Starting /dee2/code/volunteer_pipeline.sh SRR5423385 current disk space = 3049675620352 free memory = 1581982488 SRR5423385 SRAfilesize 2320e9bf244610b124ad5abc589e7050 SRR5423385.sra SRR5423385.sra file validated SRR5423385 is single end SRR5423385 is conventional basespace SRR5423385 read1 length is 52 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR5423385_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 31.97025 33.0 31.0 34.0 30.0 34.0 2 32.06525 34.0 31.0 34.0 30.0 34.0 3 32.2845 34.0 31.0 34.0 30.0 34.0 4 35.09675 37.0 35.0 37.0 32.0 37.0 5 35.64275 37.0 35.0 37.0 33.0 37.0 6 35.72575 37.0 35.0 37.0 35.0 37.0 7 35.61475 37.0 35.0 37.0 33.0 37.0 8 35.7625 37.0 35.0 37.0 35.0 37.0 9 37.326 39.0 37.0 39.0 34.0 39.0 10 37.39975 39.0 37.0 39.0 34.0 39.0 11 37.3185 39.0 37.0 39.0 34.0 39.0 12 37.42975 39.0 37.0 39.0 35.0 39.0 13 37.187 39.0 37.0 39.0 33.0 39.0 14 38.6005 40.0 38.0 41.0 34.0 41.0 15 38.80625 40.0 38.0 41.0 35.0 41.0 16 38.548 40.0 38.0 41.0 34.0 41.0 17 38.49825 40.0 38.0 41.0 34.0 41.0 18 38.651 40.0 38.0 41.0 34.0 41.0 19 38.68825 40.0 38.0 41.0 34.0 41.0 20 38.61925 40.0 38.0 41.0 34.0 41.0 21 38.5445 40.0 38.0 41.0 34.0 41.0 22 38.72425 40.0 38.0 41.0 35.0 41.0 23 38.4745 40.0 38.0 41.0 34.0 41.0 24 38.4905 40.0 38.0 41.0 34.0 41.0 25 38.434 40.0 38.0 41.0 34.0 41.0 26 38.42875 40.0 38.0 41.0 34.0 41.0 27 38.44775 40.0 38.0 41.0 34.0 41.0 28 38.38625 40.0 38.0 41.0 34.0 41.0 29 38.30175 40.0 38.0 41.0 33.0 41.0 30 38.2215 40.0 38.0 41.0 34.0 41.0 31 37.7695 40.0 37.0 41.0 32.0 41.0 32 37.83025 40.0 37.0 41.0 33.0 41.0 33 37.99425 40.0 38.0 41.0 33.0 41.0 34 37.93125 40.0 37.0 41.0 33.0 41.0 35 37.993 40.0 37.0 41.0 33.0 41.0 36 37.89625 40.0 38.0 41.0 33.0 41.0 37 37.8225 40.0 37.0 41.0 32.0 41.0 38 37.88925 40.0 38.0 41.0 33.0 41.0 39 37.63425 40.0 37.0 41.0 32.0 41.0 40 37.357 40.0 37.0 41.0 31.0 41.0 41 37.52 40.0 37.0 41.0 31.0 41.0 42 37.5575 40.0 37.0 41.0 31.0 41.0 43 37.501 40.0 37.0 41.0 31.0 41.0 44 37.35625 40.0 37.0 41.0 32.0 41.0 45 37.3705 40.0 36.0 41.0 31.0 41.0 46 37.1915 40.0 36.0 41.0 31.0 41.0 47 37.04275 40.0 36.0 41.0 30.0 41.0 48 37.21125 39.0 36.0 41.0 31.0 41.0 49 37.12875 39.0 36.0 41.0 31.0 41.0 50 36.98725 39.0 36.0 41.0 31.0 41.0 51 37.099 39.0 36.0 41.0 31.0 41.0 52 36.14175 38.0 35.0 40.0 29.0 41.0 >>END_MODULE >>Per tile sequence quality pass #Tile Base Mean 2107 1 0.0 2107 2 0.0 2107 3 0.0 2107 4 0.0 2107 5 0.0 2107 6 0.0 2107 7 0.0 2107 8 0.0 2107 9 0.0 2107 10 0.0 2107 11 0.0 2107 12 0.0 2107 13 0.0 2107 14 0.0 2107 15 0.0 2107 16 0.0 2107 17 0.0 2107 18 0.0 2107 19 0.0 2107 20 0.0 2107 21 0.0 2107 22 0.0 2107 23 0.0 2107 24 0.0 2107 25 0.0 2107 26 0.0 2107 27 0.0 2107 28 0.0 2107 29 0.0 2107 30 0.0 2107 31 0.0 2107 32 0.0 2107 33 0.0 2107 34 0.0 2107 35 0.0 2107 36 0.0 2107 37 0.0 2107 38 0.0 2107 39 0.0 2107 40 0.0 2107 41 0.0 2107 42 0.0 2107 43 0.0 2107 44 0.0 2107 45 0.0 2107 46 0.0 2107 47 0.0 2107 48 0.0 2107 49 0.0 2107 50 0.0 2107 51 0.0 2107 52 0.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 12 1.0 13 1.0 14 0.0 15 0.0 16 0.0 17 1.0 18 0.0 19 0.0 20 1.0 21 1.0 22 7.0 23 11.0 24 4.0 25 7.0 26 21.0 27 25.0 28 30.0 29 42.0 30 60.0 31 83.0 32 118.0 33 114.0 34 175.0 35 216.0 36 299.0 37 432.0 38 734.0 39 1612.0 40 5.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 44.310776942355886 13.859649122807017 5.989974937343359 35.83959899749373 2 21.625 14.799999999999999 34.975 28.599999999999998 3 19.75 18.9 25.4 35.949999999999996 4 25.624999999999996 27.025 21.45 25.900000000000002 5 23.3 33.425 22.225 21.05 6 20.375 36.325 22.225 21.075 7 15.825 23.974999999999998 41.8 18.4 8 17.775 22.875 29.375 29.975 9 18.35 22.15 32.45 27.05 10 20.025000000000002 38.975 21.575 19.425 11 23.599999999999998 28.9 19.625 27.875 12 20.7 24.075 27.3 27.925 13 19.825 28.65 27.925 23.599999999999998 14 20.45 29.299999999999997 26.825 23.425 15 23.325000000000003 24.65 26.924999999999997 25.1 16 21.7 26.375 25.324999999999996 26.6 17 22.525000000000002 24.925 26.25 26.3 18 21.075 26.3 26.200000000000003 26.424999999999997 19 22.95 27.400000000000002 25.650000000000002 24.0 20 21.95 27.35 25.874999999999996 24.825 21 21.55 26.900000000000002 25.974999999999998 25.575 22 20.280070017504375 28.057014253563388 24.706176544136035 26.9567391847962 23 21.5 27.750000000000004 25.374999999999996 25.374999999999996 24 22.400000000000002 26.974999999999998 25.674999999999997 24.95 25 21.425 27.474999999999998 25.55 25.55 26 22.6 26.85 25.575 24.975 27 21.125 27.825 26.25 24.8 28 21.65 28.1 25.724999999999998 24.525 29 21.475 27.625 27.075 23.825 30 20.849999999999998 24.875 27.400000000000002 26.875 31 20.200000000000003 28.275 25.35 26.174999999999997 32 21.425 27.700000000000003 26.474999999999998 24.4 33 21.45 26.375 26.85 25.324999999999996 34 22.475 26.174999999999997 26.8 24.55 35 20.75 27.875 23.724999999999998 27.650000000000002 36 21.349999999999998 28.15 24.4 26.1 37 22.8 26.0 25.424999999999997 25.775 38 21.775 27.35 25.3 25.575 39 21.775 25.45 25.674999999999997 27.1 40 20.849999999999998 27.575 25.55 26.025 41 22.75 25.900000000000002 24.775 26.575 42 20.875 25.8 26.775 26.55 43 22.125 26.625 26.275 24.975 44 21.475 28.275 25.0 25.25 45 21.85 27.825 24.6 25.724999999999998 46 23.305826456614152 26.9567391847962 24.90622655663916 24.831207801950487 47 24.05 27.625 23.674999999999997 24.65 48 22.625 26.424999999999997 25.05 25.900000000000002 49 22.58064516129032 26.331582895723933 24.356089022255563 26.731682920730183 50 23.3 26.450000000000003 23.875 26.375 51 22.25 25.35 25.025 27.375 52 23.925 26.575 24.85 24.65 >>END_MODULE >>Per sequence GC content pass #GC Content Count 0 2.0 1 1.5 2 1.0 3 1.5 4 2.0 5 1.5 6 1.0 7 2.5 8 4.0 9 2.5 10 1.0 11 1.0 12 1.0 13 0.5 14 1.5 15 3.0 16 4.5 17 6.0 18 4.5 19 3.0 20 6.0 21 9.0 22 9.5 23 10.0 24 14.5 25 19.0 26 19.0 27 19.0 28 27.5 29 36.0 30 49.0 31 62.0 32 76.0 33 90.0 34 110.5 35 131.0 36 144.5 37 158.0 38 184.0 39 214.5 40 219.0 41 224.0 42 229.0 43 265.5 44 302.0 45 306.0 46 310.0 47 302.5 48 295.0 49 311.0 50 327.0 51 311.0 52 295.0 53 308.0 54 321.0 55 285.5 56 250.0 57 223.0 58 196.0 59 174.5 60 153.0 61 143.5 62 134.0 63 107.5 64 64.5 65 48.0 66 38.0 67 28.0 68 20.0 69 12.0 70 13.0 71 14.0 72 12.0 73 10.0 74 6.0 75 2.0 76 1.5 77 1.0 78 1.0 79 1.0 80 0.5 81 0.0 82 0.5 83 1.0 84 1.0 85 1.0 86 0.5 87 0.0 88 0.5 89 0.5 90 0.0 91 0.5 92 1.0 93 0.5 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 0.025 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 0.025 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 87.2 #Duplication Level Percentage of deduplicated Percentage of total 1 92.74655963302753 80.875 2 4.3577981651376145 7.6 3 1.2901376146788992 3.375 4 0.573394495412844 2.0 5 0.45871559633027525 2.0 6 0.22935779816513763 1.2 7 0.05733944954128441 0.35000000000000003 8 0.05733944954128441 0.4 9 0.028669724770642203 0.22499999999999998 >10 0.20068807339449543 1.975 >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 GTCCACACAGTTGTCCATGTACCAGTAGAAGATTCAGCAGCTACTGCGGCCC 13 0.325 No Hit CTCGTATTTTCCCCTCTGCCTCGGGTTGTCTCGCGATACCTTCTACAGCTTG 12 0.3 No Hit CCAGCAACGGGCTCGATGTCGTAGCATCGTCCCTTATAACGATCAAGACTGG 12 0.3 No Hit GGGTAAGCTACATAAGCAATAAATTGATTTTCTTCTCCAGCAACGGGCTCGA 12 0.3 No Hit CGTCGGTCCACACAGTTGTCCATGTACCAGTAGAAGATTCAGCAGCTACTGC 10 0.25 No Hit CTAACATGTGAAATGGGTGCATAAGGATGTTGTGCTCAGCCTGGAATACAAT 10 0.25 No Hit AGCACGGTTAATAATATCAGCCCAGGTATTAATTACACGACCTTGACTATCA 10 0.25 No Hit CCCTGATCAAACTAGAGGTTACCAAAGAACCATGCATAGCACTGAATAGGGA 9 0.22499999999999998 No Hit GCCAGACTAAGCAATAAAGTACCTCGTATTTTCCCCTCTGCCTCGGGTTGTC 8 0.2 No Hit GCTCCATTTGCTAGCTTCACGGATAATTTCATTACCCTCACGAGCAAGATCA 8 0.2 No Hit GTCCCTTATAACGATCAAGACTGGTAAGCCCGTCGGTCCACACAGTTGTCCA 7 0.17500000000000002 No Hit ATAACGATCAAGACTGGTAAGCCCGTCGGTCCACACAGTTGTCCATGTACCA 7 0.17500000000000002 No Hit GTCCCTCATTACGAGCTTGTACACATGCTTCTAGAGCTACTCGATTAGCAAC 6 0.15 No Hit GATCAAACTAGAGGTTACCAAAGAACCATGCATAGCACTGAATAGGGAGCCG 6 0.15 No Hit CTCACGAGCAAGATCACGTCCCTCATTACGAGCTTGTACACATGCTTCTAGA 6 0.15 No Hit ATAATATCAGCCCAGGTATTAATTACACGACCTTGACTATCAACTACAGATT 6 0.15 No Hit CCCGTCGGTCCACACAGTTGTCCATGTACCAGTAGAAGATTCAGCAGCTACT 6 0.15 No Hit GCACGGTTAATAATATCAGCCCAGGTATTAATTACACGACCTTGACTATCAA 6 0.15 No Hit CCGCATTTCGCTAAAGGGTTGAAGGAGGATAGTGCATCAAGCTGTTCGCAAG 6 0.15 No Hit GCCGAATACACCAGCTACGCCTAACATGTGAAATGGGTGCATAAGGATGTTG 6 0.15 No Hit GGTTAATAATATCAGCCCAGGTATTAATTACACGACCTTGACTATCAACTAC 5 0.125 No Hit GTCCATGTACCAGTAGAAGATTCAGCAGCTACTGCGGCCCCTGCTTCCTCGG 5 0.125 No Hit GGGTAAACCACCGCCTCTCGGGCCCCCGACTGATTCTACCATAGAGGCCGAC 5 0.125 No Hit AGAGATTCCTAGAGGCATCCCATCCGAAAAACTTCCTTGACCGATTGGATAA 5 0.125 No Hit GTGCTGAGTTGGAATCCCATTCTAACTAAGGATTCTTGTGGTTCCGGAGGAT 5 0.125 No Hit CCCAGGTATTAATTACACGACCTTGACTATCAACTACAGATTGGTTGAAATT 5 0.125 No Hit GTCCGCGACCCCTGGATGCCGAAGGCGTCCTTGGGGCGATCTCGTAGTTCCT 5 0.125 No Hit GGGGTAAGCTACATAAGCAATAAATTGATTTTCTTCTCCAGCAACGGGCTCG 5 0.125 No Hit CGAAAAACTTCCTTGACCGATTGGATAAATCAAGAAAACAGCAGTAGCCGCC 5 0.125 No Hit CAGCAACGGGCTCGATGTCGTAGCATCGTCCCTTATAACGATCAAGACTGGT 5 0.125 No Hit CCTGATCAAACTAGAGGTTACCAAAGAACCATGCATAGCACTGAATAGGGAG 5 0.125 No Hit CATGCATAGCACTGAATAGGGAGCCGCCGAATACACCAGCTACGCCTAACAT 5 0.125 No Hit GTCATTGTTAGCCTTTCTGGTGACCGGGAAAGCTGAGGTAGACTTGAGGCCG 5 0.125 No Hit GTGCATAAGGATGTTGTGCTCAGCCTGGAATACAATCATAAAGTTAAAAGTA 5 0.125 No Hit ATCAAACTAGAGGTTACCAAAGAACCATGCATAGCACTGAATAGGGAGCCGC 5 0.125 No Hit GTTAAAACTAGCATATTGGAAGATCAATCGGCCAAAATAACCATGAGCGGCT 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 0.025 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 SRR5423385.sra Written 200000 spots for SRR5423385.sra Read 200000 spots for SRR5423385.sra Written 200000 spots for SRR5423385.sra Read 200000 spots for SRR5423385.sra Written 200000 spots for SRR5423385.sra Read 200000 spots for SRR5423385.sra Written 200000 spots for SRR5423385.sra Read 200000 spots for SRR5423385.sra Written 200000 spots for SRR5423385.sra Read 200000 spots for SRR5423385.sra Written 200000 spots for SRR5423385.sra Read 200000 spots for SRR5423385.sra Written 200000 spots for SRR5423385.sra Read 200000 spots for SRR5423385.sra Written 200000 spots for SRR5423385.sra Read 200000 spots for SRR5423385.sra Written 200000 spots for SRR5423385.sra Read 200000 spots for SRR5423385.sra Written 200000 spots for SRR5423385.sra Read 200000 spots for SRR5423385.sra Written 200000 spots for SRR5423385.sra Read 200000 spots for SRR5423385.sra Written 200000 spots for SRR5423385.sra Read 200000 spots for SRR5423385.sra Written 200000 spots for SRR5423385.sra Read 200000 spots for SRR5423385.sra Written 200000 spots for SRR5423385.sra Read 200000 spots for SRR5423385.sra Written 200000 spots for SRR5423385.sra Read 200000 spots for SRR5423385.sra Written 200000 spots for SRR5423385.sra Read 200000 spots for SRR5423385.sra Written 200000 spots for SRR5423385.sra Read 200000 spots for SRR5423385.sra Written 200000 spots for SRR5423385.sra Read 200000 spots for SRR5423385.sra Written 200000 spots for SRR5423385.sra Read 200000 spots for SRR5423385.sra Written 200000 spots for SRR5423385.sra SRR ids: ['SRR5423385.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_8atg_zl3 SRR5423385.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]] SRR5423385 file size 703989 SRR5423385 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 SRR5423385 SRR5423385_1.fastq Input file: SRR5423385_1.fastq trimmed: SRR5423385-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 09:07:22 2025 >> started Wed Feb 12 09:07:25 2025 >> done (2.784s) 4000000 reads processed; of these: 98 ( 0.00%) short reads filtered out after trimming by size control 850 ( 0.02%) empty reads filtered out after trimming by size control 3999052 (99.98%) reads available; of these: 81351 ( 2.03%) trimmed reads available after processing 3917701 (97.97%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 9 0.00% 19 3 0.00% 20 3 0.00% 21 1 0.00% 22 0 0.00% 23 2 0.00% 24 5 0.00% 25 7 0.00% 26 4 0.00% 27 2 0.00% 28 9 0.00% 29 3 0.00% 30 7 0.00% 31 15 0.00% 32 17 0.00% 33 17 0.00% 34 18 0.00% 35 27 0.00% 36 37 0.00% 37 35 0.00% 38 53 0.00% 39 78 0.00% 40 70 0.00% 41 95 0.00% 42 134 0.00% 43 206 0.01% 44 316 0.01% 45 407 0.01% 46 524 0.01% 47 890 0.02% 48 1643 0.04% 49 3379 0.08% 50 10181 0.25% 51 63154 1.58% 52 3917701 97.97% 3999052 reads passed initial QC criterion=sequence-density sequence-density=0.38 sequence-density-rank=1 fanout-score=1.91 fanout-score-rank=29 prefix-density=0.35 prefix-fanout=1.9 sequence=TGGCACCGGCCCGTAATCCTTCCACTGCCAGGAGCGGGAGGTGATCGCTGCTCTGTGAGACCAGCCTCACGCTGTGCCCTCCCCTCTAGGAGCCACGACACC criterion=fanout-score sequence-density=0.01 sequence-density-rank=37 fanout-score=19.86 fanout-score-rank=1 prefix-density=0.04 prefix-fanout=3.0 sequence=AAGAAGTTCACACTTTCTGGCGACGTCTTTCTTTTTCTTCAAAACCCCAATCCGCTCTCGCTCGCCGCTACTAACGGGGTCTCGGTTGATTTCCCTTCCTTTAGCTAGTCAGATGTTTCAGTTCGCTAAGTTTGAAAAGTCCAAAGAGCGCAGACTCGCCACGGAGCTTGGAGACGGTTTCCCGATCGGAGATCCATGGATCACAGACGGTATCTCCCCATGGCCTTTCGCC Started job on | Feb 12 09:07:38 Started mapping on | Feb 12 09:07:38 Finished on | Feb 12 09:07:43 Mapping speed, Million of reads per hour | 2879.32 Number of input reads | 3999052 Average input read length | 51 UNIQUE READS: Uniquely mapped reads number | 3002248 Uniquely mapped reads % | 75.07% Average mapped length | 51.78 Number of splices: Total | 256644 Number of splices: Annotated (sjdb) | 253306 Number of splices: GT/AG | 248799 Number of splices: GC/AG | 6254 Number of splices: AT/AC | 917 Number of splices: Non-canonical | 674 Mismatch rate per base, % | 0.42% Deletion rate per base | 0.01% Deletion average length | 2.35 Insertion rate per base | 0.00% Insertion average length | 1.33 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 845617 % of reads mapped to multiple loci | 21.15% Number of reads mapped to too many loci | 73841 % of reads mapped to too many loci | 1.85% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.82% % of reads unmapped: other | 0.12% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 151187 151187 151187 N_multimapping 845617 845617 845617 N_noFeature 454568 2931932 514030 N_ambiguous 22069 160 11063 UnstrandedReadsAssigned:2525611 PositiveStrandReadsAssigned:70156 NegativeStrandReadsAssigned:2477155 Dataset is classified negative stranded MeadianReadLen=52 20thPercentileLength=52 echo kmer=47 SRR5423385 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: SRR5423385-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 3,999,052 reads, 3,146,805 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,067 rounds 52401 SRR5423385.ke.tsv 34699 SRR5423385.se.tsv 87100 total ==> SRR5423385.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1919 87 12.1357 Potri.005G024800.1.v4.1 1035 936 2 0.571971 Potri.004G059700.1.v4.1 961 862 2 0.621073 Potri.007G009000.2.v4.1 1416 1317 0 0 Potri.003G141000.2.v4.1 2943 2844 63.3174 5.95954 Potri.016G087400.1.v4.1 270 171 17 26.6117 Potri.015G069301.1.v4.1 564 465 0 0 Potri.010G195200.1.v4.1 1773 1674 3 0.479717 Potri.012G127500.1.v4.1 977 878 7 2.13414 ==> SRR5423385.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 4 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 18 Potri.001G212900.v4.1 2 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 SRR5423385 completed mapping pipeline successfully