Starting /dee2/code/volunteer_pipeline.sh SRR5423443 current disk space = 3051252031488 free memory = 1581996040 SRR5423443 SRAfilesize 1835ce20aac29b087ce4c851314dcbb6 SRR5423443.sra SRR5423443.sra file validated SRR5423443 is single end SRR5423443 is conventional basespace SRR5423443 read1 length is 52 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR5423443_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 32.49575 34.0 31.0 34.0 31.0 34.0 2 32.56575 34.0 31.0 34.0 31.0 34.0 3 32.615 34.0 31.0 34.0 31.0 34.0 4 35.92725 37.0 35.0 37.0 35.0 37.0 5 35.91025 37.0 35.0 37.0 35.0 37.0 6 35.9345 37.0 35.0 37.0 35.0 37.0 7 35.9335 37.0 35.0 37.0 35.0 37.0 8 35.94875 37.0 35.0 37.0 35.0 37.0 9 37.63275 39.0 37.0 39.0 35.0 39.0 10 37.4575 39.0 37.0 39.0 34.0 39.0 11 37.58225 39.0 37.0 39.0 35.0 39.0 12 37.62125 39.0 37.0 39.0 35.0 39.0 13 37.4925 39.0 37.0 39.0 35.0 39.0 14 38.93225 40.0 38.0 41.0 36.0 41.0 15 38.80775 40.0 38.0 41.0 34.0 41.0 16 38.85325 40.0 38.0 41.0 35.0 41.0 17 38.831 40.0 38.0 41.0 35.0 41.0 18 38.7875 40.0 38.0 41.0 35.0 41.0 19 38.67425 40.0 38.0 41.0 34.0 41.0 20 38.734 40.0 38.0 41.0 34.0 41.0 21 38.801 40.0 38.0 41.0 35.0 41.0 22 38.8605 40.0 38.0 41.0 35.0 41.0 23 38.707 40.0 38.0 41.0 34.0 41.0 24 38.72225 40.0 38.0 41.0 34.0 41.0 25 38.7095 40.0 38.0 41.0 34.0 41.0 26 38.56725 40.0 38.0 41.0 34.0 41.0 27 38.427 40.0 38.0 41.0 34.0 41.0 28 38.52125 40.0 38.0 41.0 34.0 41.0 29 38.4465 40.0 38.0 41.0 34.0 41.0 30 38.35675 40.0 38.0 41.0 34.0 41.0 31 38.3815 40.0 38.0 41.0 34.0 41.0 32 38.344 40.0 38.0 41.0 34.0 41.0 33 38.2955 40.0 38.0 41.0 34.0 41.0 34 38.18825 40.0 38.0 41.0 33.0 41.0 35 38.1265 40.0 38.0 41.0 33.0 41.0 36 38.17925 40.0 38.0 41.0 33.0 41.0 37 37.93475 40.0 38.0 41.0 33.0 41.0 38 37.906 40.0 38.0 41.0 33.0 41.0 39 37.94675 40.0 38.0 41.0 33.0 41.0 40 37.804 40.0 38.0 41.0 33.0 41.0 41 37.85125 40.0 38.0 41.0 33.0 41.0 42 37.5455 40.0 37.0 41.0 31.0 41.0 43 37.69975 40.0 37.0 41.0 32.0 41.0 44 37.65375 40.0 37.0 41.0 32.0 41.0 45 37.54475 40.0 37.0 41.0 32.0 41.0 46 37.47875 40.0 37.0 41.0 32.0 41.0 47 37.43925 40.0 37.0 41.0 32.0 41.0 48 37.556 40.0 37.0 41.0 32.0 41.0 49 37.112 40.0 36.0 41.0 31.0 41.0 50 37.26075 40.0 36.0 41.0 31.0 41.0 51 37.42475 40.0 37.0 41.0 31.0 41.0 52 36.1785 39.0 35.0 40.0 28.0 41.0 >>END_MODULE >>Per tile sequence quality pass #Tile Base Mean 2305 1 0.0 2305 2 0.0 2305 3 0.0 2305 4 0.0 2305 5 0.0 2305 6 0.0 2305 7 0.0 2305 8 0.0 2305 9 0.0 2305 10 0.0 2305 11 0.0 2305 12 0.0 2305 13 0.0 2305 14 0.0 2305 15 0.0 2305 16 0.0 2305 17 0.0 2305 18 0.0 2305 19 0.0 2305 20 0.0 2305 21 0.0 2305 22 0.0 2305 23 0.0 2305 24 0.0 2305 25 0.0 2305 26 0.0 2305 27 0.0 2305 28 0.0 2305 29 0.0 2305 30 0.0 2305 31 0.0 2305 32 0.0 2305 33 0.0 2305 34 0.0 2305 35 0.0 2305 36 0.0 2305 37 0.0 2305 38 0.0 2305 39 0.0 2305 40 0.0 2305 41 0.0 2305 42 0.0 2305 43 0.0 2305 44 0.0 2305 45 0.0 2305 46 0.0 2305 47 0.0 2305 48 0.0 2305 49 0.0 2305 50 0.0 2305 51 0.0 2305 52 0.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 14 1.0 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 5.0 24 9.0 25 12.0 26 15.0 27 20.0 28 33.0 29 34.0 30 63.0 31 72.0 32 90.0 33 106.0 34 138.0 35 197.0 36 263.0 37 414.0 38 740.0 39 1778.0 40 4.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 37.20290217663248 9.782336752564422 5.754315736802602 47.2604453340005 2 22.75 14.399999999999999 35.775 27.075 3 20.974999999999998 18.375 22.95 37.7 4 25.124999999999996 24.5 21.3 29.075 5 24.75 31.1 22.95 21.2 6 19.525000000000002 31.624999999999996 25.074999999999996 23.775 7 15.6 24.025 41.3 19.075 8 18.5 22.35 29.849999999999998 29.299999999999997 9 17.125 20.325 34.675 27.875 10 18.375 37.1 24.95 19.575 11 22.575 27.750000000000004 21.475 28.199999999999996 12 21.925 24.2 26.075 27.800000000000004 13 19.675 27.474999999999998 27.925 24.925 14 19.45 27.500000000000004 28.375 24.675 15 20.5 27.700000000000003 27.200000000000003 24.6 16 20.225 27.175 26.75 25.85 17 21.3 27.325 26.650000000000002 24.725 18 21.275 25.874999999999996 27.175 25.674999999999997 19 20.849999999999998 27.400000000000002 25.8 25.95 20 21.5 26.825 25.174999999999997 26.5 21 20.9 26.375 26.125 26.6 22 21.525 27.625 24.175 26.674999999999997 23 20.8 28.025 25.75 25.424999999999997 24 22.0 26.3 25.5 26.200000000000003 25 20.925 27.825 25.650000000000002 25.6 26 22.675 27.900000000000002 25.35 24.075 27 20.65 27.775 27.325 24.25 28 21.175 27.775 27.375 23.674999999999997 29 22.475 26.974999999999998 27.025 23.525 30 20.525 25.074999999999996 27.575 26.825 31 21.55 26.400000000000002 27.3 24.75 32 20.424999999999997 27.950000000000003 26.775 24.85 33 20.575 26.05 26.974999999999998 26.400000000000002 34 20.3 25.825 27.625 26.25 35 19.775000000000002 26.325 27.35 26.55 36 19.950000000000003 27.35 25.2 27.500000000000004 37 21.05 25.874999999999996 26.424999999999997 26.650000000000002 38 20.5 26.25 26.825 26.424999999999997 39 21.45 24.7 25.8 28.050000000000004 40 20.525 27.800000000000004 24.775 26.900000000000002 41 21.5 26.174999999999997 25.724999999999998 26.6 42 19.275000000000002 25.974999999999998 27.700000000000003 27.05 43 21.325 27.85 24.8 26.025 44 22.5 26.85 25.474999999999998 25.174999999999997 45 22.475 26.025 25.6 25.900000000000002 46 23.150000000000002 26.875 25.4 24.575 47 22.7 26.85 25.825 24.625 48 21.825 26.275 25.074999999999996 26.825 49 20.775 26.6 25.95 26.674999999999997 50 22.175 26.224999999999998 25.6 26.0 51 21.85 24.85 25.324999999999996 27.975 52 23.150000000000002 25.724999999999998 24.525 26.6 >>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 1.5 17 2.0 18 2.0 19 2.0 20 4.5 21 7.0 22 9.5 23 12.0 24 10.5 25 9.0 26 13.5 27 18.0 28 27.0 29 36.0 30 43.0 31 50.0 32 59.0 33 68.0 34 90.5 35 113.0 36 147.0 37 181.0 38 202.0 39 240.5 40 258.0 41 260.5 42 263.0 43 278.0 44 293.0 45 299.5 46 306.0 47 311.5 48 317.0 49 312.5 50 308.0 51 332.5 52 357.0 53 349.0 54 341.0 55 287.5 56 234.0 57 204.5 58 175.0 59 158.5 60 142.0 61 139.0 62 136.0 63 95.0 64 44.5 65 35.0 66 30.0 67 25.0 68 21.0 69 17.0 70 11.0 71 5.0 72 5.0 73 5.0 74 3.0 75 1.0 76 2.0 77 3.0 78 2.5 79 2.0 80 1.0 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 0.075 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 87.6 #Duplication Level Percentage of deduplicated Percentage of total 1 93.57876712328768 81.975 2 3.65296803652968 6.4 3 1.2271689497716893 3.225 4 0.5422374429223744 1.9 5 0.28538812785388123 1.25 6 0.3139269406392694 1.6500000000000001 7 0.1141552511415525 0.7000000000000001 8 0.05707762557077625 0.4 9 0.028538812785388126 0.22499999999999998 >10 0.1997716894977169 2.275 >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 17 0.42500000000000004 No Hit GGGGTAAGCTACATAAGCAATAAATTGATTTTCTTCTCCAGCAACGGGCTCG 16 0.4 No Hit GGGTAAGCTACATAAGCAATAAATTGATTTTCTTCTCCAGCAACGGGCTCGA 15 0.375 No Hit CTGCAAAGGATTCTACCCGCCGCTCGGTGGGAATTGTACTTCAAGGCGGCCC 11 0.27499999999999997 No Hit CCCGTCGGTCCACACAGTTGTCCATGTACCAGTAGAAGATTCAGCAGCTACT 11 0.27499999999999997 No Hit GTGCATAAGGATGTTGTGCTCAGCCTGGAATACAATCATAAAGTTAAAAGTA 11 0.27499999999999997 No Hit CAGGGCTCCATTTGCTAGCTTCACGGATAATTTCATTACCCTCACGAGCAAG 10 0.25 No Hit GCTCCATTTGCTAGCTTCACGGATAATTTCATTACCCTCACGAGCAAGATCA 9 0.22499999999999998 No Hit GTCGCGTATTTAAGTCGTCTGCAAAGGATTCTACCCGCCGCTCGGTGGGAAT 8 0.2 No Hit CTCGGTTGCTGGAACCTCCATGACTCCAGTGTAGACATGGCTCTTCTCAGTC 8 0.2 No Hit CGCAGAAGTAGGAATAATGGCACCAGAAATGATATTGTTTCCATAAAGTAGA 7 0.17500000000000002 No Hit GTCCCTTATAACGATCAAGACTGGTAAGCCCGTCGGTCCACACAGTTGTCCA 7 0.17500000000000002 No Hit GTCCACACAGTTGTCCATGTACCAGTAGAAGATTCAGCAGCTACTGCGGCCC 7 0.17500000000000002 No Hit GTGAAGATACGTTGTTAGGTGCTCCATTTTATTTTCCCATTGAGGCCGAACC 7 0.17500000000000002 No Hit CTCGTATTTTCCCCTCTGCCTCGGGTTGTCTCGCGATACCTTCTACAGCTTG 6 0.15 No Hit GCCCGTCGGTCCACACAGTTGTCCATGTACCAGTAGAAGATTCAGCAGCTAC 6 0.15 No Hit AAAGGATTCTACCCGCCGCTCGGTGGGAATTGTACTTCAAGGCGGCCCGCGC 6 0.15 No Hit GATCAAACTAGAGGTTACCAAAGAACCATGCATAGCACTGAATAGGGAGCCG 6 0.15 No Hit CGCGTATTTAAGTCGTCTGCAAAGGATTCTACCCGCCGCTCGGTGGGAATTG 6 0.15 No Hit CCATGTACCAGTAGAAGATTCAGCAGCTACTGCGGCCCCTGCTTCCTCGGGC 6 0.15 No Hit GCATAAGGATGTTGTGCTCAGCCTGGAATACAATCATAAAGTTAAAAGTACC 6 0.15 No Hit CCGTAATCCTTCCACTGCCAGGAGCGGGAGGTGATCGCTGCTCTGTGAGACC 6 0.15 No Hit CTCCAGCAACGGGCTCGATGTCGTAGCATCGTCCCTTATAACGATCAAGACT 6 0.15 No Hit GTCGTCTGCAAAGGATTCTACCCGCCGCTCGGTGGGAATTGTACTTCAAGGC 6 0.15 No Hit GTTAAAACTAGCATATTGGAAGATCAATCGGCCAAAATAACCATGAGCGGCT 6 0.15 No Hit GTCCCTCATTACGAGCTTGTACACATGCTTCTAGAGCTACTCGATTAGCAAC 5 0.125 No Hit GGTGCATAAGGATGTTGTGCTCAGCCTGGAATACAATCATAAAGTTAAAAGT 5 0.125 No Hit CTCACGAGCAAGATCACGTCCCTCATTACGAGCTTGTACACATGCTTCTAGA 5 0.125 No Hit GCCCCATGTAACAAGCTACACCAAGTAAGAAGTGTAGAACAATTAGCTCATA 5 0.125 No Hit CCCGAAGCCACGGGTAGAACACCCGGTAGAGAGACCCAATCTTGAGTGAAAT 5 0.125 No Hit CCAGCAACGGGCTCGATGTCGTAGCATCGTCCCTTATAACGATCAAGACTGG 5 0.125 No Hit GTAAGCTACATAAGCAATAAATTGATTTTCTTCTCCAGCAACGGGCTCGATG 5 0.125 No Hit CGCAAATAAAAGTGCTAATGCTACAACCAGTCCATAAATTGTTAAAGCTTCC 5 0.125 No Hit GTCGGTCCATGGATTTTCCTTCCTTTTTCCGCATTTCGCTAAAGGGTTGAAG 5 0.125 No Hit CTCAGCCTGGAATACAATCATAAAGTTAAAAGTACCAGAGATTCCTAGAGGC 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 0.025 0.0 0.0 0.0 0.0 15 0.025 0.0 0.0 0.0 0.0 16 0.025 0.0 0.0 0.0 0.0 17 0.025 0.0 0.0 0.0 0.0 18 0.025 0.0 0.0 0.0 0.0 19 0.025 0.0 0.0 0.0 0.0 20 0.025 0.0 0.0 0.0 0.0 21 0.025 0.0 0.0 0.0 0.0 22 0.025 0.0 0.0 0.0 0.0 23 0.025 0.0 0.0 0.0 0.0 24 0.025 0.0 0.0 0.0 0.0 25 0.025 0.0 0.0 0.0 0.0 26 0.025 0.0 0.0 0.0 0.0 27 0.025 0.0 0.0 0.0 0.0 28 0.025 0.0 0.0 0.0 0.0 29 0.025 0.0 0.0 0.0 0.0 30 0.025 0.0 0.0 0.0 0.0 31 0.025 0.0 0.0 0.0 0.0 32 0.025 0.0 0.0 0.0 0.0 33 0.025 0.0 0.0 0.0 0.0 34 0.025 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 SRR5423443.sra Written 200000 spots for SRR5423443.sra Read 200000 spots for SRR5423443.sra Written 200000 spots for SRR5423443.sra Read 200000 spots for SRR5423443.sra Written 200000 spots for SRR5423443.sra Read 200000 spots for SRR5423443.sra Written 200000 spots for SRR5423443.sra Read 200000 spots for SRR5423443.sra Written 200000 spots for SRR5423443.sra Read 200000 spots for SRR5423443.sra Written 200000 spots for SRR5423443.sra Read 200000 spots for SRR5423443.sra Written 200000 spots for SRR5423443.sra Read 200000 spots for SRR5423443.sra Written 200000 spots for SRR5423443.sra Read 200000 spots for SRR5423443.sra Written 200000 spots for SRR5423443.sra Read 200000 spots for SRR5423443.sra Written 200000 spots for SRR5423443.sra Read 200000 spots for SRR5423443.sra Written 200000 spots for SRR5423443.sra Read 200000 spots for SRR5423443.sra Written 200000 spots for SRR5423443.sra Read 200000 spots for SRR5423443.sra Written 200000 spots for SRR5423443.sra Read 200000 spots for SRR5423443.sra Written 200000 spots for SRR5423443.sra Read 200000 spots for SRR5423443.sra Written 200000 spots for SRR5423443.sra Read 200000 spots for SRR5423443.sra Written 200000 spots for SRR5423443.sra Read 200000 spots for SRR5423443.sra Written 200000 spots for SRR5423443.sra Read 200000 spots for SRR5423443.sra Written 200000 spots for SRR5423443.sra Read 200000 spots for SRR5423443.sra Written 200000 spots for SRR5423443.sra Read 200000 spots for SRR5423443.sra Written 200000 spots for SRR5423443.sra SRR ids: ['SRR5423443.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_qh68747_ SRR5423443.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]] SRR5423443 file size 703949 SRR5423443 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 SRR5423443 SRR5423443_1.fastq Input file: SRR5423443_1.fastq trimmed: SRR5423443-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 12:59:16 2025 >> started Wed Feb 12 12:59:18 2025 >> done (2.020s) 4000000 reads processed; of these: 150 ( 0.00%) short reads filtered out after trimming by size control 215 ( 0.01%) empty reads filtered out after trimming by size control 3999635 (99.99%) reads available; of these: 67433 ( 1.69%) trimmed reads available after processing 3932202 (98.31%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 14 0.00% 19 2 0.00% 20 5 0.00% 21 0 0.00% 22 1 0.00% 23 1 0.00% 24 0 0.00% 25 1 0.00% 26 2 0.00% 27 1 0.00% 28 1 0.00% 29 3 0.00% 30 2 0.00% 31 2 0.00% 32 2 0.00% 33 6 0.00% 34 6 0.00% 35 11 0.00% 36 10 0.00% 37 13 0.00% 38 19 0.00% 39 26 0.00% 40 46 0.00% 41 46 0.00% 42 69 0.00% 43 89 0.00% 44 166 0.00% 45 210 0.01% 46 298 0.01% 47 551 0.01% 48 1082 0.03% 49 2715 0.07% 50 8103 0.20% 51 53930 1.35% 52 3932202 98.31% 3999635 reads passed initial QC criterion=sequence-density sequence-density=0.18 sequence-density-rank=1 fanout-score=6.58 fanout-score-rank=7 prefix-density=0.78 prefix-fanout=1.5 sequence=ACGTGCTTAATACGTGCTTAA criterion=fanout-score sequence-density=0.02 sequence-density-rank=24 fanout-score=20.74 fanout-score-rank=1 prefix-density=0.31 prefix-fanout=1.2 sequence=CATTTTATTTCTATCTTTCCATACATAACCAAAAAATGGAAAAGATTCTTCAAGAGTCTCGGGTCCTAGAAGTGCATGATAAATACCGCCAAAGCCCAATACTGCAGAGGAAATTAAGTGAAGTACGCCAGATACAAAGTATGGAAAGGTGTCTATGACTTCCCCGCCAGGACCCACCCCCCAACCTAGAGTAGCTAGGTGGGGAAGTAAAATTAATCCTTGTTCATACATTGGCTTCTCCGGTACGAAATGGGCCACTTCAAATAGGTTCATTGCTCCGGCCCAGAATACGATTAATCCAGCATGGGCTACATGAGCTCCCAGCAG Started job on | Feb 12 12:59:34 Started mapping on | Feb 12 12:59:34 Finished on | Feb 12 12:59:39 Mapping speed, Million of reads per hour | 2879.74 Number of input reads | 3999635 Average input read length | 51 UNIQUE READS: Uniquely mapped reads number | 3140079 Uniquely mapped reads % | 78.51% Average mapped length | 51.75 Number of splices: Total | 297156 Number of splices: Annotated (sjdb) | 292444 Number of splices: GT/AG | 290451 Number of splices: GC/AG | 5327 Number of splices: AT/AC | 880 Number of splices: Non-canonical | 498 Mismatch rate per base, % | 0.36% Deletion rate per base | 0.01% Deletion average length | 2.32 Insertion rate per base | 0.00% Insertion average length | 1.35 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 676717 % of reads mapped to multiple loci | 16.92% Number of reads mapped to too many loci | 109983 % of reads mapped to too many loci | 2.75% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.81% % of reads unmapped: other | 0.01% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 182839 182839 182839 N_multimapping 676717 676717 676717 N_noFeature 409393 3093464 445661 N_ambiguous 19838 111 9390 UnstrandedReadsAssigned:2710848 PositiveStrandReadsAssigned:46504 NegativeStrandReadsAssigned:2685028 Dataset is classified negative stranded MeadianReadLen=52 20thPercentileLength=52 echo kmer=47 SRR5423443 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: SRR5423443-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 3,999,635 reads, 3,260,931 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,148 rounds 52401 SRR5423443.ke.tsv 34699 SRR5423443.se.tsv 87100 total ==> SRR5423443.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1919 169 23.7332 Potri.005G024800.1.v4.1 1035 936 13 3.74293 Potri.004G059700.1.v4.1 961 862 0 0 Potri.007G009000.2.v4.1 1416 1317 0 0 Potri.003G141000.2.v4.1 2943 2844 66.3335 6.28561 Potri.016G087400.1.v4.1 270 171 9 14.1837 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 2 0.613874 ==> SRR5423443.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 0 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 27 Potri.001G212900.v4.1 1 Potri.001G182400.v4.1 0 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 1 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 0 SRR5423443 completed mapping pipeline successfully