Starting /dee2/code/volunteer_pipeline.sh SRR5423451 current disk space = 3051698110464 free memory = 1581068960 SRR5423451 SRAfilesize 89fa84d5d3808d3b6e8664db6a0c54e7 SRR5423451.sra SRR5423451.sra file validated SRR5423451 is single end SRR5423451 is conventional basespace SRR5423451 read1 length is 52 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR5423451_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 32.08575 34.0 31.0 34.0 30.0 34.0 2 32.12875 34.0 31.0 34.0 30.0 34.0 3 32.1065 34.0 31.0 34.0 30.0 34.0 4 35.67575 37.0 35.0 37.0 33.0 37.0 5 35.63575 37.0 35.0 37.0 33.0 37.0 6 35.53925 37.0 35.0 37.0 33.0 37.0 7 35.6835 37.0 35.0 37.0 33.0 37.0 8 35.723 37.0 35.0 37.0 35.0 37.0 9 37.371 39.0 37.0 39.0 34.0 39.0 10 37.217 39.0 37.0 39.0 33.0 39.0 11 37.268 39.0 37.0 39.0 33.0 39.0 12 37.261 39.0 37.0 39.0 33.0 39.0 13 37.27525 39.0 37.0 39.0 33.0 39.0 14 38.46325 40.0 38.0 41.0 33.0 41.0 15 38.5025 40.0 38.0 41.0 34.0 41.0 16 38.36025 40.0 38.0 41.0 34.0 41.0 17 38.43025 40.0 38.0 41.0 34.0 41.0 18 38.53875 40.0 38.0 41.0 34.0 41.0 19 38.539 40.0 38.0 41.0 34.0 41.0 20 38.30175 40.0 38.0 41.0 34.0 41.0 21 38.464 40.0 38.0 41.0 34.0 41.0 22 38.4515 40.0 38.0 41.0 34.0 41.0 23 38.3515 40.0 38.0 41.0 34.0 41.0 24 38.22625 40.0 38.0 41.0 33.0 41.0 25 38.14175 40.0 38.0 41.0 33.0 41.0 26 37.73075 40.0 37.0 41.0 32.0 41.0 27 37.91275 40.0 38.0 41.0 33.0 41.0 28 37.94 40.0 37.0 41.0 33.0 41.0 29 38.021 40.0 38.0 41.0 33.0 41.0 30 37.97175 40.0 38.0 41.0 33.0 41.0 31 37.89875 40.0 37.0 41.0 33.0 41.0 32 37.75975 40.0 37.0 41.0 33.0 41.0 33 37.90225 40.0 37.0 41.0 33.0 41.0 34 37.903 40.0 37.0 41.0 33.0 41.0 35 37.6735 40.0 37.0 41.0 32.0 41.0 36 37.571 40.0 37.0 41.0 32.0 41.0 37 37.521 40.0 37.0 41.0 31.0 41.0 38 37.469 40.0 37.0 41.0 31.0 41.0 39 37.56225 40.0 37.0 41.0 32.0 41.0 40 37.4795 40.0 37.0 41.0 32.0 41.0 41 37.4425 40.0 37.0 41.0 32.0 41.0 42 37.3485 40.0 37.0 41.0 31.0 41.0 43 37.34425 40.0 37.0 41.0 31.0 41.0 44 37.23625 40.0 36.0 41.0 31.0 41.0 45 37.1945 40.0 36.0 41.0 31.0 41.0 46 36.95675 39.0 36.0 41.0 30.0 41.0 47 36.90725 39.0 36.0 41.0 30.0 41.0 48 36.78 39.0 35.0 41.0 30.0 41.0 49 36.78625 39.0 36.0 41.0 30.0 41.0 50 36.8345 39.0 35.0 41.0 30.0 41.0 51 36.53425 39.0 35.0 41.0 29.0 41.0 52 35.4225 38.0 33.0 40.0 27.0 41.0 >>END_MODULE >>Per tile sequence quality pass #Tile Base Mean 2209 1 0.0 2209 2 0.0 2209 3 0.0 2209 4 0.0 2209 5 0.0 2209 6 0.0 2209 7 0.0 2209 8 0.0 2209 9 0.0 2209 10 0.0 2209 11 0.0 2209 12 0.0 2209 13 0.0 2209 14 0.0 2209 15 0.0 2209 16 0.0 2209 17 0.0 2209 18 0.0 2209 19 0.0 2209 20 0.0 2209 21 0.0 2209 22 0.0 2209 23 0.0 2209 24 0.0 2209 25 0.0 2209 26 0.0 2209 27 0.0 2209 28 0.0 2209 29 0.0 2209 30 0.0 2209 31 0.0 2209 32 0.0 2209 33 0.0 2209 34 0.0 2209 35 0.0 2209 36 0.0 2209 37 0.0 2209 38 0.0 2209 39 0.0 2209 40 0.0 2209 41 0.0 2209 42 0.0 2209 43 0.0 2209 44 0.0 2209 45 0.0 2209 46 0.0 2209 47 0.0 2209 48 0.0 2209 49 0.0 2209 50 0.0 2209 51 0.0 2209 52 0.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 19 3.0 20 4.0 21 1.0 22 4.0 23 7.0 24 10.0 25 10.0 26 24.0 27 29.0 28 30.0 29 52.0 30 59.0 31 86.0 32 107.0 33 149.0 34 183.0 35 236.0 36 327.0 37 478.0 38 725.0 39 1473.0 40 3.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 36.62324649298597 9.544088176352705 6.5881763527054105 47.24448897795591 2 24.0 13.725000000000001 34.825 27.450000000000003 3 23.925 18.875 20.625 36.575 4 25.45 25.525 20.025000000000002 28.999999999999996 5 24.975 30.925000000000004 24.349999999999998 19.75 6 20.775 32.05 23.200000000000003 23.974999999999998 7 14.575 23.150000000000002 42.575 19.7 8 16.6 21.525 31.674999999999997 30.2 9 19.0 21.224999999999998 32.425 27.35 10 17.8 38.2 24.9 19.1 11 22.225 28.975 22.2 26.6 12 22.675 24.375 25.724999999999998 27.224999999999998 13 18.55 28.15 27.675 25.624999999999996 14 20.349999999999998 27.775 27.775 24.099999999999998 15 21.475 26.900000000000002 26.974999999999998 24.65 16 20.65 27.725 26.35 25.275 17 22.35 26.325 26.900000000000002 24.425 18 20.575 26.8 25.8 26.825 19 20.474999999999998 26.424999999999997 27.0 26.1 20 20.599999999999998 26.05 26.6 26.75 21 21.325 26.85 26.25 25.575 22 20.8 28.225 26.325 24.65 23 21.8 27.500000000000004 25.724999999999998 24.975 24 21.525 26.700000000000003 26.200000000000003 25.575 25 21.725 27.625 26.075 24.575 26 21.275 26.35 27.474999999999998 24.9 27 21.85 25.85 26.400000000000002 25.900000000000002 28 20.150000000000002 28.225 27.175 24.45 29 21.6 27.775 27.625 23.0 30 20.349999999999998 27.0 26.974999999999998 25.674999999999997 31 20.8 27.224999999999998 26.75 25.224999999999998 32 20.575 26.924999999999997 27.700000000000003 24.8 33 20.175 27.55 27.125 25.15 34 20.275000000000002 26.625 27.325 25.775 35 20.599999999999998 27.35 25.724999999999998 26.325 36 19.925 27.0 25.0 28.075 37 20.45 27.275 25.624999999999996 26.650000000000002 38 20.875 25.5 26.474999999999998 27.150000000000002 39 20.349999999999998 25.75 25.924999999999997 27.975 40 22.2 25.8 26.325 25.674999999999997 41 21.725 27.025 24.099999999999998 27.150000000000002 42 20.474999999999998 26.55 25.7 27.275 43 21.955488872218055 26.556639159789945 25.506376594148538 25.98149537384346 44 21.975 25.924999999999997 26.05 26.05 45 22.80570142535634 25.6064016004001 25.98149537384346 25.6064016004001 46 23.55588897224306 26.60665166291573 24.131032758189548 25.70642660665166 47 22.330582645661416 25.156289072268066 25.70642660665166 26.806701675418854 48 22.83070767691923 27.00675168792198 24.081020255063766 26.081520380095025 49 21.880470117529384 25.881470367591895 24.956239059764943 27.28182045511378 50 22.725 25.575 25.3 26.400000000000002 51 22.20555138784696 24.88122030507627 25.806451612903224 27.106776694173547 52 21.6 26.474999999999998 24.925 27.0 >>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 0.5 10 1.0 11 0.5 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 5.0 21 5.0 22 5.5 23 6.0 24 8.0 25 10.0 26 13.0 27 16.0 28 22.5 29 29.0 30 43.5 31 58.0 32 66.5 33 75.0 34 92.5 35 110.0 36 132.0 37 154.0 38 186.5 39 236.5 40 254.0 41 260.5 42 267.0 43 284.5 44 302.0 45 332.0 46 362.0 47 348.5 48 335.0 49 326.0 50 317.0 51 328.0 52 339.0 53 333.5 54 328.0 55 263.0 56 198.0 57 188.0 58 178.0 59 168.5 60 159.0 61 133.5 62 108.0 63 81.5 64 44.0 65 33.0 66 29.0 67 25.0 68 21.5 69 18.0 70 15.5 71 13.0 72 9.0 73 5.0 74 6.5 75 8.0 76 5.0 77 2.0 78 3.0 79 4.0 80 2.5 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 0.2 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 0.025 44 0.0 45 0.025 46 0.025 47 0.025 48 0.025 49 0.025 50 0.0 51 0.025 52 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 52 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 88.97500000000001 #Duplication Level Percentage of deduplicated Percentage of total 1 94.12756392245014 83.75 2 3.2593425119415564 5.800000000000001 3 1.1801067715650464 3.15 4 0.5338578252318067 1.9 5 0.39336892385501543 1.7500000000000002 6 0.1685866816521495 0.8999999999999999 7 0.1685866816521495 1.05 8 0.02809778027535825 0.2 9 0.02809778027535825 0.22499999999999998 >10 0.112391121101433 1.275 >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 18 0.44999999999999996 No Hit GGGTAAGCTACATAAGCAATAAATTGATTTTCTTCTCCAGCAACGGGCTCGA 13 0.325 No Hit GTCGCGTATTTAAGTCGTCTGCAAAGGATTCTACCCGCCGCTCGGTGGGAAT 10 0.25 No Hit GTGCATAAGGATGTTGTGCTCAGCCTGGAATACAATCATAAAGTTAAAAGTA 10 0.25 No Hit GGGGTAAGCTACATAAGCAATAAATTGATTTTCTTCTCCAGCAACGGGCTCG 9 0.22499999999999998 No Hit CGCGTATTTAAGTCGTCTGCAAAGGATTCTACCCGCCGCTCGGTGGGAATTG 8 0.2 No Hit GGGCTCCATTTGCTAGCTTCACGGATAATTTCATTACCCTCACGAGCAAGAT 7 0.17500000000000002 No Hit CCATGTACCAGTAGAAGATTCAGCAGCTACTGCGGCCCCTGCTTCCTCGGGC 7 0.17500000000000002 No Hit CTGCAAAGGATTCTACCCGCCGCTCGGTGGGAATTGTACTTCAAGGCGGCCC 7 0.17500000000000002 No Hit CTCGGTTGCTGGAACCTCCATGACTCCAGTGTAGACATGGCTCTTCTCAGTC 7 0.17500000000000002 No Hit GTCCACACAGTTGTCCATGTACCAGTAGAAGATTCAGCAGCTACTGCGGCCC 7 0.17500000000000002 No Hit CTCAGCCTGGAATACAATCATAAAGTTAAAAGTACCAGAGATTCCTAGAGGC 7 0.17500000000000002 No Hit CTCGTATTTTCCCCTCTGCCTCGGGTTGTCTCGCGATACCTTCTACAGCTTG 6 0.15 No Hit GTGCTCAGCCTGGAATACAATCATAAAGTTAAAAGTACCAGAGATTCCTAGA 6 0.15 No Hit CTCCATTTGCTAGCTTCACGGATAATTTCATTACCCTCACGAGCAAGATCAC 6 0.15 No Hit CACTTTTTGGTCTTAAGAATGCTGGTTTTAAGAATGAGTGATTGCCCTTCTC 6 0.15 No Hit GCCAGATACAAAGTATGGAAAGGTGTCTATGACTTCCCCGCCAGGACCCACC 6 0.15 No Hit AGCACGGTTAATAATATCAGCCCAGGTATTAATTACACGACCTTGACTATCA 6 0.15 No Hit GTCCCTCATTACGAGCTTGTACACATGCTTCTAGAGCTACTCGATTAGCAAC 5 0.125 No Hit CTCACGAGCAAGATCACGTCCCTCATTACGAGCTTGTACACATGCTTCTAGA 5 0.125 No Hit GCCGACTCCAACTATCGTCCATGTACGATCCATACTAGATCTGACCAACTGC 5 0.125 No Hit GTGCTGAGTTGGAATCCCATTCTAACTAAGGATTCTTGTGGTTCCGGAGGAT 5 0.125 No Hit CCAGTCCATAAATTGTTAAAGCTTCCATAAAAGCCAGACTAAGCAATAAAGT 5 0.125 No Hit CAGAAATGATATTGTTTCCATAAAGTAGAGATCCAGAAACAGGTTCACGAAT 5 0.125 No Hit CCCTGATCAAACTAGAGGTTACCAAAGAACCATGCATAGCACTGAATAGGGA 5 0.125 No Hit CCAGCAACGGGCTCGATGTCGTAGCATCGTCCCTTATAACGATCAAGACTGG 5 0.125 No Hit CTCATTACGAGCTTGTACACATGCTTCTAGAGCTACTCGATTAGCAACGGCA 5 0.125 No Hit GCAAAGGATTCTACCCGCCGCTCGGTGGGAATTGTACTTCAAGGCGGCCCGC 5 0.125 No Hit CCCGTCGGTCCACACAGTTGTCCATGTACCAGTAGAAGATTCAGCAGCTACT 5 0.125 No Hit CCTCTGCCTCGGGTTGTCTCGCGATACCTTCTACAGCTTGGCCCGCAGCAGT 5 0.125 No Hit CTCTGCCTCGGGTTGTCTCGCGATACCTTCTACAGCTTGGCCCGCAGCAGTA 5 0.125 No Hit GCTCCATTTGCTAGCTTCACGGATAATTTCATTACCCTCACGAGCAAGATCA 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 SRR5423451.sra Written 200000 spots for SRR5423451.sra Read 200000 spots for SRR5423451.sra Written 200000 spots for SRR5423451.sra Read 200000 spots for SRR5423451.sra Written 200000 spots for SRR5423451.sra Read 200000 spots for SRR5423451.sra Written 200000 spots for SRR5423451.sra Read 200000 spots for SRR5423451.sra Written 200000 spots for SRR5423451.sra Read 200000 spots for SRR5423451.sra Written 200000 spots for SRR5423451.sra Read 200000 spots for SRR5423451.sra Written 200000 spots for SRR5423451.sra Read 200000 spots for SRR5423451.sra Written 200000 spots for SRR5423451.sra Read 200000 spots for SRR5423451.sra Written 200000 spots for SRR5423451.sra Read 200000 spots for SRR5423451.sra Written 200000 spots for SRR5423451.sra Read 200000 spots for SRR5423451.sra Written 200000 spots for SRR5423451.sra Read 200000 spots for SRR5423451.sra Written 200000 spots for SRR5423451.sra Read 200000 spots for SRR5423451.sra Written 200000 spots for SRR5423451.sra Read 200000 spots for SRR5423451.sra Written 200000 spots for SRR5423451.sra Read 200000 spots for SRR5423451.sra Written 200000 spots for SRR5423451.sra Read 200000 spots for SRR5423451.sra Written 200000 spots for SRR5423451.sra Read 200000 spots for SRR5423451.sra Written 200000 spots for SRR5423451.sra Read 200000 spots for SRR5423451.sra Written 200000 spots for SRR5423451.sra Read 200000 spots for SRR5423451.sra Written 200000 spots for SRR5423451.sra Read 200000 spots for SRR5423451.sra Written 200000 spots for SRR5423451.sra SRR ids: ['SRR5423451.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_ywl00ezh SRR5423451.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]] SRR5423451 file size 703953 SRR5423451 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 SRR5423451 SRR5423451_1.fastq Input file: SRR5423451_1.fastq trimmed: SRR5423451-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 14:36:13 2025 >> started Wed Feb 12 14:36:15 2025 >> done (2.039s) 4000000 reads processed; of these: 163 ( 0.00%) short reads filtered out after trimming by size control 210 ( 0.01%) empty reads filtered out after trimming by size control 3999627 (99.99%) reads available; of these: 109078 ( 2.73%) trimmed reads available after processing 3890549 (97.27%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 13 0.00% 19 5 0.00% 20 8 0.00% 21 2 0.00% 22 0 0.00% 23 2 0.00% 24 2 0.00% 25 1 0.00% 26 7 0.00% 27 2 0.00% 28 3 0.00% 29 4 0.00% 30 3 0.00% 31 9 0.00% 32 6 0.00% 33 12 0.00% 34 25 0.00% 35 20 0.00% 36 30 0.00% 37 29 0.00% 38 50 0.00% 39 62 0.00% 40 87 0.00% 41 97 0.00% 42 149 0.00% 43 199 0.00% 44 383 0.01% 45 522 0.01% 46 693 0.02% 47 1226 0.03% 48 2307 0.06% 49 4989 0.12% 50 14287 0.36% 51 83844 2.10% 52 3890549 97.27% 3999627 reads passed initial QC criterion=sequence-density sequence-density=0.18 sequence-density-rank=1 fanout-score=6.57 fanout-score-rank=8 prefix-density=0.78 prefix-fanout=1.5 sequence=ACGTGCTTAATACGTGCTTAA criterion=fanout-score sequence-density=0.02 sequence-density-rank=25 fanout-score=21.40 fanout-score-rank=1 prefix-density=0.31 prefix-fanout=1.3 sequence=CATTTTATTTCTATCTTTCCATACATAACCAAAAAATGGAAAAGATTCTTCAAGAGTCTCGGGTCCTAGAAGTGCATGATAAATACCGCCAAAGCCCAATACTGCAGAGGAAATTAAGTGAAGTACGCCAGATACAAAGTATGGAAAGGTGTCTATGACTTCCCCGCCAGGACCCACCCCCCAACCTAGAGTAGCTAGGTGGGGAAGTAAAATTAATCCTTGTTCATACATTGGCTTCTCCGGTACGAAATGGGCCACTTCAAATAGGTTCATTGCTCCGGCCCAGAATACGATTAATCCAGCATGGGCTACATGAGCTCCCAGCAG Started job on | Feb 12 14:36:27 Started mapping on | Feb 12 14:36:27 Finished on | Feb 12 14:36:32 Mapping speed, Million of reads per hour | 2879.73 Number of input reads | 3999627 Average input read length | 51 UNIQUE READS: Uniquely mapped reads number | 3137012 Uniquely mapped reads % | 78.43% Average mapped length | 51.73 Number of splices: Total | 298963 Number of splices: Annotated (sjdb) | 294133 Number of splices: GT/AG | 292355 Number of splices: GC/AG | 5251 Number of splices: AT/AC | 851 Number of splices: Non-canonical | 506 Mismatch rate per base, % | 0.40% Deletion rate per base | 0.01% Deletion average length | 2.36 Insertion rate per base | 0.00% Insertion average length | 1.36 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 681814 % of reads mapped to multiple loci | 17.05% Number of reads mapped to too many loci | 105292 % of reads mapped to too many loci | 2.63% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.88% % of reads unmapped: other | 0.01% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 180801 180801 180801 N_multimapping 681814 681814 681814 N_noFeature 407118 3090379 443273 N_ambiguous 19959 126 9364 UnstrandedReadsAssigned:2709935 PositiveStrandReadsAssigned:46507 NegativeStrandReadsAssigned:2684375 Dataset is classified negative stranded MeadianReadLen=52 20thPercentileLength=52 echo kmer=47 SRR5423451 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: SRR5423451-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 3,999,627 reads, 3,248,709 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,159 rounds 52401 SRR5423451.ke.tsv 34699 SRR5423451.se.tsv 87100 total ==> SRR5423451.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1919 141 20.0727 Potri.005G024800.1.v4.1 1035 936 19 5.54549 Potri.004G059700.1.v4.1 961 862 9 2.85231 Potri.007G009000.2.v4.1 1416 1317 0 0 Potri.003G141000.2.v4.1 2943 2844 44.3264 4.2579 Potri.016G087400.1.v4.1 270 171 18 28.7567 Potri.015G069301.1.v4.1 564 465 0 0 Potri.010G195200.1.v4.1 1773 1674 2 0.32639 Potri.012G127500.1.v4.1 977 878 5 1.55574 ==> SRR5423451.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 1 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 41 Potri.001G212900.v4.1 2 Potri.001G182400.v4.1 0 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 0 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 0 SRR5423451 completed mapping pipeline successfully