Starting /dee2/code/volunteer_pipeline.sh ERR6133542 current disk space = 1544470994944 free memory = 1417580220 ERR6133542 SRAfilesize 903711c80f2b76778988d49cd71252f2 ERR6133542.sra ERR6133542.sra file validated ERR6133542 is single end ERR6133542 is conventional basespace ERR6133542 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133542_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 33.9435 37.0 33.0 37.0 27.0 37.0 2 36.008 37.0 37.0 37.0 33.0 37.0 3 34.98875 37.0 33.0 37.0 33.0 37.0 4 35.169 37.0 37.0 37.0 33.0 37.0 5 35.05825 37.0 37.0 37.0 33.0 37.0 6 35.5005 37.0 37.0 37.0 33.0 37.0 7 37.27025 37.0 37.0 40.0 33.0 40.0 8 37.24875 37.0 37.0 40.0 33.0 40.0 9 37.264 37.0 37.0 40.0 33.0 40.0 10-11 37.269999999999996 37.0 37.0 40.0 33.0 40.0 12-13 37.18475 37.0 37.0 40.0 33.0 40.0 14-15 37.208 37.0 37.0 40.0 33.0 40.0 16-17 37.232625 37.0 37.0 40.0 33.0 40.0 18-19 37.199375 37.0 37.0 40.0 33.0 40.0 20-21 37.074875000000006 37.0 37.0 40.0 33.0 40.0 22-23 36.919125 37.0 37.0 40.0 33.0 40.0 24-25 37.062124999999995 37.0 37.0 40.0 33.0 40.0 26-27 37.0155 37.0 37.0 40.0 33.0 40.0 28-29 36.96875 37.0 37.0 40.0 33.0 40.0 30-31 36.871125 37.0 37.0 40.0 33.0 40.0 32-33 36.768 37.0 37.0 40.0 33.0 40.0 34-35 36.597375 37.0 37.0 40.0 33.0 40.0 36-37 36.39575 37.0 37.0 40.0 33.0 40.0 38-39 36.350625 37.0 37.0 40.0 33.0 40.0 40-41 36.192125000000004 37.0 37.0 40.0 33.0 40.0 42-43 36.0745 37.0 37.0 40.0 33.0 40.0 44-45 35.9345 37.0 35.0 40.0 33.0 40.0 46-47 35.528999999999996 37.0 33.0 37.0 33.0 40.0 48-49 35.4585 37.0 33.0 37.0 33.0 40.0 50-51 35.4655 37.0 33.0 37.0 33.0 40.0 52-53 35.147875 37.0 33.0 37.0 30.0 40.0 54-55 35.032624999999996 37.0 33.0 37.0 27.0 40.0 56-57 34.836125 37.0 33.0 37.0 27.0 37.0 58-59 34.163375 37.0 33.0 37.0 27.0 37.0 60-61 34.37025 37.0 33.0 37.0 27.0 37.0 62-63 34.370000000000005 37.0 33.0 37.0 27.0 37.0 64-65 34.44975 37.0 33.0 37.0 27.0 37.0 66-67 34.320375 37.0 33.0 37.0 27.0 37.0 68-69 33.558 35.0 33.0 37.0 27.0 37.0 70-71 33.74704803822938 35.0 33.0 37.0 27.0 37.0 72-73 34.12031758658381 37.0 33.0 37.0 27.0 37.0 74-75 34.14062771549591 37.0 33.0 37.0 27.0 37.0 76-77 33.96054850926437 37.0 33.0 37.0 27.0 37.0 78-79 33.892216457102464 37.0 33.0 37.0 27.0 37.0 80-81 33.99003372831146 37.0 33.0 37.0 27.0 37.0 82-83 33.840878678060704 37.0 33.0 37.0 27.0 37.0 84-85 33.75662280276644 37.0 33.0 37.0 27.0 37.0 86-87 33.70521992580816 37.0 33.0 37.0 27.0 37.0 88-89 33.71992580816111 37.0 33.0 37.0 27.0 37.0 90-91 33.50993640699524 37.0 33.0 37.0 27.0 37.0 92-93 33.53378378378378 37.0 33.0 37.0 27.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 13.0 21 18.0 22 22.0 23 26.0 24 22.0 25 42.0 26 29.0 27 49.0 28 51.0 29 88.0 30 80.0 31 107.0 32 153.0 33 148.0 34 233.0 35 406.0 36 929.0 37 897.0 38 669.0 39 18.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 90.17500000000001 2.075 2.45 5.3 2 77.05 13.55 5.8500000000000005 3.55 3 37.1 39.825 13.600000000000001 9.475 4 32.725 29.599999999999998 18.0 19.675 5 23.75 31.5 27.150000000000002 17.599999999999998 6 20.849999999999998 37.5 25.974999999999998 15.675 7 38.65 28.425 18.875 14.05 8 31.2 31.474999999999998 23.5 13.825000000000001 9 28.775000000000002 28.15 28.175 14.899999999999999 10-11 25.874999999999996 28.725 28.349999999999998 17.05 12-13 28.3375 26.1125 29.612500000000004 15.937499999999998 14-15 21.212500000000002 29.799999999999997 30.925000000000004 18.0625 16-17 23.125 31.9875 26.387500000000003 18.5 18-19 23.0375 26.2875 29.849999999999998 20.825 20-21 25.11877969492373 26.006501625406354 29.794948737184296 19.079769942485623 22-23 26.437500000000004 23.8625 29.4125 20.2875 24-25 25.0375 25.3125 28.975 20.674999999999997 26-27 24.9 26.075 31.374999999999996 17.65 28-29 24.725 27.187499999999996 29.3375 18.75 30-31 26.224999999999998 25.637500000000003 28.925 19.2125 32-33 22.775000000000002 27.275 29.675 20.275000000000002 34-35 23.814884302689183 26.12883051907442 28.993120700437775 21.063164477798622 36-37 23.799999999999997 24.9375 29.45 21.8125 38-39 25.424999999999997 25.650000000000002 30.612499999999997 18.3125 40-41 26.525762881440716 24.662331165582792 28.414207103551774 20.39769884942471 42-43 23.945424959319066 26.962072850168983 29.60320440605833 19.489297784453623 44-45 22.998999499749875 26.038019009504755 30.777888944472238 20.185092546273136 46-47 23.962500000000002 25.162499999999998 28.9375 21.9375 48-49 24.24053006625828 25.55319414926866 31.391423927990996 18.814851856482058 50-51 24.7875 26.575 29.4 19.2375 52-53 24.130597948461347 26.882661996497376 28.33375031273455 20.65298974230673 54-55 24.25 28.349999999999998 29.262500000000003 18.1375 56-57 24.45 25.2875 30.599999999999998 19.662499999999998 58-59 23.75 25.624999999999996 29.849999999999998 20.775 60-61 23.974999999999998 26.575 30.525000000000002 18.925 62-63 22.7 27.150000000000002 31.4 18.75 64-65 23.724999999999998 27.1375 30.55 18.587500000000002 66-67 23.75 27.1 30.1375 19.0125 68-69 21.7875 27.474999999999998 29.5 21.2375 70-71 23.395185556670008 25.90270812437312 30.127883650952857 20.574222668004012 72-73 24.320566300088483 26.317785362153963 30.29958285930982 19.06206547844773 74-75 22.566258919469927 26.044852191641183 31.05249745158002 20.33639143730887 76-77 22.878086419753085 26.311728395061728 31.147119341563783 19.6630658436214 78-79 23.814459704586678 25.03239181135009 31.76988857216896 19.383259911894275 80-81 22.733794182861615 29.085691926437978 29.7508803965045 18.429633494195905 82-83 22.871014302584964 27.227397979267813 30.310982810654767 19.590604907492455 84-85 22.980298823218302 24.46119264841994 31.905328573317465 20.653179955044294 86-87 21.449390567037625 26.90779014308426 31.756756756756754 19.886062533121358 88-89 20.800211976682565 28.07366189719131 31.53153153153153 19.594594594594593 90-91 24.019607843137255 27.835188129305777 29.040805511393746 19.104398516163222 92-93 22.469528351881294 28.908320084790674 30.23317435082141 18.388977212506624 >>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 0.5 17 5.0 18 7.5 19 2.5 20 1.0 21 1.5 22 0.5 23 2.0 24 3.5 25 5.5 26 7.0 27 11.5 28 23.0 29 29.0 30 31.0 31 46.5 32 65.0 33 83.0 34 103.0 35 125.0 36 134.5 37 146.5 38 192.0 39 214.0 40 219.5 41 209.5 42 230.0 43 269.0 44 235.0 45 215.5 46 226.5 47 188.5 48 151.0 49 156.5 50 143.5 51 128.0 52 126.0 53 116.5 54 97.0 55 64.0 56 45.5 57 44.0 58 46.0 59 40.0 60 32.0 61 26.5 62 25.0 63 29.0 64 26.0 65 19.0 66 12.5 67 10.5 68 7.5 69 5.0 70 3.5 71 2.0 72 3.0 73 3.0 74 3.5 75 3.0 76 0.5 77 0.0 78 0.0 79 0.0 80 0.0 81 0.5 82 0.5 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 0.025 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 0.0625 36-37 0.0 38-39 0.0 40-41 0.05 42-43 0.13749999999999998 44-45 0.05 46-47 0.0 48-49 0.0125 50-51 0.0 52-53 0.075 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 24.0 71 14.0 72 13.0 73 19.0 74 12.0 75 21.0 76 18.0 77 15.0 78 10.0 79 13.0 80 15.0 81 10.0 82 11.0 83 16.0 84 15.0 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 3774.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 82.075 #Duplication Level Percentage of deduplicated Percentage of total 1 92.96375266524521 76.3 2 3.929332927200731 6.45 3 1.1270179713676516 2.775 4 0.6091989034419738 2.0 5 0.3045994517209869 1.25 6 0.15229972586049345 0.75 7 0.18275967103259214 1.05 8 0.15229972586049345 1.0 9 0.06091989034419738 0.44999999999999996 >10 0.5178190679256778 7.9750000000000005 >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 GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 48 1.2 No Hit GGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGG 33 0.8250000000000001 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 27 0.675 No Hit GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGC 27 0.675 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 20 0.5 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 18 0.44999999999999996 No Hit GGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTT 18 0.44999999999999996 No Hit GGGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTG 17 0.42500000000000004 No Hit GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 16 0.4 No Hit GGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTT 15 0.375 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 14 0.35000000000000003 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 13 0.325 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 12 0.3 No Hit GGAGTATCCTTGATATATAAATATATAGATAAATAGATTTAAATGGAAAA 11 0.27499999999999997 No Hit GGGAAAAGAGGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTT 10 0.25 No Hit GGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAACCCTCTTAACT 10 0.25 No Hit GGAAAAGAGGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTTG 10 0.25 No Hit GGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGC 9 0.22499999999999998 No Hit GGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGGG 9 0.22499999999999998 No Hit GGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAAA 8 0.2 No Hit GGCCTGTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCG 8 0.2 No Hit GGTGGGGCAATGGGCATTCCGTTGAGTTTGTATGGTGGGTGCTGTTTTGC 8 0.2 No Hit GGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAA 8 0.2 No Hit GGGCCGGGTATCTCTCTGCATGTACGTATGCCTGTAATGTACGTAGCTAC 8 0.2 No Hit GGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAAGGCGATCAAATTC 7 0.17500000000000002 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 7 0.17500000000000002 No Hit GGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAA 7 0.17500000000000002 No Hit GCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATC 7 0.17500000000000002 No Hit GGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAA 7 0.17500000000000002 No Hit GGTTTTGAAAAGGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAA 7 0.17500000000000002 No Hit GGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCG 6 0.15 No Hit CAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCT 6 0.15 No Hit GGAACAAACGAGGATAAGATAAAATTTCTTTAAATTTATTTTGCCCAAGT 6 0.15 No Hit GGGGCAGAGGGAATTTCCGGTGGAGCGGTGAAATGCATTGAGATCGGAAA 6 0.15 No Hit GGAAATGGTGAAGATGATACGAATATGCCGGCCGGGTGCTGATATTGTGA 6 0.15 No Hit CAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATAT 5 0.125 No Hit GGAGAAAAACAGTTGTTATAGTTCTTCTGCTTATGATGATTTACCAGTCG 5 0.125 No Hit GAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGC 5 0.125 No Hit GGAGAACGAGTCTTGCACTATGCTGTTGCCCGTCTACCAGTTGACTACGA 5 0.125 No Hit GGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTTGAAATCGGA 5 0.125 No Hit GGGATTGAGATGTCTGGCTGCAGTTTTAGTGTTTACTAAGTTTTGTCTAT 5 0.125 No Hit GGAGTGGGGGTGCCATACGCAAAAAGGAAGCGACTCATAGAATGGCAGAG 5 0.125 No Hit GGGCAAGTTCATGTAAACATAGATCGATATATGGCGGAGCGCCATTTTAT 5 0.125 No Hit GGGCACTGTAGCCAGTGTGTCAGTCGTTGTTAAATTACAGGTTGAGATCA 5 0.125 No Hit GGGACTCCCGATTTCAATTCCAATTCCAAAGTTTGATGATGTACTTTGCT 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 0.0 0.0 0.0 0.0 68-69 0.0 0.0 0.0 0.0 0.0 70-71 0.0 0.0 0.0 0.0 0.0 72-73 0.0 0.0 0.0 0.0 0.0 74-75 0.0 0.0 0.0 0.0 0.0 76-77 0.0 0.0 0.0 0.0 0.0 78-79 0.0 0.0 0.0 0.0 0.0 80-81 0.0 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position AAAAAAA 20 6.3625263E-4 45.335526 86-87 >>END_MODULE Rejected 305933 READS because READLEN < 1 Read 305933 spots for ERR6133542.sra Written 305933 spots for ERR6133542.sra Rejected 305933 READS because READLEN < 1 Read 305933 spots for ERR6133542.sra Written 305933 spots for ERR6133542.sra Rejected 305933 READS because READLEN < 1 Read 305933 spots for ERR6133542.sra Written 305933 spots for ERR6133542.sra Rejected 305933 READS because READLEN < 1 Read 305933 spots for ERR6133542.sra Written 305933 spots for ERR6133542.sra Rejected 305933 READS because READLEN < 1 Read 305933 spots for ERR6133542.sra Written 305933 spots for ERR6133542.sra Rejected 305933 READS because READLEN < 1 Read 305933 spots for ERR6133542.sra Written 305933 spots for ERR6133542.sra Rejected 305933 READS because READLEN < 1 Read 305933 spots for ERR6133542.sra Written 305933 spots for ERR6133542.sra Rejected 305933 READS because READLEN < 1 Read 305933 spots for ERR6133542.sra Written 305933 spots for ERR6133542.sra Rejected 305933 READS because READLEN < 1 Read 305933 spots for ERR6133542.sra Written 305933 spots for ERR6133542.sra Rejected 305933 READS because READLEN < 1 Rejected 305933 READS because READLEN < 1 Read 305933 spots for ERR6133542.sra Read 305933 spots for ERR6133542.sra Written 305933 spots for ERR6133542.sra Written 305933 spots for ERR6133542.sra Rejected 305933 READS because READLEN < 1 Read 305933 spots for ERR6133542.sra Written 305933 spots for ERR6133542.sra Rejected 305933 READS because READLEN < 1 Read 305933 spots for ERR6133542.sra Written 305933 spots for ERR6133542.sra Rejected 305951 READS because READLEN < 1 Read 305951 spots for ERR6133542.sra Written 305951 spots for ERR6133542.sra Rejected 305933 READS because READLEN < 1 Read 305933 spots for ERR6133542.sra Written 305933 spots for ERR6133542.sra Rejected 305933 READS because READLEN < 1 Read 305933 spots for ERR6133542.sra Written 305933 spots for ERR6133542.sra Rejected 305933 READS because READLEN < 1 Read 305933 spots for ERR6133542.sra Written 305933 spots for ERR6133542.sra Rejected 305933 READS because READLEN < 1 Read 305933 spots for ERR6133542.sra Written 305933 spots for ERR6133542.sra Rejected 305933 READS because READLEN < 1 Read 305933 spots for ERR6133542.sra Written 305933 spots for ERR6133542.sra Rejected 305933 READS because READLEN < 1 Read 305933 spots for ERR6133542.sra Written 305933 spots for ERR6133542.sra SRR ids: ['ERR6133542.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_3y_jxfzs ERR6133542.sra spots: 6118678 blocks: [[1, 305933], [305934, 611866], [611867, 917799], [917800, 1223732], [1223733, 1529665], [1529666, 1835598], [1835599, 2141531], [2141532, 2447464], [2447465, 2753397], [2753398, 3059330], [3059331, 3365263], [3365264, 3671196], [3671197, 3977129], [3977130, 4283062], [4283063, 4588995], [4588996, 4894928], [4894929, 5200861], [5200862, 5506794], [5506795, 5812727], [5812728, 6118678]] ERR6133542 file size 1349481 ERR6133542 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 ERR6133542 ERR6133542_1.fastq Input file: ERR6133542_1.fastq trimmed: ERR6133542-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 08:17:15 2024 >> started Sat Dec 7 08:17:20 2024 >> done (5.251s) 6118678 reads processed; of these: 106 ( 0.00%) short reads filtered out after trimming by size control 15 ( 0.00%) empty reads filtered out after trimming by size control 6118557 (100.00%) reads available; of these: 103400 ( 1.69%) trimmed reads available after processing 6015157 (98.31%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 14 0.00% 19 87 0.00% 20 22 0.00% 21 17 0.00% 22 27 0.00% 23 4 0.00% 24 5 0.00% 25 7 0.00% 26 3 0.00% 27 5 0.00% 28 7 0.00% 29 19 0.00% 30 11 0.00% 31 15 0.00% 32 26 0.00% 33 10 0.00% 34 24 0.00% 35 100 0.00% 36 531 0.01% 37 23 0.00% 38 42 0.00% 39 109 0.00% 40 147 0.00% 41 41 0.00% 42 15 0.00% 43 15 0.00% 44 16 0.00% 45 11 0.00% 46 10 0.00% 47 8 0.00% 48 8 0.00% 49 8 0.00% 50 11 0.00% 51 74 0.00% 52 15 0.00% 53 10 0.00% 54 6 0.00% 55 6 0.00% 56 9 0.00% 57 12 0.00% 58 17 0.00% 59 11 0.00% 60 18 0.00% 61 16 0.00% 62 2 0.00% 63 9 0.00% 64 10 0.00% 65 8 0.00% 66 11 0.00% 67 37 0.00% 68 71 0.00% 69 260 0.00% 70 22127 0.36% 71 22654 0.37% 72 22199 0.36% 73 20560 0.34% 74 22012 0.36% 75 21817 0.36% 76 19742 0.32% 77 20714 0.34% 78 23411 0.38% 79 25909 0.42% 80 22775 0.37% 81 24780 0.40% 82 27928 0.46% 83 28851 0.47% 84 24288 0.40% 85 223 0.00% 86 423 0.01% 87 677 0.01% 88 1231 0.02% 89 2379 0.04% 90 5500 0.09% 91 16467 0.27% 92 70402 1.15% 93 5669488 92.66% 6118557 reads passed initial QC criterion=sequence-density sequence-density=0.45 sequence-density-rank=1 fanout-score=1.98 fanout-score-rank=36 prefix-density=0.45 prefix-fanout=2.0 sequence=CAAGGCTAAATAC criterion=fanout-score sequence-density=0.02 sequence-density-rank=25 fanout-score=191.37 fanout-score-rank=1 prefix-density=0.52 prefix-fanout=7.8 sequence=GAAGAAGAAAAGTTTTCTCAACATGGGGAGGAAGTCCCTCCGAAATTTGATTTGTTATTGTATTGTAAGGGGCTTTTTTAGTATTTATCTAAAGGAAGGAACAAACGAGGATAAGATAAAATTTCTTTAAATTTATTTTGCCCAAGTGGGATATATGGCATACTATTCTTTCCATTTTCATCTTTTTTTCTATTCCACTCCATCTAGATATAAGAAAGAACCCAATGCAATGAAATTCCACTAATATACAATACAAAAAAGAAGAATAGATACAGGGTCTCAAACCTTGCTATAGAGTTTTTGCTT Started job on | Dec 07 08:17:41 Started mapping on | Dec 07 08:17:41 Finished on | Dec 07 08:17:49 Mapping speed, Million of reads per hour | 2753.35 Number of input reads | 6118557 Average input read length | 92 UNIQUE READS: Uniquely mapped reads number | 4659804 Uniquely mapped reads % | 76.16% Average mapped length | 91.53 Number of splices: Total | 149165 Number of splices: Annotated (sjdb) | 121282 Number of splices: GT/AG | 139457 Number of splices: GC/AG | 5162 Number of splices: AT/AC | 75 Number of splices: Non-canonical | 4471 Mismatch rate per base, % | 0.51% Deletion rate per base | 0.05% Deletion average length | 1.88 Insertion rate per base | 0.03% Insertion average length | 1.79 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 1303635 % of reads mapped to multiple loci | 21.31% Number of reads mapped to too many loci | 56981 % of reads mapped to too many loci | 0.93% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.54% % of reads unmapped: other | 0.06% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 155118 155118 155118 N_multimapping 1303635 1303635 1303635 N_noFeature 340915 383046 4437062 N_ambiguous 201908 21434 706 UnstrandedReadsAssigned:4116981 PositiveStrandReadsAssigned:4255324 NegativeStrandReadsAssigned:222036 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=93 echo kmer=89 ERR6133542 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: ERR6133542-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 6,118,557 reads, 5,120,073 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,089 rounds 52973 ERR6133542.ke.tsv 35125 ERR6133542.se.tsv 88098 total ==> ERR6133542.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 133 26.0159 PNS24243 293 194 0 0 KQK14069 1603 1504 30 5.35321 KQK14071 474 375 0 0 ==> ERR6133542.se.tsv <== BRADI_1g14170v3 30 BRADI_1g53295v3 181 BRADI_1g59795v3 19 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 136 BRADI_1g74790v3 58 BRADI_1g09890v3 0 BRADI_1g77505v3 138 BRADI_1g48960v3 0 ERR6133542 completed mapping pipeline successfully