Starting /dee2/code/volunteer_pipeline.sh SRR5423415 current disk space = 3052699721728 free memory = 1580040184 SRR5423415 SRAfilesize 9df0f71c02db6bb66fe827bfbf6ce76c SRR5423415.sra SRR5423415.sra file validated SRR5423415 is single end SRR5423415 is conventional basespace SRR5423415 read1 length is 52 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR5423415_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 30.75375 31.0 30.0 33.0 28.0 34.0 2 31.1975 31.0 31.0 34.0 28.0 34.0 3 31.49125 31.0 31.0 34.0 30.0 34.0 4 30.71075 35.0 28.0 37.0 16.0 37.0 5 33.65825 35.0 33.0 37.0 28.0 37.0 6 34.687 35.0 35.0 37.0 32.0 37.0 7 34.8895 35.0 35.0 37.0 32.0 37.0 8 35.10425 36.0 35.0 37.0 32.0 37.0 9 36.83825 39.0 35.0 39.0 33.0 39.0 10 36.53625 39.0 35.0 39.0 32.0 39.0 11 36.374 38.0 35.0 39.0 32.0 39.0 12 36.34325 38.0 35.0 39.0 32.0 39.0 13 36.41225 38.0 35.0 39.0 32.0 39.0 14 37.5435 39.0 36.0 41.0 32.0 41.0 15 37.3975 39.0 36.0 41.0 32.0 41.0 16 37.43275 39.0 36.0 41.0 32.0 41.0 17 37.507 39.0 36.0 41.0 32.0 41.0 18 37.5575 39.0 36.0 41.0 32.0 41.0 19 37.58275 39.0 37.0 41.0 32.0 41.0 20 37.4605 39.0 36.0 41.0 32.0 41.0 21 37.49125 39.0 36.0 41.0 32.0 41.0 22 37.6335 39.0 37.0 41.0 32.0 41.0 23 36.90775 39.0 36.0 40.0 30.0 41.0 24 37.4755 39.0 36.0 41.0 32.0 41.0 25 37.492 39.0 36.0 41.0 32.0 41.0 26 37.54825 39.0 37.0 41.0 32.0 41.0 27 36.9435 39.0 36.0 40.0 30.0 41.0 28 37.414 39.0 36.0 40.0 32.0 41.0 29 37.29675 39.0 36.0 40.0 32.0 41.0 30 37.261 39.0 36.0 40.0 31.0 41.0 31 37.16325 39.0 36.0 40.0 31.0 41.0 32 37.16575 39.0 36.0 40.0 31.0 41.0 33 37.02375 39.0 36.0 40.0 30.0 41.0 34 37.025 39.0 36.0 40.0 30.0 41.0 35 37.09375 39.0 36.0 40.0 30.0 41.0 36 36.793 39.0 35.0 40.0 30.0 41.0 37 36.6945 39.0 35.0 40.0 30.0 41.0 38 37.0915 39.0 36.0 40.0 31.0 41.0 39 37.13575 39.0 36.0 40.0 31.0 41.0 40 36.55375 39.0 35.0 40.0 30.0 41.0 41 36.88975 39.0 35.0 40.0 30.0 41.0 42 36.84675 39.0 35.0 40.0 30.0 41.0 43 36.75075 39.0 35.0 40.0 30.0 41.0 44 36.5785 39.0 35.0 40.0 30.0 41.0 45 36.566 39.0 35.0 40.0 30.0 41.0 46 36.81875 39.0 35.0 40.0 30.0 41.0 47 36.607 39.0 35.0 40.0 30.0 41.0 48 36.3995 39.0 35.0 40.0 30.0 41.0 49 35.8275 38.0 34.0 40.0 27.0 41.0 50 36.222 38.0 35.0 40.0 29.0 41.0 51 36.1985 38.0 35.0 40.0 29.0 41.0 52 35.4115 38.0 34.0 40.0 27.0 41.0 >>END_MODULE >>Per tile sequence quality pass #Tile Base Mean 2215 1 0.0 2215 2 0.0 2215 3 0.0 2215 4 0.0 2215 5 0.0 2215 6 0.0 2215 7 0.0 2215 8 0.0 2215 9 0.0 2215 10 0.0 2215 11 0.0 2215 12 0.0 2215 13 0.0 2215 14 0.0 2215 15 0.0 2215 16 0.0 2215 17 0.0 2215 18 0.0 2215 19 0.0 2215 20 0.0 2215 21 0.0 2215 22 0.0 2215 23 0.0 2215 24 0.0 2215 25 0.0 2215 26 0.0 2215 27 0.0 2215 28 0.0 2215 29 0.0 2215 30 0.0 2215 31 0.0 2215 32 0.0 2215 33 0.0 2215 34 0.0 2215 35 0.0 2215 36 0.0 2215 37 0.0 2215 38 0.0 2215 39 0.0 2215 40 0.0 2215 41 0.0 2215 42 0.0 2215 43 0.0 2215 44 0.0 2215 45 0.0 2215 46 0.0 2215 47 0.0 2215 48 0.0 2215 49 0.0 2215 50 0.0 2215 51 0.0 2215 52 0.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 11 1.0 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 2.0 22 3.0 23 3.0 24 8.0 25 16.0 26 31.0 27 47.0 28 44.0 29 68.0 30 94.0 31 128.0 32 172.0 33 209.0 34 271.0 35 338.0 36 408.0 37 573.0 38 736.0 39 847.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 28.435544430538172 10.087609511889863 6.858573216520651 54.61827284105132 2 20.849999999999998 13.875000000000002 37.225 28.050000000000004 3 21.725 17.575 22.375 38.324999999999996 4 27.224999999999998 25.775 19.950000000000003 27.05 5 23.974999999999998 30.85 23.674999999999997 21.5 6 19.025 33.175 26.200000000000003 21.6 7 15.575 23.375 41.4 19.650000000000002 8 17.625 22.925 32.175 27.275 9 17.849999999999998 22.1 33.85 26.200000000000003 10 18.099999999999998 38.574999999999996 23.35 19.975 11 23.275000000000002 27.525 22.725 26.474999999999998 12 22.125 24.45 26.025 27.400000000000002 13 18.575 28.075 28.4 24.95 14 19.975 28.449999999999996 27.275 24.3 15 20.200000000000003 25.424999999999997 29.25 25.124999999999996 16 20.5 29.075 25.8 24.625 17 20.849999999999998 28.075 26.924999999999997 24.15 18 19.775000000000002 27.675 27.800000000000004 24.75 19 21.075 26.650000000000002 26.1 26.174999999999997 20 19.575 28.175 26.224999999999998 26.025 21 20.7 26.950000000000003 26.25 26.1 22 21.175 28.349999999999998 25.624999999999996 24.85 23 22.875 27.700000000000003 26.224999999999998 23.200000000000003 24 22.55 26.1 25.95 25.4 25 21.425 28.275 25.025 25.275 26 22.125 27.474999999999998 27.250000000000004 23.150000000000002 27 20.925 26.174999999999997 27.6 25.3 28 20.225 28.599999999999998 26.474999999999998 24.7 29 20.5 28.95 25.7 24.85 30 19.900000000000002 26.275 26.974999999999998 26.85 31 20.474999999999998 28.299999999999997 26.025 25.2 32 21.525 27.400000000000002 26.625 24.45 33 21.125 24.675 26.700000000000003 27.500000000000004 34 19.775000000000002 26.625 28.299999999999997 25.3 35 21.325 26.275 26.400000000000002 26.0 36 21.8 25.95 25.874999999999996 26.375 37 21.325 25.474999999999998 26.674999999999997 26.525 38 21.25 26.325 25.775 26.650000000000002 39 21.224999999999998 26.150000000000002 25.1 27.525 40 20.65 28.349999999999998 25.5 25.5 41 20.674999999999997 27.150000000000002 26.25 25.924999999999997 42 20.4 26.650000000000002 26.55 26.400000000000002 43 21.2 27.725 24.85 26.224999999999998 44 21.9 28.449999999999996 26.325 23.325000000000003 45 21.4 26.474999999999998 25.624999999999996 26.5 46 22.425 26.724999999999998 24.525 26.325 47 22.525000000000002 29.475 23.95 24.05 48 23.225 27.075 24.425 25.275 49 21.4 26.825 25.4 26.375 50 22.925 27.950000000000003 25.424999999999997 23.7 51 23.575 24.25 25.85 26.325 52 22.425 26.474999999999998 25.05 26.05 >>END_MODULE >>Per sequence GC content pass #GC Content Count 0 0.0 1 0.0 2 0.0 3 0.5 4 1.0 5 0.5 6 0.0 7 0.0 8 0.0 9 0.0 10 0.0 11 0.5 12 1.0 13 0.5 14 0.0 15 0.0 16 0.0 17 0.0 18 3.5 19 7.0 20 7.5 21 8.0 22 7.0 23 6.0 24 8.5 25 11.0 26 15.5 27 20.0 28 33.0 29 46.0 30 48.0 31 50.0 32 71.5 33 93.0 34 110.0 35 127.0 36 152.5 37 178.0 38 191.0 39 240.0 40 276.0 41 262.5 42 249.0 43 284.5 44 320.0 45 324.5 46 329.0 47 328.5 48 328.0 49 328.5 50 329.0 51 331.5 52 334.0 53 328.5 54 323.0 55 265.0 56 207.0 57 198.0 58 189.0 59 162.5 60 136.0 61 113.0 62 90.0 63 71.0 64 44.0 65 36.0 66 28.5 67 21.0 68 18.0 69 15.0 70 10.5 71 6.0 72 5.0 73 4.0 74 3.0 75 2.0 76 2.0 77 2.0 78 1.0 79 0.0 80 0.0 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 0.125 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 89.4 #Duplication Level Percentage of deduplicated Percentage of total 1 94.26733780760627 84.275 2 3.4395973154362416 6.15 3 1.0626398210290828 2.85 4 0.33557046979865773 1.2 5 0.2796420581655481 1.25 6 0.2796420581655481 1.5 7 0.13982102908277405 0.8750000000000001 8 0.05592841163310962 0.4 9 0.02796420581655481 0.22499999999999998 >10 0.11185682326621924 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 CTCGTATTTTCCCCTCTGCCTCGGGTTGTCTCGCGATACCTTCTACAGCTTG 17 0.42500000000000004 No Hit CGCAGAAGTAGGAATAATGGCACCAGAAATGATATTGTTTCCATAAAGTAGA 12 0.3 No Hit CCCGTCGGTCCACACAGTTGTCCATGTACCAGTAGAAGATTCAGCAGCTACT 11 0.27499999999999997 No Hit CGTCGGTCCACACAGTTGTCCATGTACCAGTAGAAGATTCAGCAGCTACTGC 11 0.27499999999999997 No Hit CCTCATTACGAGCTTGTACACATGCTTCTAGAGCTACTCGATTAGCAACGGC 9 0.22499999999999998 No Hit CCAGCAACGGGCTCGATGTCGTAGCATCGTCCCTTATAACGATCAAGACTGG 8 0.2 No Hit CTGGTTTTAAGAATGAGTGATTGCCCTTCTCCGACCCTTACTGCCCAACCTG 8 0.2 No Hit CTCACGAGCAAGATCACGTCCCTCATTACGAGCTTGTACACATGCTTCTAGA 7 0.17500000000000002 No Hit CCCTGATCAAACTAGAGGTTACCAAAGAACCATGCATAGCACTGAATAGGGA 7 0.17500000000000002 No Hit CTCATTACGAGCTTGTACACATGCTTCTAGAGCTACTCGATTAGCAACGGCA 7 0.17500000000000002 No Hit GGGTAAGCTACATAAGCAATAAATTGATTTTCTTCTCCAGCAACGGGCTCGA 7 0.17500000000000002 No Hit CTCAGCCTGGAATACAATCATAAAGTTAAAAGTACCAGAGATTCCTAGAGGC 7 0.17500000000000002 No Hit GCCCGTCGGTCCACACAGTTGTCCATGTACCAGTAGAAGATTCAGCAGCTAC 6 0.15 No Hit CAGGGCTCCATTTGCTAGCTTCACGGATAATTTCATTACCCTCACGAGCAAG 6 0.15 No Hit GTCGGTCCACACAGTTGTCCATGTACCAGTAGAAGATTCAGCAGCTACTGCG 6 0.15 No Hit GTCCCTTATAACGATCAAGACTGGTAAGCCCGTCGGTCCACACAGTTGTCCA 6 0.15 No Hit CCCGAAGCCACGGGTAGAACACCCGGTAGAGAGACCCAATCTTGAGTGAAAT 6 0.15 No Hit GTAAGCTACATAAGCAATAAATTGATTTTCTTCTCCAGCAACGGGCTCGATG 6 0.15 No Hit GGGGTAAGCTACATAAGCAATAAATTGATTTTCTTCTCCAGCAACGGGCTCG 6 0.15 No Hit CTCGTACACACTAAGAAAAAAGCCTTATCCATTTACAAAAGTCTTATCCATT 6 0.15 No Hit GGGCGATCTCGTAGTTCCTACGGGGTGGAGACGATGGGGTCGGTCCATGGAT 6 0.15 No Hit CTCCAGCAACGGGCTCGATGTCGTAGCATCGTCCCTTATAACGATCAAGACT 6 0.15 No Hit GTCCCTCATTACGAGCTTGTACACATGCTTCTAGAGCTACTCGATTAGCAAC 5 0.125 No Hit CTCCATTTTATTTTCCCATTGAGGCCGAACCTAAACCTGTGCTCGAGAGATA 5 0.125 No Hit GTCCGCGACCCCTGGATGCCGAAGGCGTCCTTGGGGCGATCTCGTAGTTCCT 5 0.125 No Hit CCCGAACACAGCTTACAACTTTCATCGTACTGTGCTCTCCAAAGAGCAACTC 5 0.125 No Hit CTGGAATACAATCATAAAGTTAAAAGTACCAGAGATTCCTAGAGGCATCCCA 5 0.125 No Hit CCAGGTATTAATTACACGACCTTGACTATCAACTACAGATTGGTTGAAATTG 5 0.125 No Hit CCCACTTTTTGGTCTTAAGAATGCTGGTTTTAAGAATGAGTGATTGCCCTTC 5 0.125 No Hit CTCTGCCTCGGGTTGTCTCGCGATACCTTCTACAGCTTGGCCCGCAGCAGTA 5 0.125 No Hit GCTCCATTTGCTAGCTTCACGGATAATTTCATTACCCTCACGAGCAAGATCA 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 0.025 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 SRR5423415.sra Written 200000 spots for SRR5423415.sra Read 200000 spots for SRR5423415.sra Written 200000 spots for SRR5423415.sra Read 200000 spots for SRR5423415.sra Written 200000 spots for SRR5423415.sra Read 200000 spots for SRR5423415.sra Written 200000 spots for SRR5423415.sra Read 200000 spots for SRR5423415.sra Written 200000 spots for SRR5423415.sra Read 200000 spots for SRR5423415.sra Written 200000 spots for SRR5423415.sra Read 200000 spots for SRR5423415.sra Written 200000 spots for SRR5423415.sra Read 200000 spots for SRR5423415.sra Written 200000 spots for SRR5423415.sra Read 200000 spots for SRR5423415.sra Written 200000 spots for SRR5423415.sra Read 200000 spots for SRR5423415.sra Written 200000 spots for SRR5423415.sra Read 200000 spots for SRR5423415.sra Written 200000 spots for SRR5423415.sra Read 200000 spots for SRR5423415.sra Written 200000 spots for SRR5423415.sra Read 200000 spots for SRR5423415.sra Written 200000 spots for SRR5423415.sra Read 200000 spots for SRR5423415.sra Written 200000 spots for SRR5423415.sra Read 200000 spots for SRR5423415.sra Written 200000 spots for SRR5423415.sra Read 200000 spots for SRR5423415.sra Written 200000 spots for SRR5423415.sra Read 200000 spots for SRR5423415.sra Written 200000 spots for SRR5423415.sra Read 200000 spots for SRR5423415.sra Written 200000 spots for SRR5423415.sra Read 200000 spots for SRR5423415.sra Written 200000 spots for SRR5423415.sra Read 200000 spots for SRR5423415.sra Written 200000 spots for SRR5423415.sra SRR ids: ['SRR5423415.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_xvav61i7 SRR5423415.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]] SRR5423415 file size 703949 SRR5423415 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 SRR5423415 SRR5423415_1.fastq Input file: SRR5423415_1.fastq trimmed: SRR5423415-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 08:00:36 2025 >> started Thu Feb 13 08:17:40 2025 >> done (1024.680s) 4000000 reads processed; of these: 117 ( 0.00%) short reads filtered out after trimming by size control 45 ( 0.00%) empty reads filtered out after trimming by size control 3999838 (100.00%) reads available; of these: 100171 ( 2.50%) trimmed reads available after processing 3899667 (97.50%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 9 0.00% 19 7 0.00% 20 1 0.00% 21 0 0.00% 22 1 0.00% 23 7 0.00% 24 2 0.00% 25 2 0.00% 26 2 0.00% 27 2 0.00% 28 6 0.00% 29 4 0.00% 30 6 0.00% 31 5 0.00% 32 7 0.00% 33 13 0.00% 34 28 0.00% 35 22 0.00% 36 19 0.00% 37 37 0.00% 38 46 0.00% 39 58 0.00% 40 65 0.00% 41 94 0.00% 42 151 0.00% 43 186 0.00% 44 516 0.01% 45 624 0.02% 46 753 0.02% 47 982 0.02% 48 1887 0.05% 49 4220 0.11% 50 12351 0.31% 51 78058 1.95% 52 3899667 97.50% 3999838 reads passed initial QC criterion=sequence-density sequence-density=0.34 sequence-density-rank=1 fanout-score=3.64 fanout-score-rank=13 prefix-density=0.42 prefix-fanout=2.9 sequence=CCATTGCTTGCAATGGAAGTAATGTCATT criterion=fanout-score sequence-density=0.01 sequence-density-rank=28 fanout-score=30.68 fanout-score-rank=1 prefix-density=0.38 prefix-fanout=1.1 sequence=CATTTTATTTCTATCTTTCCATACATAACCAAAAAATGGAAAAGATTCTTCAAGAGTCTCGGGTCCTAGAAGTGCATGATAAATACCGCCAAAGCCCAATACTGCAGAGGAAATTAAGTGAAGTACGCCAGATACAAAGTATGGAAAGGTGTCTATGACTTCCCCGCCAGGACCCACCCCCCAACCTAGAGTAGCTAGGTGGGGAAGTAAAATTAATCCTTGTTCATACATTGGCTTCTCCGGTACGAAATGGGCCACTTCAAATAGGTTCATTGCTCCGGCCCAGAATACGATTAATCCAGCATGGGCTACATGAGCTCCCAGCAG Started job on | Feb 13 08:21:29 Started mapping on | Feb 13 08:21:46 Finished on | Feb 13 08:37:37 Mapping speed, Million of reads per hour | 15.14 Number of input reads | 3999838 Average input read length | 51 UNIQUE READS: Uniquely mapped reads number | 3115084 Uniquely mapped reads % | 77.88% Average mapped length | 51.80 Number of splices: Total | 278029 Number of splices: Annotated (sjdb) | 274406 Number of splices: GT/AG | 270151 Number of splices: GC/AG | 6240 Number of splices: AT/AC | 1084 Number of splices: Non-canonical | 554 Mismatch rate per base, % | 0.35% Deletion rate per base | 0.02% Deletion average length | 2.78 Insertion rate per base | 0.00% Insertion average length | 1.36 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 768236 % of reads mapped to multiple loci | 19.21% Number of reads mapped to too many loci | 52876 % of reads mapped to too many loci | 1.32% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.58% % of reads unmapped: other | 0.01% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 116518 116518 116518 N_multimapping 768236 768236 768236 N_noFeature 401977 3074537 431237 N_ambiguous 22512 171 11068 UnstrandedReadsAssigned:2690595 PositiveStrandReadsAssigned:40376 NegativeStrandReadsAssigned:2672779 Dataset is classified negative stranded MeadianReadLen=52 20thPercentileLength=52 echo kmer=47 SRR5423415 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: SRR5423415-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 3,999,838 reads, 3,275,709 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,058 rounds 52401 SRR5423415.ke.tsv 34699 SRR5423415.se.tsv 87100 total ==> SRR5423415.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1919 73 10.2867 Potri.005G024800.1.v4.1 1035 936 1 0.288903 Potri.004G059700.1.v4.1 961 862 3 0.941115 Potri.007G009000.2.v4.1 1416 1317 0 0 Potri.003G141000.2.v4.1 2943 2844 66.3217 6.30601 Potri.016G087400.1.v4.1 270 171 10 15.8137 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 5 1.53994 ==> SRR5423415.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 1 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 26 Potri.001G212900.v4.1 0 Potri.001G182400.v4.1 1 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 3 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 1 SRR5423415 completed mapping pipeline successfully