Starting /dee2/code/volunteer_pipeline.sh SRR5423447 current disk space = 3051544940544 free memory = 1582209260 SRR5423447 SRAfilesize aa9b969d32b2471106f3c2a4e2893fae SRR5423447.sra SRR5423447.sra file validated SRR5423447 is single end SRR5423447 is conventional basespace SRR5423447 read1 length is 52 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR5423447_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 31.938 33.0 31.0 34.0 30.0 34.0 2 32.1085 34.0 31.0 34.0 30.0 34.0 3 32.13225 34.0 31.0 34.0 30.0 34.0 4 35.23075 37.0 35.0 37.0 32.0 37.0 5 35.53575 37.0 35.0 37.0 33.0 37.0 6 35.596 37.0 35.0 37.0 33.0 37.0 7 35.67825 37.0 35.0 37.0 33.0 37.0 8 35.56825 37.0 35.0 37.0 33.0 37.0 9 37.341 39.0 37.0 39.0 34.0 39.0 10 37.10225 39.0 37.0 39.0 33.0 39.0 11 37.386 39.0 37.0 39.0 34.0 39.0 12 37.25875 39.0 37.0 39.0 33.0 39.0 13 37.2025 39.0 37.0 39.0 33.0 39.0 14 38.6405 40.0 38.0 41.0 34.0 41.0 15 38.53225 40.0 38.0 41.0 34.0 41.0 16 38.56525 40.0 38.0 41.0 34.0 41.0 17 38.496 40.0 38.0 41.0 34.0 41.0 18 38.542 40.0 38.0 41.0 34.0 41.0 19 38.305 40.0 38.0 41.0 33.0 41.0 20 38.39225 40.0 38.0 41.0 34.0 41.0 21 38.47125 40.0 38.0 41.0 34.0 41.0 22 38.44125 40.0 38.0 41.0 34.0 41.0 23 38.43225 40.0 38.0 41.0 34.0 41.0 24 38.3285 40.0 38.0 41.0 34.0 41.0 25 38.26075 40.0 38.0 41.0 33.0 41.0 26 38.1675 40.0 38.0 41.0 33.0 41.0 27 37.95075 40.0 37.0 41.0 32.0 41.0 28 37.979 40.0 37.0 41.0 33.0 41.0 29 38.0135 40.0 37.0 41.0 33.0 41.0 30 38.00825 40.0 38.0 41.0 33.0 41.0 31 37.9565 40.0 37.0 41.0 33.0 41.0 32 37.767 40.0 37.0 41.0 32.0 41.0 33 37.62575 40.0 37.0 41.0 32.0 41.0 34 37.803 40.0 37.0 41.0 33.0 41.0 35 37.771 40.0 37.0 41.0 33.0 41.0 36 37.766 40.0 37.0 41.0 33.0 41.0 37 37.682 40.0 37.0 41.0 32.0 41.0 38 37.46175 40.0 37.0 41.0 31.0 41.0 39 37.478 40.0 37.0 41.0 31.0 41.0 40 37.475 40.0 37.0 41.0 31.0 41.0 41 37.44975 40.0 37.0 41.0 32.0 41.0 42 37.381 40.0 37.0 41.0 31.0 41.0 43 37.336 40.0 36.0 41.0 31.0 41.0 44 37.22625 40.0 36.0 41.0 31.0 41.0 45 36.95575 39.0 36.0 41.0 30.0 41.0 46 36.9575 39.0 36.0 41.0 30.0 41.0 47 37.15425 39.0 36.0 41.0 31.0 41.0 48 36.8995 39.0 35.0 41.0 31.0 41.0 49 36.4295 39.0 35.0 41.0 29.0 41.0 50 36.55175 39.0 35.0 41.0 30.0 41.0 51 36.65675 39.0 35.0 41.0 30.0 41.0 52 35.2935 38.0 34.0 40.0 27.0 41.0 >>END_MODULE >>Per tile sequence quality pass #Tile Base Mean 1209 1 0.0 1209 2 0.0 1209 3 0.0 1209 4 0.0 1209 5 0.0 1209 6 0.0 1209 7 0.0 1209 8 0.0 1209 9 0.0 1209 10 0.0 1209 11 0.0 1209 12 0.0 1209 13 0.0 1209 14 0.0 1209 15 0.0 1209 16 0.0 1209 17 0.0 1209 18 0.0 1209 19 0.0 1209 20 0.0 1209 21 0.0 1209 22 0.0 1209 23 0.0 1209 24 0.0 1209 25 0.0 1209 26 0.0 1209 27 0.0 1209 28 0.0 1209 29 0.0 1209 30 0.0 1209 31 0.0 1209 32 0.0 1209 33 0.0 1209 34 0.0 1209 35 0.0 1209 36 0.0 1209 37 0.0 1209 38 0.0 1209 39 0.0 1209 40 0.0 1209 41 0.0 1209 42 0.0 1209 43 0.0 1209 44 0.0 1209 45 0.0 1209 46 0.0 1209 47 0.0 1209 48 0.0 1209 49 0.0 1209 50 0.0 1209 51 0.0 1209 52 0.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 18 1.0 19 2.0 20 1.0 21 3.0 22 4.0 23 5.0 24 8.0 25 13.0 26 15.0 27 25.0 28 45.0 29 53.0 30 81.0 31 90.0 32 109.0 33 129.0 34 201.0 35 211.0 36 321.0 37 453.0 38 747.0 39 1473.0 40 10.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 35.60511150087697 10.097719869706841 6.188925081433225 48.10824354798296 2 22.8 13.950000000000001 36.225 27.025 3 22.05 17.549999999999997 23.5 36.9 4 26.275 25.85 20.7 27.175 5 25.25 30.725 23.125 20.9 6 19.85 32.324999999999996 24.099999999999998 23.724999999999998 7 14.799999999999999 23.849999999999998 42.05 19.3 8 18.0 24.075 29.925 28.000000000000004 9 17.925 22.7 32.300000000000004 27.075 10 18.125 38.05 25.2 18.625 11 23.125 28.249999999999996 21.15 27.474999999999998 12 23.1 24.425 25.7 26.775 13 18.975 28.275 27.750000000000004 25.0 14 19.85 29.475 27.625 23.05 15 21.9 26.5 26.474999999999998 25.124999999999996 16 20.65 27.750000000000004 26.025 25.575 17 21.825 25.924999999999997 27.725 24.525 18 21.224999999999998 27.450000000000003 25.95 25.374999999999996 19 21.275 27.474999999999998 25.2 26.05 20 19.675 27.725 25.474999999999998 27.125 21 20.825 27.175 26.1 25.900000000000002 22 21.525 27.85 24.3 26.325 23 21.025 28.349999999999998 25.1 25.525 24 21.15 27.1 25.75 26.0 25 22.15 27.275 25.7 24.875 26 22.675 26.875 25.874999999999996 24.575 27 20.724999999999998 27.500000000000004 26.174999999999997 25.6 28 20.549999999999997 27.700000000000003 27.200000000000003 24.55 29 21.075 28.349999999999998 26.25 24.325 30 21.4 24.474999999999998 27.975 26.150000000000002 31 21.5 28.125 25.4 24.975 32 21.4 27.675 26.75 24.175 33 20.225 26.875 26.674999999999997 26.224999999999998 34 20.9 27.425 26.450000000000003 25.224999999999998 35 20.349999999999998 27.0 25.3 27.35 36 21.15 27.425 24.875 26.55 37 21.25 26.424999999999997 25.224999999999998 27.1 38 20.225 25.900000000000002 26.25 27.625 39 20.599999999999998 25.275 26.825 27.3 40 21.55 27.224999999999998 24.075 27.150000000000002 41 22.1 26.375 25.124999999999996 26.400000000000002 42 20.75 24.975 26.8 27.474999999999998 43 21.725 27.224999999999998 26.025 25.025 44 22.35 26.25 26.224999999999998 25.174999999999997 45 22.775000000000002 24.425 26.35 26.450000000000003 46 23.825 26.0 25.45 24.725 47 23.724999999999998 26.125 24.775 25.374999999999996 48 22.425 27.250000000000004 23.575 26.75 49 22.15 25.95 25.275 26.625 50 22.375 27.900000000000002 25.6 24.125 51 23.25 25.575 25.4 25.775 52 21.875 26.174999999999997 25.95 26.0 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 1.0 1 0.5 2 0.0 3 0.0 4 0.0 5 1.0 6 2.0 7 1.5 8 1.0 9 0.5 10 0.0 11 0.0 12 0.0 13 0.0 14 0.5 15 1.0 16 1.5 17 2.0 18 2.5 19 3.0 20 4.0 21 5.0 22 9.0 23 13.0 24 10.0 25 7.0 26 11.0 27 15.0 28 24.5 29 34.0 30 42.0 31 50.0 32 62.0 33 74.0 34 96.5 35 119.0 36 130.0 37 141.0 38 193.0 39 249.5 40 254.0 41 259.0 42 264.0 43 292.5 44 321.0 45 326.5 46 332.0 47 321.0 48 310.0 49 319.5 50 329.0 51 315.0 52 301.0 53 326.0 54 351.0 55 289.0 56 227.0 57 198.0 58 169.0 59 146.0 60 123.0 61 126.0 62 129.0 63 98.5 64 56.5 65 45.0 66 32.5 67 20.0 68 17.0 69 14.0 70 11.5 71 9.0 72 7.5 73 6.0 74 5.5 75 5.0 76 4.0 77 3.0 78 3.0 79 3.0 80 3.0 81 3.0 82 2.0 83 1.0 84 0.5 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 0.22499999999999998 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 87.02499999999999 #Duplication Level Percentage of deduplicated Percentage of total 1 92.73197357081298 80.7 2 4.481470841712152 7.8 3 1.292731973570813 3.375 4 0.4883654122378627 1.7000000000000002 5 0.3447285262855501 1.5 6 0.14363688595231255 0.75 7 0.2010916403332376 1.225 8 0.08618213157138753 0.6 9 0.08618213157138753 0.675 >10 0.14363688595231255 1.675 >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 16 0.4 No Hit GGGGTAAGCTACATAAGCAATAAATTGATTTTCTTCTCCAGCAACGGGCTCG 15 0.375 No Hit GGGTAAGCTACATAAGCAATAAATTGATTTTCTTCTCCAGCAACGGGCTCGA 14 0.35000000000000003 No Hit CTGCAAAGGATTCTACCCGCCGCTCGGTGGGAATTGTACTTCAAGGCGGCCC 12 0.3 No Hit GTCGCGTATTTAAGTCGTCTGCAAAGGATTCTACCCGCCGCTCGGTGGGAAT 10 0.25 No Hit CGCGTATTTAAGTCGTCTGCAAAGGATTCTACCCGCCGCTCGGTGGGAATTG 9 0.22499999999999998 No Hit CTCGGTTGCTGGAACCTCCATGACTCCAGTGTAGACATGGCTCTTCTCAGTC 9 0.22499999999999998 No Hit CTCAGCCTGGAATACAATCATAAAGTTAAAAGTACCAGAGATTCCTAGAGGC 9 0.22499999999999998 No Hit GTGCTCAGCCTGGAATACAATCATAAAGTTAAAAGTACCAGAGATTCCTAGA 8 0.2 No Hit GTAAGCTACATAAGCAATAAATTGATTTTCTTCTCCAGCAACGGGCTCGATG 8 0.2 No Hit GCTCCATTTGCTAGCTTCACGGATAATTTCATTACCCTCACGAGCAAGATCA 8 0.2 No Hit CTCGTATTTTCCCCTCTGCCTCGGGTTGTCTCGCGATACCTTCTACAGCTTG 7 0.17500000000000002 No Hit CCCTACGCCACACACATGACGGTTTACGTGCTTAATGACCGCATGTGCAGGT 7 0.17500000000000002 No Hit GCCCGTCGGTCCACACAGTTGTCCATGTACCAGTAGAAGATTCAGCAGCTAC 7 0.17500000000000002 No Hit AAAGGATTCTACCCGCCGCTCGGTGGGAATTGTACTTCAAGGCGGCCCGCGC 7 0.17500000000000002 No Hit CCAGCAACGGGCTCGATGTCGTAGCATCGTCCCTTATAACGATCAAGACTGG 7 0.17500000000000002 No Hit CTCATTACGAGCTTGTACACATGCTTCTAGAGCTACTCGATTAGCAACGGCA 7 0.17500000000000002 No Hit CCTCTGCCTCGGGTTGTCTCGCGATACCTTCTACAGCTTGGCCCGCAGCAGT 7 0.17500000000000002 No Hit CGCAGAAGTAGGAATAATGGCACCAGAAATGATATTGTTTCCATAAAGTAGA 6 0.15 No Hit GTCCATGTACCAGTAGAAGATTCAGCAGCTACTGCGGCCCCTGCTTCCTCGG 6 0.15 No Hit CACACAGTTGTCCATGTACCAGTAGAAGATTCAGCAGCTACTGCGGCCCCTG 6 0.15 No Hit CCCACTTTTTGGTCTTAAGAATGCTGGTTTTAAGAATGAGTGATTGCCCTTC 6 0.15 No Hit GTGCATAAGGATGTTGTGCTCAGCCTGGAATACAATCATAAAGTTAAAAGTA 6 0.15 No Hit CTACGCCACACACATGACGGTTTACGTGCTTAATGACCGCATGTGCAGGTAG 5 0.125 No Hit GTCCCTCATTACGAGCTTGTACACATGCTTCTAGAGCTACTCGATTAGCAAC 5 0.125 No Hit CTCGGGTCCTAGAAGTGCATGATAAATACCGCCAAAGCCCAATACTGCAGAG 5 0.125 No Hit CTCACGAGCAAGATCACGTCCCTCATTACGAGCTTGTACACATGCTTCTAGA 5 0.125 No Hit CCCTCATTACGAGCTTGTACACATGCTTCTAGAGCTACTCGATTAGCAACGG 5 0.125 No Hit CTCTTGACCAAATCTGTAACCTTCATTAGCAGATTCATTTTCTGTGGTTTCC 5 0.125 No Hit CCAGAAATGATATTGTTTCCATAAAGTAGAGATCCAGAAACAGGTTCACGAA 5 0.125 No Hit GGCTCCATTTGCTAGCTTCACGGATAATTTCATTACCCTCACGAGCAAGATC 5 0.125 No Hit GTCCACACAGTTGTCCATGTACCAGTAGAAGATTCAGCAGCTACTGCGGCCC 5 0.125 No Hit ATCAAACTAGAGGTTACCAAAGAACCATGCATAGCACTGAATAGGGAGCCGC 5 0.125 No Hit CTAACATGTGAAATGGGTGCATAAGGATGTTGTGCTCAGCCTGGAATACAAT 5 0.125 No Hit GTAACCTTCATTAGCAGATTCATTTTCTGTGGTTTCCCTGATCAAACTAGAG 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 SRR5423447.sra Written 200000 spots for SRR5423447.sra Read 200000 spots for SRR5423447.sra Written 200000 spots for SRR5423447.sra Read 200000 spots for SRR5423447.sra Written 200000 spots for SRR5423447.sra Read 200000 spots for SRR5423447.sra Written 200000 spots for SRR5423447.sra Read 200000 spots for SRR5423447.sra Written 200000 spots for SRR5423447.sra Read 200000 spots for SRR5423447.sra Written 200000 spots for SRR5423447.sra Read 200000 spots for SRR5423447.sra Written 200000 spots for SRR5423447.sra Read 200000 spots for SRR5423447.sra Written 200000 spots for SRR5423447.sra Read 200000 spots for SRR5423447.sra Written 200000 spots for SRR5423447.sra Read 200000 spots for SRR5423447.sra Written 200000 spots for SRR5423447.sra Read 200000 spots for SRR5423447.sra Written 200000 spots for SRR5423447.sra Read 200000 spots for SRR5423447.sra Written 200000 spots for SRR5423447.sra Read 200000 spots for SRR5423447.sra Written 200000 spots for SRR5423447.sra Read 200000 spots for SRR5423447.sra Written 200000 spots for SRR5423447.sra Read 200000 spots for SRR5423447.sra Written 200000 spots for SRR5423447.sra Read 200000 spots for SRR5423447.sra Written 200000 spots for SRR5423447.sra Read 200000 spots for SRR5423447.sra Written 200000 spots for SRR5423447.sra Read 200000 spots for SRR5423447.sra Written 200000 spots for SRR5423447.sra Read 200000 spots for SRR5423447.sra Written 200000 spots for SRR5423447.sra Read 200000 spots for SRR5423447.sra Written 200000 spots for SRR5423447.sra SRR ids: ['SRR5423447.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_4jjb3u7q SRR5423447.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]] SRR5423447 file size 703961 SRR5423447 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 SRR5423447 SRR5423447_1.fastq Input file: SRR5423447_1.fastq trimmed: SRR5423447-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 14:00:02 2025 >> started Wed Feb 12 14:00:04 2025 >> done (1.874s) 4000000 reads processed; of these: 182 ( 0.00%) short reads filtered out after trimming by size control 198 ( 0.00%) empty reads filtered out after trimming by size control 3999620 (99.99%) reads available; of these: 100423 ( 2.51%) trimmed reads available after processing 3899197 (97.49%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 4 0.00% 19 3 0.00% 20 4 0.00% 21 0 0.00% 22 0 0.00% 23 4 0.00% 24 3 0.00% 25 1 0.00% 26 3 0.00% 27 2 0.00% 28 4 0.00% 29 6 0.00% 30 5 0.00% 31 9 0.00% 32 9 0.00% 33 13 0.00% 34 21 0.00% 35 16 0.00% 36 27 0.00% 37 32 0.00% 38 36 0.00% 39 50 0.00% 40 61 0.00% 41 82 0.00% 42 163 0.00% 43 169 0.00% 44 352 0.01% 45 480 0.01% 46 611 0.02% 47 1059 0.03% 48 1884 0.05% 49 4512 0.11% 50 12971 0.32% 51 77827 1.95% 52 3899197 97.49% 3999620 reads passed initial QC criterion=sequence-density sequence-density=0.19 sequence-density-rank=1 fanout-score=6.50 fanout-score-rank=7 prefix-density=0.79 prefix-fanout=1.5 sequence=ACGTGCTTAATACGTGCTTAA criterion=fanout-score sequence-density=0.02 sequence-density-rank=25 fanout-score=21.36 fanout-score-rank=1 prefix-density=0.31 prefix-fanout=1.3 sequence=CATTTTATTTCTATCTTTCCATACATAACCAAAAAATGGAAAAGATTCTTCAAGAGTCTCGGGTCCTAGAAGTGCATGATAAATACCGCCAAAGCCCAATACTGCAGAGGAAATTAAGTGAAGTACGCCAGATACAAAGTATGGAAAGGTGTCTATGACTTCCCCGCCAGGACCCACCCCCCAACCTAGAGTAGCTAGGTGGGGAAGTAAAATTAATCCTTGTTCATACATTGGCTTCTCCGGTACGAAATGGGCCACTTCAAATAGGTTCATTGCTCCGGCCCAGAATACGATTAATCCAGCATGGGCTACATGAGCTCCCAGCAG Started job on | Feb 12 14:00:15 Started mapping on | Feb 12 14:00:15 Finished on | Feb 12 14:00:20 Mapping speed, Million of reads per hour | 2879.73 Number of input reads | 3999620 Average input read length | 51 UNIQUE READS: Uniquely mapped reads number | 3139520 Uniquely mapped reads % | 78.50% Average mapped length | 51.73 Number of splices: Total | 297989 Number of splices: Annotated (sjdb) | 293274 Number of splices: GT/AG | 291509 Number of splices: GC/AG | 5191 Number of splices: AT/AC | 813 Number of splices: Non-canonical | 476 Mismatch rate per base, % | 0.37% Deletion rate per base | 0.01% Deletion average length | 2.34 Insertion rate per base | 0.00% Insertion average length | 1.39 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 678955 % of reads mapped to multiple loci | 16.98% Number of reads mapped to too many loci | 107308 % of reads mapped to too many loci | 2.68% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.83% % of reads unmapped: other | 0.01% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 181145 181145 181145 N_multimapping 678955 678955 678955 N_noFeature 408832 3092788 445173 N_ambiguous 20121 137 9606 UnstrandedReadsAssigned:2710567 PositiveStrandReadsAssigned:46595 NegativeStrandReadsAssigned:2684741 Dataset is classified negative stranded MeadianReadLen=52 20thPercentileLength=52 echo kmer=47 SRR5423447 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: SRR5423447-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 3,999,620 reads, 3,255,110 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,316 rounds 52401 SRR5423447.ke.tsv 34699 SRR5423447.se.tsv 87100 total ==> SRR5423447.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1919 153 21.6481 Potri.005G024800.1.v4.1 1035 936 19 5.51163 Potri.004G059700.1.v4.1 961 862 3 0.944967 Potri.007G009000.2.v4.1 1416 1317 0 0 Potri.003G141000.2.v4.1 2943 2844 57.3292 5.47329 Potri.016G087400.1.v4.1 270 171 8 12.7027 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 6 1.85549 ==> SRR5423447.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 1 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 44 Potri.001G212900.v4.1 0 Potri.001G182400.v4.1 1 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 2 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 0 SRR5423447 completed mapping pipeline successfully