Starting /dee2/code/volunteer_pipeline.sh SRR5423400 current disk space = 3049676853248 free memory = 1303326416 SRR5423400 SRAfilesize 8c1ffdf3f2f4c4a96b2ce2bdba068f12 SRR5423400.sra SRR5423400.sra file validated SRR5423400 is single end SRR5423400 is conventional basespace SRR5423400 read1 length is 52 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR5423400_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 31.772 31.0 31.0 34.0 30.0 34.0 2 31.79 31.0 31.0 34.0 30.0 34.0 3 31.89375 33.0 31.0 34.0 30.0 34.0 4 34.612 37.0 35.0 37.0 30.0 37.0 5 35.2415 37.0 35.0 37.0 32.0 37.0 6 35.42375 37.0 35.0 37.0 33.0 37.0 7 35.46825 37.0 35.0 37.0 33.0 37.0 8 35.56225 37.0 35.0 37.0 33.0 37.0 9 37.11575 39.0 37.0 39.0 33.0 39.0 10 37.024 39.0 37.0 39.0 33.0 39.0 11 37.17325 39.0 37.0 39.0 33.0 39.0 12 36.997 39.0 37.0 39.0 33.0 39.0 13 36.78225 39.0 37.0 39.0 32.0 39.0 14 38.15125 40.0 37.0 41.0 33.0 41.0 15 37.58675 40.0 36.0 41.0 32.0 41.0 16 38.0705 40.0 37.0 41.0 33.0 41.0 17 38.09625 40.0 37.0 41.0 33.0 41.0 18 37.817 40.0 37.0 41.0 33.0 41.0 19 38.11425 40.0 37.0 41.0 33.0 41.0 20 38.0755 40.0 37.0 41.0 33.0 41.0 21 38.152 40.0 37.0 41.0 33.0 41.0 22 38.1795 40.0 38.0 41.0 33.0 41.0 23 37.8965 40.0 37.0 41.0 32.0 41.0 24 38.10725 40.0 37.0 41.0 33.0 41.0 25 38.01475 40.0 37.0 41.0 33.0 41.0 26 37.808 40.0 37.0 41.0 32.0 41.0 27 37.94075 40.0 37.0 41.0 33.0 41.0 28 38.00075 40.0 37.0 41.0 33.0 41.0 29 37.992 40.0 37.0 41.0 33.0 41.0 30 37.54875 40.0 37.0 41.0 31.0 41.0 31 37.9145 40.0 37.0 41.0 33.0 41.0 32 37.9805 40.0 37.0 41.0 33.0 41.0 33 37.6805 40.0 37.0 41.0 32.0 41.0 34 37.9 40.0 37.0 41.0 33.0 41.0 35 37.77475 40.0 37.0 41.0 33.0 41.0 36 37.60325 40.0 37.0 41.0 32.0 41.0 37 37.40275 40.0 37.0 41.0 31.0 41.0 38 37.3635 40.0 37.0 41.0 31.0 41.0 39 37.366 39.0 36.0 41.0 31.0 41.0 40 37.107 39.0 36.0 41.0 30.0 41.0 41 37.28425 39.0 36.0 41.0 31.0 41.0 42 37.1835 39.0 36.0 41.0 31.0 41.0 43 37.29525 39.0 36.0 41.0 31.0 41.0 44 37.1005 39.0 36.0 41.0 31.0 41.0 45 36.998 39.0 36.0 41.0 30.0 41.0 46 36.86975 39.0 35.0 41.0 30.0 41.0 47 36.90375 39.0 35.0 41.0 30.0 41.0 48 36.7425 39.0 35.0 40.0 30.0 41.0 49 36.6505 39.0 35.0 41.0 30.0 41.0 50 36.5385 39.0 35.0 40.0 30.0 41.0 51 36.6755 39.0 35.0 40.0 30.0 41.0 52 35.61475 38.0 34.0 40.0 28.0 41.0 >>END_MODULE >>Per tile sequence quality pass #Tile Base Mean 1112 1 0.0 1112 2 0.0 1112 3 0.0 1112 4 0.0 1112 5 0.0 1112 6 0.0 1112 7 0.0 1112 8 0.0 1112 9 0.0 1112 10 0.0 1112 11 0.0 1112 12 0.0 1112 13 0.0 1112 14 0.0 1112 15 0.0 1112 16 0.0 1112 17 0.0 1112 18 0.0 1112 19 0.0 1112 20 0.0 1112 21 0.0 1112 22 0.0 1112 23 0.0 1112 24 0.0 1112 25 0.0 1112 26 0.0 1112 27 0.0 1112 28 0.0 1112 29 0.0 1112 30 0.0 1112 31 0.0 1112 32 0.0 1112 33 0.0 1112 34 0.0 1112 35 0.0 1112 36 0.0 1112 37 0.0 1112 38 0.0 1112 39 0.0 1112 40 0.0 1112 41 0.0 1112 42 0.0 1112 43 0.0 1112 44 0.0 1112 45 0.0 1112 46 0.0 1112 47 0.0 1112 48 0.0 1112 49 0.0 1112 50 0.0 1112 51 0.0 1112 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 0.0 21 1.0 22 3.0 23 3.0 24 10.0 25 13.0 26 23.0 27 27.0 28 45.0 29 52.0 30 84.0 31 95.0 32 133.0 33 155.0 34 191.0 35 283.0 36 361.0 37 492.0 38 702.0 39 1320.0 40 6.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 29.584168336673343 9.193386773547093 7.039078156312625 54.18336673346693 2 22.15 13.5 37.25 27.1 3 20.075000000000003 18.224999999999998 22.475 39.225 4 25.624999999999996 25.3 20.474999999999998 28.599999999999998 5 24.175 30.325000000000003 24.55 20.95 6 20.125 32.824999999999996 25.3 21.75 7 16.175 22.900000000000002 39.925 21.0 8 19.1 23.5 30.599999999999998 26.8 9 18.75 20.275000000000002 34.675 26.3 10 17.625 38.800000000000004 23.474999999999998 20.1 11 23.3 27.6 22.575 26.525 12 21.275 24.6 27.375 26.75 13 20.424999999999997 28.175 26.900000000000002 24.5 14 19.85 28.749999999999996 26.875 24.525 15 20.925 26.575 27.075 25.424999999999997 16 21.175 27.275 25.974999999999998 25.575 17 20.95 27.625 27.800000000000004 23.625 18 21.825 26.825 27.025 24.325 19 20.625 27.750000000000004 25.900000000000002 25.724999999999998 20 21.0 27.900000000000002 26.025 25.074999999999996 21 20.65 25.85 27.1 26.400000000000002 22 21.2 27.325 24.75 26.724999999999998 23 22.1 27.425 24.85 25.624999999999996 24 22.2 26.674999999999997 25.6 25.525 25 21.375 27.825 24.425 26.375 26 22.525000000000002 25.724999999999998 26.85 24.9 27 20.549999999999997 27.925 26.474999999999998 25.05 28 20.95 28.749999999999996 25.8 24.5 29 20.200000000000003 28.025 27.400000000000002 24.375 30 19.900000000000002 24.775 27.900000000000002 27.425 31 21.65 27.900000000000002 26.85 23.599999999999998 32 20.825 27.55 26.8 24.825 33 19.575 26.974999999999998 28.449999999999996 25.0 34 21.0 27.200000000000003 25.224999999999998 26.575 35 20.075000000000003 27.375 25.650000000000002 26.900000000000002 36 20.175 28.299999999999997 25.374999999999996 26.150000000000002 37 21.05 26.974999999999998 25.525 26.450000000000003 38 21.575 26.825 26.0 25.6 39 21.349999999999998 26.35 25.25 27.05 40 20.200000000000003 28.349999999999998 25.95 25.5 41 21.675 27.224999999999998 25.624999999999996 25.474999999999998 42 19.775000000000002 25.05 27.35 27.825 43 20.974999999999998 26.8 26.075 26.150000000000002 44 22.075 27.450000000000003 25.974999999999998 24.5 45 22.650000000000002 24.875 26.525 25.95 46 22.2 26.75 25.324999999999996 25.724999999999998 47 24.025 26.400000000000002 24.5 25.074999999999996 48 22.15 25.624999999999996 24.975 27.250000000000004 49 19.775000000000002 27.250000000000004 25.874999999999996 27.1 50 21.45 28.675 25.474999999999998 24.4 51 23.35 25.374999999999996 24.275 27.0 52 22.2 26.8 25.525 25.474999999999998 >>END_MODULE >>Per sequence GC content pass #GC Content Count 0 1.0 1 0.5 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 1.0 12 1.0 13 0.5 14 0.0 15 0.0 16 1.0 17 2.0 18 4.5 19 7.0 20 7.5 21 8.0 22 9.5 23 11.0 24 13.5 25 16.0 26 21.5 27 27.0 28 30.5 29 34.0 30 37.0 31 40.0 32 64.5 33 89.0 34 96.0 35 103.0 36 135.5 37 168.0 38 194.5 39 227.5 40 234.0 41 243.0 42 252.0 43 288.5 44 325.0 45 334.0 46 343.0 47 348.0 48 353.0 49 332.5 50 312.0 51 330.5 52 349.0 53 321.0 54 293.0 55 257.0 56 221.0 57 208.5 58 196.0 59 174.5 60 153.0 61 124.0 62 95.0 63 71.5 64 43.5 65 39.0 66 35.5 67 32.0 68 24.0 69 16.0 70 10.5 71 5.0 72 3.5 73 2.0 74 1.5 75 1.0 76 1.5 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 0.2 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 0.0 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 86.3 #Duplication Level Percentage of deduplicated Percentage of total 1 92.67091541135574 79.975 2 4.345307068366164 7.5 3 1.3035921205098495 3.375 4 0.5793742757821553 2.0 5 0.3765932792584009 1.625 6 0.2607184241019699 1.35 7 0.14484356894553882 0.8750000000000001 8 0.08690614136732329 0.6 9 0.057937427578215524 0.44999999999999996 >10 0.17381228273464658 2.25 >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 21 0.525 No Hit CCCGTCGGTCCACACAGTTGTCCATGTACCAGTAGAAGATTCAGCAGCTACT 17 0.42500000000000004 No Hit CTCGTATTTTCCCCTCTGCCTCGGGTTGTCTCGCGATACCTTCTACAGCTTG 16 0.4 No Hit GGGTAAGCTACATAAGCAATAAATTGATTTTCTTCTCCAGCAACGGGCTCGA 15 0.375 No Hit CTCGTACACACTAAGAAAAAAGCCTTATCCATTTACAAAAGTCTTATCCATT 11 0.27499999999999997 No Hit CTGCAAAGGATTCTACCCGCCGCTCGGTGGGAATTGTACTTCAAGGCGGCCC 10 0.25 No Hit CGCAGAAGTAGGAATAATGGCACCAGAAATGATATTGTTTCCATAAAGTAGA 9 0.22499999999999998 No Hit CTCCAGCAACGGGCTCGATGTCGTAGCATCGTCCCTTATAACGATCAAGACT 9 0.22499999999999998 No Hit CCTCATTACGAGCTTGTACACATGCTTCTAGAGCTACTCGATTAGCAACGGC 8 0.2 No Hit GTCCGCGACCCCTGGATGCCGAAGGCGTCCTTGGGGCGATCTCGTAGTTCCT 8 0.2 No Hit CTCATTACGAGCTTGTACACATGCTTCTAGAGCTACTCGATTAGCAACGGCA 8 0.2 No Hit CTCCATTTTATTTTCCCATTGAGGCCGAACCTAAACCTGTGCTCGAGAGATA 7 0.17500000000000002 No Hit CTCACGAGCAAGATCACGTCCCTCATTACGAGCTTGTACACATGCTTCTAGA 7 0.17500000000000002 No Hit CTGGAATACAATCATAAAGTTAAAAGTACCAGAGATTCCTAGAGGCATCCCA 7 0.17500000000000002 No Hit CCGTCGGTCCACACAGTTGTCCATGTACCAGTAGAAGATTCAGCAGCTACTG 7 0.17500000000000002 No Hit AGCACGGTTAATAATATCAGCCCAGGTATTAATTACACGACCTTGACTATCA 7 0.17500000000000002 No Hit GTCCATGTACCAGTAGAAGATTCAGCAGCTACTGCGGCCCCTGCTTCCTCGG 6 0.15 No Hit GATCAAACTAGAGGTTACCAAAGAACCATGCATAGCACTGAATAGGGAGCCG 6 0.15 No Hit GCCTCCTCAAGCTCAAGCAACACTTGAGATGCCTCAGTGCATCCAAACATGG 6 0.15 No Hit CCTCTGCCTCGGGTTGTCTCGCGATACCTTCTACAGCTTGGCCCGCAGCAGT 6 0.15 No Hit CATGAATGTGATGGACCAAAAAATCCGCGGTTCCTAATGGAATAGGTAACAA 6 0.15 No Hit CCCACTTTTTGGTCTTAAGAATGCTGGTTTTAAGAATGAGTGATTGCCCTTC 6 0.15 No Hit GTCCACACAGTTGTCCATGTACCAGTAGAAGATTCAGCAGCTACTGCGGCCC 6 0.15 No Hit ATCAAACTAGAGGTTACCAAAGAACCATGCATAGCACTGAATAGGGAGCCGC 6 0.15 No Hit CTCTGCCTCGGGTTGTCTCGCGATACCTTCTACAGCTTGGCCCGCAGCAGTA 6 0.15 No Hit GTCCCTCATTACGAGCTTGTACACATGCTTCTAGAGCTACTCGATTAGCAAC 5 0.125 No Hit GCCCGTCGGTCCACACAGTTGTCCATGTACCAGTAGAAGATTCAGCAGCTAC 5 0.125 No Hit CAGGGCTCCATTTGCTAGCTTCACGGATAATTTCATTACCCTCACGAGCAAG 5 0.125 No Hit CTTAAGAATGCTGGTTTTAAGAATGAGTGATTGCCCTTCTCCGACCCTTACT 5 0.125 No Hit GTCGAATCCAATGATACGGATAAAGGAGTTAGGGTAAGCTTTCTTCGCCTCC 5 0.125 No Hit CCAGCAACGGGCTCGATGTCGTAGCATCGTCCCTTATAACGATCAAGACTGG 5 0.125 No Hit GTAAGCTACATAAGCAATAAATTGATTTTCTTCTCCAGCAACGGGCTCGATG 5 0.125 No Hit GGGGTAAGCTACATAAGCAATAAATTGATTTTCTTCTCCAGCAACGGGCTCG 5 0.125 No Hit GTCCTAGAAGTGCATGATAAATACCGCCAAAGCCCAATACTGCAGAGGAAAT 5 0.125 No Hit GCTGGTTTTAAGAATGAGTGATTGCCCTTCTCCGACCCTTACTGCCCAACCT 5 0.125 No Hit CTCGATTAGCAACGGCACCGGGTGCATTTCCCCAAGGGTGCCCTAAAGTTCC 5 0.125 No Hit GTGCATAAGGATGTTGTGCTCAGCCTGGAATACAATCATAAAGTTAAAAGTA 5 0.125 No Hit ATAACGATCAAGACTGGTAAGCCCGTCGGTCCACACAGTTGTCCATGTACCA 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 SRR5423400.sra Written 200000 spots for SRR5423400.sra Read 200000 spots for SRR5423400.sra Written 200000 spots for SRR5423400.sra Read 200000 spots for SRR5423400.sra Written 200000 spots for SRR5423400.sra Read 200000 spots for SRR5423400.sra Written 200000 spots for SRR5423400.sra Read 200000 spots for SRR5423400.sra Written 200000 spots for SRR5423400.sra Read 200000 spots for SRR5423400.sra Written 200000 spots for SRR5423400.sra Read 200000 spots for SRR5423400.sra Written 200000 spots for SRR5423400.sra Read 200000 spots for SRR5423400.sra Written 200000 spots for SRR5423400.sra Read 200000 spots for SRR5423400.sra Written 200000 spots for SRR5423400.sra Read 200000 spots for SRR5423400.sra Written 200000 spots for SRR5423400.sra Read 200000 spots for SRR5423400.sra Written 200000 spots for SRR5423400.sra Read 200000 spots for SRR5423400.sra Written 200000 spots for SRR5423400.sra Read 200000 spots for SRR5423400.sra Written 200000 spots for SRR5423400.sra Read 200000 spots for SRR5423400.sra Written 200000 spots for SRR5423400.sra Read 200000 spots for SRR5423400.sra Written 200000 spots for SRR5423400.sra Read 200000 spots for SRR5423400.sra Written 200000 spots for SRR5423400.sra Read 200000 spots for SRR5423400.sra Written 200000 spots for SRR5423400.sra Read 200000 spots for SRR5423400.sra Written 200000 spots for SRR5423400.sra Read 200000 spots for SRR5423400.sra Written 200000 spots for SRR5423400.sra Read 200000 spots for SRR5423400.sra Written 200000 spots for SRR5423400.sra SRR ids: ['SRR5423400.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_1ypzz3y6 SRR5423400.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]] SRR5423400 file size 704026 SRR5423400 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 SRR5423400 SRR5423400_1.fastq Input file: SRR5423400_1.fastq trimmed: SRR5423400-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 08:44:42 2025 >> started Wed Feb 12 08:44:44 2025 >> done (2.058s) 4000000 reads processed; of these: 153 ( 0.00%) short reads filtered out after trimming by size control 41 ( 0.00%) empty reads filtered out after trimming by size control 3999806 (100.00%) reads available; of these: 82294 ( 2.06%) trimmed reads available after processing 3917512 (97.94%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 6 0.00% 19 2 0.00% 20 4 0.00% 21 0 0.00% 22 1 0.00% 23 1 0.00% 24 1 0.00% 25 1 0.00% 26 2 0.00% 27 2 0.00% 28 5 0.00% 29 6 0.00% 30 3 0.00% 31 5 0.00% 32 3 0.00% 33 16 0.00% 34 18 0.00% 35 15 0.00% 36 21 0.00% 37 18 0.00% 38 27 0.00% 39 27 0.00% 40 61 0.00% 41 72 0.00% 42 110 0.00% 43 134 0.00% 44 458 0.01% 45 385 0.01% 46 546 0.01% 47 862 0.02% 48 1485 0.04% 49 3372 0.08% 50 9902 0.25% 51 64723 1.62% 52 3917512 97.94% 3999806 reads passed initial QC criterion=sequence-density sequence-density=0.33 sequence-density-rank=1 fanout-score=3.69 fanout-score-rank=11 prefix-density=0.41 prefix-fanout=3.0 sequence=CCATTGCTTGCAATGGAAGTAATGTCATT criterion=fanout-score sequence-density=0.01 sequence-density-rank=28 fanout-score=28.70 fanout-score-rank=1 prefix-density=0.36 prefix-fanout=1.1 sequence=CATTTTATTTCTATCTTTCCATACATAACCAAAAAATGGAAAAGATTCTTCAAGAGTCTCGGGTCCTAGAAGTGCATGATAAATACCGCCAAAGCCCAATACTGCAGAGGAAATTAAGTGAAGTACGCCAGATACAAAGTATGGAAAGGTGTCTATGACTTCCCCGCCAGGACCCACCCCCCAACCTAGAGTAGCTAGGTGGGGAAGTAAAATTAATCCTTGTTCATACATTGGCTTCTCCGGTACGAAATGGGCCACTTCAAATAGGTTCATTGCTCCGGCCCAGAATACGATTAATCCAGCATGGGCTACATGAGCTCCCAGCAG Started job on | Feb 12 08:44:57 Started mapping on | Feb 12 08:44:57 Finished on | Feb 12 08:45:03 Mapping speed, Million of reads per hour | 2399.88 Number of input reads | 3999806 Average input read length | 51 UNIQUE READS: Uniquely mapped reads number | 3118423 Uniquely mapped reads % | 77.96% Average mapped length | 51.80 Number of splices: Total | 276158 Number of splices: Annotated (sjdb) | 272663 Number of splices: GT/AG | 268336 Number of splices: GC/AG | 6224 Number of splices: AT/AC | 1126 Number of splices: Non-canonical | 472 Mismatch rate per base, % | 0.38% Deletion rate per base | 0.01% Deletion average length | 2.75 Insertion rate per base | 0.00% Insertion average length | 1.34 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 764067 % of reads mapped to multiple loci | 19.10% Number of reads mapped to too many loci | 55038 % of reads mapped to too many loci | 1.38% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.54% % of reads unmapped: other | 0.01% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 117316 117316 117316 N_multimapping 764067 764067 764067 N_noFeature 403208 3077635 432757 N_ambiguous 22597 156 11211 UnstrandedReadsAssigned:2692618 PositiveStrandReadsAssigned:40632 NegativeStrandReadsAssigned:2674455 Dataset is classified negative stranded MeadianReadLen=52 20thPercentileLength=52 echo kmer=47 SRR5423400 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: SRR5423400-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 3,999,806 reads, 3,266,893 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,060 rounds 52401 SRR5423400.ke.tsv 34699 SRR5423400.se.tsv 87100 total ==> SRR5423400.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1919 76 10.7081 Potri.005G024800.1.v4.1 1035 936 2 0.577732 Potri.004G059700.1.v4.1 961 862 1 0.313664 Potri.007G009000.2.v4.1 1416 1317 0 0 Potri.003G141000.2.v4.1 2943 2844 84.3891 8.02286 Potri.016G087400.1.v4.1 270 171 8 12.6493 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 1.53974 ==> SRR5423400.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 3 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 19 Potri.001G212900.v4.1 0 Potri.001G182400.v4.1 0 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 5 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 0 SRR5423400 completed mapping pipeline successfully