Starting /dee2/code/volunteer_pipeline.sh SRR5423399 current disk space = 3049827274752 free memory = 1582487388 SRR5423399 SRAfilesize 7732e85b86653a5ccbe7351a7ef850b5 SRR5423399.sra SRR5423399.sra file validated SRR5423399 is single end SRR5423399 is conventional basespace SRR5423399 read1 length is 52 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR5423399_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 30.0945 34.0 31.0 34.0 26.0 34.0 2 31.424 34.0 31.0 34.0 26.0 34.0 3 32.37975 34.0 31.0 34.0 28.0 34.0 4 35.98075 37.0 35.0 37.0 35.0 37.0 5 36.0205 37.0 35.0 37.0 35.0 37.0 6 36.0635 37.0 35.0 37.0 35.0 37.0 7 36.07175 37.0 35.0 37.0 35.0 37.0 8 36.052 37.0 35.0 37.0 35.0 37.0 9 37.8065 39.0 38.0 39.0 35.0 39.0 10 37.63025 39.0 37.0 39.0 35.0 39.0 11 37.76525 39.0 38.0 39.0 35.0 39.0 12 37.75925 39.0 38.0 39.0 35.0 39.0 13 37.734 39.0 38.0 39.0 35.0 39.0 14 39.16425 40.0 39.0 41.0 36.0 41.0 15 39.10775 40.0 39.0 41.0 36.0 41.0 16 39.047 40.0 38.0 41.0 36.0 41.0 17 39.0935 40.0 39.0 41.0 36.0 41.0 18 38.98225 40.0 38.0 41.0 35.0 41.0 19 39.12525 40.0 39.0 41.0 36.0 41.0 20 38.8565 40.0 38.0 41.0 35.0 41.0 21 38.97 40.0 39.0 41.0 35.0 41.0 22 38.96375 40.0 39.0 41.0 35.0 41.0 23 38.879 40.0 38.0 41.0 35.0 41.0 24 38.795 40.0 38.0 41.0 35.0 41.0 25 38.75975 40.0 38.0 41.0 34.0 41.0 26 38.7495 40.0 38.0 41.0 35.0 41.0 27 38.66425 40.0 38.0 41.0 34.0 41.0 28 38.5245 40.0 38.0 41.0 34.0 41.0 29 38.74725 40.0 38.0 41.0 35.0 41.0 30 38.67325 40.0 38.0 41.0 34.0 41.0 31 38.3925 40.0 38.0 41.0 34.0 41.0 32 38.31525 40.0 38.0 41.0 34.0 41.0 33 38.40675 40.0 38.0 41.0 34.0 41.0 34 38.36575 40.0 38.0 41.0 34.0 41.0 35 38.41025 40.0 38.0 41.0 34.0 41.0 36 38.33775 40.0 38.0 41.0 34.0 41.0 37 38.088 40.0 38.0 41.0 33.0 41.0 38 38.00675 40.0 38.0 41.0 33.0 41.0 39 37.96975 40.0 38.0 41.0 33.0 41.0 40 37.836 40.0 38.0 41.0 32.0 41.0 41 37.85375 40.0 38.0 41.0 33.0 41.0 42 37.73425 40.0 37.0 41.0 32.0 41.0 43 37.56575 40.0 37.0 41.0 32.0 41.0 44 37.646 40.0 37.0 41.0 32.0 41.0 45 37.538 40.0 37.0 41.0 31.0 41.0 46 37.14975 40.0 37.0 41.0 31.0 41.0 47 37.24025 40.0 37.0 41.0 31.0 41.0 48 37.06525 40.0 37.0 41.0 30.0 41.0 49 36.889 40.0 36.0 41.0 30.0 41.0 50 36.93025 40.0 36.0 41.0 30.0 41.0 51 36.85425 40.0 36.0 41.0 30.0 41.0 52 34.747 38.0 33.0 40.0 24.0 41.0 >>END_MODULE >>Per tile sequence quality pass #Tile Base Mean 1101 1 0.0 1101 2 0.0 1101 3 0.0 1101 4 0.0 1101 5 0.0 1101 6 0.0 1101 7 0.0 1101 8 0.0 1101 9 0.0 1101 10 0.0 1101 11 0.0 1101 12 0.0 1101 13 0.0 1101 14 0.0 1101 15 0.0 1101 16 0.0 1101 17 0.0 1101 18 0.0 1101 19 0.0 1101 20 0.0 1101 21 0.0 1101 22 0.0 1101 23 0.0 1101 24 0.0 1101 25 0.0 1101 26 0.0 1101 27 0.0 1101 28 0.0 1101 29 0.0 1101 30 0.0 1101 31 0.0 1101 32 0.0 1101 33 0.0 1101 34 0.0 1101 35 0.0 1101 36 0.0 1101 37 0.0 1101 38 0.0 1101 39 0.0 1101 40 0.0 1101 41 0.0 1101 42 0.0 1101 43 0.0 1101 44 0.0 1101 45 0.0 1101 46 0.0 1101 47 0.0 1101 48 0.0 1101 49 0.0 1101 50 0.0 1101 51 0.0 1101 52 0.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 19 1.0 20 0.0 21 7.0 22 4.0 23 6.0 24 9.0 25 11.0 26 19.0 27 17.0 28 28.0 29 40.0 30 46.0 31 68.0 32 84.0 33 107.0 34 137.0 35 208.0 36 287.0 37 424.0 38 816.0 39 1677.0 40 4.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 28.938028938028935 8.5995085995086 6.934206934206934 55.528255528255535 2 22.075 13.450000000000001 36.325 28.15 3 21.625 16.900000000000002 22.725 38.75 4 24.25 24.675 20.8 30.275000000000002 5 24.224999999999998 29.95 23.625 22.2 6 19.125 33.675 25.424999999999997 21.775 7 14.924999999999999 24.875 40.65 19.55 8 19.275000000000002 22.55 29.825000000000003 28.349999999999998 9 17.8 20.724999999999998 35.15 26.325 10 18.15 38.125 22.925 20.8 11 22.3 28.999999999999996 21.3 27.400000000000002 12 22.0 24.925 25.4 27.675 13 19.55 28.199999999999996 27.075 25.174999999999997 14 19.825 28.325 27.450000000000003 24.4 15 22.225 26.075 27.725 23.974999999999998 16 19.900000000000002 28.275 26.025 25.8 17 22.075 26.85 26.424999999999997 24.65 18 20.95 27.150000000000002 25.900000000000002 26.0 19 21.3 28.299999999999997 25.3 25.1 20 20.424999999999997 27.775 25.8 26.0 21 20.599999999999998 26.375 25.924999999999997 27.1 22 20.45 28.15 25.174999999999997 26.224999999999998 23 22.025 26.950000000000003 25.525 25.5 24 21.325 27.425 25.525 25.724999999999998 25 21.725 28.000000000000004 25.025 25.25 26 21.45 26.8 26.224999999999998 25.525 27 20.575 26.674999999999997 27.275 25.474999999999998 28 22.400000000000002 28.575 25.724999999999998 23.3 29 20.424999999999997 28.799999999999997 26.724999999999998 24.05 30 21.4 25.374999999999996 26.900000000000002 26.325 31 21.8 27.950000000000003 25.974999999999998 24.275 32 21.325 28.075 26.025 24.575 33 21.95 26.924999999999997 26.650000000000002 24.474999999999998 34 21.275 27.575 25.45 25.7 35 22.400000000000002 25.3 25.825 26.474999999999998 36 21.25 26.825 25.275 26.650000000000002 37 20.3 27.575 25.924999999999997 26.200000000000003 38 21.775 26.724999999999998 25.525 25.974999999999998 39 21.224999999999998 25.724999999999998 25.924999999999997 27.125 40 21.275 28.65 25.224999999999998 24.85 41 22.525000000000002 26.650000000000002 25.05 25.775 42 21.2 26.174999999999997 25.650000000000002 26.974999999999998 43 21.675 26.875 25.324999999999996 26.125 44 21.65 27.875 27.275 23.200000000000003 45 22.625 26.125 25.650000000000002 25.6 46 23.275000000000002 26.3 24.975 25.45 47 22.425 28.349999999999998 24.375 24.85 48 22.35 26.950000000000003 23.875 26.825 49 21.675 25.575 26.424999999999997 26.325 50 23.525 27.250000000000004 24.325 24.9 51 22.625 25.324999999999996 25.25 26.8 52 23.3 26.775 25.624999999999996 24.3 >>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 0.5 6 1.0 7 0.5 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 2.0 19 4.0 20 5.0 21 6.0 22 8.5 23 11.0 24 12.5 25 14.0 26 15.5 27 17.0 28 25.5 29 34.0 30 35.5 31 37.0 32 54.0 33 71.0 34 95.0 35 119.0 36 143.0 37 167.0 38 193.0 39 226.5 40 234.0 41 269.0 42 304.0 43 317.0 44 330.0 45 329.5 46 329.0 47 332.0 48 335.0 49 328.5 50 322.0 51 339.0 52 356.0 53 322.5 54 289.0 55 252.0 56 215.0 57 203.5 58 192.0 59 169.0 60 146.0 61 124.0 62 102.0 63 79.5 64 48.5 65 40.0 66 32.0 67 24.0 68 17.5 69 11.0 70 7.5 71 4.0 72 4.0 73 4.0 74 2.5 75 1.0 76 1.5 77 2.0 78 1.5 79 1.0 80 0.5 81 0.0 82 0.5 83 1.0 84 0.5 85 0.0 86 0.0 87 0.0 88 0.0 89 0.5 90 1.0 91 0.5 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 warn #Base N-Count 1 8.425 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 88.425 #Duplication Level Percentage of deduplicated Percentage of total 1 93.97794741306191 83.1 2 3.5623409669211195 6.3 3 1.1591744416171896 3.075 4 0.31099802092168505 1.0999999999999999 5 0.3958156629912355 1.7500000000000002 6 0.22618037885213457 1.2 7 0.11309018942606729 0.7000000000000001 8 0.05654509471303364 0.4 9 0.05654509471303364 0.44999999999999996 >10 0.14136273678258413 1.925 >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 19 0.475 No Hit CCCGTCGGTCCACACAGTTGTCCATGTACCAGTAGAAGATTCAGCAGCTACT 17 0.42500000000000004 No Hit CTCCAGCAACGGGCTCGATGTCGTAGCATCGTCCCTTATAACGATCAAGACT 15 0.375 No Hit GGGGTAAGCTACATAAGCAATAAATTGATTTTCTTCTCCAGCAACGGGCTCG 14 0.35000000000000003 No Hit CTCGTATTTTCCCCTCTGCCTCGGGTTGTCTCGCGATACCTTCTACAGCTTG 12 0.3 No Hit CCTCATTACGAGCTTGTACACATGCTTCTAGAGCTACTCGATTAGCAACGGC 9 0.22499999999999998 No Hit CTCATTACGAGCTTGTACACATGCTTCTAGAGCTACTCGATTAGCAACGGCA 9 0.22499999999999998 No Hit CGCAGAAGTAGGAATAATGGCACCAGAAATGATATTGTTTCCATAAAGTAGA 8 0.2 No Hit GGGTAAGCTACATAAGCAATAAATTGATTTTCTTCTCCAGCAACGGGCTCGA 8 0.2 No Hit GTCCCTCATTACGAGCTTGTACACATGCTTCTAGAGCTACTCGATTAGCAAC 7 0.17500000000000002 No Hit CCCTGATCAAACTAGAGGTTACCAAAGAACCATGCATAGCACTGAATAGGGA 7 0.17500000000000002 No Hit CTCTTGACCAAATCTGTAACCTTCATTAGCAGATTCATTTTCTGTGGTTTCC 7 0.17500000000000002 No Hit CTTATAACGATCAAGACTGGTAAGCCCGTCGGTCCACACAGTTGTCCATGTA 7 0.17500000000000002 No Hit GCCCGTCGGTCCACACAGTTGTCCATGTACCAGTAGAAGATTCAGCAGCTAC 6 0.15 No Hit GTCCCTTATAACGATCAAGACTGGTAAGCCCGTCGGTCCACACAGTTGTCCA 6 0.15 No Hit CCCGAAGCCACGGGTAGAACACCCGGTAGAGAGACCCAATCTTGAGTGAAAT 6 0.15 No Hit GTGCTCAGCCTGGAATACAATCATAAAGTTAAAAGTACCAGAGATTCCTAGA 6 0.15 No Hit CTCGTACACACTAAGAAAAAAGCCTTATCCATTTACAAAAGTCTTATCCATT 6 0.15 No Hit GTGCATAAGGATGTTGTGCTCAGCCTGGAATACAATCATAAAGTTAAAAGTA 6 0.15 No Hit GTTAAAACTAGCATATTGGAAGATCAATCGGCCAAAATAACCATGAGCGGCT 6 0.15 No Hit GCCGCTTCCCATATTGGGTAAAAGTGCAACCCTATAGCCGCAGAAGTAGGAA 6 0.15 No Hit CTCCATTTTATTTTCCCATTGAGGCCGAACCTAAACCTGTGCTCGAGAGATA 5 0.125 No Hit CTTCCATACTTCACAAGCAGCAGCTAGTTCAGGGCTCCATTTGCTAGCTTCA 5 0.125 No Hit CTCACGAGCAAGATCACGTCCCTCATTACGAGCTTGTACACATGCTTCTAGA 5 0.125 No Hit CCACTTTTTGGTCTTAAGAATGCTGGTTTTAAGAATGAGTGATTGCCCTTCT 5 0.125 No Hit GTCGGTCCACACAGTTGTCCATGTACCAGTAGAAGATTCAGCAGCTACTGCG 5 0.125 No Hit CCCTCATTACGAGCTTGTACACATGCTTCTAGAGCTACTCGATTAGCAACGG 5 0.125 No Hit CACACAGTTGTCCATGTACCAGTAGAAGATTCAGCAGCTACTGCGGCCCCTG 5 0.125 No Hit CTACGATATTATAAGTTTCTTCCTCTTGACCAAATCTGTAACCTTCATTAGC 5 0.125 No Hit CCCTTCTCCGACCCTTACTGCCCAACCTGAGAGCGGACAGCTAATGCGTTCC 5 0.125 No Hit GTAAGCTACATAAGCAATAAATTGATTTTCTTCTCCAGCAACGGGCTCGATG 5 0.125 No Hit CTGGTTTTAAGAATGAGTGATTGCCCTTCTCCGACCCTTACTGCCCAACCTG 5 0.125 No Hit CGCCGAATACACCAGCTACGCCTAACATGTGAAATGGGTGCATAAGGATGTT 5 0.125 No Hit GTGAAGATACGTTGTTAGGTGCTCCATTTTATTTTCCCATTGAGGCCGAACC 5 0.125 No Hit GCCCCATCTATCCTCCTGAGGAGAAGTTTGGTTTCAAACCCCGGTTCGAACA 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 0.025 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 SRR5423399.sra Written 200000 spots for SRR5423399.sra Read 200000 spots for SRR5423399.sra Written 200000 spots for SRR5423399.sra Read 200000 spots for SRR5423399.sra Written 200000 spots for SRR5423399.sra Read 200000 spots for SRR5423399.sra Written 200000 spots for SRR5423399.sra Read 200000 spots for SRR5423399.sra Written 200000 spots for SRR5423399.sra Read 200000 spots for SRR5423399.sra Written 200000 spots for SRR5423399.sra Read 200000 spots for SRR5423399.sra Written 200000 spots for SRR5423399.sra Read 200000 spots for SRR5423399.sra Written 200000 spots for SRR5423399.sra Read 200000 spots for SRR5423399.sra Written 200000 spots for SRR5423399.sra Read 200000 spots for SRR5423399.sra Written 200000 spots for SRR5423399.sra Read 200000 spots for SRR5423399.sra Written 200000 spots for SRR5423399.sra Read 200000 spots for SRR5423399.sra Written 200000 spots for SRR5423399.sra Read 200000 spots for SRR5423399.sra Written 200000 spots for SRR5423399.sra Read 200000 spots for SRR5423399.sra Written 200000 spots for SRR5423399.sra Read 200000 spots for SRR5423399.sra Written 200000 spots for SRR5423399.sra Read 200000 spots for SRR5423399.sra Written 200000 spots for SRR5423399.sra Read 200000 spots for SRR5423399.sra Written 200000 spots for SRR5423399.sra Read 200000 spots for SRR5423399.sra Written 200000 spots for SRR5423399.sra Read 200000 spots for SRR5423399.sra Written 200000 spots for SRR5423399.sra Read 200000 spots for SRR5423399.sra Written 200000 spots for SRR5423399.sra SRR ids: ['SRR5423399.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_zi580au6 SRR5423399.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]] SRR5423399 file size 703971 SRR5423399 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 SRR5423399 SRR5423399_1.fastq Input file: SRR5423399_1.fastq trimmed: SRR5423399-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 09:51:46 2025 >> started Wed Feb 12 09:51:48 2025 >> done (1.966s) 4000000 reads processed; of these: 130 ( 0.00%) short reads filtered out after trimming by size control 36 ( 0.00%) empty reads filtered out after trimming by size control 3999834 (100.00%) reads available; of these: 82302 ( 2.06%) trimmed reads available after processing 3917532 (97.94%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 10 0.00% 19 2 0.00% 20 2 0.00% 21 0 0.00% 22 0 0.00% 23 1 0.00% 24 1 0.00% 25 5 0.00% 26 2 0.00% 27 3 0.00% 28 4 0.00% 29 4 0.00% 30 5 0.00% 31 9 0.00% 32 6 0.00% 33 17 0.00% 34 10 0.00% 35 21 0.00% 36 24 0.00% 37 29 0.00% 38 22 0.00% 39 41 0.00% 40 36 0.00% 41 81 0.00% 42 103 0.00% 43 129 0.00% 44 395 0.01% 45 443 0.01% 46 640 0.02% 47 704 0.02% 48 1355 0.03% 49 3480 0.09% 50 9938 0.25% 51 64780 1.62% 52 3917532 97.94% 3999834 reads passed initial QC criterion=sequence-density sequence-density=0.25 sequence-density-rank=1 fanout-score=2.15 fanout-score-rank=20 prefix-density=0.17 prefix-fanout=2.1 sequence=GGCCACACCTGCATGCATTGAACTC criterion=fanout-score sequence-density=0.01 sequence-density-rank=29 fanout-score=29.36 fanout-score-rank=1 prefix-density=0.38 prefix-fanout=1.1 sequence=CATTTTATTTCTATCTTTCCATACATAACCAAAAAATGGAAAAGATTCTTCAAGAGTCTCGGGTCCTAGAAGTGCATGATAAATACCGCCAAAGCCCAATACTGCAGAGGAAATTAAGTGAAGTACGCCAGATACAAAGTATGGAAAGGTGTCTATGACTTCCCCGCCAGGACCCACCCCCCAACCTAGAGTAGCTAGGTGGGGAAGTAAAATTAATCCTTGTTCATACATTGGCTTCTCCGGTACGAAATGGGCCACTTCAAATAGGTTCATTGCTCCGGCCCAGAATACGATTAATCCAGCATGGGCTACATGAGCTCCCAGCAG Started job on | Feb 12 09:52:01 Started mapping on | Feb 12 09:52:01 Finished on | Feb 12 09:52:06 Mapping speed, Million of reads per hour | 2879.88 Number of input reads | 3999834 Average input read length | 51 UNIQUE READS: Uniquely mapped reads number | 3118514 Uniquely mapped reads % | 77.97% Average mapped length | 51.80 Number of splices: Total | 277657 Number of splices: Annotated (sjdb) | 274188 Number of splices: GT/AG | 269849 Number of splices: GC/AG | 6268 Number of splices: AT/AC | 1046 Number of splices: Non-canonical | 494 Mismatch rate per base, % | 0.30% Deletion rate per base | 0.01% Deletion average length | 2.75 Insertion rate per base | 0.00% Insertion average length | 1.34 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 764860 % of reads mapped to multiple loci | 19.12% Number of reads mapped to too many loci | 53946 % of reads mapped to too many loci | 1.35% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.55% % of reads unmapped: other | 0.01% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 116460 116460 116460 N_multimapping 764860 764860 764860 N_noFeature 404087 3077330 433858 N_ambiguous 22517 149 10961 UnstrandedReadsAssigned:2691910 PositiveStrandReadsAssigned:41035 NegativeStrandReadsAssigned:2673695 Dataset is classified negative stranded MeadianReadLen=52 20thPercentileLength=52 echo kmer=47 SRR5423399 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: SRR5423399-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 3,999,834 reads, 3,293,018 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,071 rounds 52401 SRR5423399.ke.tsv 34699 SRR5423399.se.tsv 87100 total ==> SRR5423399.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1919 79 11.0391 Potri.005G024800.1.v4.1 1035 936 4 1.14595 Potri.004G059700.1.v4.1 961 862 2 0.622162 Potri.007G009000.2.v4.1 1416 1317 0 0 Potri.003G141000.2.v4.1 2943 2844 69.3258 6.53651 Potri.016G087400.1.v4.1 270 171 15 23.5221 Potri.015G069301.1.v4.1 564 465 0 0 Potri.010G195200.1.v4.1 1773 1674 1 0.160186 Potri.012G127500.1.v4.1 977 878 7 2.13788 ==> SRR5423399.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 1 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 16 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 SRR5423399 completed mapping pipeline successfully