Starting /dee2/code/volunteer_pipeline.sh SRR5423409 current disk space = 3052623781888 free memory = 1575078992 SRR5423409 SRAfilesize b7afd8a3e3c98e444b981c7b2b53f85d SRR5423409.sra SRR5423409.sra file validated SRR5423409 is single end SRR5423409 is conventional basespace SRR5423409 read1 length is 52 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR5423409_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 28.613 31.0 30.0 34.0 10.0 34.0 2 30.1925 31.0 30.0 34.0 19.0 34.0 3 31.2325 31.0 31.0 34.0 27.0 34.0 4 33.96875 35.0 35.0 37.0 28.0 37.0 5 34.95125 35.0 35.0 37.0 32.0 37.0 6 35.18825 37.0 35.0 37.0 32.0 37.0 7 34.9325 37.0 35.0 37.0 32.0 37.0 8 35.3225 37.0 35.0 37.0 33.0 37.0 9 36.41875 39.0 35.0 39.0 32.0 39.0 10 36.7615 39.0 37.0 39.0 32.0 39.0 11 36.9105 39.0 37.0 39.0 33.0 39.0 12 36.49875 39.0 35.0 39.0 32.0 39.0 13 36.81375 39.0 37.0 39.0 32.0 39.0 14 38.02975 40.0 37.0 41.0 33.0 41.0 15 38.01375 40.0 37.0 41.0 33.0 41.0 16 37.89775 40.0 37.0 41.0 33.0 41.0 17 38.18575 40.0 37.0 41.0 33.0 41.0 18 38.126 40.0 37.0 41.0 33.0 41.0 19 38.21725 40.0 37.0 41.0 33.0 41.0 20 37.927 40.0 37.0 41.0 33.0 41.0 21 37.7665 40.0 37.0 41.0 32.0 41.0 22 37.8625 40.0 37.0 41.0 33.0 41.0 23 37.97075 40.0 37.0 41.0 33.0 41.0 24 37.9205 40.0 37.0 41.0 33.0 41.0 25 37.67925 40.0 37.0 41.0 32.0 41.0 26 37.65525 40.0 37.0 41.0 32.0 41.0 27 37.725 40.0 37.0 41.0 32.0 41.0 28 37.64375 40.0 37.0 41.0 32.0 41.0 29 37.8485 40.0 37.0 41.0 33.0 41.0 30 37.6195 40.0 37.0 41.0 32.0 41.0 31 37.1535 39.0 36.0 41.0 31.0 41.0 32 37.27275 39.0 36.0 41.0 31.0 41.0 33 37.37225 39.0 36.0 41.0 31.0 41.0 34 37.2625 39.0 36.0 41.0 31.0 41.0 35 37.44375 39.0 37.0 41.0 31.0 41.0 36 37.524 39.0 37.0 41.0 32.0 41.0 37 37.53025 40.0 37.0 41.0 32.0 41.0 38 37.512 39.0 36.0 41.0 32.0 41.0 39 37.54825 40.0 37.0 41.0 32.0 41.0 40 37.1205 39.0 36.0 40.0 31.0 41.0 41 37.351 39.0 36.0 40.0 31.0 41.0 42 37.30575 39.0 36.0 40.0 31.0 41.0 43 36.9485 39.0 36.0 40.0 30.0 41.0 44 36.92725 39.0 35.0 40.0 31.0 41.0 45 37.11325 39.0 36.0 40.0 31.0 41.0 46 36.95025 39.0 35.0 40.0 30.0 41.0 47 36.56825 39.0 35.0 40.0 30.0 41.0 48 36.5675 39.0 35.0 40.0 30.0 41.0 49 36.50475 39.0 35.0 40.0 30.0 41.0 50 36.48025 39.0 35.0 40.0 30.0 41.0 51 36.448 39.0 35.0 40.0 29.0 41.0 52 35.8305 38.0 34.0 40.0 28.0 41.0 >>END_MODULE >>Per tile sequence quality warn #Tile Base Mean 1111 1 1.2731829573934839 1111 2 1.855889724310778 1111 3 -0.14285714285714235 1111 4 0.4273182957393473 1111 5 0.9473684210526301 1111 6 0.8521303258145352 1111 7 0.9899749373433622 1111 8 0.7919799498746869 1111 9 0.7192982456140342 1111 10 1.0676691729323267 1111 11 0.5 1111 12 0.6716791979949903 1111 13 -1.0175438596491233 1111 14 -0.7067669172932369 1111 15 0.2857142857142847 1111 16 1.0626566416040077 1111 17 0.8157894736842053 1111 18 -0.05263157894736992 1111 19 0.42481203007518786 1111 20 0.441102756892235 1111 21 1.0200501253132828 1111 22 0.9812030075188005 1111 23 1.5162907268170471 1111 24 -0.047619047619051 1111 25 0.573934837092736 1111 26 0.16290726817042867 1111 27 -1.7969924812030058 1111 28 0.13784461152881988 1111 29 0.5075187969924855 1111 30 1.1516290726817004 1111 31 1.9273182957393473 1111 32 -1.196741854636592 1111 33 -4.324561403508767 1111 34 0.42606516290726404 1111 35 0.7493734335839548 1111 36 1.1842105263157947 1111 37 -2.2355889724310742 1111 38 0.8157894736842053 1111 39 1.191729323308266 1111 40 0.6390977443609032 1111 41 -0.18922305764411362 1111 42 -1.2781954887218063 1111 43 -0.6115288220551349 1111 44 -1.2305764411027553 1111 45 -0.13909774436090316 1111 46 -5.615288220551378 1111 47 0.2844611528822014 1111 48 1.1854636591478709 1111 49 -2.4348370927318257 1111 50 -1.4561403508771917 1111 51 -1.404761904761905 1111 52 -7.513784461152881 1112 1 -1.2731829573934839 1112 2 -1.8558897243107744 1112 3 0.14285714285714235 1112 4 -0.4273182957393473 1112 5 -0.9473684210526301 1112 6 -0.8521303258145352 1112 7 -0.9899749373433551 1112 8 -0.7919799498746869 1112 9 -0.7192982456140342 1112 10 -1.0676691729323338 1112 11 -0.5 1112 12 -0.6716791979949832 1112 13 1.0175438596491233 1112 14 0.7067669172932298 1112 15 -0.2857142857142847 1112 16 -1.0626566416040149 1112 17 -0.8157894736842124 1112 18 0.05263157894736992 1112 19 -0.42481203007518786 1112 20 -0.4411027568922279 1112 21 -1.0200501253132828 1112 22 -0.9812030075187934 1112 23 -1.51629072681704 1112 24 0.0476190476190439 1112 25 -0.5739348370927289 1112 26 -0.16290726817042156 1112 27 1.7969924812030058 1112 28 -0.137844611528827 1112 29 -0.5075187969924784 1112 30 -1.1516290726817076 1112 31 -1.9273182957393473 1112 32 1.196741854636592 1112 33 4.324561403508774 1112 34 -0.42606516290727114 1112 35 -0.7493734335839619 1112 36 -1.1842105263157876 1112 37 2.2355889724310813 1112 38 -0.8157894736842124 1112 39 -1.191729323308273 1112 40 -0.6390977443609032 1112 41 0.18922305764410652 1112 42 1.2781954887217992 1112 43 0.611528822055142 1112 44 1.2305764411027553 1112 45 0.13909774436090316 1112 46 5.615288220551378 1112 47 -0.2844611528822085 1112 48 -1.1854636591478709 1112 49 2.434837092731833 1112 50 1.4561403508771917 1112 51 1.404761904761905 1112 52 7.513784461152881 >>END_MODULE >>Per sequence quality scores pass #Quality Count 21 1.0 22 2.0 23 2.0 24 5.0 25 16.0 26 18.0 27 26.0 28 46.0 29 52.0 30 94.0 31 104.0 32 147.0 33 190.0 34 222.0 35 330.0 36 437.0 37 538.0 38 756.0 39 1010.0 40 4.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 29.628603104212857 10.08869179600887 7.067627494456763 53.215077605321504 2 20.075000000000003 13.200000000000001 39.0 27.725 3 21.0 17.925 23.05 38.025 4 24.7 25.1 20.674999999999997 29.525000000000002 5 24.025 30.75 24.275 20.95 6 18.725 33.1 25.674999999999997 22.5 7 14.875 23.775 41.75 19.6 8 18.224999999999998 22.0 31.15 28.625 9 18.425 21.8 34.2 25.575 10 18.075 38.175 23.425 20.325 11 21.75 27.85 22.025 28.375 12 21.325 23.974999999999998 27.075 27.625 13 19.900000000000002 27.725 27.150000000000002 25.224999999999998 14 20.599999999999998 29.475 26.775 23.150000000000002 15 21.025 27.200000000000003 26.8 24.975 16 19.85 28.199999999999996 27.35 24.6 17 21.725 26.85 27.1 24.325 18 21.0 26.625 26.700000000000003 25.674999999999997 19 20.525 28.425 25.45 25.6 20 19.725 27.025 27.125 26.125 21 19.975 28.349999999999998 26.075 25.6 22 20.724999999999998 29.075 24.425 25.775 23 21.975 27.675 25.25 25.1 24 22.05 26.474999999999998 25.650000000000002 25.825 25 21.05 27.0 26.224999999999998 25.724999999999998 26 21.525 27.150000000000002 26.3 25.025 27 21.75543885971493 25.731432858214554 26.881720430107524 25.63140785196299 28 20.130032508127034 29.00725181295324 25.831457864466117 25.03125781445361 29 20.305076269067268 28.157039259814955 27.131782945736433 24.406101525381345 30 20.455113778444613 26.60665166291573 26.9567391847962 25.98149537384346 31 21.099999999999998 28.1 26.724999999999998 24.075 32 20.555138784696176 28.307076769192296 25.731432858214554 25.406351587896975 33 21.125 25.6 28.075 25.2 34 20.974999999999998 28.225 26.174999999999997 24.625 35 19.675 27.650000000000002 26.650000000000002 26.025 36 20.674999999999997 27.150000000000002 26.075 26.1 37 21.75 26.200000000000003 24.675 27.375 38 20.875 26.650000000000002 25.775 26.700000000000003 39 20.95 26.3 25.624999999999996 27.125 40 21.7 27.425 25.674999999999997 25.2 41 20.974999999999998 27.700000000000003 24.95 26.375 42 20.575 26.424999999999997 26.6 26.400000000000002 43 21.475 26.8 25.85 25.874999999999996 44 22.2 29.175 25.575 23.05 45 23.400000000000002 25.775 26.650000000000002 24.175 46 23.25 28.125 23.400000000000002 25.224999999999998 47 23.075000000000003 28.15 25.2 23.575 48 21.2 27.200000000000003 25.674999999999997 25.924999999999997 49 21.7 26.224999999999998 25.2 26.875 50 22.75 28.025 25.0 24.224999999999998 51 21.224999999999998 27.150000000000002 25.624999999999996 26.0 52 21.55 28.7 23.75 26.0 >>END_MODULE >>Per sequence GC content pass #GC Content Count 0 1.0 1 1.0 2 1.0 3 0.5 4 0.0 5 0.5 6 1.0 7 1.5 8 2.0 9 1.5 10 1.0 11 1.5 12 2.0 13 1.0 14 2.5 15 5.0 16 5.5 17 6.0 18 7.0 19 8.0 20 13.0 21 18.0 22 15.0 23 12.0 24 13.0 25 14.0 26 16.5 27 19.0 28 31.0 29 43.0 30 45.0 31 47.0 32 61.0 33 75.0 34 101.5 35 128.0 36 148.5 37 169.0 38 207.5 39 234.0 40 222.0 41 250.0 42 278.0 43 302.5 44 327.0 45 325.5 46 324.0 47 327.0 48 330.0 49 315.0 50 300.0 51 313.5 52 327.0 53 324.5 54 322.0 55 279.0 56 236.0 57 208.5 58 181.0 59 157.0 60 133.0 61 112.5 62 92.0 63 70.0 64 39.0 65 30.0 66 27.5 67 25.0 68 21.5 69 18.0 70 11.0 71 4.0 72 3.0 73 2.0 74 1.5 75 1.0 76 1.0 77 1.0 78 0.5 79 0.0 80 0.5 81 1.0 82 0.5 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 warn #Base N-Count 1 9.8 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 0.025 28 0.025 29 0.025 30 0.025 31 0.0 32 0.025 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 88.375 #Duplication Level Percentage of deduplicated Percentage of total 1 93.06930693069307 82.25 2 4.441301272984441 7.85 3 1.1598302687411597 3.075 4 0.48090523338048086 1.7000000000000002 5 0.33946251768033947 1.5 6 0.16973125884016974 0.8999999999999999 7 0.11315417256011315 0.7000000000000001 8 0.056577086280056574 0.4 9 0.056577086280056574 0.44999999999999996 >10 0.11315417256011315 1.175 >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 14 0.35000000000000003 No Hit CTCATTACGAGCTTGTACACATGCTTCTAGAGCTACTCGATTAGCAACGGCA 12 0.3 No Hit CTCCAGCAACGGGCTCGATGTCGTAGCATCGTCCCTTATAACGATCAAGACT 11 0.27499999999999997 No Hit CCCGTCGGTCCACACAGTTGTCCATGTACCAGTAGAAGATTCAGCAGCTACT 10 0.25 No Hit CGCAGAAGTAGGAATAATGGCACCAGAAATGATATTGTTTCCATAAAGTAGA 9 0.22499999999999998 No Hit GTCCACACAGTTGTCCATGTACCAGTAGAAGATTCAGCAGCTACTGCGGCCC 9 0.22499999999999998 No Hit GTCCCTCATTACGAGCTTGTACACATGCTTCTAGAGCTACTCGATTAGCAAC 8 0.2 No Hit CTCGTATTTTCCCCTCTGCCTCGGGTTGTCTCGCGATACCTTCTACAGCTTG 8 0.2 No Hit CCTCATTACGAGCTTGTACACATGCTTCTAGAGCTACTCGATTAGCAACGGC 7 0.17500000000000002 No Hit CCCGAAGCCACGGGTAGAACACCCGGTAGAGAGACCCAATCTTGAGTGAAAT 7 0.17500000000000002 No Hit GGGTAAGCTACATAAGCAATAAATTGATTTTCTTCTCCAGCAACGGGCTCGA 7 0.17500000000000002 No Hit AGCACGGTTAATAATATCAGCCCAGGTATTAATTACACGACCTTGACTATCA 7 0.17500000000000002 No Hit CTGCAAAGGATTCTACCCGCCGCTCGGTGGGAATTGTACTTCAAGGCGGCCC 6 0.15 No Hit CTTATAACGATCAAGACTGGTAAGCCCGTCGGTCCACACAGTTGTCCATGTA 6 0.15 No Hit GGGGTAAGCTACATAAGCAATAAATTGATTTTCTTCTCCAGCAACGGGCTCG 6 0.15 No Hit CTCGTACACACTAAGAAAAAAGCCTTATCCATTTACAAAAGTCTTATCCATT 6 0.15 No Hit ATCAAACTAGAGGTTACCAAAGAACCATGCATAGCACTGAATAGGGAGCCGC 6 0.15 No Hit GCTCCATTTGCTAGCTTCACGGATAATTTCATTACCCTCACGAGCAAGATCA 6 0.15 No Hit GCCCGTCGGTCCACACAGTTGTCCATGTACCAGTAGAAGATTCAGCAGCTAC 5 0.125 No Hit CTCACGAGCAAGATCACGTCCCTCATTACGAGCTTGTACACATGCTTCTAGA 5 0.125 No Hit GTCGCGTATTTAAGTCGTCTGCAAAGGATTCTACCCGCCGCTCGGTGGGAAT 5 0.125 No Hit CCATGTACCAGTAGAAGATTCAGCAGCTACTGCGGCCCCTGCTTCCTCGGGC 5 0.125 No Hit GTCCCTTATAACGATCAAGACTGGTAAGCCCGTCGGTCCACACAGTTGTCCA 5 0.125 No Hit CCAGCAACGGGCTCGATGTCGTAGCATCGTCCCTTATAACGATCAAGACTGG 5 0.125 No Hit GCCTCCTCGAGCTCAATCAGCACCTGAGATGCCTCAGTGCATCCAAACATGG 5 0.125 No Hit NGTCGGTCCACACAGTTGTCCATGTACCAGTAGAAGATTCAGCAGCTACTGC 5 0.125 No Hit CTCGATTAGCAACGGCACCGGGTGCATTTCCCCAAGGGTGCCCTAAAGTTCC 5 0.125 No Hit CCGCATTTCGCTAAAGGGTTGAAGGAGGATAGTGCATCAAGCTGTTCGCAAG 5 0.125 No Hit GCCAGATACAAAGTATGGAAAGGTGTCTATGACTTCCCCGCCAGGACCCACC 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 0.0 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 SRR5423409.sra Written 200000 spots for SRR5423409.sra Read 200000 spots for SRR5423409.sra Written 200000 spots for SRR5423409.sra Read 200000 spots for SRR5423409.sra Written 200000 spots for SRR5423409.sra Read 200000 spots for SRR5423409.sra Written 200000 spots for SRR5423409.sra Read 200000 spots for SRR5423409.sra Written 200000 spots for SRR5423409.sra Read 200000 spots for SRR5423409.sra Written 200000 spots for SRR5423409.sra Read 200000 spots for SRR5423409.sra Written 200000 spots for SRR5423409.sra Read 200000 spots for SRR5423409.sra Written 200000 spots for SRR5423409.sra Read 200000 spots for SRR5423409.sra Written 200000 spots for SRR5423409.sra Read 200000 spots for SRR5423409.sra Written 200000 spots for SRR5423409.sra Read 200000 spots for SRR5423409.sra Written 200000 spots for SRR5423409.sra Read 200000 spots for SRR5423409.sra Written 200000 spots for SRR5423409.sra Read 200000 spots for SRR5423409.sra Written 200000 spots for SRR5423409.sra Read 200000 spots for SRR5423409.sra Written 200000 spots for SRR5423409.sra Read 200000 spots for SRR5423409.sra Written 200000 spots for SRR5423409.sra Read 200000 spots for SRR5423409.sra Written 200000 spots for SRR5423409.sra Read 200000 spots for SRR5423409.sra Written 200000 spots for SRR5423409.sra Read 200000 spots for SRR5423409.sra Written 200000 spots for SRR5423409.sra Read 200000 spots for SRR5423409.sra Written 200000 spots for SRR5423409.sra Read 200000 spots for SRR5423409.sra Written 200000 spots for SRR5423409.sra SRR ids: ['SRR5423409.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_j7mq2i2c SRR5423409.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]] SRR5423409 file size 703991 SRR5423409 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 SRR5423409 SRR5423409_1.fastq Input file: SRR5423409_1.fastq trimmed: SRR5423409-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 07:26:22 2025 >> started Thu Feb 13 07:26:24 2025 >> done (1.606s) 4000000 reads processed; of these: 122 ( 0.00%) short reads filtered out after trimming by size control 41 ( 0.00%) empty reads filtered out after trimming by size control 3999837 (100.00%) reads available; of these: 98701 ( 2.47%) trimmed reads available after processing 3901136 (97.53%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 9 0.00% 19 5 0.00% 20 2 0.00% 21 1 0.00% 22 0 0.00% 23 1 0.00% 24 5 0.00% 25 3 0.00% 26 2 0.00% 27 7 0.00% 28 7 0.00% 29 4 0.00% 30 6 0.00% 31 11 0.00% 32 9 0.00% 33 13 0.00% 34 16 0.00% 35 17 0.00% 36 18 0.00% 37 36 0.00% 38 34 0.00% 39 49 0.00% 40 51 0.00% 41 65 0.00% 42 125 0.00% 43 187 0.00% 44 458 0.01% 45 530 0.01% 46 755 0.02% 47 974 0.02% 48 1744 0.04% 49 4120 0.10% 50 12692 0.32% 51 76745 1.92% 52 3901136 97.53% 3999837 reads passed initial QC criterion=sequence-density sequence-density=0.47 sequence-density-rank=1 fanout-score=1.96 fanout-score-rank=21 prefix-density=0.48 prefix-fanout=1.9 sequence=TGAGATGCCTCAGTGCATCCAAACATGGGTAG criterion=fanout-score sequence-density=0.01 sequence-density-rank=26 fanout-score=31.48 fanout-score-rank=1 prefix-density=0.36 prefix-fanout=1.1 sequence=CATTTTATTTCTATCTTTCCATACATAACCAAAAAATGGAAAAGATTCTTCAAGAGTCTCGGGTCCTAGAAGTGCATGATAAATACCGCCAAAGCCCAATACTGCAGAGGAAATTAAGTGAAGTACGCCAGATACAAAGTATGGAAAGGTGTCTATGACTTCCCCGCCAGGACCCACCCCCCAACCTAGAGTAGCTAGGTGGGGAAGTAAAATTAATCCTTGTTCATACATTGGCTTCTCCGGTACGAAATGGGCCACTTCAAATAGGTTCATTGCTCCGGCCCAGAATACGATTAATCCAGCATGGGCTACATGAGCTCCCAGCAG Started job on | Feb 13 07:26:34 Started mapping on | Feb 13 07:26:34 Finished on | Feb 13 07:26:42 Mapping speed, Million of reads per hour | 1799.93 Number of input reads | 3999837 Average input read length | 51 UNIQUE READS: Uniquely mapped reads number | 3112297 Uniquely mapped reads % | 77.81% Average mapped length | 51.79 Number of splices: Total | 274771 Number of splices: Annotated (sjdb) | 271365 Number of splices: GT/AG | 267099 Number of splices: GC/AG | 6201 Number of splices: AT/AC | 999 Number of splices: Non-canonical | 472 Mismatch rate per base, % | 0.50% Deletion rate per base | 0.01% Deletion average length | 2.75 Insertion rate per base | 0.00% Insertion average length | 1.33 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 767222 % of reads mapped to multiple loci | 19.18% Number of reads mapped to too many loci | 53968 % of reads mapped to too many loci | 1.35% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.65% % of reads unmapped: other | 0.01% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 120318 120318 120318 N_multimapping 767222 767222 767222 N_noFeature 402664 3071738 431914 N_ambiguous 22371 130 10935 UnstrandedReadsAssigned:2687262 PositiveStrandReadsAssigned:40429 NegativeStrandReadsAssigned:2669448 Dataset is classified negative stranded MeadianReadLen=52 20thPercentileLength=52 echo kmer=47 SRR5423409 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: SRR5423409-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 3,999,837 reads, 3,250,434 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,113 rounds 52401 SRR5423409.ke.tsv 34699 SRR5423409.se.tsv 87100 total ==> SRR5423409.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1919 90 12.7787 Potri.005G024800.1.v4.1 1035 936 2.00606 0.583965 Potri.004G059700.1.v4.1 961 862 4 1.26436 Potri.007G009000.2.v4.1 1416 1317 0 0 Potri.003G141000.2.v4.1 2943 2844 58.5773 5.61202 Potri.016G087400.1.v4.1 270 171 12 19.1207 Potri.015G069301.1.v4.1 564 465 0 0 Potri.010G195200.1.v4.1 1773 1674 1 0.162766 Potri.012G127500.1.v4.1 977 878 4 1.24132 ==> SRR5423409.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 1 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 27 Potri.001G212900.v4.1 0 Potri.001G182400.v4.1 1 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 4 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 0 SRR5423409 completed mapping pipeline successfully