sra spots: 976064 blocks: [[1, 48803], [48804, 97606], [97607, 146409], [146410, 195212], [195213, 244015], [244016, 292818], [292819, 341621], [341622, 390424], [390425, 439227], [439228, 488030], [488031, 536833], [536834, 585636], [585637, 634439], [634440, 683242], [683243, 732045], [732046, 780848], [780849, 829651], [829652, 878454], [878455, 927257], [927258, 976064]] ERR6133336 file size 214576 ERR6133336 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 ERR6133336 ERR6133336_1.fastq Input file: ERR6133336_1.fastq trimmed: ERR6133336-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 00:55:13 2024 >> started Sat Dec 7 00:55:13 2024 >> done (0.654s) 976064 reads processed; of these: 163 ( 0.02%) short reads filtered out after trimming by size control 7 ( 0.00%) empty reads filtered out after trimming by size control 975894 (99.98%) reads available; of these: 14644 ( 1.50%) trimmed reads available after processing 961250 (98.50%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 11 0.00% 19 15 0.00% 20 10 0.00% 21 16 0.00% 22 12 0.00% 23 9 0.00% 24 3 0.00% 25 8 0.00% 26 6 0.00% 27 2 0.00% 28 9 0.00% 29 9 0.00% 30 5 0.00% 31 6 0.00% 32 9 0.00% 33 12 0.00% 34 11 0.00% 35 15 0.00% 36 8 0.00% 37 8 0.00% 38 9 0.00% 39 13 0.00% 40 6 0.00% 41 8 0.00% 42 4 0.00% 43 4 0.00% 44 8 0.00% 45 5 0.00% 46 4 0.00% 47 6 0.00% 48 4 0.00% 49 0 0.00% 50 6 0.00% 51 2 0.00% 52 5 0.00% 53 5 0.00% 54 3 0.00% 55 4 0.00% 56 4 0.00% 57 3 0.00% 58 9 0.00% 59 3 0.00% 60 3 0.00% 61 1 0.00% 62 0 0.00% 63 0 0.00% 64 0 0.00% 65 1 0.00% 66 3 0.00% 67 2 0.00% 68 1 0.00% 69 9 0.00% 70 1230 0.13% 71 1187 0.12% 72 1241 0.13% 73 1235 0.13% 74 1189 0.12% 75 1200 0.12% 76 1174 0.12% 77 1347 0.14% 78 1343 0.14% 79 1410 0.14% 80 1352 0.14% 81 1637 0.17% 82 1708 0.18% 83 1633 0.17% 84 1737 0.18% 85 12 0.00% 86 21 0.00% 87 39 0.00% 88 87 0.01% 89 205 0.02% 90 519 0.05% 91 1940 0.20% 92 11326 1.16% 93 940803 96.40% 975894 reads passed initial QC criterion=sequence-density sequence-density=0.33 sequence-density-rank=1 fanout-score=2.00 fanout-score-rank=22 prefix-density=0.34 prefix-fanout=2.0 sequence=CAAGGCTAAATAC criterion=fanout-score sequence-density=0.01 sequence-density-rank=29 fanout-score=114.71 fanout-score-rank=1 prefix-density=0.38 prefix-fanout=4.0 sequence=GAAGAAGAAAAGTTTTCTCAACATGGGGAGGAAGTCCCTCCGAAATTTGATTTGTTATTGTATTGTAAGGGGCTTTTTTAGTATTTATCTAAAGGAAGGAACAAACGAGGATAAGATAAAATTTCTTTAAATTTATTTTGCCCAAGTGGGATATATGGCATACTATTCTTTCCATTTTCATCTTTTTTTCTATTCCACTCCATCTAGATATAAGAAAGAACCCAATGCAATGAAATTCCACTAATATACAATACAAAAAAGAAGAATAGATACAGGGTCTCAAACCTTGCTATAGAGTTTTTGCTT Started job on | Dec 07 00:55:27 Started mapping on | Dec 07 00:55:27 Finished on | Dec 07 00:55:30 Mapping speed, Million of reads per hour | 1171.07 Number of input reads | 975894 Average input read length | 92 UNIQUE READS: Uniquely mapped reads number | 552215 Uniquely mapped reads % | 56.59% Average mapped length | 92.01 Number of splices: Total | 25374 Number of splices: Annotated (sjdb) | 19789 Number of splices: GT/AG | 24165 Number of splices: GC/AG | 478 Number of splices: AT/AC | 34 Number of splices: Non-canonical | 697 Mismatch rate per base, % | 0.39% Deletion rate per base | 0.04% Deletion average length | 1.64 Insertion rate per base | 0.02% Insertion average length | 1.66 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 402074 % of reads mapped to multiple loci | 41.20% Number of reads mapped to too many loci | 5809 % of reads mapped to too many loci | 0.60% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.59% % of reads unmapped: other | 0.03% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 21605 21605 21605 N_multimapping 402074 402074 402074 N_noFeature 38761 43702 530660 N_ambiguous 18866 2259 76 UnstrandedReadsAssigned:494588 PositiveStrandReadsAssigned:506254 NegativeStrandReadsAssigned:21479 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=93 echo kmer=89 ERR6133336 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: ERR6133336-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 975,894 reads, 766,754 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,039 rounds 52973 ERR6133336.ke.tsv 35125 ERR6133336.se.tsv 88098 total ==> ERR6133336.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 12 14.9047 PNS24243 293 194 0 0 KQK14069 1603 1504 8 9.06438 KQK14071 474 375 0 0 ==> ERR6133336.se.tsv <== BRADI_1g14170v3 8 BRADI_1g53295v3 2 BRADI_1g59795v3 4 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 6 BRADI_1g74790v3 5 BRADI_1g09890v3 0 BRADI_1g77505v3 10 BRADI_1g48960v3 0 ERR6133336 completed mapping pipeline successfully