Starting /dee2/code/volunteer_pipeline.sh ERR6133455 current disk space = 1545648680960 free memory = 1460668328 ERR6133455 SRAfilesize 647e36875cff6af36dfaa1345eb1162a ERR6133455.sra ERR6133455.sra file validated ERR6133455 is single end ERR6133455 is conventional basespace ERR6133455 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133455_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 47 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 34.5705 33.0 33.0 37.0 33.0 37.0 2 36.044 37.0 37.0 37.0 33.0 37.0 3 35.437 37.0 33.0 37.0 33.0 37.0 4 35.19475 37.0 37.0 37.0 33.0 37.0 5 35.00725 37.0 37.0 37.0 33.0 37.0 6 35.31775 37.0 37.0 37.0 33.0 37.0 7 36.822 37.0 37.0 40.0 33.0 40.0 8 37.10475 37.0 37.0 40.0 33.0 40.0 9 37.2405 37.0 37.0 40.0 33.0 40.0 10-11 37.204375 37.0 37.0 40.0 33.0 40.0 12-13 37.150375 37.0 37.0 40.0 33.0 40.0 14-15 36.979124999999996 37.0 37.0 40.0 33.0 40.0 16-17 36.810125 37.0 37.0 40.0 33.0 40.0 18-19 36.489625000000004 37.0 37.0 40.0 33.0 40.0 20-21 36.382374999999996 37.0 37.0 40.0 33.0 40.0 22-23 36.034625 37.0 35.0 40.0 33.0 40.0 24-25 36.047375 37.0 37.0 40.0 33.0 40.0 26-27 36.240875 37.0 37.0 40.0 33.0 40.0 28-29 36.158249999999995 37.0 37.0 40.0 33.0 40.0 30-31 36.242875 37.0 37.0 40.0 33.0 40.0 32-33 36.109375 37.0 35.0 40.0 33.0 40.0 34-35 36.189375 37.0 35.0 40.0 33.0 40.0 36-37 36.139375 37.0 37.0 40.0 33.0 40.0 38-39 36.032624999999996 37.0 35.0 40.0 33.0 40.0 40-41 35.9855 37.0 33.0 40.0 33.0 40.0 42-43 35.856750000000005 37.0 33.0 40.0 33.0 40.0 44-45 35.554 37.0 33.0 40.0 30.0 40.0 46-47 35.525375 37.0 33.0 40.0 33.0 40.0 48-49 35.448875 37.0 33.0 37.0 33.0 40.0 50-51 35.366749999999996 37.0 33.0 37.0 33.0 40.0 52-53 35.069 37.0 33.0 37.0 30.0 40.0 54-55 34.976375000000004 37.0 33.0 37.0 30.0 40.0 56-57 34.756625 37.0 33.0 37.0 27.0 40.0 58-59 34.151625 37.0 33.0 37.0 27.0 37.0 60-61 34.347375 37.0 33.0 37.0 27.0 37.0 62-63 34.228624999999994 37.0 33.0 37.0 27.0 37.0 64-65 33.968875 37.0 33.0 37.0 27.0 37.0 66-67 33.83925 37.0 33.0 37.0 27.0 37.0 68-69 33.11625 35.0 33.0 37.0 27.0 37.0 70-71 33.2031768018018 33.0 33.0 37.0 27.0 37.0 72-73 33.56415056843086 37.0 33.0 37.0 27.0 37.0 74-75 33.699180752545814 37.0 33.0 37.0 27.0 37.0 76-77 33.68224429497046 37.0 33.0 37.0 27.0 37.0 78-79 33.5851284056165 37.0 33.0 37.0 27.0 37.0 80-81 33.42258079039006 37.0 33.0 37.0 27.0 37.0 82-83 33.20068398499052 33.0 33.0 37.0 27.0 37.0 84-85 33.05685591061257 33.0 33.0 37.0 27.0 37.0 86-87 32.886040609137055 33.0 33.0 37.0 27.0 37.0 88-89 33.003934010152285 33.0 33.0 37.0 27.0 37.0 90-91 32.73223350253807 33.0 33.0 37.0 27.0 37.0 92-93 32.71662436548223 33.0 33.0 37.0 27.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 14.0 21 21.0 22 12.0 23 33.0 24 33.0 25 37.0 26 42.0 27 60.0 28 70.0 29 73.0 30 109.0 31 125.0 32 177.0 33 215.0 34 303.0 35 519.0 36 763.0 37 893.0 38 495.0 39 6.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 81.5 4.9 5.1 8.5 2 60.550000000000004 22.05 11.15 6.25 3 32.625 37.85 14.875 14.649999999999999 4 34.4 24.55 19.5 21.55 5 26.775 30.225 25.324999999999996 17.675 6 19.15 38.775 24.65 17.424999999999997 7 32.574999999999996 29.625 21.15 16.650000000000002 8 30.125 27.425 25.45 17.0 9 26.1 26.5 26.825 20.575 10-11 24.9875 26.424999999999997 28.1875 20.4 12-13 29.349999999999998 23.9875 25.937500000000004 20.724999999999998 14-15 24.3125 28.6625 27.575 19.45 16-17 25.724999999999998 29.612500000000004 24.925 19.7375 18-19 23.65 27.400000000000002 26.1625 22.787499999999998 20-21 24.4125 25.687500000000004 27.275 22.625 22-23 27.800000000000004 23.2625 26.825 22.112499999999997 24-25 27.474999999999998 25.087500000000002 25.8 21.637500000000003 26-27 26.85 25.825 27.950000000000003 19.375 28-29 27.0125 26.0375 25.424999999999997 21.525 30-31 28.262500000000003 25.7125 25.025 21.0 32-33 25.937500000000004 26.5875 27.0875 20.3875 34-35 26.25 25.3125 25.362499999999997 23.075000000000003 36-37 25.1875 25.25 27.675 21.8875 38-39 26.200000000000003 25.412499999999998 28.725 19.662499999999998 40-41 26.6625 26.6 25.2 21.5375 42-43 26.957718288716535 28.471353515136354 23.30497873405054 21.26594946209657 44-45 23.7375 26.0 26.6125 23.65 46-47 26.087500000000002 23.45 26.974999999999998 23.4875 48-49 25.525 24.6 27.85 22.025 50-51 26.025 25.85 27.175 20.95 52-53 25.55986488177155 27.67421493807081 24.25872638558739 22.50719379457025 54-55 25.362499999999997 27.35 26.0625 21.224999999999998 56-57 25.6 26.087500000000002 26.325 21.987499999999997 58-59 25.5 24.4875 28.0875 21.925 60-61 24.587500000000002 26.0125 27.6625 21.7375 62-63 23.0125 27.787499999999998 29.5875 19.6125 64-65 24.025 27.2625 27.537499999999998 21.175 66-67 25.900000000000002 27.224999999999998 25.412499999999998 21.462500000000002 68-69 23.8625 27.0125 25.1875 23.9375 70-71 26.32566283141571 25.850425212606304 25.7503751875938 22.07353676838419 72-73 26.214929859719437 24.423847695390783 26.966432865731466 22.394789579158317 74-75 22.675879396984925 29.334170854271356 27.462311557788944 20.527638190954775 76-77 23.191141311186612 24.852145463696992 27.721152636214924 24.23556058890147 78-79 27.637051039697543 24.574669187145556 26.918714555765593 20.869565217391305 80-81 25.656565656565654 26.666666666666668 29.103535353535353 18.57323232323232 82-83 25.85988872028326 24.013657056145675 27.807283763277695 22.319170460293375 84-85 25.155318879168252 22.619500443768224 29.922657537720298 22.302523139343222 86-87 24.53045685279188 25.368020304568528 29.708121827411166 20.393401015228427 88-89 23.248730964467004 28.464467005076145 28.134517766497463 20.15228426395939 90-91 27.220812182741117 26.68781725888325 26.20558375634518 19.885786802030456 92-93 24.35279187817259 28.895939086294415 27.00507614213198 19.746192893401016 >>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 0.5 13 0.5 14 0.0 15 0.0 16 0.5 17 10.5 18 12.0 19 3.0 20 1.5 21 3.0 22 4.0 23 5.0 24 8.0 25 5.5 26 3.0 27 11.5 28 18.0 29 18.0 30 18.5 31 19.5 32 24.5 33 29.0 34 51.0 35 71.5 36 93.0 37 139.5 38 161.0 39 145.5 40 144.5 41 165.5 42 171.0 43 166.5 44 162.5 45 156.5 46 191.5 47 198.0 48 154.0 49 159.0 50 185.5 51 189.5 52 175.5 53 175.5 54 163.0 55 115.5 56 85.5 57 80.5 58 77.0 59 65.0 60 54.5 61 57.5 62 54.5 63 42.5 64 36.5 65 37.0 66 32.5 67 22.0 68 21.0 69 22.5 70 15.5 71 10.0 72 9.5 73 11.0 74 9.0 75 5.0 76 3.5 77 1.5 78 1.0 79 1.5 80 2.0 81 1.0 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 0.075 44-45 0.0 46-47 0.0 48-49 0.0 50-51 0.0 52-53 0.08750000000000001 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 4.0 71 3.0 72 2.0 73 8.0 74 6.0 75 2.0 76 3.0 77 4.0 78 1.0 79 6.0 80 2.0 81 4.0 82 2.0 83 6.0 84 7.0 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 3940.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 79.05 #Duplication Level Percentage of deduplicated Percentage of total 1 93.9911448450348 74.3 2 3.6053130929791273 5.7 3 0.9487666034155597 2.25 4 0.31625553447185323 1.0 5 0.1265022137887413 0.5 6 0.09487666034155598 0.44999999999999996 7 0.15812776723592661 0.8750000000000001 8 0.0 0.0 9 0.06325110689437065 0.44999999999999996 >10 0.6641366223908919 13.05 >50 0.031625553447185324 1.425 >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 57 1.425 No Hit GTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAA 44 1.0999999999999999 No Hit GGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGG 43 1.075 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 39 0.975 No Hit GTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCT 38 0.95 No Hit GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGC 35 0.8750000000000001 No Hit GGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAA 34 0.8500000000000001 No Hit GGCCTGTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCG 29 0.7250000000000001 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 28 0.7000000000000001 No Hit GGGAGTATTATGAAAGGAGATTAATCATAGATTATCAAAAACCCTAGAAA 27 0.675 No Hit GGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGGG 27 0.675 No Hit GGGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTG 27 0.675 No Hit GGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTT 24 0.6 No Hit GGAGTATCCTTGATATATAAATATATAGATAAATAGATTTAAATGGAAAA 20 0.5 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 17 0.42500000000000004 No Hit GGGGGTCGCAGTGACCAGGCCCGGGCGACTGTTTACCAAAAACACAGGTC 17 0.42500000000000004 No Hit GGTGGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGC 14 0.35000000000000003 No Hit GACCACAGCGCATTCCCAATTAGCATCTAAGCTCTCGTTGACATTTCCTT 12 0.3 No Hit GGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCG 12 0.3 No Hit GGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAAATGGATTC 12 0.3 No Hit GGCTGCTTGGCCTGTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTA 12 0.3 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 11 0.27499999999999997 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 9 0.22499999999999998 No Hit GTATTTAGCCTTGCAAGGTGGTCCTTGCTGATTCACACGGGATTCCACGT 9 0.22499999999999998 No Hit GAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAAT 7 0.17500000000000002 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 7 0.17500000000000002 No Hit GGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAAA 7 0.17500000000000002 No Hit CAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTG 7 0.17500000000000002 No Hit TCAAAAGAGGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGGA 7 0.17500000000000002 No Hit GGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGT 6 0.15 No Hit GGGGAAGTACACCAGCGACGGCGAGGCCGCCGCCGCCAAGGAAGGCATGT 6 0.15 No Hit GGAAAAGAAAGCAAAAGCGATTCCCGTAGTAGCGGCGAGCGAAATGGGAG 6 0.15 No Hit CAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCT 5 0.125 No Hit GGGCCATTCACAGACACACACAACTACACAAGAGCTCTCAGCTGCTGCCC 5 0.125 No Hit GACAGACACACACAACTACACAAGAGCTCTCAGCTGCTGCCCACTTCTCT 5 0.125 No Hit GGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTG 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 0.025 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 0.025 0.0 0.0 0.0 0.0 36-37 0.037500000000000006 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 0.075 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 0.0875 0.0 0.0 0.0 0.0 64-65 0.1 0.0 0.0 0.0 0.0 66-67 0.1 0.0 0.0 0.0 0.0 68-69 0.1 0.0 0.0 0.0 0.0 70-71 0.1 0.0 0.0 0.0 0.0 72-73 0.1 0.0 0.0 0.0 0.0 74-75 0.1 0.0 0.0 0.0 0.0 76-77 0.1 0.0 0.0 0.0 0.0 78-79 0.1 0.0 0.0 0.0 0.0 80-81 0.1 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TCGTGAA 25 0.0021127714 35.533333 82-83 TTGCTCG 25 0.0021127714 35.533333 78-79 GAAGGTA 25 0.0021127714 35.533333 86-87 GCGATCT 25 0.002250884 35.083546 72-73 GCGCGAT 25 0.002250884 35.083546 70-71 AGAAGCC 25 0.0023960548 34.645 40-41 AACGAAG 25 0.0023960548 34.645 62-63 GTGTACA 25 0.0023960548 34.645 48-49 CGAAGGG 25 0.0023960548 34.645 64-65 GCTCGTA 25 0.0023960548 34.645 56-57 ACAAGCT 25 0.0023960548 34.645 52-53 TCGTAAC 25 0.0023960548 34.645 58-59 GGGCGCG 25 0.0023960548 34.645 68-69 GCCTGTG 25 0.0023960548 34.645 44-45 AAGCCTG 25 0.0023960548 34.645 42-43 GTAACGA 25 0.0023960548 34.645 60-61 GCTCGTG 30 0.0051628454 29.611113 80-81 TCTTGCT 30 0.0051628454 29.611113 76-77 GTGAAGG 30 0.0051628454 29.611113 84-85 GATCTTG 30 0.0053288396 29.422504 74-75 >>END_MODULE Rejected 110382 READS because READLEN < 1 Read 110382 spots for ERR6133455.sra Written 110382 spots for ERR6133455.sra Rejected 110382 READS because READLEN < 1 Read 110382 spots for ERR6133455.sra Written 110382 spots for ERR6133455.sra Rejected 110382 READS because READLEN < 1 Read 110382 spots for ERR6133455.sra Written 110382 spots for ERR6133455.sra Rejected 110382 READS because READLEN < 1 Read 110382 spots for ERR6133455.sra Written 110382 spots for ERR6133455.sra Rejected 110382 READS because READLEN < 1 Read 110382 spots for ERR6133455.sra Written 110382 spots for ERR6133455.sra Rejected 110382 READS because READLEN < 1 Read 110382 spots for ERR6133455.sra Written 110382 spots for ERR6133455.sra Rejected 110382 READS because READLEN < 1 Read 110382 spots for ERR6133455.sra Written 110382 spots for ERR6133455.sra Rejected 110382 READS because READLEN < 1 Read 110382 spots for ERR6133455.sra Written 110382 spots for ERR6133455.sra Rejected 110382 READS because READLEN < 1 Read 110382 spots for ERR6133455.sra Written 110382 spots for ERR6133455.sra Rejected 110382 READS because READLEN < 1 Read 110382 spots for ERR6133455.sra Written 110382 spots for ERR6133455.sra Rejected 110382 READS because READLEN < 1 Read 110382 spots for ERR6133455.sra Written 110382 spots for ERR6133455.sra Rejected 110382 READS because READLEN < 1 Read 110382 spots for ERR6133455.sra Written 110382 spots for ERR6133455.sra Rejected 110400 READS because READLEN < 1 Read 110400 spots for ERR6133455.sra Written 110400 spots for ERR6133455.sra Rejected 110382 READS because READLEN < 1 Read 110382 spots for ERR6133455.sra Written 110382 spots for ERR6133455.sra Rejected 110382 READS because READLEN < 1 Read 110382 spots for ERR6133455.sra Written 110382 spots for ERR6133455.sra Rejected 110382 READS because READLEN < 1 Read 110382 spots for ERR6133455.sra Written 110382 spots for ERR6133455.sra Rejected 110382 READS because READLEN < 1 Read 110382 spots for ERR6133455.sra Written 110382 spots for ERR6133455.sra Rejected 110382 READS because READLEN < 1 Read 110382 spots for ERR6133455.sra Written 110382 spots for ERR6133455.sra Rejected 110382 READS because READLEN < 1 Read 110382 spots for ERR6133455.sra Written 110382 spots for ERR6133455.sra Rejected 110382 READS because READLEN < 1 Read 110382 spots for ERR6133455.sra Written 110382 spots for ERR6133455.sra SRR ids: ['ERR6133455.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_y4b45pva ERR6133455.sra spots: 2207658 blocks: [[1, 110382], [110383, 220764], [220765, 331146], [331147, 441528], [441529, 551910], [551911, 662292], [662293, 772674], [772675, 883056], [883057, 993438], [993439, 1103820], [1103821, 1214202], [1214203, 1324584], [1324585, 1434966], [1434967, 1545348], [1545349, 1655730], [1655731, 1766112], [1766113, 1876494], [1876495, 1986876], [1986877, 2097258], [2097259, 2207658]] ERR6133455 file size 488037 ERR6133455 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 ERR6133455 ERR6133455_1.fastq Input file: ERR6133455_1.fastq trimmed: ERR6133455-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 06:22:43 2024 >> started Sat Dec 7 06:22:49 2024 >> done (5.831s) 2207658 reads processed; of these: 216 ( 0.01%) short reads filtered out after trimming by size control 17 ( 0.00%) empty reads filtered out after trimming by size control 2207425 (99.99%) reads available; of these: 41626 ( 1.89%) trimmed reads available after processing 2165799 (98.11%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 11 0.00% 19 42 0.00% 20 16 0.00% 21 29 0.00% 22 17 0.00% 23 13 0.00% 24 16 0.00% 25 18 0.00% 26 9 0.00% 27 15 0.00% 28 55 0.00% 29 42 0.00% 30 20 0.00% 31 19 0.00% 32 17 0.00% 33 37 0.00% 34 26 0.00% 35 80 0.00% 36 525 0.02% 37 20 0.00% 38 16 0.00% 39 68 0.00% 40 26 0.00% 41 46 0.00% 42 8 0.00% 43 23 0.00% 44 26 0.00% 45 14 0.00% 46 30 0.00% 47 8 0.00% 48 6 0.00% 49 7 0.00% 50 9 0.00% 51 40 0.00% 52 14 0.00% 53 8 0.00% 54 5 0.00% 55 7 0.00% 56 16 0.00% 57 29 0.00% 58 7 0.00% 59 7 0.00% 60 7 0.00% 61 12 0.00% 62 2 0.00% 63 5 0.00% 64 3 0.00% 65 5 0.00% 66 6 0.00% 67 8 0.00% 68 9 0.00% 69 39 0.00% 70 3140 0.14% 71 3163 0.14% 72 3071 0.14% 73 2966 0.13% 74 2961 0.13% 75 3062 0.14% 76 2610 0.12% 77 2482 0.11% 78 2503 0.11% 79 2659 0.12% 80 2448 0.11% 81 2521 0.11% 82 3153 0.14% 83 3278 0.15% 84 2622 0.12% 85 135 0.01% 86 252 0.01% 87 434 0.02% 88 695 0.03% 89 1273 0.06% 90 2651 0.12% 91 7304 0.33% 92 26427 1.20% 93 2124072 96.22% 2207425 reads passed initial QC criterion=sequence-density sequence-density=0.37 sequence-density-rank=1 fanout-score=17.03 fanout-score-rank=5 prefix-density=1.12 prefix-fanout=5.6 sequence=GAAGAAGAAGAAACAACTCCGGCCATGGCGGGCATCATCCACAAGATCGAGG criterion=fanout-score sequence-density=0.02 sequence-density-rank=28 fanout-score=34.30 fanout-score-rank=1 prefix-density=0.08 prefix-fanout=6.4 sequence=AGTTTGTTGACAAGTACGGCGCCAACGTCGACGGCTACAGCCCGATCTACACGCCGGAGGTATGGTCCGAATCTGGCGACCGCTACGCCGGTGGGACGACGGGGCTCCTGATCTGGGCCGTCACCCTGGCCGGCCTCCTCGGCGGCGGCGCCCTCCTCGTCTACAACACCAGCGCTCTCGCCGGCTAATTAAGAATCAAGTCATCTCATTCTCATCTATGCAATTGCAAACACAACACAGGGCCGGGTATCTCTCTGCATGTACGTATGCCTGTAATGTACGTAGCTACCTGCTGTGAAATGTACGTATGTGATCGATGATGCCAAGTACTTGATCGAAACGCATCGCTTAATTTTATGTATGTAT Started job on | Dec 07 06:23:10 Started mapping on | Dec 07 06:23:10 Finished on | Dec 07 06:23:32 Mapping speed, Million of reads per hour | 361.22 Number of input reads | 2207425 Average input read length | 92 UNIQUE READS: Uniquely mapped reads number | 1404283 Uniquely mapped reads % | 63.62% Average mapped length | 92.38 Number of splices: Total | 153232 Number of splices: Annotated (sjdb) | 130528 Number of splices: GT/AG | 149380 Number of splices: GC/AG | 2167 Number of splices: AT/AC | 54 Number of splices: Non-canonical | 1631 Mismatch rate per base, % | 0.49% Deletion rate per base | 0.04% Deletion average length | 1.77 Insertion rate per base | 0.02% Insertion average length | 1.87 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 720374 % of reads mapped to multiple loci | 32.63% Number of reads mapped to too many loci | 15212 % of reads mapped to too many loci | 0.69% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 3.00% % of reads unmapped: other | 0.06% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 82768 82768 82768 N_multimapping 720374 720374 720374 N_noFeature 83952 98686 1346240 N_ambiguous 50487 7138 196 UnstrandedReadsAssigned:1269844 PositiveStrandReadsAssigned:1298459 NegativeStrandReadsAssigned:57847 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=93 echo kmer=89 ERR6133455 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: ERR6133455-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 2,207,425 reads, 1,844,714 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 982 rounds 52973 ERR6133455.ke.tsv 35125 ERR6133455.se.tsv 88098 total ==> ERR6133455.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 837 0 0 PNS24247 1044 945 0.706885 0.521554 PNS24249 1928 1829 0 0 PNS24246 1044 945 0.706885 0.521554 PNS24248 1044 945 0.706885 0.521554 PNS24244 1471 1372 40.8793 20.7745 PNS24243 293 194 0 0 KQK14069 1603 1504 7 3.24513 KQK14071 474 375 0 0 ==> ERR6133455.se.tsv <== BRADI_1g14170v3 7 BRADI_1g53295v3 9 BRADI_1g59795v3 14 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 12 BRADI_1g74790v3 17 BRADI_1g09890v3 0 BRADI_1g77505v3 41 BRADI_1g48960v3 0 ERR6133455 completed mapping pipeline successfully