Starting /dee2/code/volunteer_pipeline.sh SRR5423440 current disk space = 3062701228032 free memory = 1422352972 SRR5423440 SRAfilesize eb9089b009cec7336eb3c5f687e7c54b SRR5423440.sra SRR5423440.sra file validated SRR5423440 is single end SRR5423440 is conventional basespace SRR5423440 read1 length is 52 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR5423440_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 32.3585 34.0 31.0 34.0 30.0 34.0 2 32.50575 34.0 31.0 34.0 30.0 34.0 3 32.587 34.0 31.0 34.0 31.0 34.0 4 36.00725 37.0 35.0 37.0 35.0 37.0 5 35.968 37.0 35.0 37.0 35.0 37.0 6 35.841 37.0 35.0 37.0 35.0 37.0 7 35.87275 37.0 35.0 37.0 35.0 37.0 8 35.94925 37.0 35.0 37.0 35.0 37.0 9 37.6065 39.0 37.0 39.0 35.0 39.0 10 37.517 39.0 37.0 39.0 35.0 39.0 11 37.569 39.0 37.0 39.0 35.0 39.0 12 37.68325 39.0 37.0 39.0 35.0 39.0 13 37.38675 39.0 37.0 39.0 34.0 39.0 14 38.76825 40.0 38.0 41.0 34.0 41.0 15 38.845 40.0 38.0 41.0 35.0 41.0 16 38.81925 40.0 38.0 41.0 35.0 41.0 17 38.7445 40.0 38.0 41.0 35.0 41.0 18 38.804 40.0 38.0 41.0 35.0 41.0 19 38.793 40.0 38.0 41.0 35.0 41.0 20 38.73775 40.0 38.0 41.0 34.0 41.0 21 38.45125 40.0 38.0 41.0 34.0 41.0 22 38.46475 40.0 38.0 41.0 34.0 41.0 23 38.57975 40.0 38.0 41.0 34.0 41.0 24 38.73025 40.0 38.0 41.0 35.0 41.0 25 38.32125 40.0 38.0 41.0 34.0 41.0 26 38.40825 40.0 38.0 41.0 34.0 41.0 27 38.4815 40.0 38.0 41.0 34.0 41.0 28 38.41075 40.0 38.0 41.0 34.0 41.0 29 38.26675 40.0 38.0 41.0 34.0 41.0 30 38.2635 40.0 38.0 41.0 34.0 41.0 31 38.0935 40.0 38.0 41.0 33.0 41.0 32 38.22025 40.0 38.0 41.0 34.0 41.0 33 37.97725 40.0 38.0 41.0 33.0 41.0 34 37.9335 40.0 38.0 41.0 33.0 41.0 35 37.55475 40.0 37.0 41.0 31.0 41.0 36 37.822 40.0 38.0 41.0 33.0 41.0 37 37.66475 40.0 37.0 41.0 32.0 41.0 38 37.5675 40.0 37.0 41.0 32.0 41.0 39 37.28075 40.0 37.0 41.0 30.0 41.0 40 37.3945 40.0 37.0 41.0 31.0 41.0 41 36.96575 40.0 36.0 41.0 30.0 41.0 42 37.30825 40.0 37.0 41.0 31.0 41.0 43 37.27075 40.0 37.0 41.0 31.0 41.0 44 36.95975 40.0 36.0 41.0 30.0 41.0 45 37.00525 40.0 36.0 41.0 30.0 41.0 46 36.8325 40.0 36.0 41.0 30.0 41.0 47 36.943 40.0 36.0 41.0 30.0 41.0 48 36.583 39.0 35.0 41.0 29.0 41.0 49 36.493 39.0 35.0 41.0 29.0 41.0 50 36.47325 39.0 35.0 41.0 29.0 41.0 51 36.22925 39.0 35.0 41.0 28.0 41.0 52 34.5505 38.0 33.0 40.0 24.0 41.0 >>END_MODULE >>Per tile sequence quality pass #Tile Base Mean 2101 1 0.0 2101 2 0.0 2101 3 0.0 2101 4 0.0 2101 5 0.0 2101 6 0.0 2101 7 0.0 2101 8 0.0 2101 9 0.0 2101 10 0.0 2101 11 0.0 2101 12 0.0 2101 13 0.0 2101 14 0.0 2101 15 0.0 2101 16 0.0 2101 17 0.0 2101 18 0.0 2101 19 0.0 2101 20 0.0 2101 21 0.0 2101 22 0.0 2101 23 0.0 2101 24 0.0 2101 25 0.0 2101 26 0.0 2101 27 0.0 2101 28 0.0 2101 29 0.0 2101 30 0.0 2101 31 0.0 2101 32 0.0 2101 33 0.0 2101 34 0.0 2101 35 0.0 2101 36 0.0 2101 37 0.0 2101 38 0.0 2101 39 0.0 2101 40 0.0 2101 41 0.0 2101 42 0.0 2101 43 0.0 2101 44 0.0 2101 45 0.0 2101 46 0.0 2101 47 0.0 2101 48 0.0 2101 49 0.0 2101 50 0.0 2101 51 0.0 2101 52 0.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 9 1.0 10 0.0 11 0.0 12 0.0 13 0.0 14 1.0 15 0.0 16 0.0 17 0.0 18 2.0 19 1.0 20 2.0 21 2.0 22 6.0 23 9.0 24 7.0 25 15.0 26 25.0 27 28.0 28 36.0 29 60.0 30 63.0 31 81.0 32 92.0 33 115.0 34 149.0 35 196.0 36 301.0 37 431.0 38 737.0 39 1638.0 40 2.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 35.51378446115288 10.426065162907268 6.090225563909774 47.96992481203007 2 23.35 13.625000000000002 35.225 27.800000000000004 3 20.4 18.525 22.5 38.574999999999996 4 26.325 24.8 21.325 27.55 5 24.975 31.075000000000003 23.225 20.724999999999998 6 19.85 32.9 23.549999999999997 23.7 7 15.15 23.724999999999998 41.9 19.225 8 18.4 22.825 30.65 28.125 9 18.3 21.075 33.5 27.125 10 17.150000000000002 38.4 23.474999999999998 20.974999999999998 11 22.925 28.299999999999997 22.125 26.650000000000002 12 20.7 24.775 26.05 28.475 13 18.825 27.1 29.475 24.6 14 19.75 29.625 27.650000000000002 22.975 15 22.05 26.275 26.974999999999998 24.7 16 20.1 29.049999999999997 25.3 25.55 17 21.55 27.6 25.8 25.05 18 20.599999999999998 25.825 26.8 26.775 19 20.25 28.925 25.55 25.275 20 21.725 26.150000000000002 26.974999999999998 25.15 21 20.674999999999997 27.525 26.1 25.7 22 20.724999999999998 27.500000000000004 25.7 26.075 23 21.575 29.2 25.275 23.95 24 22.25 25.0 25.275 27.474999999999998 25 21.05 27.500000000000004 25.0 26.450000000000003 26 21.2 26.825 27.675 24.3 27 19.575 26.450000000000003 28.449999999999996 25.525 28 21.15 27.3 26.700000000000003 24.85 29 21.575 27.950000000000003 26.400000000000002 24.075 30 20.849999999999998 25.424999999999997 27.150000000000002 26.575 31 21.099999999999998 27.775 24.925 26.200000000000003 32 21.475 27.125 26.224999999999998 25.174999999999997 33 20.875 25.224999999999998 27.474999999999998 26.424999999999997 34 21.75 27.500000000000004 25.025 25.724999999999998 35 20.849999999999998 28.525 25.424999999999997 25.2 36 20.724999999999998 26.775 25.0 27.500000000000004 37 21.2 27.224999999999998 25.025 26.55 38 22.15 26.200000000000003 24.95 26.700000000000003 39 20.1 25.7 26.25 27.950000000000003 40 21.15 27.025 25.624999999999996 26.200000000000003 41 21.55 27.425 25.05 25.974999999999998 42 21.224999999999998 26.05 25.025 27.700000000000003 43 22.400000000000002 26.200000000000003 26.125 25.275 44 22.275 27.05 25.3 25.374999999999996 45 23.0 25.15 25.724999999999998 26.125 46 22.875 27.250000000000004 23.375 26.5 47 23.95 26.174999999999997 24.775 25.1 48 20.575 26.924999999999997 25.474999999999998 27.025 49 21.75 26.55 24.975 26.724999999999998 50 22.1 26.05 26.625 25.224999999999998 51 22.125 24.474999999999998 26.575 26.825 52 23.325000000000003 25.374999999999996 23.974999999999998 27.325 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 1.0 1 0.5 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 0.5 17 1.0 18 3.0 19 5.0 20 6.0 21 7.0 22 8.0 23 9.0 24 11.0 25 13.0 26 16.5 27 20.0 28 22.0 29 24.0 30 37.0 31 50.0 32 69.0 33 88.0 34 86.0 35 84.0 36 124.5 37 165.0 38 207.5 39 248.0 40 246.0 41 253.0 42 260.0 43 266.0 44 272.0 45 302.0 46 332.0 47 329.5 48 327.0 49 334.5 50 342.0 51 356.0 52 370.0 53 350.5 54 331.0 55 262.5 56 194.0 57 185.0 58 176.0 59 163.5 60 151.0 61 131.0 62 111.0 63 86.0 64 51.5 65 42.0 66 33.5 67 25.0 68 20.0 69 15.0 70 14.0 71 13.0 72 7.5 73 2.0 74 3.0 75 4.0 76 4.5 77 5.0 78 4.5 79 4.0 80 2.0 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 0.25 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 89.05 #Duplication Level Percentage of deduplicated Percentage of total 1 94.13250982594047 83.825 2 3.3408197641774287 5.949999999999999 3 1.2071869736103313 3.225 4 0.4772599663110612 1.7000000000000002 5 0.25266704098820886 1.125 6 0.22459292532285235 1.2 7 0.1403705783267827 0.8750000000000001 8 0.11229646266142618 0.8 9 0.0 0.0 >10 0.11229646266142618 1.3 >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 17 0.42500000000000004 No Hit GGGTAAGCTACATAAGCAATAAATTGATTTTCTTCTCCAGCAACGGGCTCGA 14 0.35000000000000003 No Hit CGCGTATTTAAGTCGTCTGCAAAGGATTCTACCCGCCGCTCGGTGGGAATTG 11 0.27499999999999997 No Hit CTCAGCCTGGAATACAATCATAAAGTTAAAAGTACCAGAGATTCCTAGAGGC 10 0.25 No Hit CGCAGAAGTAGGAATAATGGCACCAGAAATGATATTGTTTCCATAAAGTAGA 8 0.2 No Hit CCAGCAACGGGCTCGATGTCGTAGCATCGTCCCTTATAACGATCAAGACTGG 8 0.2 No Hit GTAAGCTACATAAGCAATAAATTGATTTTCTTCTCCAGCAACGGGCTCGATG 8 0.2 No Hit CCCGTCGGTCCACACAGTTGTCCATGTACCAGTAGAAGATTCAGCAGCTACT 8 0.2 No Hit CCACACAGTTGTCCATGTACCAGTAGAAGATTCAGCAGCTACTGCGGCCCCT 7 0.17500000000000002 No Hit CTCGGGTCCTAGAAGTGCATGATAAATACCGCCAAAGCCCAATACTGCAGAG 7 0.17500000000000002 No Hit CCTCATTACGAGCTTGTACACATGCTTCTAGAGCTACTCGATTAGCAACGGC 7 0.17500000000000002 No Hit GTCCTAGAAGTGCATGATAAATACCGCCAAAGCCCAATACTGCAGAGGAAAT 7 0.17500000000000002 No Hit GTCCACACAGTTGTCCATGTACCAGTAGAAGATTCAGCAGCTACTGCGGCCC 7 0.17500000000000002 No Hit GTCCCTCATTACGAGCTTGTACACATGCTTCTAGAGCTACTCGATTAGCAAC 6 0.15 No Hit CTCGTATTTTCCCCTCTGCCTCGGGTTGTCTCGCGATACCTTCTACAGCTTG 6 0.15 No Hit CTTCCATACTTCACAAGCAGCAGCTAGTTCAGGGCTCCATTTGCTAGCTTCA 6 0.15 No Hit CCCGAAGCCACGGGTAGAACACCCGGTAGAGAGACCCAATCTTGAGTGAAAT 6 0.15 No Hit CTTATAACGATCAAGACTGGTAAGCCCGTCGGTCCACACAGTTGTCCATGTA 6 0.15 No Hit CTGGAATACAATCATAAAGTTAAAAGTACCAGAGATTCCTAGAGGCATCCCA 6 0.15 No Hit CTCATTACGAGCTTGTACACATGCTTCTAGAGCTACTCGATTAGCAACGGCA 6 0.15 No Hit GCTCCATTTGCTAGCTTCACGGATAATTTCATTACCCTCACGAGCAAGATCA 6 0.15 No Hit GCCCGTCGGTCCACACAGTTGTCCATGTACCAGTAGAAGATTCAGCAGCTAC 5 0.125 No Hit CAGGGCTCCATTTGCTAGCTTCACGGATAATTTCATTACCCTCACGAGCAAG 5 0.125 No Hit CTCACGAGCAAGATCACGTCCCTCATTACGAGCTTGTACACATGCTTCTAGA 5 0.125 No Hit GTCGGTCCACACAGTTGTCCATGTACCAGTAGAAGATTCAGCAGCTACTGCG 5 0.125 No Hit GGCTCCATTTGCTAGCTTCACGGATAATTTCATTACCCTCACGAGCAAGATC 5 0.125 No Hit CTCCAGCAACGGGCTCGATGTCGTAGCATCGTCCCTTATAACGATCAAGACT 5 0.125 No Hit CTCGATTAGCAACGGCACCGGGTGCATTTCCCCAAGGGTGCCCTAAAGTTCC 5 0.125 No Hit GTGCATAAGGATGTTGTGCTCAGCCTGGAATACAATCATAAAGTTAAAAGTA 5 0.125 No Hit GCCAGATACAAAGTATGGAAAGGTGTCTATGACTTCCCCGCCAGGACCCACC 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 SRR5423440.sra Written 200000 spots for SRR5423440.sra Read 200000 spots for SRR5423440.sra Written 200000 spots for SRR5423440.sra Read 200000 spots for SRR5423440.sra Written 200000 spots for SRR5423440.sra Read 200000 spots for SRR5423440.sra Written 200000 spots for SRR5423440.sra Read 200000 spots for SRR5423440.sra Written 200000 spots for SRR5423440.sra Read 200000 spots for SRR5423440.sra Read 200000 spots for SRR5423440.sra Written 200000 spots for SRR5423440.sra Written 200000 spots for SRR5423440.sra Read 200000 spots for SRR5423440.sra Written 200000 spots for SRR5423440.sra Read 200000 spots for SRR5423440.sra Written 200000 spots for SRR5423440.sra Read 200000 spots for SRR5423440.sra Written 200000 spots for SRR5423440.sra Read 200000 spots for SRR5423440.sra Written 200000 spots for SRR5423440.sra Read 200000 spots for SRR5423440.sra Written 200000 spots for SRR5423440.sra Read 200000 spots for SRR5423440.sra Written 200000 spots for SRR5423440.sra Read 200000 spots for SRR5423440.sra Written 200000 spots for SRR5423440.sra Read 200000 spots for SRR5423440.sra Written 200000 spots for SRR5423440.sra Read 200000 spots for SRR5423440.sra Written 200000 spots for SRR5423440.sra Read 200000 spots for SRR5423440.sra Written 200000 spots for SRR5423440.sra Read 200000 spots for SRR5423440.sra Written 200000 spots for SRR5423440.sra Read 200000 spots for SRR5423440.sra Written 200000 spots for SRR5423440.sra Read 200000 spots for SRR5423440.sra Written 200000 spots for SRR5423440.sra SRR ids: ['SRR5423440.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_kmytwh1r SRR5423440.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]] SRR5423440 file size 703959 SRR5423440 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 SRR5423440 SRR5423440_1.fastq Input file: SRR5423440_1.fastq trimmed: SRR5423440-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 08:48:25 2025 >> started Thu Feb 13 08:52:45 2025 >> done (260.594s) 4000000 reads processed; of these: 148 ( 0.00%) short reads filtered out after trimming by size control 226 ( 0.01%) empty reads filtered out after trimming by size control 3999626 (99.99%) reads available; of these: 91357 ( 2.28%) trimmed reads available after processing 3908269 (97.72%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 10 0.00% 19 6 0.00% 20 6 0.00% 21 0 0.00% 22 2 0.00% 23 3 0.00% 24 2 0.00% 25 5 0.00% 26 0 0.00% 27 8 0.00% 28 0 0.00% 29 0 0.00% 30 5 0.00% 31 9 0.00% 32 8 0.00% 33 10 0.00% 34 19 0.00% 35 21 0.00% 36 24 0.00% 37 33 0.00% 38 52 0.00% 39 56 0.00% 40 81 0.00% 41 100 0.00% 42 131 0.00% 43 196 0.00% 44 397 0.01% 45 481 0.01% 46 651 0.02% 47 990 0.02% 48 1949 0.05% 49 4251 0.11% 50 11939 0.30% 51 69912 1.75% 52 3908269 97.72% 3999626 reads passed initial QC criterion=sequence-density sequence-density=0.19 sequence-density-rank=1 fanout-score=6.49 fanout-score-rank=5 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=0.32 prefix-fanout=1.2 sequence=CATTTTATTTCTATCTTTCCATACATAACCAAAAAATGGAAAAGATTCTTCAAGAGTCTCGGGTCCTAGAAGTGCATGATAAATACCGCCAAAGCCCAATACTGCAGAGGAAATTAAGTGAAGTACGCCAGATACAAAGTATGGAAAGGTGTCTATGACTTCCCCGCCAGGACCCACCCCCCAACCTAGAGTAGCTAGGTGGGGAAGTAAAATTAATCCTTGTTCATACATTGGCTTCTCCGGTACGAAATGGGCCACTTCAAATAGGTTCATTGCTCCGGCCCAGAATACGATTAATCCAGCATGGGCTACATGAGCTCCCAGCAG Started job on | Feb 13 08:55:57 Started mapping on | Feb 13 08:56:19 Finished on | Feb 13 08:59:04 Mapping speed, Million of reads per hour | 87.26 Number of input reads | 3999626 Average input read length | 51 UNIQUE READS: Uniquely mapped reads number | 3143146 Uniquely mapped reads % | 78.59% Average mapped length | 51.73 Number of splices: Total | 298894 Number of splices: Annotated (sjdb) | 294197 Number of splices: GT/AG | 292412 Number of splices: GC/AG | 5213 Number of splices: AT/AC | 805 Number of splices: Non-canonical | 464 Mismatch rate per base, % | 0.34% Deletion rate per base | 0.01% Deletion average length | 2.40 Insertion rate per base | 0.00% Insertion average length | 1.38 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 677454 % of reads mapped to multiple loci | 16.94% Number of reads mapped to too many loci | 104439 % of reads mapped to too many loci | 2.61% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.85% % of reads unmapped: other | 0.01% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 179026 179026 179026 N_multimapping 677454 677454 677454 N_noFeature 407152 3096498 443433 N_ambiguous 19767 141 9269 UnstrandedReadsAssigned:2716227 PositiveStrandReadsAssigned:46507 NegativeStrandReadsAssigned:2690444 Dataset is classified negative stranded MeadianReadLen=52 20thPercentileLength=52 echo kmer=47 SRR5423440 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: SRR5423440-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 3,999,626 reads, 3,264,266 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,332 rounds 52401 SRR5423440.ke.tsv 34699 SRR5423440.se.tsv 87100 total ==> SRR5423440.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1919 150 21.2149 Potri.005G024800.1.v4.1 1035 936 20 5.79935 Potri.004G059700.1.v4.1 961 862 4 1.25944 Potri.007G009000.2.v4.1 1416 1317 0 0 Potri.003G141000.2.v4.1 2943 2844 56.6154 5.40294 Potri.016G087400.1.v4.1 270 171 19 30.1566 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 3 0.927368 ==> SRR5423440.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 1 Potri.001G182400.v4.1 0 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 0 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 1 SRR5423440 completed mapping pipeline successfully