Starting /dee2/code/volunteer_pipeline.sh ERR6133424 current disk space = 1547148734464 free memory = 1600238924 ERR6133424 SRAfilesize a4d027aa17575e0da7ece8a13a807e4e ERR6133424.sra ERR6133424.sra file validated ERR6133424 is single end ERR6133424 is conventional basespace ERR6133424 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133424_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 35.25625 37.0 33.0 37.0 33.0 37.0 2 36.397 37.0 37.0 37.0 33.0 37.0 3 35.79175 37.0 37.0 37.0 33.0 37.0 4 35.6085 37.0 37.0 37.0 33.0 37.0 5 35.50025 37.0 37.0 37.0 33.0 37.0 6 35.714 37.0 37.0 37.0 33.0 37.0 7 37.376 37.0 37.0 40.0 33.0 40.0 8 37.35825 37.0 37.0 40.0 33.0 40.0 9 37.453 37.0 37.0 40.0 33.0 40.0 10-11 37.4045 37.0 37.0 40.0 33.0 40.0 12-13 37.307249999999996 37.0 37.0 40.0 33.0 40.0 14-15 37.2825 37.0 37.0 40.0 33.0 40.0 16-17 37.2035 37.0 37.0 40.0 33.0 40.0 18-19 37.353624999999994 37.0 37.0 40.0 33.0 40.0 20-21 37.526125 37.0 37.0 40.0 33.0 40.0 22-23 37.380250000000004 37.0 37.0 40.0 33.0 40.0 24-25 37.3775 37.0 37.0 40.0 33.0 40.0 26-27 37.222875 37.0 37.0 40.0 33.0 40.0 28-29 37.333375000000004 37.0 37.0 40.0 33.0 40.0 30-31 37.272375 37.0 37.0 40.0 33.0 40.0 32-33 37.212625 37.0 37.0 40.0 33.0 40.0 34-35 37.028125 37.0 37.0 40.0 33.0 40.0 36-37 36.9865 37.0 37.0 40.0 33.0 40.0 38-39 36.7435 37.0 37.0 40.0 33.0 40.0 40-41 36.606375 37.0 37.0 40.0 33.0 40.0 42-43 36.516125 37.0 37.0 40.0 33.0 40.0 44-45 36.337125 37.0 37.0 40.0 33.0 40.0 46-47 36.204875 37.0 37.0 37.0 33.0 40.0 48-49 36.00425 37.0 37.0 37.0 33.0 40.0 50-51 35.801 37.0 35.0 37.0 33.0 40.0 52-53 35.653999999999996 37.0 33.0 37.0 33.0 40.0 54-55 35.574875000000006 37.0 33.0 37.0 33.0 40.0 56-57 35.402874999999995 37.0 33.0 37.0 33.0 37.0 58-59 34.95375 37.0 33.0 37.0 33.0 37.0 60-61 34.896249999999995 37.0 33.0 37.0 33.0 37.0 62-63 34.8545 37.0 33.0 37.0 33.0 37.0 64-65 34.520875000000004 37.0 33.0 37.0 33.0 37.0 66-67 34.54925 37.0 33.0 37.0 33.0 37.0 68-69 33.221125 35.0 33.0 35.0 30.0 37.0 70-71 33.49383674555472 33.0 33.0 37.0 27.0 37.0 72-73 34.22468671679198 37.0 33.0 37.0 33.0 37.0 74-75 34.46649286218501 37.0 33.0 37.0 33.0 37.0 76-77 34.23689478653199 37.0 33.0 37.0 30.0 37.0 78-79 34.300585567636936 37.0 33.0 37.0 30.0 37.0 80-81 34.33611786520001 37.0 33.0 37.0 33.0 37.0 82-83 34.09431051986362 37.0 33.0 37.0 30.0 37.0 84-85 34.09356773487698 37.0 33.0 37.0 30.0 37.0 86-87 34.00329865516366 37.0 33.0 37.0 30.0 37.0 88-89 33.93986297893936 37.0 33.0 37.0 30.0 37.0 90-91 33.665820857650345 35.0 33.0 37.0 27.0 37.0 92-93 33.46257295102766 33.0 33.0 37.0 27.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 4.0 21 9.0 22 13.0 23 14.0 24 14.0 25 23.0 26 20.0 27 28.0 28 32.0 29 57.0 30 66.0 31 100.0 32 143.0 33 170.0 34 247.0 35 479.0 36 1010.0 37 1138.0 38 427.0 39 6.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 88.97500000000001 2.8000000000000003 2.4250000000000003 5.800000000000001 2 73.58679339669834 15.657828914457228 6.678339169584792 4.07703851925963 3 35.85 39.475 13.425 11.25 4 35.75 27.525 16.55 20.175 5 25.8 30.599999999999998 25.374999999999996 18.224999999999998 6 20.775 38.4 24.75 16.075 7 36.8 28.125 18.35 16.725 8 30.725 29.725 23.225 16.325 9 26.55 28.175 26.150000000000002 19.125 10-11 25.7125 27.325 27.2625 19.7 12-13 28.8625 26.224999999999998 26.787499999999998 18.125 14-15 22.412499999999998 30.099999999999998 27.950000000000003 19.537499999999998 16-17 25.362499999999997 31.3125 24.5625 18.7625 18-19 23.825 27.3375 27.0875 21.75 20-21 25.474999999999998 27.125 26.987499999999997 20.4125 22-23 27.0625 24.2 26.3125 22.425 24-25 26.174999999999997 23.625 28.3625 21.837500000000002 26-27 24.462500000000002 26.5 30.2375 18.8 28-29 25.162499999999998 27.537499999999998 27.400000000000002 19.900000000000002 30-31 27.025 25.324999999999996 25.8125 21.837500000000002 32-33 24.8125 27.175 26.937499999999996 21.075 34-35 24.837500000000002 26.05 28.287499999999998 20.825 36-37 26.1625 24.025 27.125 22.6875 38-39 25.8625 24.3125 31.0625 18.7625 40-41 27.075 24.875 26.887499999999996 21.1625 42-43 24.337500000000002 27.3875 27.500000000000004 20.775 44-45 23.8125 25.074999999999996 29.349999999999998 21.762500000000003 46-47 24.775 23.35 27.712500000000002 24.1625 48-49 24.8625 24.8 29.2 21.1375 50-51 24.837500000000002 26.650000000000002 28.537499999999998 19.975 52-53 25.1 26.375 27.437499999999996 21.087500000000002 54-55 24.2875 27.05 27.3875 21.275 56-57 26.187500000000004 25.937500000000004 28.349999999999998 19.525000000000002 58-59 24.1375 24.25 28.962500000000002 22.650000000000002 60-61 25.1875 24.775 28.475 21.5625 62-63 22.95 26.775 30.912499999999998 19.3625 64-65 23.6375 26.387500000000003 29.625 20.349999999999998 66-67 25.112499999999997 26.637499999999996 28.299999999999997 19.950000000000003 68-69 22.85 27.325 28.075 21.75 70-71 25.447266358063303 25.39722256974853 28.787689228074566 20.3678218441136 72-73 25.86466165413534 24.273182957393484 28.696741854636592 21.165413533834588 74-75 23.480662983425415 27.54897036664992 28.176795580110497 20.793571069814163 76-77 23.101106639839035 26.131790744466798 28.596579476861166 22.170523138832998 78-79 23.662680931403397 24.707363121460038 30.786658275645063 20.843297671491502 80-81 23.57539082198689 28.189611699445283 30.168935955622793 18.06606152294503 82-83 22.931143398610235 25.306380290587494 30.410612760581174 21.351863550221097 84-85 24.55006337135615 23.11787072243346 31.368821292775667 20.96324461343473 86-87 22.088302461304238 25.843694493783303 32.52981476782543 19.538188277087034 88-89 21.96143110885562 28.660238518142606 30.347627505709212 19.030702867292565 90-91 26.871352448617102 24.892159350418673 29.370718091854858 18.865770109109363 92-93 22.31667089571175 27.69601623953311 30.398376046688657 19.58893681806648 >>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 7.0 18 8.0 19 2.5 20 1.5 21 3.0 22 4.0 23 5.0 24 5.5 25 3.5 26 7.0 27 10.5 28 19.5 29 28.5 30 27.0 31 32.5 32 47.5 33 59.0 34 61.5 35 62.5 36 89.0 37 128.5 38 154.5 39 160.0 40 180.0 41 198.0 42 207.0 43 223.0 44 192.0 45 166.5 46 209.0 47 225.5 48 197.5 49 176.0 50 158.5 51 148.5 52 135.5 53 158.0 54 151.5 55 99.5 56 71.0 57 59.5 58 62.0 59 58.0 60 51.5 61 47.0 62 35.5 63 28.5 64 32.0 65 32.5 66 24.5 67 17.0 68 10.0 69 11.0 70 11.5 71 7.0 72 5.0 73 4.5 74 3.5 75 1.5 76 1.5 77 0.5 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 0.05 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 7.0 71 3.0 72 0.0 73 7.0 74 2.0 75 4.0 76 2.0 77 2.0 78 1.0 79 5.0 80 2.0 81 5.0 82 5.0 83 6.0 84 8.0 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 3941.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 81.475 #Duplication Level Percentage of deduplicated Percentage of total 1 92.94262043571648 75.725 2 4.173059220619822 6.800000000000001 3 1.1660018410555384 2.85 4 0.490948143602332 1.6 5 0.245474071801166 1.0 6 0.21478981282602025 1.05 7 0.15342129487572875 0.8750000000000001 8 0.03068425897514575 0.2 9 0.0 0.0 >10 0.5523166615526235 8.25 >50 0.03068425897514575 1.6500000000000001 >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 66 1.6500000000000001 No Hit GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGC 38 0.95 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 26 0.65 No Hit GGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGG 25 0.625 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 24 0.6 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 24 0.6 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 23 0.575 No Hit GGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGGG 23 0.575 No Hit GGGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTG 19 0.475 No Hit GGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACAAGCTCGTAA 17 0.42500000000000004 No Hit GGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTT 16 0.4 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 15 0.375 No Hit GGAAGAGCCCGAGCTGCTGCAGCAGGTTTTGAAAAGGGAATCGATCGTGA 14 0.35000000000000003 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 12 0.3 No Hit GGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAA 12 0.3 No Hit GGAGTCCCATATATATATGTATAAGATGCCAGCCCGGTTTCGTCAACCAT 11 0.27499999999999997 No Hit GGAGTATCCTTGATATATAAATATATAGATAAATAGATTTAAATGGAAAA 11 0.27499999999999997 No Hit GGGAGTATTATGAAAGGAGATTAATCATAGATTATCAAAAACCCTAGAAA 10 0.25 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 10 0.25 No Hit GGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAACCCTCTTAACT 8 0.2 No Hit CAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATAT 7 0.17500000000000002 No Hit GGGATGGAGCGACAGAAGTATGGAAATAGGATAAGGTAGCGGCGAGACGA 7 0.17500000000000002 No Hit GAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGC 7 0.17500000000000002 No Hit GGAAAAGAGGGGTTACTTTTTTTCATTTTTCCCTTAAAAGATAGGCTTTG 7 0.17500000000000002 No Hit GGTTTTGAAAAGGGAATCGATCGTGATTTAGAACCTGTTCTTTACATGAA 7 0.17500000000000002 No Hit GGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAAA 6 0.15 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 6 0.15 No Hit GGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGC 6 0.15 No Hit GGAGTGGGGGTGCCATACGCAAAAAGGAAGCGACTCATAGAATGGCAGAG 6 0.15 No Hit GGGCCGGGTATCTCTCTGCATGTACGTATGCCTGTAATGTACGTAGCTAC 6 0.15 No Hit GGAAATGGTGAAGATGATACGAATATGCCGGCCGGGTGCTGATATTGTGA 6 0.15 No Hit GGGGAAGTACACCAGCGACGGCGAGGCCGCCGCCGCCAAGGAAGGCATGT 6 0.15 No Hit GGAAGAGACTTATAATATTGTGGCTGCTCATGGTTATTTTGGCCGATTAA 5 0.125 No Hit GGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCG 5 0.125 No Hit GAAGCCTGTGTACAAGCTCGTAACGAAGGGCGCGATCTTGCTCGTGAAGG 5 0.125 No Hit GGGCAAGGAGAAGTACAAGTGCGGATCCAACGTCTTCTGGAAATGGTGAA 5 0.125 No Hit GGGAAACAACGAGGTCATCATCGACATGATATATTGCTGCTATTTTCCAC 5 0.125 No Hit GAAGGAACAAACGAGGATAAGATAAAATTTCTTTAAATTTATTTTGCCCA 5 0.125 No Hit GGAACAAACGAGGATAAGATAAAATTTCTTTAAATTTATTTTGCCCAAGT 5 0.125 No Hit GGGCAAGTTCATGTAAACATAGATCGATATATGGCGGAGCGCCATTTTAT 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 0.025 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 0.0625 0.0 0.0 0.0 0.0 20-21 0.075 0.0 0.0 0.0 0.0 22-23 0.075 0.0 0.0 0.0 0.0 24-25 0.075 0.0 0.0 0.0 0.0 26-27 0.075 0.0 0.0 0.0 0.0 28-29 0.075 0.0 0.0 0.0 0.0 30-31 0.075 0.0 0.0 0.0 0.0 32-33 0.075 0.0 0.0 0.0 0.0 34-35 0.075 0.0 0.0 0.0 0.0 36-37 0.075 0.0 0.0 0.0 0.0 38-39 0.075 0.0 0.0 0.0 0.0 40-41 0.075 0.0 0.0 0.0 0.0 42-43 0.075 0.0 0.0 0.0 0.0 44-45 0.075 0.0 0.0 0.0 0.0 46-47 0.075 0.0 0.0 0.0 0.0 48-49 0.075 0.0 0.0 0.0 0.0 50-51 0.075 0.0 0.0 0.0 0.0 52-53 0.075 0.0 0.0 0.0 0.0 54-55 0.075 0.0 0.0 0.0 0.0 56-57 0.075 0.0 0.0 0.0 0.0 58-59 0.075 0.0 0.0 0.0 0.0 60-61 0.075 0.0 0.0 0.0 0.0 62-63 0.075 0.0 0.0 0.0 0.0 64-65 0.075 0.0 0.0 0.0 0.0 66-67 0.075 0.0 0.0 0.0 0.0 68-69 0.075 0.0 0.0 0.0 0.0 70-71 0.075 0.0 0.0 0.0 0.0 72-73 0.075 0.0 0.0 0.0 0.0 74-75 0.075 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 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GGAACTT 25 0.006763133 51.8925 1 >>END_MODULE Rejected 182038 READS because READLEN < 1 Read 182038 spots for ERR6133424.sra Written 182038 spots for ERR6133424.sra Rejected 182038 READS because READLEN < 1 Read 182038 spots for ERR6133424.sra Written 182038 spots for ERR6133424.sra Rejected 182038 READS because READLEN < 1 Read 182038 spots for ERR6133424.sra Written 182038 spots for ERR6133424.sra Rejected 182038 READS because READLEN < 1 Read 182038 spots for ERR6133424.sra Written 182038 spots for ERR6133424.sra Rejected 182038 READS because READLEN < 1 Read 182038 spots for ERR6133424.sra Written 182038 spots for ERR6133424.sra Rejected 182038 READS because READLEN < 1 Read 182038 spots for ERR6133424.sra Written 182038 spots for ERR6133424.sra Rejected 182038 READS because READLEN < 1 Read 182038 spots for ERR6133424.sra Written 182038 spots for ERR6133424.sra Rejected 182038 READS because READLEN < 1 Read 182038 spots for ERR6133424.sra Written 182038 spots for ERR6133424.sra Rejected 182038 READS because READLEN < 1 Read 182038 spots for ERR6133424.sra Written 182038 spots for ERR6133424.sra Rejected 182038 READS because READLEN < 1 Read 182038 spots for ERR6133424.sra Written 182038 spots for ERR6133424.sra Rejected 182038 READS because READLEN < 1 Read 182038 spots for ERR6133424.sra Written 182038 spots for ERR6133424.sra Rejected 182038 READS because READLEN < 1 Read 182038 spots for ERR6133424.sra Written 182038 spots for ERR6133424.sra Rejected 182038 READS because READLEN < 1 Read 182038 spots for ERR6133424.sra Written 182038 spots for ERR6133424.sra Rejected 182038 READS because READLEN < 1 Read 182038 spots for ERR6133424.sra Written 182038 spots for ERR6133424.sra Rejected 182038 READS because READLEN < 1 Read 182038 spots for ERR6133424.sra Written 182038 spots for ERR6133424.sra Rejected 182038 READS because READLEN < 1 Read 182038 spots for ERR6133424.sra Written 182038 spots for ERR6133424.sra Rejected 182043 READS because READLEN < 1 Read 182043 spots for ERR6133424.sra Written 182043 spots for ERR6133424.sra Rejected 182038 READS because READLEN < 1 Read 182038 spots for ERR6133424.sra Written 182038 spots for ERR6133424.sra Rejected 182038 READS because READLEN < 1 Read 182038 spots for ERR6133424.sra Written 182038 spots for ERR6133424.sra Rejected 182038 READS because READLEN < 1 Read 182038 spots for ERR6133424.sra Written 182038 spots for ERR6133424.sra SRR ids: ['ERR6133424.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_o4yd06rl ERR6133424.sra spots: 3640765 blocks: [[1, 182038], [182039, 364076], [364077, 546114], [546115, 728152], [728153, 910190], [910191, 1092228], [1092229, 1274266], [1274267, 1456304], [1456305, 1638342], [1638343, 1820380], [1820381, 2002418], [2002419, 2184456], [2184457, 2366494], [2366495, 2548532], [2548533, 2730570], [2730571, 2912608], [2912609, 3094646], [3094647, 3276684], [3276685, 3458722], [3458723, 3640765]] ERR6133424 file size 806547 ERR6133424 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 ERR6133424 ERR6133424_1.fastq Input file: ERR6133424_1.fastq trimmed: ERR6133424-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 04:32:29 2024 >> started Sat Dec 7 04:32:31 2024 >> done (2.573s) 3640765 reads processed; of these: 2118 ( 0.06%) short reads filtered out after trimming by size control 34 ( 0.00%) empty reads filtered out after trimming by size control 3638613 (99.94%) reads available; of these: 46625 ( 1.28%) trimmed reads available after processing 3591988 (98.72%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 51 0.00% 19 42 0.00% 20 19 0.00% 21 15 0.00% 22 20 0.00% 23 19 0.00% 24 11 0.00% 25 9 0.00% 26 17 0.00% 27 9 0.00% 28 7 0.00% 29 75 0.00% 30 11 0.00% 31 7 0.00% 32 12 0.00% 33 23 0.00% 34 12 0.00% 35 11 0.00% 36 17 0.00% 37 7 0.00% 38 9 0.00% 39 27 0.00% 40 33 0.00% 41 27 0.00% 42 20 0.00% 43 35 0.00% 44 15 0.00% 45 33 0.00% 46 23 0.00% 47 20 0.00% 48 24 0.00% 49 34 0.00% 50 29 0.00% 51 34 0.00% 52 22 0.00% 53 22 0.00% 54 30 0.00% 55 30 0.00% 56 21 0.00% 57 16 0.00% 58 21 0.00% 59 22 0.00% 60 25 0.00% 61 16 0.00% 62 3 0.00% 63 0 0.00% 64 4 0.00% 65 3 0.00% 66 5 0.00% 67 12 0.00% 68 13 0.00% 69 60 0.00% 70 4036 0.11% 71 3708 0.10% 72 3828 0.11% 73 3484 0.10% 74 3883 0.11% 75 3810 0.10% 76 3433 0.09% 77 3559 0.10% 78 3965 0.11% 79 4888 0.13% 80 4201 0.12% 81 4286 0.12% 82 4925 0.14% 83 5402 0.15% 84 4123 0.11% 85 101 0.00% 86 217 0.01% 87 280 0.01% 88 560 0.02% 89 1076 0.03% 90 2641 0.07% 91 7635 0.21% 92 32208 0.89% 93 3531282 97.05% 3638613 reads passed initial QC criterion=sequence-density sequence-density=0.27 sequence-density-rank=1 fanout-score=2.84 fanout-score-rank=28 prefix-density=0.33 prefix-fanout=2.3 sequence=TGTACATTTGAACCCTGACTACACATATACACACATATACATGTAATATTATACAATCTGTCGAGTATGTGTTGGTTCA criterion=fanout-score sequence-density=0.03 sequence-density-rank=20 fanout-score=33.77 fanout-score-rank=1 prefix-density=0.22 prefix-fanout=4.2 sequence=GCTCAAGGACGTCGGGTACCCGGTGAAGCTGGGGAGCGGCGTGGCAGCTGCCGCCGCGTACCTTTCCAATGCCACGCCCCTCATCCCGTCCAGGATCTGATCTGATCCAGCAAATTCGACGAAATTCATCGGGATTACGACGAGAAAGAAGAAGAA Started job on | Dec 07 04:32:44 Started mapping on | Dec 07 04:32:44 Finished on | Dec 07 04:32:50 Mapping speed, Million of reads per hour | 2183.17 Number of input reads | 3638613 Average input read length | 92 UNIQUE READS: Uniquely mapped reads number | 2658597 Uniquely mapped reads % | 73.07% Average mapped length | 92.40 Number of splices: Total | 164834 Number of splices: Annotated (sjdb) | 140284 Number of splices: GT/AG | 158437 Number of splices: GC/AG | 3865 Number of splices: AT/AC | 71 Number of splices: Non-canonical | 2461 Mismatch rate per base, % | 0.40% Deletion rate per base | 0.04% Deletion average length | 1.85 Insertion rate per base | 0.02% Insertion average length | 2.03 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 913355 % of reads mapped to multiple loci | 25.10% Number of reads mapped to too many loci | 11071 % of reads mapped to too many loci | 0.30% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.51% % of reads unmapped: other | 0.02% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 66661 66661 66661 N_multimapping 913355 913355 913355 N_noFeature 151633 176782 2538647 N_ambiguous 105070 10373 244 UnstrandedReadsAssigned:2401894 PositiveStrandReadsAssigned:2471442 NegativeStrandReadsAssigned:119706 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=93 echo kmer=89 ERR6133424 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: ERR6133424-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 3,638,613 reads, 3,138,169 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 991 rounds 52973 ERR6133424.ke.tsv 35125 ERR6133424.se.tsv 88098 total ==> ERR6133424.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 83 25.5872 PNS24243 293 194 0 0 KQK14069 1603 1504 66 18.5607 KQK14071 474 375 0 0 ==> ERR6133424.se.tsv <== BRADI_1g14170v3 66 BRADI_1g53295v3 38 BRADI_1g59795v3 15 BRADI_1g07683v3 0 BRADI_1g00485v3 1 BRADI_1g20270v3 25 BRADI_1g74790v3 37 BRADI_1g09890v3 0 BRADI_1g77505v3 64 BRADI_1g48960v3 0 ERR6133424 completed mapping pipeline successfully