Starting /dee2/code/volunteer_pipeline.sh SRR5423439 current disk space = 3051213025280 free memory = 1581009004 SRR5423439 SRAfilesize 24dc0a6793355e2991690296391ee751 SRR5423439.sra SRR5423439.sra file validated SRR5423439 is single end SRR5423439 is conventional basespace SRR5423439 read1 length is 52 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR5423439_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 32.222 34.0 31.0 34.0 30.0 34.0 2 32.49525 34.0 31.0 34.0 30.0 34.0 3 32.51075 34.0 31.0 34.0 30.0 34.0 4 35.99875 37.0 35.0 37.0 35.0 37.0 5 35.92175 37.0 35.0 37.0 35.0 37.0 6 35.91 37.0 35.0 37.0 35.0 37.0 7 35.933 37.0 35.0 37.0 35.0 37.0 8 35.89825 37.0 35.0 37.0 35.0 37.0 9 37.5875 39.0 37.0 39.0 35.0 39.0 10 37.59 39.0 37.0 39.0 35.0 39.0 11 37.4635 39.0 37.0 39.0 35.0 39.0 12 37.54925 39.0 37.0 39.0 35.0 39.0 13 37.63975 39.0 37.0 39.0 35.0 39.0 14 38.885 40.0 38.0 41.0 35.0 41.0 15 38.79175 40.0 38.0 41.0 35.0 41.0 16 38.85825 40.0 38.0 41.0 35.0 41.0 17 38.683 40.0 38.0 41.0 34.0 41.0 18 38.81775 40.0 38.0 41.0 35.0 41.0 19 38.85775 40.0 38.0 41.0 35.0 41.0 20 38.85675 40.0 38.0 41.0 35.0 41.0 21 38.87 40.0 38.0 41.0 35.0 41.0 22 38.79325 40.0 38.0 41.0 34.0 41.0 23 38.73475 40.0 38.0 41.0 34.0 41.0 24 38.7405 40.0 38.0 41.0 35.0 41.0 25 38.91825 40.0 38.0 41.0 35.0 41.0 26 38.62375 40.0 38.0 41.0 34.0 41.0 27 38.59825 40.0 38.0 41.0 34.0 41.0 28 38.5225 40.0 38.0 41.0 34.0 41.0 29 38.2615 40.0 38.0 41.0 33.0 41.0 30 38.43675 40.0 38.0 41.0 34.0 41.0 31 38.38075 40.0 38.0 41.0 34.0 41.0 32 38.48 40.0 38.0 41.0 34.0 41.0 33 38.37625 40.0 38.0 41.0 34.0 41.0 34 38.36175 40.0 38.0 41.0 34.0 41.0 35 38.32425 40.0 38.0 41.0 34.0 41.0 36 38.1015 40.0 38.0 41.0 33.0 41.0 37 38.03125 40.0 38.0 41.0 33.0 41.0 38 38.04925 40.0 38.0 41.0 33.0 41.0 39 37.9575 40.0 38.0 41.0 33.0 41.0 40 37.92725 40.0 37.0 41.0 33.0 41.0 41 37.91875 40.0 38.0 41.0 33.0 41.0 42 37.792 40.0 37.0 41.0 33.0 41.0 43 37.797 40.0 37.0 41.0 33.0 41.0 44 37.71525 40.0 37.0 41.0 33.0 41.0 45 37.55275 40.0 37.0 41.0 31.0 41.0 46 37.53625 40.0 37.0 41.0 32.0 41.0 47 37.5015 40.0 37.0 41.0 31.0 41.0 48 37.29325 40.0 36.0 41.0 31.0 41.0 49 37.1555 40.0 36.0 41.0 31.0 41.0 50 37.38175 40.0 36.0 41.0 31.0 41.0 51 37.2125 40.0 36.0 41.0 31.0 41.0 52 35.9805 38.0 35.0 40.0 28.0 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 10 1.0 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 1.0 21 1.0 22 3.0 23 4.0 24 6.0 25 13.0 26 22.0 27 21.0 28 23.0 29 39.0 30 52.0 31 66.0 32 85.0 33 119.0 34 143.0 35 186.0 36 272.0 37 431.0 38 754.0 39 1750.0 40 8.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 36.926548007019306 10.629230383554775 6.192028077212334 46.25219353221359 2 22.925 13.675 35.475 27.925 3 21.825 17.75 22.725 37.7 4 26.224999999999998 24.6 20.75 28.425 5 25.3 30.049999999999997 23.974999999999998 20.674999999999997 6 17.525 33.875 24.25 24.349999999999998 7 14.625 22.825 43.25 19.3 8 17.424999999999997 22.725 29.25 30.599999999999998 9 19.2 20.175 34.050000000000004 26.575 10 17.9 37.225 24.2 20.674999999999997 11 21.675 27.55 22.075 28.7 12 21.95 24.3 26.3 27.450000000000003 13 19.275000000000002 26.075 28.325 26.325 14 19.275000000000002 29.2 26.6 24.925 15 20.875 25.55 28.125 25.45 16 19.325 27.85 28.175 24.65 17 21.625 27.625 27.525 23.225 18 22.45 25.1 27.725 24.725 19 20.75 28.275 25.724999999999998 25.25 20 21.525 26.150000000000002 26.275 26.05 21 20.25 26.450000000000003 27.200000000000003 26.1 22 21.175 28.299999999999997 24.85 25.674999999999997 23 21.2 27.725 26.150000000000002 24.925 24 21.375 26.974999999999998 24.85 26.8 25 20.775 26.650000000000002 27.325 25.25 26 21.6 27.224999999999998 26.650000000000002 24.525 27 20.724999999999998 27.200000000000003 26.125 25.95 28 21.125 28.125 25.124999999999996 25.624999999999996 29 22.6 27.625 26.200000000000003 23.575 30 22.025 26.125 25.75 26.1 31 19.975 28.95 26.0 25.074999999999996 32 22.075 27.250000000000004 26.875 23.799999999999997 33 21.15 26.1 27.425 25.324999999999996 34 20.75 26.650000000000002 26.35 26.25 35 22.1 26.25 26.05 25.6 36 22.25 24.8 26.35 26.6 37 20.549999999999997 28.050000000000004 25.45 25.95 38 22.575 26.1 25.874999999999996 25.45 39 20.525 26.85 26.125 26.5 40 21.4 26.25 24.6 27.750000000000004 41 22.05 26.625 24.099999999999998 27.224999999999998 42 21.349999999999998 25.624999999999996 27.1 25.924999999999997 43 21.85 27.05 24.25 26.85 44 22.825 27.85 24.375 24.95 45 23.075000000000003 25.874999999999996 25.5 25.55 46 23.575 25.650000000000002 24.15 26.625 47 21.65 26.775 26.0 25.575 48 22.825 26.55 24.675 25.95 49 21.45 27.05 24.525 26.974999999999998 50 21.625 26.575 26.35 25.45 51 22.125 25.124999999999996 25.95 26.8 52 20.9 26.674999999999997 25.5 26.924999999999997 >>END_MODULE >>Per sequence GC content fail #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 3.0 19 6.0 20 7.5 21 9.0 22 10.5 23 12.0 24 12.5 25 13.0 26 17.5 27 22.0 28 23.5 29 25.0 30 40.0 31 55.0 32 71.5 33 88.0 34 97.5 35 107.0 36 137.0 37 167.0 38 184.0 39 211.0 40 221.0 41 240.0 42 259.0 43 282.5 44 306.0 45 308.5 46 311.0 47 332.0 48 353.0 49 337.5 50 322.0 51 347.0 52 372.0 53 357.0 54 342.0 55 268.0 56 194.0 57 188.0 58 182.0 59 165.5 60 149.0 61 137.0 62 125.0 63 90.0 64 48.0 65 41.0 66 33.5 67 26.0 68 19.5 69 13.0 70 8.5 71 4.0 72 4.5 73 5.0 74 6.5 75 8.0 76 5.0 77 2.0 78 2.0 79 2.0 80 1.5 81 1.0 82 0.5 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 0.27499999999999997 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 88.6 #Duplication Level Percentage of deduplicated Percentage of total 1 93.93340857787811 83.22500000000001 2 3.639954853273138 6.45 3 1.0158013544018059 2.7 4 0.536117381489842 1.9 5 0.33860045146726864 1.5 6 0.16930022573363432 0.8999999999999999 7 0.14108352144469527 0.8750000000000001 8 0.0564334085778781 0.4 9 0.0564334085778781 0.44999999999999996 >10 0.1128668171557562 1.6 >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 24 0.6 No Hit CCCGTCGGTCCACACAGTTGTCCATGTACCAGTAGAAGATTCAGCAGCTACT 15 0.375 No Hit GGGTAAGCTACATAAGCAATAAATTGATTTTCTTCTCCAGCAACGGGCTCGA 14 0.35000000000000003 No Hit CTCGGTTGCTGGAACCTCCATGACTCCAGTGTAGACATGGCTCTTCTCAGTC 11 0.27499999999999997 No Hit GTCCCTTATAACGATCAAGACTGGTAAGCCCGTCGGTCCACACAGTTGTCCA 9 0.22499999999999998 No Hit GGGGTAAGCTACATAAGCAATAAATTGATTTTCTTCTCCAGCAACGGGCTCG 9 0.22499999999999998 No Hit GTCCTAGAAGTGCATGATAAATACCGCCAAAGCCCAATACTGCAGAGGAAAT 8 0.2 No Hit GTCCACACAGTTGTCCATGTACCAGTAGAAGATTCAGCAGCTACTGCGGCCC 8 0.2 No Hit CAGGGCTCCATTTGCTAGCTTCACGGATAATTTCATTACCCTCACGAGCAAG 7 0.17500000000000002 No Hit CTCATTACGAGCTTGTACACATGCTTCTAGAGCTACTCGATTAGCAACGGCA 7 0.17500000000000002 No Hit CCGTCGGTCCACACAGTTGTCCATGTACCAGTAGAAGATTCAGCAGCTACTG 7 0.17500000000000002 No Hit CTCCAGCAACGGGCTCGATGTCGTAGCATCGTCCCTTATAACGATCAAGACT 7 0.17500000000000002 No Hit GCTCCATTTGCTAGCTTCACGGATAATTTCATTACCCTCACGAGCAAGATCA 7 0.17500000000000002 No Hit CGCGTATTTAAGTCGTCTGCAAAGGATTCTACCCGCCGCTCGGTGGGAATTG 6 0.15 No Hit CTGCAAAGGATTCTACCCGCCGCTCGGTGGGAATTGTACTTCAAGGCGGCCC 6 0.15 No Hit CCAGCAACGGGCTCGATGTCGTAGCATCGTCCCTTATAACGATCAAGACTGG 6 0.15 No Hit GTGCATAAGGATGTTGTGCTCAGCCTGGAATACAATCATAAAGTTAAAAGTA 6 0.15 No Hit GCCGAATACACCAGCTACGCCTAACATGTGAAATGGGTGCATAAGGATGTTG 6 0.15 No Hit CTCAGCCTGGAATACAATCATAAAGTTAAAAGTACCAGAGATTCCTAGAGGC 6 0.15 No Hit CTACGCCACACACATGACGGTTTACGTGCTTAATGACCGCATGTGCAGGTAG 5 0.125 No Hit CGCAGAAGTAGGAATAATGGCACCAGAAATGATATTGTTTCCATAAAGTAGA 5 0.125 No Hit CTCGTATTTTCCCCTCTGCCTCGGGTTGTCTCGCGATACCTTCTACAGCTTG 5 0.125 No Hit CCACACAGTTGTCCATGTACCAGTAGAAGATTCAGCAGCTACTGCGGCCCCT 5 0.125 No Hit GCCCGTCGGTCCACACAGTTGTCCATGTACCAGTAGAAGATTCAGCAGCTAC 5 0.125 No Hit CTCACGAGCAAGATCACGTCCCTCATTACGAGCTTGTACACATGCTTCTAGA 5 0.125 No Hit GTCGGTCCACACAGTTGTCCATGTACCAGTAGAAGATTCAGCAGCTACTGCG 5 0.125 No Hit CTCTTGACCAAATCTGTAACCTTCATTAGCAGATTCATTTTCTGTGGTTTCC 5 0.125 No Hit GTGCTCAGCCTGGAATACAATCATAAAGTTAAAAGTACCAGAGATTCCTAGA 5 0.125 No Hit CTCCATTTGCTAGCTTCACGGATAATTTCATTACCCTCACGAGCAAGATCAC 5 0.125 No Hit GTTCAATTAGATCAGCCCATCAGGCCATGCGGATCCAGGTGGCACCGGCCCG 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 0.025 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 SRR5423439.sra Written 200000 spots for SRR5423439.sra Read 200000 spots for SRR5423439.sra Written 200000 spots for SRR5423439.sra Read 200000 spots for SRR5423439.sra Written 200000 spots for SRR5423439.sra Read 200000 spots for SRR5423439.sra Written 200000 spots for SRR5423439.sra Read 200000 spots for SRR5423439.sra Written 200000 spots for SRR5423439.sra Read 200000 spots for SRR5423439.sra Written 200000 spots for SRR5423439.sra Read 200000 spots for SRR5423439.sra Written 200000 spots for SRR5423439.sra Read 200000 spots for SRR5423439.sra Written 200000 spots for SRR5423439.sra Read 200000 spots for SRR5423439.sra Written 200000 spots for SRR5423439.sra Read 200000 spots for SRR5423439.sra Written 200000 spots for SRR5423439.sra Read 200000 spots for SRR5423439.sra Written 200000 spots for SRR5423439.sra Read 200000 spots for SRR5423439.sra Written 200000 spots for SRR5423439.sra Read 200000 spots for SRR5423439.sra Written 200000 spots for SRR5423439.sra Read 200000 spots for SRR5423439.sra Written 200000 spots for SRR5423439.sra Read 200000 spots for SRR5423439.sra Written 200000 spots for SRR5423439.sra Read 200000 spots for SRR5423439.sra Written 200000 spots for SRR5423439.sra Read 200000 spots for SRR5423439.sra Written 200000 spots for SRR5423439.sra Read 200000 spots for SRR5423439.sra Written 200000 spots for SRR5423439.sra Read 200000 spots for SRR5423439.sra Written 200000 spots for SRR5423439.sra Read 200000 spots for SRR5423439.sra Written 200000 spots for SRR5423439.sra SRR ids: ['SRR5423439.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_zclmoi6t SRR5423439.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]] SRR5423439 file size 703963 SRR5423439 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 SRR5423439 SRR5423439_1.fastq Input file: SRR5423439_1.fastq trimmed: SRR5423439-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 12:52:58 2025 >> started Wed Feb 12 12:53:00 2025 >> done (1.890s) 4000000 reads processed; of these: 159 ( 0.00%) short reads filtered out after trimming by size control 212 ( 0.01%) empty reads filtered out after trimming by size control 3999629 (99.99%) reads available; of these: 67353 ( 1.68%) trimmed reads available after processing 3932276 (98.32%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 15 0.00% 19 5 0.00% 20 4 0.00% 21 1 0.00% 22 0 0.00% 23 0 0.00% 24 4 0.00% 25 0 0.00% 26 1 0.00% 27 0 0.00% 28 1 0.00% 29 2 0.00% 30 2 0.00% 31 5 0.00% 32 4 0.00% 33 6 0.00% 34 4 0.00% 35 7 0.00% 36 11 0.00% 37 11 0.00% 38 23 0.00% 39 28 0.00% 40 41 0.00% 41 39 0.00% 42 54 0.00% 43 74 0.00% 44 146 0.00% 45 156 0.00% 46 286 0.01% 47 485 0.01% 48 1018 0.03% 49 2445 0.06% 50 8139 0.20% 51 54336 1.36% 52 3932276 98.32% 3999629 reads passed initial QC criterion=sequence-density sequence-density=0.19 sequence-density-rank=1 fanout-score=6.44 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=19.93 fanout-score-rank=1 prefix-density=0.31 prefix-fanout=1.3 sequence=CATTTTATTTCTATCTTTCCATACATAACCAAAAAATGGAAAAGATTCTTCAAGAGTCTCGGGTCCTAGAAGTGCATGATAAATACCGCCAAAGCCCAATACTGCAGAGGAAATTAAGTGAAGTACGCCAGATACAAAGTATGGAAAGGTGTCTATGACTTCCCCGCCAGGACCCACCCCCCAACCTAGAGTAGCTAGGTGGGGAAGTAAAATTAATCCTTGTTCATACATTGGCTTCTCCGGTACGAAATGGGCCACTTCAAATAGGTTCATTGCTCCGGCCCAGAATACGATTAATCCAGCATGGGCTACATGAGCTCCCAGCAG Started job on | Feb 12 12:53:13 Started mapping on | Feb 12 12:53:13 Finished on | Feb 12 12:53:18 Mapping speed, Million of reads per hour | 2879.73 Number of input reads | 3999629 Average input read length | 51 UNIQUE READS: Uniquely mapped reads number | 3140382 Uniquely mapped reads % | 78.52% Average mapped length | 51.75 Number of splices: Total | 297650 Number of splices: Annotated (sjdb) | 292949 Number of splices: GT/AG | 291025 Number of splices: GC/AG | 5250 Number of splices: AT/AC | 871 Number of splices: Non-canonical | 504 Mismatch rate per base, % | 0.32% Deletion rate per base | 0.01% Deletion average length | 2.34 Insertion rate per base | 0.00% Insertion average length | 1.37 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 675331 % of reads mapped to multiple loci | 16.88% Number of reads mapped to too many loci | 111826 % of reads mapped to too many loci | 2.80% 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 183916 183916 183916 N_multimapping 675331 675331 675331 N_noFeature 411021 3093276 447827 N_ambiguous 19821 141 9396 UnstrandedReadsAssigned:2709540 PositiveStrandReadsAssigned:46965 NegativeStrandReadsAssigned:2683159 Dataset is classified negative stranded MeadianReadLen=52 20thPercentileLength=52 echo kmer=47 SRR5423439 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: SRR5423439-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 3,999,629 reads, 3,264,572 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,254 rounds 52401 SRR5423439.ke.tsv 34699 SRR5423439.se.tsv 87100 total ==> SRR5423439.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1919 163 22.8201 Potri.005G024800.1.v4.1 1035 936 21 6.02765 Potri.004G059700.1.v4.1 961 862 3 0.935016 Potri.007G009000.2.v4.1 1416 1317 0 0 Potri.003G141000.2.v4.1 2943 2844 54 5.10116 Potri.016G087400.1.v4.1 270 171 9 14.1401 Potri.015G069301.1.v4.1 564 465 0 0 Potri.010G195200.1.v4.1 1773 1674 4.50458 0.722943 Potri.012G127500.1.v4.1 977 878 2 0.611984 ==> SRR5423439.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 1 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 29 Potri.001G212900.v4.1 2 Potri.001G182400.v4.1 1 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 0 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 1 SRR5423439 completed mapping pipeline successfully