Starting /dee2/code/volunteer_pipeline.sh SRR5423448 current disk space = 3051503013888 free memory = 1581639076 SRR5423448 SRAfilesize 2de82eb7930ff56669d4badf1667e934 SRR5423448.sra SRR5423448.sra file validated SRR5423448 is single end SRR5423448 is conventional basespace SRR5423448 read1 length is 52 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR5423448_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 32.2435 34.0 31.0 34.0 30.0 34.0 2 32.36425 34.0 31.0 34.0 30.0 34.0 3 32.42175 34.0 31.0 34.0 30.0 34.0 4 35.7915 37.0 35.0 37.0 33.0 37.0 5 35.82075 37.0 35.0 37.0 33.0 37.0 6 35.89725 37.0 35.0 37.0 35.0 37.0 7 35.82 37.0 35.0 37.0 35.0 37.0 8 35.845 37.0 35.0 37.0 35.0 37.0 9 37.5355 39.0 37.0 39.0 35.0 39.0 10 37.4685 39.0 37.0 39.0 34.0 39.0 11 37.40525 39.0 37.0 39.0 34.0 39.0 12 37.39725 39.0 37.0 39.0 34.0 39.0 13 37.5395 39.0 37.0 39.0 35.0 39.0 14 38.679 40.0 38.0 41.0 34.0 41.0 15 38.76725 40.0 38.0 41.0 34.0 41.0 16 38.73375 40.0 38.0 41.0 34.0 41.0 17 38.6945 40.0 38.0 41.0 34.0 41.0 18 38.56 40.0 38.0 41.0 34.0 41.0 19 38.613 40.0 38.0 41.0 34.0 41.0 20 38.644 40.0 38.0 41.0 34.0 41.0 21 38.60475 40.0 38.0 41.0 34.0 41.0 22 38.6895 40.0 38.0 41.0 34.0 41.0 23 38.63475 40.0 38.0 41.0 34.0 41.0 24 38.7245 40.0 38.0 41.0 34.0 41.0 25 38.64 40.0 38.0 41.0 35.0 41.0 26 38.4795 40.0 38.0 41.0 34.0 41.0 27 38.51675 40.0 38.0 41.0 34.0 41.0 28 38.47725 40.0 38.0 41.0 34.0 41.0 29 38.29975 40.0 38.0 41.0 34.0 41.0 30 38.20775 40.0 38.0 41.0 33.0 41.0 31 38.063 40.0 38.0 41.0 33.0 41.0 32 37.981 40.0 38.0 41.0 33.0 41.0 33 37.907 40.0 38.0 41.0 33.0 41.0 34 37.91025 40.0 38.0 41.0 33.0 41.0 35 37.94825 40.0 38.0 41.0 33.0 41.0 36 37.827 40.0 38.0 41.0 32.0 41.0 37 37.7725 40.0 38.0 41.0 33.0 41.0 38 37.80775 40.0 38.0 41.0 33.0 41.0 39 37.59275 40.0 37.0 41.0 31.0 41.0 40 37.52625 40.0 37.0 41.0 31.0 41.0 41 37.54325 40.0 37.0 41.0 31.0 41.0 42 37.30325 40.0 37.0 41.0 31.0 41.0 43 37.28625 40.0 37.0 41.0 31.0 41.0 44 37.17525 40.0 37.0 41.0 30.0 41.0 45 37.30125 40.0 37.0 41.0 31.0 41.0 46 37.2805 40.0 37.0 41.0 31.0 41.0 47 37.19475 40.0 36.0 41.0 31.0 41.0 48 37.07075 40.0 36.0 41.0 31.0 41.0 49 37.1445 40.0 36.0 41.0 31.0 41.0 50 36.94725 39.0 36.0 41.0 30.0 41.0 51 36.79975 39.0 36.0 41.0 30.0 41.0 52 35.25075 38.0 34.0 40.0 26.0 41.0 >>END_MODULE >>Per tile sequence quality pass #Tile Base Mean 1305 1 0.0 1305 2 0.0 1305 3 0.0 1305 4 0.0 1305 5 0.0 1305 6 0.0 1305 7 0.0 1305 8 0.0 1305 9 0.0 1305 10 0.0 1305 11 0.0 1305 12 0.0 1305 13 0.0 1305 14 0.0 1305 15 0.0 1305 16 0.0 1305 17 0.0 1305 18 0.0 1305 19 0.0 1305 20 0.0 1305 21 0.0 1305 22 0.0 1305 23 0.0 1305 24 0.0 1305 25 0.0 1305 26 0.0 1305 27 0.0 1305 28 0.0 1305 29 0.0 1305 30 0.0 1305 31 0.0 1305 32 0.0 1305 33 0.0 1305 34 0.0 1305 35 0.0 1305 36 0.0 1305 37 0.0 1305 38 0.0 1305 39 0.0 1305 40 0.0 1305 41 0.0 1305 42 0.0 1305 43 0.0 1305 44 0.0 1305 45 0.0 1305 46 0.0 1305 47 0.0 1305 48 0.0 1305 49 0.0 1305 50 0.0 1305 51 0.0 1305 52 0.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 19 1.0 20 2.0 21 1.0 22 2.0 23 6.0 24 10.0 25 16.0 26 16.0 27 25.0 28 43.0 29 40.0 30 81.0 31 59.0 32 91.0 33 136.0 34 148.0 35 189.0 36 328.0 37 415.0 38 757.0 39 1633.0 40 1.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 36.493246623311656 10.630315157578789 5.52776388194097 47.34867433716858 2 21.099999999999998 14.174999999999999 35.875 28.849999999999998 3 22.3 17.424999999999997 22.225 38.05 4 25.825 24.925 20.625 28.625 5 24.15 31.35 23.225 21.275 6 18.25 33.775 23.425 24.55 7 14.799999999999999 23.599999999999998 42.199999999999996 19.400000000000002 8 17.224999999999998 23.025000000000002 30.5 29.25 9 18.325 21.375 33.4 26.900000000000002 10 17.974999999999998 38.75 23.674999999999997 19.6 11 22.075 28.125 22.025 27.775 12 20.25 24.575 26.125 29.049999999999997 13 18.925 27.725 28.4 24.95 14 19.725 28.275 27.700000000000003 24.3 15 20.925 27.025 26.6 25.45 16 20.5 27.224999999999998 27.425 24.85 17 21.275 27.775 26.275 24.675 18 21.375 26.825 25.575 26.224999999999998 19 21.2 28.575 25.6 24.625 20 21.475 27.525 25.724999999999998 25.275 21 20.474999999999998 28.225 26.075 25.224999999999998 22 20.474999999999998 28.025 26.375 25.124999999999996 23 21.275 27.525 25.15 26.05 24 21.45 26.375 25.424999999999997 26.75 25 20.45 28.249999999999996 27.200000000000003 24.099999999999998 26 21.05 28.349999999999998 25.650000000000002 24.95 27 20.7 27.425 27.3 24.575 28 21.725 27.525 27.400000000000002 23.35 29 20.125 27.375 27.325 25.174999999999997 30 21.65 25.900000000000002 26.35 26.1 31 21.475 27.150000000000002 27.05 24.325 32 21.2 27.200000000000003 28.15 23.45 33 21.349999999999998 27.425 26.025 25.2 34 19.900000000000002 27.6 27.725 24.775 35 20.95 26.775 26.25 26.025 36 21.4 25.974999999999998 25.2 27.425 37 20.474999999999998 26.200000000000003 26.974999999999998 26.35 38 21.325 25.95 25.55 27.175 39 21.7 25.474999999999998 25.95 26.875 40 20.7 27.500000000000004 24.2 27.6 41 21.25 26.85 25.074999999999996 26.825 42 20.65 26.275 26.924999999999997 26.150000000000002 43 20.925 27.125 25.75 26.200000000000003 44 23.425 26.35 26.025 24.2 45 22.275 24.8 25.7 27.224999999999998 46 21.7 27.675 25.074999999999996 25.55 47 22.925 27.025 24.375 25.674999999999997 48 22.45 27.375 23.674999999999997 26.5 49 21.525 27.150000000000002 25.25 26.075 50 21.775 27.725 25.124999999999996 25.374999999999996 51 20.825 27.375 24.125 27.675 52 21.875 28.299999999999997 24.3 25.525 >>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 0.5 12 1.0 13 1.0 14 1.0 15 1.0 16 2.0 17 3.0 18 2.5 19 2.0 20 5.0 21 8.0 22 11.0 23 14.0 24 13.5 25 13.0 26 17.0 27 21.0 28 29.0 29 37.0 30 44.5 31 52.0 32 69.5 33 87.0 34 93.5 35 100.0 36 131.5 37 163.0 38 201.0 39 234.5 40 230.0 41 250.5 42 271.0 43 294.5 44 318.0 45 319.5 46 321.0 47 329.0 48 337.0 49 326.5 50 316.0 51 331.5 52 347.0 53 345.0 54 343.0 55 276.5 56 210.0 57 192.0 58 174.0 59 163.0 60 152.0 61 117.5 62 83.0 63 76.5 64 49.5 65 29.0 66 28.5 67 28.0 68 21.5 69 15.0 70 9.0 71 3.0 72 2.5 73 2.0 74 2.5 75 3.0 76 2.5 77 2.0 78 1.5 79 1.0 80 1.0 81 1.0 82 0.5 83 0.0 84 0.5 85 1.0 86 0.5 87 0.0 88 0.0 89 0.0 90 0.0 91 0.5 92 1.0 93 0.5 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 0.05 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 88.5 #Duplication Level Percentage of deduplicated Percentage of total 1 93.78531073446328 83.0 2 3.8135593220338984 6.75 3 0.9887005649717515 2.625 4 0.39548022598870053 1.4000000000000001 5 0.39548022598870053 1.7500000000000002 6 0.1694915254237288 0.8999999999999999 7 0.14124293785310735 0.8750000000000001 8 0.11299435028248588 0.8 9 0.0847457627118644 0.675 >10 0.11299435028248588 1.225 >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 CCCGTCGGTCCACACAGTTGTCCATGTACCAGTAGAAGATTCAGCAGCTACT 14 0.35000000000000003 No Hit GGGGTAAGCTACATAAGCAATAAATTGATTTTCTTCTCCAGCAACGGGCTCG 12 0.3 No Hit CGTCGGTCCACACAGTTGTCCATGTACCAGTAGAAGATTCAGCAGCTACTGC 12 0.3 No Hit GGGTAAGCTACATAAGCAATAAATTGATTTTCTTCTCCAGCAACGGGCTCGA 11 0.27499999999999997 No Hit CTACGCCACACACATGACGGTTTACGTGCTTAATGACCGCATGTGCAGGTAG 9 0.22499999999999998 No Hit GTCGCGTATTTAAGTCGTCTGCAAAGGATTCTACCCGCCGCTCGGTGGGAAT 9 0.22499999999999998 No Hit CTGCAAAGGATTCTACCCGCCGCTCGGTGGGAATTGTACTTCAAGGCGGCCC 9 0.22499999999999998 No Hit CAGGGCTCCATTTGCTAGCTTCACGGATAATTTCATTACCCTCACGAGCAAG 8 0.2 No Hit GTCCTAGAAGTGCATGATAAATACCGCCAAAGCCCAATACTGCAGAGGAAAT 8 0.2 No Hit GTGCATAAGGATGTTGTGCTCAGCCTGGAATACAATCATAAAGTTAAAAGTA 8 0.2 No Hit GCTCCATTTGCTAGCTTCACGGATAATTTCATTACCCTCACGAGCAAGATCA 8 0.2 No Hit CGCGTATTTAAGTCGTCTGCAAAGGATTCTACCCGCCGCTCGGTGGGAATTG 7 0.17500000000000002 No Hit GCCCCATGTAACAAGCTACACCAAGTAAGAAGTGTAGAACAATTAGCTCATA 7 0.17500000000000002 No Hit CTCATTACGAGCTTGTACACATGCTTCTAGAGCTACTCGATTAGCAACGGCA 7 0.17500000000000002 No Hit CTCGTACACACTAAGAAAAAAGCCTTATCCATTTACAAAAGTCTTATCCATT 7 0.17500000000000002 No Hit CTCTGCCTCGGGTTGTCTCGCGATACCTTCTACAGCTTGGCCCGCAGCAGTA 7 0.17500000000000002 No Hit GTCCCTCATTACGAGCTTGTACACATGCTTCTAGAGCTACTCGATTAGCAAC 6 0.15 No Hit CTCACGAGCAAGATCACGTCCCTCATTACGAGCTTGTACACATGCTTCTAGA 6 0.15 No Hit GTCGGTCCACACAGTTGTCCATGTACCAGTAGAAGATTCAGCAGCTACTGCG 6 0.15 No Hit CTGGAATACAATCATAAAGTTAAAAGTACCAGAGATTCCTAGAGGCATCCCA 6 0.15 No Hit CAGCAACGGGCTCGATGTCGTAGCATCGTCCCTTATAACGATCAAGACTGGT 6 0.15 No Hit GTCCACACAGTTGTCCATGTACCAGTAGAAGATTCAGCAGCTACTGCGGCCC 6 0.15 No Hit CCACACAGTTGTCCATGTACCAGTAGAAGATTCAGCAGCTACTGCGGCCCCT 5 0.125 No Hit GCCCGTCGGTCCACACAGTTGTCCATGTACCAGTAGAAGATTCAGCAGCTAC 5 0.125 No Hit GGTGCATAAGGATGTTGTGCTCAGCCTGGAATACAATCATAAAGTTAAAAGT 5 0.125 No Hit CTTTTTTTTCCCTTCCACAAGTACTATAGCAGAAGGACACAAATTACATTAT 5 0.125 No Hit GCCGCCGCAACAGGAGCTGAATATGCAACAGCAATCCAAGGACGCATACCCA 5 0.125 No Hit CACACAGTTGTCCATGTACCAGTAGAAGATTCAGCAGCTACTGCGGCCCCTG 5 0.125 No Hit CCCTGATCAAACTAGAGGTTACCAAAGAACCATGCATAGCACTGAATAGGGA 5 0.125 No Hit GTGCTCAGCCTGGAATACAATCATAAAGTTAAAAGTACCAGAGATTCCTAGA 5 0.125 No Hit CTCCATTTGCTAGCTTCACGGATAATTTCATTACCCTCACGAGCAAGATCAC 5 0.125 No Hit GCCAGACTAAGCAATAAAGTACCTCGTATTTTCCCCTCTGCCTCGGGTTGTC 5 0.125 No Hit CTCGGTTGCTGGAACCTCCATGACTCCAGTGTAGACATGGCTCTTCTCAGTC 5 0.125 No Hit CTCCAGCAACGGGCTCGATGTCGTAGCATCGTCCCTTATAACGATCAAGACT 5 0.125 No Hit GTCGTCTGCAAAGGATTCTACCCGCCGCTCGGTGGGAATTGTACTTCAAGGC 5 0.125 No Hit GTTTCCCTGATCAAACTAGAGGTTACCAAAGAACCATGCATAGCACTGAATA 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 0.025 0.0 0.0 0.0 0.0 38 0.025 0.0 0.0 0.0 0.0 39 0.025 0.0 0.0 0.0 0.0 40 0.025 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Read 200000 spots for SRR5423448.sra Written 200000 spots for SRR5423448.sra Read 200000 spots for SRR5423448.sra Written 200000 spots for SRR5423448.sra Read 200000 spots for SRR5423448.sra Written 200000 spots for SRR5423448.sra Read 200000 spots for SRR5423448.sra Written 200000 spots for SRR5423448.sra Read 200000 spots for SRR5423448.sra Written 200000 spots for SRR5423448.sra Read 200000 spots for SRR5423448.sra Written 200000 spots for SRR5423448.sra Read 200000 spots for SRR5423448.sra Written 200000 spots for SRR5423448.sra Read 200000 spots for SRR5423448.sra Written 200000 spots for SRR5423448.sra Read 200000 spots for SRR5423448.sra Written 200000 spots for SRR5423448.sra Read 200000 spots for SRR5423448.sra Written 200000 spots for SRR5423448.sra Read 200000 spots for SRR5423448.sra Written 200000 spots for SRR5423448.sra Read 200000 spots for SRR5423448.sra Written 200000 spots for SRR5423448.sra Read 200000 spots for SRR5423448.sra Written 200000 spots for SRR5423448.sra Read 200000 spots for SRR5423448.sra Written 200000 spots for SRR5423448.sra Read 200000 spots for SRR5423448.sra Written 200000 spots for SRR5423448.sra Read 200000 spots for SRR5423448.sra Written 200000 spots for SRR5423448.sra Read 200000 spots for SRR5423448.sra Written 200000 spots for SRR5423448.sra Read 200000 spots for SRR5423448.sra Written 200000 spots for SRR5423448.sra Read 200000 spots for SRR5423448.sra Written 200000 spots for SRR5423448.sra Read 200000 spots for SRR5423448.sra Written 200000 spots for SRR5423448.sra SRR ids: ['SRR5423448.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_od695zn3 SRR5423448.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]] SRR5423448 file size 703934 SRR5423448 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 SRR5423448 SRR5423448_1.fastq Input file: SRR5423448_1.fastq trimmed: SRR5423448-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 Wed Feb 12 14:03:18 2025 >> started Wed Feb 12 14:03:20 2025 >> done (2.411s) 4000000 reads processed; of these: 143 ( 0.00%) short reads filtered out after trimming by size control 182 ( 0.00%) empty reads filtered out after trimming by size control 3999675 (99.99%) reads available; of these: 85351 ( 2.13%) trimmed reads available after processing 3914324 (97.87%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 6 0.00% 19 5 0.00% 20 5 0.00% 21 0 0.00% 22 1 0.00% 23 0 0.00% 24 3 0.00% 25 1 0.00% 26 4 0.00% 27 0 0.00% 28 1 0.00% 29 3 0.00% 30 2 0.00% 31 4 0.00% 32 3 0.00% 33 11 0.00% 34 9 0.00% 35 10 0.00% 36 10 0.00% 37 23 0.00% 38 32 0.00% 39 28 0.00% 40 38 0.00% 41 65 0.00% 42 96 0.00% 43 104 0.00% 44 181 0.00% 45 255 0.01% 46 349 0.01% 47 607 0.02% 48 1310 0.03% 49 3331 0.08% 50 10176 0.25% 51 68678 1.72% 52 3914324 97.87% 3999675 reads passed initial QC criterion=sequence-density sequence-density=0.19 sequence-density-rank=1 fanout-score=6.42 fanout-score-rank=8 prefix-density=0.79 prefix-fanout=1.5 sequence=ACGTGCTTAATACGTGCTTAA criterion=fanout-score sequence-density=0.02 sequence-density-rank=26 fanout-score=21.67 fanout-score-rank=1 prefix-density=0.31 prefix-fanout=1.3 sequence=CATTTTATTTCTATCTTTCCATACATAACCAAAAAATGGAAAAGATTCTTCAAGAGTCTCGGGTCCTAGAAGTGCATGATAAATACCGCCAAAGCCCAATACTGCAGAGGAAATTAAGTGAAGTACGCCAGATACAAAGTATGGAAAGGTGTCTATGACTTCCCCGCCAGGACCCACCCCCCAACCTAGAGTAGCTAGGTGGGGAAGTAAAATTAATCCTTGTTCATACATTGGCTTCTCCGGTACGAAATGGGCCACTTCAAATAGGTTCATTGCTCCGGCCCAGAATACGATTAATCCAGCATGGGCTACATGAGCTCCCAGCAG Started job on | Feb 12 14:03:33 Started mapping on | Feb 12 14:03:33 Finished on | Feb 12 14:03:38 Mapping speed, Million of reads per hour | 2879.77 Number of input reads | 3999675 Average input read length | 51 UNIQUE READS: Uniquely mapped reads number | 3137631 Uniquely mapped reads % | 78.45% Average mapped length | 51.74 Number of splices: Total | 298490 Number of splices: Annotated (sjdb) | 293688 Number of splices: GT/AG | 291935 Number of splices: GC/AG | 5221 Number of splices: AT/AC | 870 Number of splices: Non-canonical | 464 Mismatch rate per base, % | 0.37% Deletion rate per base | 0.01% Deletion average length | 2.33 Insertion rate per base | 0.00% Insertion average length | 1.37 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 679749 % of reads mapped to multiple loci | 17.00% Number of reads mapped to too many loci | 109827 % of reads mapped to too many loci | 2.75% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.80% % of reads unmapped: other | 0.01% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 182295 182295 182295 N_multimapping 679749 679749 679749 N_noFeature 410493 3091231 446610 N_ambiguous 19759 130 9367 UnstrandedReadsAssigned:2707379 PositiveStrandReadsAssigned:46270 NegativeStrandReadsAssigned:2681654 Dataset is classified negative stranded MeadianReadLen=52 20thPercentileLength=52 echo kmer=47 SRR5423448 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: SRR5423448-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 3,999,675 reads, 3,256,459 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,238 rounds 52401 SRR5423448.ke.tsv 34699 SRR5423448.se.tsv 87100 total ==> SRR5423448.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1919 163 22.9607 Potri.005G024800.1.v4.1 1035 936 27 7.7976 Potri.004G059700.1.v4.1 961 862 1 0.313593 Potri.007G009000.2.v4.1 1416 1317 0 0 Potri.003G141000.2.v4.1 2943 2844 53.3481 5.07064 Potri.016G087400.1.v4.1 270 171 12 18.9696 Potri.015G069301.1.v4.1 564 465 0 0 Potri.010G195200.1.v4.1 1773 1674 1.63531 0.26407 Potri.012G127500.1.v4.1 977 878 1 0.307878 ==> SRR5423448.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 0 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 45 Potri.001G212900.v4.1 0 Potri.001G182400.v4.1 0 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 1 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 0 SRR5423448 completed mapping pipeline successfully