Starting /dee2/code/volunteer_pipeline.sh SRR5423438 current disk space = 3051209179136 free memory = 1576861112 SRR5423438 SRAfilesize becf9493f6b527255ed0db8d075432ce SRR5423438.sra SRR5423438.sra file validated SRR5423438 is single end SRR5423438 is conventional basespace SRR5423438 read1 length is 52 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR5423438_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 32.00725 34.0 31.0 34.0 30.0 34.0 2 32.09125 34.0 31.0 34.0 30.0 34.0 3 32.26175 34.0 31.0 34.0 30.0 34.0 4 35.7055 37.0 35.0 37.0 33.0 37.0 5 35.547 37.0 35.0 37.0 33.0 37.0 6 35.56725 37.0 35.0 37.0 33.0 37.0 7 35.77025 37.0 35.0 37.0 35.0 37.0 8 35.635 37.0 35.0 37.0 33.0 37.0 9 37.37225 39.0 37.0 39.0 34.0 39.0 10 37.22625 39.0 37.0 39.0 33.0 39.0 11 37.24 39.0 37.0 39.0 33.0 39.0 12 37.31925 39.0 37.0 39.0 34.0 39.0 13 37.24625 39.0 37.0 39.0 33.0 39.0 14 38.272 40.0 38.0 41.0 33.0 41.0 15 38.436 40.0 38.0 41.0 33.0 41.0 16 38.308 40.0 38.0 41.0 33.0 41.0 17 38.5235 40.0 38.0 41.0 34.0 41.0 18 38.5605 40.0 38.0 41.0 34.0 41.0 19 38.58125 40.0 38.0 41.0 34.0 41.0 20 38.4675 40.0 38.0 41.0 34.0 41.0 21 38.409 40.0 38.0 41.0 34.0 41.0 22 38.4385 40.0 38.0 41.0 34.0 41.0 23 38.56825 40.0 38.0 41.0 34.0 41.0 24 38.51225 40.0 38.0 41.0 34.0 41.0 25 38.5675 40.0 38.0 41.0 34.0 41.0 26 38.4505 40.0 38.0 41.0 34.0 41.0 27 38.19225 40.0 38.0 41.0 33.0 41.0 28 38.04025 40.0 38.0 41.0 33.0 41.0 29 38.1775 40.0 38.0 41.0 33.0 41.0 30 38.19125 40.0 38.0 41.0 34.0 41.0 31 38.28475 40.0 38.0 41.0 34.0 41.0 32 38.29975 40.0 38.0 41.0 34.0 41.0 33 38.126 40.0 38.0 41.0 33.0 41.0 34 38.166 40.0 38.0 41.0 33.0 41.0 35 37.55825 40.0 37.0 41.0 31.0 41.0 36 37.831 40.0 37.0 41.0 33.0 41.0 37 37.79925 40.0 37.0 41.0 32.0 41.0 38 37.75025 40.0 37.0 41.0 33.0 41.0 39 37.8655 40.0 37.0 41.0 33.0 41.0 40 37.8875 40.0 37.0 41.0 33.0 41.0 41 37.73875 40.0 37.0 41.0 32.0 41.0 42 37.406 40.0 37.0 41.0 31.0 41.0 43 37.4335 40.0 37.0 41.0 31.0 41.0 44 37.376 40.0 37.0 41.0 31.0 41.0 45 37.465 40.0 37.0 41.0 31.0 41.0 46 37.247 40.0 36.0 41.0 31.0 41.0 47 37.034 39.0 36.0 41.0 31.0 41.0 48 37.19725 40.0 36.0 41.0 31.0 41.0 49 37.12075 39.0 36.0 41.0 31.0 41.0 50 36.72825 39.0 35.0 41.0 30.0 41.0 51 36.552 39.0 35.0 41.0 29.0 41.0 52 35.58875 38.0 34.0 40.0 28.0 41.0 >>END_MODULE >>Per tile sequence quality pass #Tile Base Mean 1209 1 0.0 1209 2 0.0 1209 3 0.0 1209 4 0.0 1209 5 0.0 1209 6 0.0 1209 7 0.0 1209 8 0.0 1209 9 0.0 1209 10 0.0 1209 11 0.0 1209 12 0.0 1209 13 0.0 1209 14 0.0 1209 15 0.0 1209 16 0.0 1209 17 0.0 1209 18 0.0 1209 19 0.0 1209 20 0.0 1209 21 0.0 1209 22 0.0 1209 23 0.0 1209 24 0.0 1209 25 0.0 1209 26 0.0 1209 27 0.0 1209 28 0.0 1209 29 0.0 1209 30 0.0 1209 31 0.0 1209 32 0.0 1209 33 0.0 1209 34 0.0 1209 35 0.0 1209 36 0.0 1209 37 0.0 1209 38 0.0 1209 39 0.0 1209 40 0.0 1209 41 0.0 1209 42 0.0 1209 43 0.0 1209 44 0.0 1209 45 0.0 1209 46 0.0 1209 47 0.0 1209 48 0.0 1209 49 0.0 1209 50 0.0 1209 51 0.0 1209 52 0.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 9 2.0 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 2.0 20 2.0 21 2.0 22 0.0 23 5.0 24 5.0 25 11.0 26 16.0 27 21.0 28 35.0 29 52.0 30 66.0 31 95.0 32 106.0 33 142.0 34 158.0 35 223.0 36 319.0 37 419.0 38 725.0 39 1591.0 40 3.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 36.065162907268174 10.12531328320802 5.7894736842105265 48.02005012531328 2 22.5 14.325 35.425000000000004 27.750000000000004 3 21.224999999999998 18.825 23.9 36.05 4 26.724999999999998 25.8 20.175 27.3 5 25.525 28.475 24.099999999999998 21.9 6 19.525000000000002 32.35 23.575 24.55 7 15.0 24.224999999999998 41.8 18.975 8 17.325 23.65 28.65 30.375000000000004 9 17.925 21.675 32.25 28.15 10 17.375 39.35 23.674999999999997 19.6 11 23.525 28.075 21.825 26.575 12 21.125 25.374999999999996 26.5 27.0 13 18.925 28.299999999999997 27.725 25.05 14 19.625 29.825000000000003 27.700000000000003 22.85 15 21.925 26.775 26.35 24.95 16 20.150000000000002 28.125 26.3 25.424999999999997 17 21.425 27.150000000000002 26.325 25.1 18 20.474999999999998 27.025 27.474999999999998 25.025 19 21.349999999999998 26.85 26.375 25.424999999999997 20 20.4 27.0 26.525 26.075 21 21.875 26.575 25.2 26.35 22 20.95 27.85 24.75 26.450000000000003 23 21.5 28.425 26.325 23.75 24 21.375 26.75 26.125 25.75 25 20.674999999999997 27.6 25.5 26.224999999999998 26 21.95 27.525 25.75 24.775 27 21.4 27.200000000000003 25.8 25.6 28 20.9 28.749999999999996 26.575 23.775 29 21.099999999999998 28.575 26.450000000000003 23.875 30 20.825 25.75 27.075 26.35 31 20.200000000000003 29.525000000000002 25.575 24.7 32 21.275 27.200000000000003 26.775 24.75 33 21.2 26.525 26.650000000000002 25.624999999999996 34 21.099999999999998 27.0 26.3 25.6 35 20.7 27.224999999999998 25.900000000000002 26.174999999999997 36 20.775 26.724999999999998 24.25 28.249999999999996 37 21.25 26.525 25.35 26.875 38 21.55 27.150000000000002 25.575 25.724999999999998 39 22.900000000000002 24.8 24.725 27.575 40 22.225 27.150000000000002 24.05 26.575 41 21.925 26.974999999999998 24.725 26.375 42 21.25 25.074999999999996 26.6 27.075 43 22.3 27.375 25.2 25.124999999999996 44 21.8 28.175 25.724999999999998 24.3 45 22.725 25.775 25.45 26.05 46 22.55563890972743 26.731682920730183 24.18104526131533 26.531632908227053 47 22.95 27.55 25.15 24.349999999999998 48 21.75 27.675 24.0 26.575 49 22.71135567783892 26.688344172086044 25.18759379689845 25.41270635317659 50 22.95573893473368 26.731682920730183 24.58114528632158 25.731432858214554 51 22.26113056528264 25.6128064032016 25.087543771885944 27.03851925962982 52 21.975 27.55 23.825 26.650000000000002 >>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 0.5 8 1.0 9 0.5 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 4.0 19 6.0 20 3.5 21 1.0 22 7.5 23 14.0 24 12.0 25 10.0 26 14.0 27 18.0 28 28.0 29 38.0 30 51.5 31 65.0 32 72.5 33 80.0 34 102.5 35 125.0 36 134.5 37 144.0 38 171.0 39 225.0 40 252.0 41 259.0 42 266.0 43 290.5 44 315.0 45 325.0 46 335.0 47 327.0 48 319.0 49 314.0 50 309.0 51 327.5 52 346.0 53 341.0 54 336.0 55 263.5 56 191.0 57 180.5 58 170.0 59 162.0 60 154.0 61 139.5 62 125.0 63 97.0 64 54.0 65 39.0 66 34.0 67 29.0 68 26.0 69 23.0 70 14.5 71 6.0 72 5.5 73 5.0 74 4.0 75 3.0 76 2.0 77 1.0 78 2.0 79 3.0 80 1.5 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 0.025 47 0.0 48 0.0 49 0.05 50 0.025 51 0.05 52 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 52 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 88.325 #Duplication Level Percentage of deduplicated Percentage of total 1 94.02773846589301 83.05 2 3.3399377299745256 5.8999999999999995 3 1.075573167279932 2.85 4 0.537786583639966 1.9 5 0.42456835550523636 1.875 6 0.2547410133031418 1.35 7 0.08491367110104728 0.525 8 0.05660911406736484 0.4 9 0.02830455703368242 0.22499999999999998 >10 0.16982734220209456 1.925 >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 22 0.5499999999999999 No Hit GGGTAAGCTACATAAGCAATAAATTGATTTTCTTCTCCAGCAACGGGCTCGA 13 0.325 No Hit CTCATTACGAGCTTGTACACATGCTTCTAGAGCTACTCGATTAGCAACGGCA 12 0.3 No Hit GTCGCGTATTTAAGTCGTCTGCAAAGGATTCTACCCGCCGCTCGGTGGGAAT 10 0.25 No Hit CTGCAAAGGATTCTACCCGCCGCTCGGTGGGAATTGTACTTCAAGGCGGCCC 10 0.25 No Hit CCCGTCGGTCCACACAGTTGTCCATGTACCAGTAGAAGATTCAGCAGCTACT 10 0.25 No Hit GGTCGGTCCGCGACCCCTGGATGCCGAAGGCGTCCTTGGGGCGATCTCGTAG 9 0.22499999999999998 No Hit CCAGCAACGGGCTCGATGTCGTAGCATCGTCCCTTATAACGATCAAGACTGG 8 0.2 No Hit CTCGGTTGCTGGAACCTCCATGACTCCAGTGTAGACATGGCTCTTCTCAGTC 8 0.2 No Hit CTCGGGTCCTAGAAGTGCATGATAAATACCGCCAAAGCCCAATACTGCAGAG 7 0.17500000000000002 No Hit GTCCTAGAAGTGCATGATAAATACCGCCAAAGCCCAATACTGCAGAGGAAAT 7 0.17500000000000002 No Hit GTCGTCTGCAAAGGATTCTACCCGCCGCTCGGTGGGAATTGTACTTCAAGGC 7 0.17500000000000002 No Hit GCTCAGCCTGGAATACAATCATAAAGTTAAAAGTACCAGAGATTCCTAGAGG 6 0.15 No Hit GTAAGCTACATAAGCAATAAATTGATTTTCTTCTCCAGCAACGGGCTCGATG 6 0.15 No Hit GGGGTAAGCTACATAAGCAATAAATTGATTTTCTTCTCCAGCAACGGGCTCG 6 0.15 No Hit GCACGGTTAATAATATCAGCCCAGGTATTAATTACACGACCTTGACTATCAA 6 0.15 No Hit CTCCAGCAACGGGCTCGATGTCGTAGCATCGTCCCTTATAACGATCAAGACT 6 0.15 No Hit GTGAAGATACGTTGTTAGGTGCTCCATTTTATTTTCCCATTGAGGCCGAACC 6 0.15 No Hit GCTCCATTTGCTAGCTTCACGGATAATTTCATTACCCTCACGAGCAAGATCA 6 0.15 No Hit GCCAGATACAAAGTATGGAAAGGTGTCTATGACTTCCCCGCCAGGACCCACC 6 0.15 No Hit CTCAGCCTGGAATACAATCATAAAGTTAAAAGTACCAGAGATTCCTAGAGGC 6 0.15 No Hit GTCCCTCATTACGAGCTTGTACACATGCTTCTAGAGCTACTCGATTAGCAAC 5 0.125 No Hit CTCGTATTTTCCCCTCTGCCTCGGGTTGTCTCGCGATACCTTCTACAGCTTG 5 0.125 No Hit CAGGGCTCCATTTGCTAGCTTCACGGATAATTTCATTACCCTCACGAGCAAG 5 0.125 No Hit AAAGGATTCTACCCGCCGCTCGGTGGGAATTGTACTTCAAGGCGGCCCGCGC 5 0.125 No Hit CGCCGCAACAGGAGCTGAATATGCAACAGCAATCCAAGGACGCATACCCAGA 5 0.125 No Hit CCCTGATCAAACTAGAGGTTACCAAAGAACCATGCATAGCACTGAATAGGGA 5 0.125 No Hit CTACGATATTATAAGTTTCTTCCTCTTGACCAAATCTGTAACCTTCATTAGC 5 0.125 No Hit GCCAGACTAAGCAATAAAGTACCTCGTATTTTCCCCTCTGCCTCGGGTTGTC 5 0.125 No Hit CTTATAACGATCAAGACTGGTAAGCCCGTCGGTCCACACAGTTGTCCATGTA 5 0.125 No Hit CTGGAATACAATCATAAAGTTAAAAGTACCAGAGATTCCTAGAGGCATCCCA 5 0.125 No Hit GGTCGGTCCATGGATTTTCCTTCCTTTTTCCGCATTTCGCTAAAGGGTTGAA 5 0.125 No Hit GGCTCCATTTGCTAGCTTCACGGATAATTTCATTACCCTCACGAGCAAGATC 5 0.125 No Hit GTGCATAAGGATGTTGTGCTCAGCCTGGAATACAATCATAAAGTTAAAAGTA 5 0.125 No Hit GGGGGCTCACCAGAGAACGGGCCCAAGTATTTAACACGGTCTGGTCCGTACC 5 0.125 No Hit AGCACGGTTAATAATATCAGCCCAGGTATTAATTACACGACCTTGACTATCA 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 SRR5423438.sra Written 200000 spots for SRR5423438.sra Read 200000 spots for SRR5423438.sra Written 200000 spots for SRR5423438.sra Read 200000 spots for SRR5423438.sra Written 200000 spots for SRR5423438.sra Read 200000 spots for SRR5423438.sra Written 200000 spots for SRR5423438.sra Read 200000 spots for SRR5423438.sra Written 200000 spots for SRR5423438.sra Read 200000 spots for SRR5423438.sra Written 200000 spots for SRR5423438.sra Read 200000 spots for SRR5423438.sra Written 200000 spots for SRR5423438.sra Read 200000 spots for SRR5423438.sra Written 200000 spots for SRR5423438.sra Read 200000 spots for SRR5423438.sra Written 200000 spots for SRR5423438.sra Read 200000 spots for SRR5423438.sra Written 200000 spots for SRR5423438.sra Read 200000 spots for SRR5423438.sra Written 200000 spots for SRR5423438.sra Read 200000 spots for SRR5423438.sra Written 200000 spots for SRR5423438.sra Read 200000 spots for SRR5423438.sra Written 200000 spots for SRR5423438.sra Read 200000 spots for SRR5423438.sra Written 200000 spots for SRR5423438.sra Read 200000 spots for SRR5423438.sra Written 200000 spots for SRR5423438.sra Read 200000 spots for SRR5423438.sra Written 200000 spots for SRR5423438.sra Read 200000 spots for SRR5423438.sra Written 200000 spots for SRR5423438.sra Read 200000 spots for SRR5423438.sra Written 200000 spots for SRR5423438.sra Read 200000 spots for SRR5423438.sra Written 200000 spots for SRR5423438.sra Read 200000 spots for SRR5423438.sra Written 200000 spots for SRR5423438.sra SRR ids: ['SRR5423438.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_othl71ff SRR5423438.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]] SRR5423438 file size 703964 SRR5423438 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 SRR5423438 SRR5423438_1.fastq Input file: SRR5423438_1.fastq trimmed: SRR5423438-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 12:22:54 2025 >> started Wed Feb 12 12:22:56 2025 >> done (1.993s) 4000000 reads processed; of these: 182 ( 0.00%) short reads filtered out after trimming by size control 221 ( 0.01%) empty reads filtered out after trimming by size control 3999597 (99.99%) reads available; of these: 77497 ( 1.94%) trimmed reads available after processing 3922100 (98.06%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 10 0.00% 19 6 0.00% 20 1 0.00% 21 0 0.00% 22 0 0.00% 23 1 0.00% 24 2 0.00% 25 5 0.00% 26 1 0.00% 27 3 0.00% 28 3 0.00% 29 2 0.00% 30 2 0.00% 31 4 0.00% 32 6 0.00% 33 4 0.00% 34 11 0.00% 35 14 0.00% 36 14 0.00% 37 21 0.00% 38 15 0.00% 39 35 0.00% 40 51 0.00% 41 63 0.00% 42 103 0.00% 43 123 0.00% 44 231 0.01% 45 271 0.01% 46 456 0.01% 47 754 0.02% 48 1429 0.04% 49 3195 0.08% 50 9822 0.25% 51 60839 1.52% 52 3922100 98.06% 3999597 reads passed initial QC criterion=sequence-density sequence-density=0.18 sequence-density-rank=1 fanout-score=6.56 fanout-score-rank=6 prefix-density=0.79 prefix-fanout=1.5 sequence=ACGTGCTTAATACGTGCTTAA criterion=fanout-score sequence-density=0.02 sequence-density-rank=24 fanout-score=20.51 fanout-score-rank=1 prefix-density=0.31 prefix-fanout=1.3 sequence=CATTTTATTTCTATCTTTCCATACATAACCAAAAAATGGAAAAGATTCTTCAAGAGTCTCGGGTCCTAGAAGTGCATGATAAATACCGCCAAAGCCCAATACTGCAGAGGAAATTAAGTGAAGTACGCCAGATACAAAGTATGGAAAGGTGTCTATGACTTCCCCGCCAGGACCCACCCCCCAACCTAGAGTAGCTAGGTGGGGAAGTAAAATTAATCCTTGTTCATACATTGGCTTCTCCGGTACGAAATGGGCCACTTCAAATAGGTTCATTGCTCCGGCCCAGAATACGATTAATCCAGCATGGGCTACATGAGCTCCCAGCAG Started job on | Feb 12 12:23:06 Started mapping on | Feb 12 12:23:06 Finished on | Feb 12 12:23:12 Mapping speed, Million of reads per hour | 2399.76 Number of input reads | 3999597 Average input read length | 51 UNIQUE READS: Uniquely mapped reads number | 3140767 Uniquely mapped reads % | 78.53% Average mapped length | 51.74 Number of splices: Total | 297734 Number of splices: Annotated (sjdb) | 292938 Number of splices: GT/AG | 291171 Number of splices: GC/AG | 5201 Number of splices: AT/AC | 878 Number of splices: Non-canonical | 484 Mismatch rate per base, % | 0.35% Deletion rate per base | 0.01% Deletion average length | 2.35 Insertion rate per base | 0.00% Insertion average length | 1.37 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 675875 % of reads mapped to multiple loci | 16.90% Number of reads mapped to too many loci | 109648 % of reads mapped to too many loci | 2.74% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.82% % of reads unmapped: other | 0.01% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 182955 182955 182955 N_multimapping 675875 675875 675875 N_noFeature 407597 3093854 444117 N_ambiguous 20096 126 9585 UnstrandedReadsAssigned:2713074 PositiveStrandReadsAssigned:46787 NegativeStrandReadsAssigned:2687065 Dataset is classified negative stranded MeadianReadLen=52 20thPercentileLength=52 echo kmer=47 SRR5423438 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: SRR5423438-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 3,999,597 reads, 3,266,509 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,159 rounds 52401 SRR5423438.ke.tsv 34699 SRR5423438.se.tsv 87100 total ==> SRR5423438.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1919 125 17.5597 Potri.005G024800.1.v4.1 1035 936 20 5.76018 Potri.004G059700.1.v4.1 961 862 3 0.938201 Potri.007G009000.2.v4.1 1416 1317 0 0 Potri.003G141000.2.v4.1 2943 2844 62.0174 5.87849 Potri.016G087400.1.v4.1 270 171 14 22.0706 Potri.015G069301.1.v4.1 564 465 0 0 Potri.010G195200.1.v4.1 1773 1674 4.14346 0.667251 Potri.012G127500.1.v4.1 977 878 2 0.614069 ==> SRR5423438.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 1 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 32 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 SRR5423438 completed mapping pipeline successfully