Starting /dee2/code/volunteer_pipeline.sh SRR5423413 current disk space = 3052660252672 free memory = 1580059004 SRR5423413 SRAfilesize 1880993144f5b49b07171e73c7e21eda SRR5423413.sra SRR5423413.sra file validated SRR5423413 is single end SRR5423413 is conventional basespace SRR5423413 read1 length is 52 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR5423413_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 52 %GC 47 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 31.85725 33.0 31.0 34.0 30.0 34.0 2 31.87275 33.0 31.0 34.0 30.0 34.0 3 32.14225 34.0 31.0 34.0 30.0 34.0 4 35.21075 37.0 35.0 37.0 32.0 37.0 5 35.492 37.0 35.0 37.0 33.0 37.0 6 35.5035 37.0 35.0 37.0 33.0 37.0 7 35.61625 37.0 35.0 37.0 33.0 37.0 8 35.5415 37.0 35.0 37.0 33.0 37.0 9 37.249 39.0 37.0 39.0 33.0 39.0 10 37.14675 39.0 37.0 39.0 33.0 39.0 11 37.05775 39.0 37.0 39.0 33.0 39.0 12 37.157 39.0 37.0 39.0 33.0 39.0 13 37.1375 39.0 37.0 39.0 33.0 39.0 14 38.563 40.0 38.0 41.0 34.0 41.0 15 38.521 40.0 38.0 41.0 34.0 41.0 16 38.439 40.0 38.0 41.0 34.0 41.0 17 38.42575 40.0 38.0 41.0 34.0 41.0 18 38.3715 40.0 38.0 41.0 33.0 41.0 19 38.40425 40.0 38.0 41.0 34.0 41.0 20 38.36725 40.0 38.0 41.0 34.0 41.0 21 38.2945 40.0 38.0 41.0 33.0 41.0 22 38.3965 40.0 38.0 41.0 34.0 41.0 23 38.3255 40.0 38.0 41.0 33.0 41.0 24 38.17575 40.0 37.0 41.0 33.0 41.0 25 37.9535 40.0 37.0 41.0 32.0 41.0 26 37.64925 40.0 37.0 41.0 32.0 41.0 27 37.79025 40.0 37.0 41.0 32.0 41.0 28 37.84225 40.0 37.0 41.0 33.0 41.0 29 37.90275 40.0 37.0 41.0 33.0 41.0 30 37.9475 40.0 38.0 41.0 33.0 41.0 31 37.7245 40.0 37.0 41.0 32.0 41.0 32 37.76875 40.0 37.0 41.0 32.0 41.0 33 37.77425 40.0 37.0 41.0 33.0 41.0 34 37.699 40.0 37.0 41.0 32.0 41.0 35 37.728 40.0 37.0 41.0 32.0 41.0 36 37.52875 40.0 37.0 41.0 31.0 41.0 37 37.51075 40.0 37.0 41.0 31.0 41.0 38 37.3155 40.0 37.0 41.0 30.0 41.0 39 37.38775 40.0 37.0 41.0 31.0 41.0 40 37.05475 40.0 36.0 41.0 30.0 41.0 41 37.234 39.0 36.0 41.0 31.0 41.0 42 37.25725 40.0 37.0 41.0 31.0 41.0 43 37.25125 40.0 36.0 41.0 31.0 41.0 44 37.11425 40.0 36.0 41.0 31.0 41.0 45 36.966 39.0 36.0 41.0 30.0 41.0 46 36.78575 39.0 36.0 41.0 30.0 41.0 47 36.75525 39.0 36.0 41.0 30.0 41.0 48 36.6485 39.0 35.0 41.0 30.0 41.0 49 36.92925 39.0 36.0 40.0 31.0 41.0 50 36.62275 39.0 35.0 41.0 30.0 41.0 51 36.368 39.0 35.0 40.0 29.0 41.0 52 35.31525 38.0 34.0 40.0 26.0 41.0 >>END_MODULE >>Per tile sequence quality pass #Tile Base Mean 2108 1 0.0 2108 2 0.0 2108 3 0.0 2108 4 0.0 2108 5 0.0 2108 6 0.0 2108 7 0.0 2108 8 0.0 2108 9 0.0 2108 10 0.0 2108 11 0.0 2108 12 0.0 2108 13 0.0 2108 14 0.0 2108 15 0.0 2108 16 0.0 2108 17 0.0 2108 18 0.0 2108 19 0.0 2108 20 0.0 2108 21 0.0 2108 22 0.0 2108 23 0.0 2108 24 0.0 2108 25 0.0 2108 26 0.0 2108 27 0.0 2108 28 0.0 2108 29 0.0 2108 30 0.0 2108 31 0.0 2108 32 0.0 2108 33 0.0 2108 34 0.0 2108 35 0.0 2108 36 0.0 2108 37 0.0 2108 38 0.0 2108 39 0.0 2108 40 0.0 2108 41 0.0 2108 42 0.0 2108 43 0.0 2108 44 0.0 2108 45 0.0 2108 46 0.0 2108 47 0.0 2108 48 0.0 2108 49 0.0 2108 50 0.0 2108 51 0.0 2108 52 0.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 18 2.0 19 0.0 20 2.0 21 3.0 22 6.0 23 5.0 24 8.0 25 17.0 26 12.0 27 34.0 28 47.0 29 77.0 30 67.0 31 92.0 32 105.0 33 133.0 34 187.0 35 237.0 36 332.0 37 463.0 38 765.0 39 1404.0 40 2.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 29.989969909729187 9.628886659979939 6.293881644934804 54.08726178535607 2 20.724999999999998 13.900000000000002 37.6 27.775 3 20.175 16.2 23.325000000000003 40.300000000000004 4 26.375 25.025 18.775 29.825000000000003 5 23.875 30.75 25.124999999999996 20.25 6 19.075 32.550000000000004 25.575 22.8 7 16.05 24.05 40.2 19.7 8 18.3 22.025 31.025000000000002 28.65 9 18.224999999999998 21.45 35.05 25.275 10 18.675 38.2 23.05 20.075000000000003 11 23.5 26.700000000000003 21.725 28.075 12 22.175 24.15 25.525 28.15 13 18.825 27.725 27.675 25.775 14 20.325 28.325 26.924999999999997 24.425 15 20.525 27.3 27.500000000000004 24.675 16 20.1 28.449999999999996 25.924999999999997 25.525 17 21.675 27.025 26.400000000000002 24.9 18 21.875 27.775 26.424999999999997 23.925 19 21.5 27.875 25.674999999999997 24.95 20 21.275 26.900000000000002 26.025 25.8 21 21.099999999999998 26.025 27.35 25.525 22 20.724999999999998 27.975 26.674999999999997 24.625 23 22.525000000000002 26.924999999999997 24.925 25.624999999999996 24 22.7 27.775 24.625 24.9 25 21.075 26.8 27.150000000000002 24.975 26 23.025000000000002 26.625 26.35 24.0 27 20.775 26.025 27.525 25.674999999999997 28 20.65 28.175 26.575 24.6 29 21.15 26.8 27.575 24.474999999999998 30 21.4 25.3 27.325 25.974999999999998 31 20.625 28.15 25.924999999999997 25.3 32 20.849999999999998 26.924999999999997 26.075 26.150000000000002 33 22.025 24.45 27.775 25.75 34 20.825 28.050000000000004 26.05 25.074999999999996 35 21.075 27.450000000000003 25.025 26.450000000000003 36 21.4 27.35 24.675 26.575 37 20.75 26.450000000000003 26.325 26.474999999999998 38 22.725 25.05 26.25 25.974999999999998 39 21.925 26.05 24.9 27.125 40 21.525 26.125 26.224999999999998 26.125 41 22.2 26.75 25.174999999999997 25.874999999999996 42 21.224999999999998 25.75 26.3 26.724999999999998 43 21.0 26.974999999999998 24.95 27.075 44 22.425 27.450000000000003 25.874999999999996 24.25 45 23.9 25.25 25.324999999999996 25.525 46 24.175 27.0 23.825 25.0 47 22.975 27.3 23.925 25.8 48 21.925 27.200000000000003 23.925 26.950000000000003 49 21.0 25.3 25.424999999999997 28.275 50 22.7 26.625 24.875 25.8 51 22.025 26.950000000000003 24.575 26.450000000000003 52 21.8 27.55 25.525 25.124999999999996 >>END_MODULE >>Per sequence GC content pass #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 0.5 14 1.0 15 1.0 16 0.5 17 0.0 18 1.0 19 2.0 20 3.0 21 4.0 22 6.5 23 9.0 24 9.0 25 9.0 26 11.5 27 14.0 28 26.5 29 39.0 30 45.5 31 52.0 32 67.0 33 82.0 34 103.0 35 124.0 36 141.0 37 158.0 38 184.5 39 221.0 40 231.0 41 240.0 42 249.0 43 276.5 44 304.0 45 328.5 46 353.0 47 345.5 48 338.0 49 325.5 50 313.0 51 333.0 52 353.0 53 340.0 54 327.0 55 268.5 56 210.0 57 195.5 58 181.0 59 171.5 60 162.0 61 134.0 62 106.0 63 80.5 64 50.0 65 45.0 66 39.0 67 33.0 68 22.5 69 12.0 70 10.0 71 8.0 72 9.0 73 10.0 74 6.0 75 2.0 76 1.5 77 1.0 78 1.0 79 1.0 80 0.5 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 0.3 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 0.0 18 0.0 19 0.0 20 0.0 21 0.0 22 0.0 23 0.0 24 0.0 25 0.0 26 0.0 27 0.0 28 0.0 29 0.0 30 0.0 31 0.0 32 0.0 33 0.0 34 0.0 35 0.0 36 0.0 37 0.0 38 0.0 39 0.0 40 0.0 41 0.0 42 0.0 43 0.0 44 0.0 45 0.0 46 0.0 47 0.0 48 0.0 49 0.0 50 0.0 51 0.0 52 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 52 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 86.075 #Duplication Level Percentage of deduplicated Percentage of total 1 92.91315713040953 79.975 2 3.8048213767063603 6.550000000000001 3 1.3941330235259948 3.5999999999999996 4 0.7841998257333721 2.7 5 0.23235550392099913 1.0 6 0.4066221318617485 2.1 7 0.17426662794074935 1.05 8 0.08713331397037467 0.6 9 0.08713331397037467 0.675 >10 0.11617775196049956 1.7500000000000002 >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 warn #Sequence Count Percentage Possible Source CGTCGGTCCACACAGTTGTCCATGTACCAGTAGAAGATTCAGCAGCTACTGC 25 0.625 No Hit CCCGTCGGTCCACACAGTTGTCCATGTACCAGTAGAAGATTCAGCAGCTACT 22 0.5499999999999999 No Hit GGGTAAGCTACATAAGCAATAAATTGATTTTCTTCTCCAGCAACGGGCTCGA 13 0.325 No Hit CTCATTACGAGCTTGTACACATGCTTCTAGAGCTACTCGATTAGCAACGGCA 10 0.25 No Hit CGCAGAAGTAGGAATAATGGCACCAGAAATGATATTGTTTCCATAAAGTAGA 9 0.22499999999999998 No Hit CTCGTATTTTCCCCTCTGCCTCGGGTTGTCTCGCGATACCTTCTACAGCTTG 9 0.22499999999999998 No Hit CCCACTTTTTGGTCTTAAGAATGCTGGTTTTAAGAATGAGTGATTGCCCTTC 9 0.22499999999999998 No Hit GCCAGACTAAGCAATAAAGTACCTCGTATTTTCCCCTCTGCCTCGGGTTGTC 8 0.2 No Hit CTCCAGCAACGGGCTCGATGTCGTAGCATCGTCCCTTATAACGATCAAGACT 8 0.2 No Hit CTCAGCCTGGAATACAATCATAAAGTTAAAAGTACCAGAGATTCCTAGAGGC 8 0.2 No Hit GCCCGTCGGTCCACACAGTTGTCCATGTACCAGTAGAAGATTCAGCAGCTAC 7 0.17500000000000002 No Hit GATCAAACTAGAGGTTACCAAAGAACCATGCATAGCACTGAATAGGGAGCCG 7 0.17500000000000002 No Hit CCTCATTACGAGCTTGTACACATGCTTCTAGAGCTACTCGATTAGCAACGGC 7 0.17500000000000002 No Hit GTCCGCGACCCCTGGATGCCGAAGGCGTCCTTGGGGCGATCTCGTAGTTCCT 7 0.17500000000000002 No Hit CTGCAAAGGATTCTACCCGCCGCTCGGTGGGAATTGTACTTCAAGGCGGCCC 7 0.17500000000000002 No Hit GGGGTAAGCTACATAAGCAATAAATTGATTTTCTTCTCCAGCAACGGGCTCG 7 0.17500000000000002 No Hit GTCCCTCATTACGAGCTTGTACACATGCTTCTAGAGCTACTCGATTAGCAAC 6 0.15 No Hit CTCCCAATCCCACATCAAACATGATAGTTGATGTGCTTGCTTAATGACCGCA 6 0.15 No Hit CTCACGAGCAAGATCACGTCCCTCATTACGAGCTTGTACACATGCTTCTAGA 6 0.15 No Hit GTGCTGAGTTGGAATCCCATTCTAACTAAGGATTCTTGTGGTTCCGGAGGAT 6 0.15 No Hit CACACAGTTGTCCATGTACCAGTAGAAGATTCAGCAGCTACTGCGGCCCCTG 6 0.15 No Hit GTCCCTTATAACGATCAAGACTGGTAAGCCCGTCGGTCCACACAGTTGTCCA 6 0.15 No Hit CCCGAAGCCACGGGTAGAACACCCGGTAGAGAGACCCAATCTTGAGTGAAAT 6 0.15 No Hit CCAGCAACGGGCTCGATGTCGTAGCATCGTCCCTTATAACGATCAAGACTGG 6 0.15 No Hit CCTCTGCCTCGGGTTGTCTCGCGATACCTTCTACAGCTTGGCCCGCAGCAGT 6 0.15 No Hit CTCGTACACACTAAGAAAAAAGCCTTATCCATTTACAAAAGTCTTATCCATT 6 0.15 No Hit ATCAAACTAGAGGTTACCAAAGAACCATGCATAGCACTGAATAGGGAGCCGC 6 0.15 No Hit CTCTGCCTCGGGTTGTCTCGCGATACCTTCTACAGCTTGGCCCGCAGCAGTA 6 0.15 No Hit GTTAAAACTAGCATATTGGAAGATCAATCGGCCAAAATAACCATGAGCGGCT 6 0.15 No Hit GCTCCATTTGCTAGCTTCACGGATAATTTCATTACCCTCACGAGCAAGATCA 6 0.15 No Hit GTCGGTCCACACAGTTGTCCATGTACCAGTAGAAGATTCAGCAGCTACTGCG 5 0.125 No Hit CTCATAAGGACCGCCGTTGTATAACCATTCATCAACGGATGCCGCTTCCCAT 5 0.125 No Hit GCCTCCTCAAGCTCAAGCAACACTTGAGATGCCTCAGTGCATCCAAACATGG 5 0.125 No Hit CTTCTCCGACCCTTACTGCCCAACCTGAGAGCGGACAGCTAATGCGTTCCAC 5 0.125 No Hit CTTATAACGATCAAGACTGGTAAGCCCGTCGGTCCACACAGTTGTCCATGTA 5 0.125 No Hit GCAAAGGATTCTACCCGCCGCTCGGTGGGAATTGTACTTCAAGGCGGCCCGC 5 0.125 No Hit GCCGCTTCCCATATTGGGTAAAAGTGCAACCCTATAGCCGCAGAAGTAGGAA 5 0.125 No Hit AAGCTACATAAGCAATAAATTGATTTTCTTCTCCAGCAACGGGCTCGATGTC 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 0.0 0.0 0.0 0.0 0.0 11 0.0 0.0 0.0 0.0 0.0 12 0.0 0.0 0.0 0.0 0.0 13 0.0 0.0 0.0 0.0 0.0 14 0.0 0.0 0.0 0.0 0.0 15 0.0 0.0 0.0 0.0 0.0 16 0.0 0.0 0.0 0.0 0.0 17 0.0 0.0 0.0 0.0 0.0 18 0.0 0.0 0.0 0.0 0.0 19 0.0 0.0 0.0 0.0 0.0 20 0.0 0.0 0.0 0.0 0.0 21 0.0 0.0 0.0 0.0 0.0 22 0.0 0.0 0.0 0.0 0.0 23 0.0 0.0 0.0 0.0 0.0 24 0.0 0.0 0.0 0.0 0.0 25 0.0 0.0 0.0 0.0 0.0 26 0.0 0.0 0.0 0.0 0.0 27 0.0 0.0 0.0 0.0 0.0 28 0.0 0.0 0.0 0.0 0.0 29 0.0 0.0 0.0 0.0 0.0 30 0.0 0.0 0.0 0.0 0.0 31 0.0 0.0 0.0 0.0 0.0 32 0.0 0.0 0.0 0.0 0.0 33 0.0 0.0 0.0 0.0 0.0 34 0.0 0.0 0.0 0.0 0.0 35 0.0 0.0 0.0 0.0 0.0 36 0.0 0.0 0.0 0.0 0.0 37 0.0 0.0 0.0 0.0 0.0 38 0.0 0.0 0.0 0.0 0.0 39 0.0 0.0 0.0 0.0 0.0 40 0.0 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Read 200000 spots for SRR5423413.sra Written 200000 spots for SRR5423413.sra Read 200000 spots for SRR5423413.sra Written 200000 spots for SRR5423413.sra Read 200000 spots for SRR5423413.sra Written 200000 spots for SRR5423413.sra Read 200000 spots for SRR5423413.sra Written 200000 spots for SRR5423413.sra Read 200000 spots for SRR5423413.sra Written 200000 spots for SRR5423413.sra Read 200000 spots for SRR5423413.sra Written 200000 spots for SRR5423413.sra Read 200000 spots for SRR5423413.sra Written 200000 spots for SRR5423413.sra Read 200000 spots for SRR5423413.sra Written 200000 spots for SRR5423413.sra Read 200000 spots for SRR5423413.sra Written 200000 spots for SRR5423413.sra Read 200000 spots for SRR5423413.sra Written 200000 spots for SRR5423413.sra Read 200000 spots for SRR5423413.sra Written 200000 spots for SRR5423413.sra Read 200000 spots for SRR5423413.sra Written 200000 spots for SRR5423413.sra Read 200000 spots for SRR5423413.sra Written 200000 spots for SRR5423413.sra Read 200000 spots for SRR5423413.sra Read 200000 spots for SRR5423413.sra Written 200000 spots for SRR5423413.sra Written 200000 spots for SRR5423413.sra Read 200000 spots for SRR5423413.sra Written 200000 spots for SRR5423413.sra Read 200000 spots for SRR5423413.sra Written 200000 spots for SRR5423413.sra Read 200000 spots for SRR5423413.sra Written 200000 spots for SRR5423413.sra Read 200000 spots for SRR5423413.sra Written 200000 spots for SRR5423413.sra Read 200000 spots for SRR5423413.sra Written 200000 spots for SRR5423413.sra SRR ids: ['SRR5423413.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_jd54345k SRR5423413.sra spots: 4000000 blocks: [[1, 200000], [200001, 400000], [400001, 600000], [600001, 800000], [800001, 1000000], [1000001, 1200000], [1200001, 1400000], [1400001, 1600000], [1600001, 1800000], [1800001, 2000000], [2000001, 2200000], [2200001, 2400000], [2400001, 2600000], [2600001, 2800000], [2800001, 3000000], [3000001, 3200000], [3200001, 3400000], [3400001, 3600000], [3600001, 3800000], [3800001, 4000000]] SRR5423413 file size 704005 SRR5423413 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 SRR5423413 SRR5423413_1.fastq Input file: SRR5423413_1.fastq trimmed: SRR5423413-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 Thu Feb 13 07:58:10 2025 >> started Thu Feb 13 07:58:51 2025 >> done (40.412s) 4000000 reads processed; of these: 117 ( 0.00%) short reads filtered out after trimming by size control 29 ( 0.00%) empty reads filtered out after trimming by size control 3999854 (100.00%) reads available; of these: 138348 ( 3.46%) trimmed reads available after processing 3861506 (96.54%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 8 0.00% 19 3 0.00% 20 5 0.00% 21 0 0.00% 22 1 0.00% 23 0 0.00% 24 0 0.00% 25 4 0.00% 26 3 0.00% 27 2 0.00% 28 3 0.00% 29 2 0.00% 30 7 0.00% 31 7 0.00% 32 8 0.00% 33 15 0.00% 34 10 0.00% 35 23 0.00% 36 23 0.00% 37 41 0.00% 38 38 0.00% 39 61 0.00% 40 71 0.00% 41 99 0.00% 42 169 0.00% 43 198 0.00% 44 445 0.01% 45 555 0.01% 46 755 0.02% 47 1083 0.03% 48 1959 0.05% 49 4488 0.11% 50 13695 0.34% 51 114567 2.86% 52 3861506 96.54% 3999854 reads passed initial QC criterion=sequence-density sequence-density=0.34 sequence-density-rank=1 fanout-score=3.65 fanout-score-rank=9 prefix-density=0.42 prefix-fanout=3.0 sequence=CCATTGCTTGCAATGGAAGTAATGTCATT criterion=fanout-score sequence-density=0.01 sequence-density-rank=25 fanout-score=31.49 fanout-score-rank=1 prefix-density=0.36 prefix-fanout=1.1 sequence=CATTTTATTTCTATCTTTCCATACATAACCAAAAAATGGAAAAGATTCTTCAAGAGTCTCGGGTCCTAGAAGTGCATGATAAATACCGCCAAAGCCCAATACTGCAGAGGAAATTAAGTGAAGTACGCCAGATACAAAGTATGGAAAGGTGTCTATGACTTCCCCGCCAGGACCCACCCCCCAACCTAGAGTAGCTAGGTGGGGAAGTAAAATTAATCCTTGTTCATACATTGGCTTCTCCGGTACGAAATGGGCCACTTCAAATAGGTTCATTGCTCCGGCCCAGAATACGATTAATCCAGCATGGGCTACATGAGCTCCCAGCAG Started job on | Feb 13 08:00:35 Started mapping on | Feb 13 08:00:41 Finished on | Feb 13 08:17:41 Mapping speed, Million of reads per hour | 14.12 Number of input reads | 3999854 Average input read length | 51 UNIQUE READS: Uniquely mapped reads number | 3106278 Uniquely mapped reads % | 77.66% Average mapped length | 51.77 Number of splices: Total | 273252 Number of splices: Annotated (sjdb) | 269730 Number of splices: GT/AG | 265483 Number of splices: GC/AG | 6248 Number of splices: AT/AC | 1013 Number of splices: Non-canonical | 508 Mismatch rate per base, % | 0.62% Deletion rate per base | 0.01% Deletion average length | 2.73 Insertion rate per base | 0.00% Insertion average length | 1.32 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 768215 % of reads mapped to multiple loci | 19.21% Number of reads mapped to too many loci | 53107 % of reads mapped to too many loci | 1.33% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.79% % of reads unmapped: other | 0.01% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 125361 125361 125361 N_multimapping 768215 768215 768215 N_noFeature 402639 3065707 431739 N_ambiguous 22630 152 11019 UnstrandedReadsAssigned:2681009 PositiveStrandReadsAssigned:40419 NegativeStrandReadsAssigned:2663520 Dataset is classified negative stranded MeadianReadLen=52 20thPercentileLength=52 echo kmer=47 SRR5423413 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: 52,400 [index] number of k-mers: 62,057,036 [index] number of equivalence classes: 130,681 [quant] running in single-end mode [quant] will process file 1: SRR5423413-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 3,999,854 reads, 3,182,461 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,051 rounds 52401 SRR5423413.ke.tsv 34699 SRR5423413.se.tsv 87100 total ==> SRR5423413.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1919 67 9.72274 Potri.005G024800.1.v4.1 1035 936 2 0.595036 Potri.004G059700.1.v4.1 961 862 3 0.969177 Potri.007G009000.2.v4.1 1416 1317 0 0 Potri.003G141000.2.v4.1 2943 2844 77.3145 7.57042 Potri.016G087400.1.v4.1 270 171 13 21.1708 Potri.015G069301.1.v4.1 564 465 0 0 Potri.010G195200.1.v4.1 1773 1674 0 0 Potri.012G127500.1.v4.1 977 878 7 2.2202 ==> SRR5423413.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 3 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 25 Potri.001G212900.v4.1 0 Potri.001G182400.v4.1 0 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 7 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 0 SRR5423413 completed mapping pipeline successfully