Starting /dee2/code/volunteer_pipeline.sh ERR6133430 current disk space = 1546489774080 free memory = 1600970604 ERR6133430 SRAfilesize 6d66466568d1b647b6b31d252092d74b ERR6133430.sra ERR6133430.sra file validated ERR6133430 is single end ERR6133430 is conventional basespace ERR6133430 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133430_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 46 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 35.24175 37.0 33.0 37.0 33.0 37.0 2 36.31375 37.0 37.0 37.0 33.0 37.0 3 35.4665 37.0 37.0 37.0 33.0 37.0 4 35.2275 37.0 37.0 37.0 33.0 37.0 5 35.017 37.0 37.0 37.0 33.0 37.0 6 35.346 37.0 37.0 37.0 33.0 37.0 7 36.974 37.0 37.0 40.0 33.0 40.0 8 37.012 37.0 37.0 40.0 33.0 40.0 9 37.05025 37.0 37.0 40.0 33.0 40.0 10-11 37.02175 37.0 37.0 40.0 33.0 40.0 12-13 36.92275 37.0 37.0 40.0 33.0 40.0 14-15 36.90875 37.0 37.0 40.0 33.0 40.0 16-17 36.757999999999996 37.0 37.0 40.0 33.0 40.0 18-19 37.090375 37.0 37.0 40.0 33.0 40.0 20-21 37.206 37.0 37.0 40.0 33.0 40.0 22-23 37.12125 37.0 37.0 40.0 33.0 40.0 24-25 37.102999999999994 37.0 37.0 40.0 33.0 40.0 26-27 36.91875 37.0 37.0 40.0 33.0 40.0 28-29 36.956 37.0 37.0 40.0 33.0 40.0 30-31 36.939875 37.0 37.0 40.0 33.0 40.0 32-33 36.73625 37.0 37.0 40.0 33.0 40.0 34-35 36.6755 37.0 37.0 40.0 33.0 40.0 36-37 36.604749999999996 37.0 37.0 40.0 33.0 40.0 38-39 36.484125000000006 37.0 37.0 40.0 33.0 40.0 40-41 36.40025 37.0 37.0 40.0 33.0 40.0 42-43 36.280375 37.0 37.0 40.0 33.0 40.0 44-45 36.012874999999994 37.0 37.0 38.5 33.0 40.0 46-47 35.925 37.0 35.0 37.0 33.0 40.0 48-49 35.765249999999995 37.0 33.0 37.0 33.0 40.0 50-51 35.615 37.0 33.0 37.0 33.0 40.0 52-53 35.47725 37.0 33.0 37.0 33.0 40.0 54-55 35.32525 37.0 33.0 37.0 33.0 38.5 56-57 35.228375 37.0 33.0 37.0 33.0 37.0 58-59 34.768625 37.0 33.0 37.0 30.0 37.0 60-61 34.674499999999995 37.0 33.0 37.0 30.0 37.0 62-63 34.636375 37.0 33.0 37.0 33.0 37.0 64-65 34.237750000000005 37.0 33.0 37.0 27.0 37.0 66-67 34.174375 37.0 33.0 37.0 27.0 37.0 68-69 32.940374999999996 35.0 33.0 35.0 27.0 37.0 70-71 33.189040038817936 33.0 33.0 37.0 27.0 37.0 72-73 34.0501857517345 37.0 33.0 37.0 27.0 37.0 74-75 34.26983048064112 37.0 33.0 37.0 30.0 37.0 76-77 34.209257948416486 37.0 33.0 37.0 30.0 37.0 78-79 34.15888807327612 37.0 33.0 37.0 30.0 37.0 80-81 34.039719337694876 37.0 33.0 37.0 27.0 37.0 82-83 33.8091997431449 37.0 33.0 37.0 27.0 37.0 84-85 33.75517669186384 35.0 33.0 37.0 27.0 37.0 86-87 33.731526463819996 37.0 33.0 37.0 27.0 37.0 88-89 33.73318844285349 37.0 33.0 37.0 27.0 37.0 90-91 33.55701866530299 33.0 33.0 37.0 27.0 37.0 92-93 33.299795448734336 33.0 33.0 37.0 27.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 10.0 21 12.0 22 13.0 23 17.0 24 16.0 25 20.0 26 32.0 27 41.0 28 45.0 29 66.0 30 75.0 31 115.0 32 165.0 33 195.0 34 249.0 35 513.0 36 1010.0 37 997.0 38 405.0 39 4.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 91.725 1.8499999999999999 1.95 4.475 2 78.36213373403456 12.8725269221137 5.08389681943401 3.6814425244177307 3 39.025 40.0 11.65 9.325 4 34.175 29.049999999999997 17.474999999999998 19.3 5 24.675 32.875 24.15 18.3 6 21.275 38.525 23.45 16.75 7 37.95 28.050000000000004 18.3 15.7 8 32.05 31.624999999999996 21.349999999999998 14.975 9 27.250000000000004 26.200000000000003 27.725 18.825 10-11 26.474999999999998 27.537499999999998 26.5375 19.45 12-13 29.099999999999998 25.900000000000002 26.700000000000003 18.3 14-15 23.1625 30.112499999999997 27.950000000000003 18.775 16-17 24.125 31.05 26.2875 18.5375 18-19 23.9 27.437499999999996 26.3625 22.3 20-21 24.525 26.525 26.987499999999997 21.9625 22-23 26.637499999999996 24.587500000000002 26.437500000000004 22.3375 24-25 26.3125 24.637500000000003 27.025 22.025 26-27 24.637500000000003 26.237500000000004 29.7375 19.3875 28-29 24.875 26.8 26.5 21.825 30-31 26.637499999999996 24.825 27.200000000000003 21.337500000000002 32-33 23.5375 27.287499999999998 28.875 20.3 34-35 25.362499999999997 24.8625 28.1 21.675 36-37 24.7 24.2 28.499999999999996 22.6 38-39 25.112499999999997 25.224999999999998 30.7625 18.9 40-41 26.974999999999998 25.75 25.5125 21.762500000000003 42-43 24.85 27.900000000000002 26.487500000000004 20.7625 44-45 23.8625 25.4 29.375 21.3625 46-47 24.224999999999998 24.0125 28.275 23.4875 48-49 23.974999999999998 25.674999999999997 30.1875 20.1625 50-51 26.0125 25.35 29.0875 19.55 52-53 25.124999999999996 27.2625 26.9625 20.65 54-55 23.325000000000003 28.787499999999998 28.9125 18.975 56-57 25.9875 25.35 28.249999999999996 20.4125 58-59 23.3375 25.55 28.475 22.6375 60-61 23.6375 25.324999999999996 29.849999999999998 21.1875 62-63 22.4625 27.650000000000002 31.937500000000004 17.95 64-65 23.5875 26.5125 29.575000000000003 20.325 66-67 23.775 27.212500000000002 28.262500000000003 20.75 68-69 23.9875 27.237499999999997 27.35 21.425 70-71 26.022769923683224 24.74665332165645 27.899411985487298 21.33116476917303 72-73 25.7243195785777 25.10974539069359 28.49617458923868 20.66976044149003 74-75 23.280955373978628 26.184789440603396 28.887492143306098 21.64676304211188 76-77 22.61559783293436 25.664608794254757 30.30112133047751 21.418672042333377 78-79 21.638681984597905 24.69385178639061 32.35702562807726 21.310440600934225 80-81 23.583829679381573 27.157521226713975 30.427068812571285 18.831580281333167 82-83 23.174926742260162 24.882150592432158 30.449738820231875 21.493183845075805 84-85 24.015848670756647 23.415132924335378 31.735685071574643 20.833333333333336 86-87 23.01201738685758 26.604448990028125 32.191255433392996 18.192278189721296 88-89 22.423932498082333 29.020710815648172 29.72385579135771 18.831500894911787 90-91 26.34875990795193 25.23651240092048 29.838915878292 18.575811812835592 92-93 22.334441319355662 28.240859115315775 29.864484786499617 19.560214778828943 >>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 1.0 17 7.0 18 7.0 19 2.0 20 1.5 21 3.0 22 3.5 23 4.0 24 6.0 25 5.0 26 8.0 27 12.0 28 21.5 29 31.0 30 28.5 31 27.5 32 43.5 33 66.0 34 75.0 35 85.5 36 99.0 37 126.5 38 155.0 39 159.0 40 186.5 41 204.0 42 212.0 43 230.5 44 210.5 45 181.0 46 195.0 47 196.5 48 179.5 49 170.5 50 150.0 51 150.0 52 147.0 53 147.0 54 116.5 55 69.0 56 66.5 57 71.5 58 71.0 59 62.0 60 55.0 61 48.5 62 43.5 63 43.5 64 38.5 65 33.5 66 22.5 67 23.0 68 20.0 69 9.0 70 6.5 71 4.0 72 2.5 73 2.5 74 2.0 75 0.5 76 0.5 77 0.5 78 0.5 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 0.17500000000000002 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 0.038328861632809505 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 7.0 71 5.0 72 3.0 73 4.0 74 7.0 75 3.0 76 5.0 77 2.0 78 7.0 79 9.0 80 5.0 81 14.0 82 9.0 83 4.0 84 5.0 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 3911.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 81.3 #Duplication Level Percentage of deduplicated Percentage of total 1 92.65067650676507 75.325 2 4.45879458794588 7.249999999999999 3 1.0762607626076262 2.625 4 0.46125461254612543 1.5 5 0.27675276752767525 1.125 6 0.21525215252152521 1.05 7 0.03075030750307503 0.17500000000000002 8 0.12300123001230012 0.8 9 0.15375153751537515 1.125 >10 0.5227552275522755 7.55 >50 0.03075030750307503 1.4749999999999999 >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 GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 59 1.4749999999999999 No Hit GGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGG 37 0.9249999999999999 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 33 0.8250000000000001 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 30 0.75 No Hit GGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAA 22 0.5499999999999999 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 20 0.5 No Hit GGGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTG 19 0.475 No Hit GGAAGAGCCCGAGCTGCTGCAGCAGGTTTTGAAAAGGGAATCGATCGTGA 18 0.44999999999999996 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 15 0.375 No Hit GGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGGG 15 0.375 No Hit GGAGTATCCTTGATATATAAATATATAGATAAATAGATTTAAATGGAAAA 14 0.35000000000000003 No Hit GGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTT 12 0.3 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 12 0.3 No Hit GGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAACCCTCTTAACT 12 0.3 No Hit GGGGAAGTACACCAGCGACGGCGAGGCCGCCGCCGCCAAGGAAGGCATGT 11 0.27499999999999997 No Hit GGGCCATTTGTGGCATGCAGGAAGAGCCCGAGCTGCTGCAGCAGGTTTTG 11 0.27499999999999997 No Hit GGTTTTGAAAAGGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAA 11 0.27499999999999997 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 10 0.25 No Hit GTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAA 9 0.22499999999999998 No Hit GGGAGGGGCTTGGCTACAATTCCGAATACGCTATTACATGTTTGCGCTAG 9 0.22499999999999998 No Hit GGGCAAGGAGAAGTACAAGTGCGGATCCAACGTCTTCTGGAAATGGTGAA 9 0.22499999999999998 No Hit GGGCTTGGCTACAATTCCGAATACGCTATTACATGTTTGCGCTAGTTTTT 9 0.22499999999999998 No Hit GGATTCTTCTTTTTTGTGGGCCATTTGTGGCATGCAGGAAGAGCCCGAGC 9 0.22499999999999998 No Hit GGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCG 8 0.2 No Hit GGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAA 8 0.2 No Hit GGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAACCCTCTTAACTA 8 0.2 No Hit GGGCCGGGTATCTCTCTGCATGTACGTATGCCTGTAATGTACGTAGCTAC 8 0.2 No Hit GGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGC 7 0.17500000000000002 No Hit GGAAGAGACTTATAATATTGTGGCTGCTCATGGTTATTTTGGCCGATTAA 6 0.15 No Hit GGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAAA 6 0.15 No Hit GGGAGTATTATGAAAGGAGATTAATCATAGATTATCAAAAACCCTAGAAA 6 0.15 No Hit GGAATAAGAATAAATCGCAACTCCTTTCCACTACACATAAAAATTGATTT 6 0.15 No Hit GGAAACAACGAGGTCATCATCGACATGATATATTGCTGCTATTTTCCACC 6 0.15 No Hit GGGACGCATGCAACGACCATCTACATATAGCTACTCGATCTACCGCTACC 6 0.15 No Hit GGAAAAGAGGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTTG 6 0.15 No Hit TAATTAAGAATCAAGTCATCTCATTCTCATCTATGCAATTGCAAACACAA 5 0.125 No Hit GGCCTGTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCG 5 0.125 No Hit GTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCT 5 0.125 No Hit CAGGAAGAGCCCGAGCTGCTGCAGCAGGTTTTGAAAAGGGAATCGATCGT 5 0.125 No Hit GGCAAAGATGATGAGTAGCCAAGCTGTGCGTGGGCCTGTTCACGCGGCCG 5 0.125 No Hit CAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAACGAAGGG 5 0.125 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 5 0.125 No Hit GGGTATCTCTCTGCATGTACGTATGCCTGTAATGTACGTAGCTACCTGCT 5 0.125 No Hit GGGCGTGGCGTTCATGAACAAGTGAAACCTTATGGCTGGATGGGTCATCG 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 0.0125 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 0.025 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 0.037500000000000006 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 pass >>END_MODULE Rejected 253821 READS because READLEN < 1 Read 253821 spots for ERR6133430.sra Written 253821 spots for ERR6133430.sra Rejected 253821 READS because READLEN < 1 Read 253821 spots for ERR6133430.sra Written 253821 spots for ERR6133430.sra Rejected 253821 READS because READLEN < 1 Read 253821 spots for ERR6133430.sra Written 253821 spots for ERR6133430.sra Rejected 253821 READS because READLEN < 1 Read 253821 spots for ERR6133430.sra Written 253821 spots for ERR6133430.sra Rejected 253821 READS because READLEN < 1 Read 253821 spots for ERR6133430.sra Written 253821 spots for ERR6133430.sra Rejected 253821 READS because READLEN < 1 Read 253821 spots for ERR6133430.sra Written 253821 spots for ERR6133430.sra Rejected 253821 READS because READLEN < 1 Read 253821 spots for ERR6133430.sra Written 253821 spots for ERR6133430.sra Rejected 253821 READS because READLEN < 1 Read 253821 spots for ERR6133430.sra Written 253821 spots for ERR6133430.sra Rejected 253821 READS because READLEN < 1 Read 253821 spots for ERR6133430.sra Written 253821 spots for ERR6133430.sra Rejected 253821 READS because READLEN < 1 Read 253821 spots for ERR6133430.sra Written 253821 spots for ERR6133430.sra Rejected 253821 READS because READLEN < 1 Read 253821 spots for ERR6133430.sra Written 253821 spots for ERR6133430.sra Rejected 253821 READS because READLEN < 1 Read 253821 spots for ERR6133430.sra Written 253821 spots for ERR6133430.sra Rejected 253821 READS because READLEN < 1 Read 253821 spots for ERR6133430.sra Written 253821 spots for ERR6133430.sra Rejected 253821 READS because READLEN < 1 Read 253821 spots for ERR6133430.sra Written 253821 spots for ERR6133430.sra Rejected 253821 READS because READLEN < 1 Read 253821 spots for ERR6133430.sra Written 253821 spots for ERR6133430.sra Rejected 253821 READS because READLEN < 1 Read 253821 spots for ERR6133430.sra Written 253821 spots for ERR6133430.sra Rejected 253821 READS because READLEN < 1 Read 253821 spots for ERR6133430.sra Written 253821 spots for ERR6133430.sra Rejected 253821 READS because READLEN < 1 Read 253821 spots for ERR6133430.sra Written 253821 spots for ERR6133430.sra Rejected 253821 READS because READLEN < 1 Read 253821 spots for ERR6133430.sra Written 253821 spots for ERR6133430.sra Rejected 253837 READS because READLEN < 1 Read 253837 spots for ERR6133430.sra Written 253837 spots for ERR6133430.sra SRR ids: ['ERR6133430.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_z_5hakcf ERR6133430.sra spots: 5076436 blocks: [[1, 253821], [253822, 507642], [507643, 761463], [761464, 1015284], [1015285, 1269105], [1269106, 1522926], [1522927, 1776747], [1776748, 2030568], [2030569, 2284389], [2284390, 2538210], [2538211, 2792031], [2792032, 3045852], [3045853, 3299673], [3299674, 3553494], [3553495, 3807315], [3807316, 4061136], [4061137, 4314957], [4314958, 4568778], [4568779, 4822599], [4822600, 5076436]] ERR6133430 file size 1123989 ERR6133430 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 ERR6133430 ERR6133430_1.fastq Input file: ERR6133430_1.fastq trimmed: ERR6133430-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 05:13:17 2024 >> started Sat Dec 7 05:13:22 2024 >> done (4.480s) 5076436 reads processed; of these: 1676 ( 0.03%) short reads filtered out after trimming by size control 21 ( 0.00%) empty reads filtered out after trimming by size control 5074739 (99.97%) reads available; of these: 68680 ( 1.35%) trimmed reads available after processing 5006059 (98.65%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 46 0.00% 19 54 0.00% 20 28 0.00% 21 18 0.00% 22 18 0.00% 23 16 0.00% 24 14 0.00% 25 8 0.00% 26 11 0.00% 27 11 0.00% 28 17 0.00% 29 19 0.00% 30 6 0.00% 31 11 0.00% 32 9 0.00% 33 24 0.00% 34 5 0.00% 35 7 0.00% 36 7 0.00% 37 11 0.00% 38 12 0.00% 39 27 0.00% 40 40 0.00% 41 24 0.00% 42 13 0.00% 43 31 0.00% 44 15 0.00% 45 15 0.00% 46 25 0.00% 47 19 0.00% 48 31 0.00% 49 32 0.00% 50 26 0.00% 51 30 0.00% 52 25 0.00% 53 24 0.00% 54 26 0.00% 55 22 0.00% 56 25 0.00% 57 19 0.00% 58 14 0.00% 59 25 0.00% 60 27 0.00% 61 18 0.00% 62 2 0.00% 63 4 0.00% 64 3 0.00% 65 7 0.00% 66 11 0.00% 67 18 0.00% 68 34 0.00% 69 124 0.00% 70 9598 0.19% 71 8568 0.17% 72 8666 0.17% 73 7698 0.15% 74 8808 0.17% 75 8482 0.17% 76 7608 0.15% 77 7766 0.15% 78 8903 0.18% 79 10101 0.20% 80 8674 0.17% 81 9052 0.18% 82 9875 0.19% 83 10360 0.20% 84 8385 0.17% 85 127 0.00% 86 268 0.01% 87 438 0.01% 88 740 0.01% 89 1606 0.03% 90 3704 0.07% 91 11293 0.22% 92 47716 0.94% 93 4875195 96.07% 5074739 reads passed initial QC criterion=sequence-density sequence-density=0.33 sequence-density-rank=1 fanout-score=5.88 fanout-score-rank=18 prefix-density=0.80 prefix-fanout=2.4 sequence=GCCGCCGCCGCCAAGGAAGGCATGTTCGTCAAGAACTACAGCTACTGATCCTAATCGCATCAAGCTTCAACGCCTGTGAGTGAAAACCAGTGATGAGAGTGCTGCTGCTAGCTAGCGCCGGCATTGATGAGCTTGAGAGGGCACTGTAGCCAGTGTGTCAGTCGTTGTTAAATTACAGGTTGAGATCATCAGCGTACTCCGATGGGAGGTGGACATCAGAAAGTATACTGTGTTTTACCACCCTAATTAAGTAAACAACTTTTGGAATGGTGATCATCTTACTGTTTTAAATAAATCTGTTTCA criterion=fanout-score sequence-density=0.04 sequence-density-rank=17 fanout-score=48.27 fanout-score-rank=1 prefix-density=1.30 prefix-fanout=1.5 sequence=TGCTGCAGCAGCTTAATTTGCATGCCAGGGACGCATGCAACGACCATCTACATATAGCTACTCGATCTACCGCTACCATGAACCGATCCAAGGCTAGCTGCACAAGCTAGGCCCTTATTTCCCT Started job on | Dec 07 05:13:35 Started mapping on | Dec 07 05:13:35 Finished on | Dec 07 05:13:43 Mapping speed, Million of reads per hour | 2283.63 Number of input reads | 5074739 Average input read length | 92 UNIQUE READS: Uniquely mapped reads number | 3901901 Uniquely mapped reads % | 76.89% Average mapped length | 92.17 Number of splices: Total | 228933 Number of splices: Annotated (sjdb) | 193516 Number of splices: GT/AG | 219629 Number of splices: GC/AG | 5938 Number of splices: AT/AC | 50 Number of splices: Non-canonical | 3316 Mismatch rate per base, % | 0.48% Deletion rate per base | 0.05% Deletion average length | 1.86 Insertion rate per base | 0.02% Insertion average length | 1.86 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 1058734 % of reads mapped to multiple loci | 20.86% Number of reads mapped to too many loci | 13705 % of reads mapped to too many loci | 0.27% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.96% % of reads unmapped: other | 0.02% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 114104 114104 114104 N_multimapping 1058734 1058734 1058734 N_noFeature 227592 269022 3723578 N_ambiguous 151670 14994 438 UnstrandedReadsAssigned:3522639 PositiveStrandReadsAssigned:3617885 NegativeStrandReadsAssigned:177885 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=93 echo kmer=89 ERR6133430 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: ERR6133430-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 5,074,739 reads, 4,403,263 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,024 rounds 52973 ERR6133430.ke.tsv 35125 ERR6133430.se.tsv 88098 total ==> ERR6133430.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 131 29.2695 PNS24243 293 194 0 0 KQK14069 1603 1504 928 189.146 KQK14071 474 375 0 0 ==> ERR6133430.se.tsv <== BRADI_1g14170v3 934 BRADI_1g53295v3 55 BRADI_1g59795v3 28 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 62 BRADI_1g74790v3 37 BRADI_1g09890v3 0 BRADI_1g77505v3 72 BRADI_1g48960v3 0 ERR6133430 completed mapping pipeline successfully