Starting /dee2/code/volunteer_pipeline.sh SRR5423420 current disk space = 3052652343296 free memory = 1572501632 SRR5423420 SRAfilesize 9cba2c8be8fe3cd42881da23d1e492b9 SRR5423420.sra SRR5423420.sra file validated SRR5423420 is single end SRR5423420 is conventional basespace SRR5423420 read1 length is 52 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR5423420_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 32.272 34.0 31.0 34.0 30.0 34.0 2 32.3805 34.0 31.0 34.0 30.0 34.0 3 32.50825 34.0 31.0 34.0 30.0 34.0 4 35.95225 37.0 35.0 37.0 35.0 37.0 5 35.8285 37.0 35.0 37.0 35.0 37.0 6 35.853 37.0 35.0 37.0 35.0 37.0 7 35.843 37.0 35.0 37.0 35.0 37.0 8 35.927 37.0 35.0 37.0 35.0 37.0 9 37.68225 39.0 37.0 39.0 35.0 39.0 10 37.5915 39.0 37.0 39.0 35.0 39.0 11 37.66325 39.0 37.0 39.0 35.0 39.0 12 37.5435 39.0 37.0 39.0 35.0 39.0 13 37.562 39.0 37.0 39.0 35.0 39.0 14 38.763 40.0 38.0 41.0 35.0 41.0 15 38.82275 40.0 38.0 41.0 35.0 41.0 16 38.80025 40.0 38.0 41.0 35.0 41.0 17 38.82875 40.0 38.0 41.0 35.0 41.0 18 38.807 40.0 38.0 41.0 35.0 41.0 19 38.81675 40.0 38.0 41.0 35.0 41.0 20 38.73075 40.0 38.0 41.0 34.0 41.0 21 38.76825 40.0 38.0 41.0 34.0 41.0 22 38.5815 40.0 38.0 41.0 34.0 41.0 23 38.54875 40.0 38.0 41.0 34.0 41.0 24 38.35025 40.0 38.0 41.0 33.0 41.0 25 38.66975 40.0 38.0 41.0 34.0 41.0 26 38.7485 40.0 38.0 41.0 35.0 41.0 27 38.63925 40.0 38.0 41.0 34.0 41.0 28 38.606 40.0 38.0 41.0 34.0 41.0 29 38.61975 40.0 38.0 41.0 34.0 41.0 30 38.5765 40.0 38.0 41.0 34.0 41.0 31 38.46875 40.0 38.0 41.0 34.0 41.0 32 38.4125 40.0 38.0 41.0 34.0 41.0 33 38.43625 40.0 38.0 41.0 34.0 41.0 34 38.31875 40.0 38.0 41.0 34.0 41.0 35 38.28475 40.0 38.0 41.0 34.0 41.0 36 38.24125 40.0 38.0 41.0 33.0 41.0 37 38.15825 40.0 38.0 41.0 33.0 41.0 38 38.00275 40.0 38.0 41.0 33.0 41.0 39 37.941 40.0 37.0 41.0 33.0 41.0 40 37.96425 40.0 38.0 41.0 33.0 41.0 41 37.859 40.0 37.0 41.0 33.0 41.0 42 37.56775 40.0 37.0 41.0 32.0 41.0 43 37.75125 40.0 37.0 41.0 33.0 41.0 44 37.6725 40.0 37.0 41.0 32.0 41.0 45 37.44525 40.0 37.0 41.0 31.0 41.0 46 37.346 40.0 36.0 41.0 31.0 41.0 47 37.462 40.0 36.0 41.0 32.0 41.0 48 37.26975 40.0 36.0 41.0 31.0 41.0 49 37.19975 40.0 36.0 41.0 31.0 41.0 50 37.03 39.0 36.0 41.0 31.0 41.0 51 37.10325 39.0 36.0 41.0 31.0 41.0 52 35.722 38.0 34.0 40.0 28.0 41.0 >>END_MODULE >>Per tile sequence quality pass #Tile Base Mean 1207 1 0.0 1207 2 0.0 1207 3 0.0 1207 4 0.0 1207 5 0.0 1207 6 0.0 1207 7 0.0 1207 8 0.0 1207 9 0.0 1207 10 0.0 1207 11 0.0 1207 12 0.0 1207 13 0.0 1207 14 0.0 1207 15 0.0 1207 16 0.0 1207 17 0.0 1207 18 0.0 1207 19 0.0 1207 20 0.0 1207 21 0.0 1207 22 0.0 1207 23 0.0 1207 24 0.0 1207 25 0.0 1207 26 0.0 1207 27 0.0 1207 28 0.0 1207 29 0.0 1207 30 0.0 1207 31 0.0 1207 32 0.0 1207 33 0.0 1207 34 0.0 1207 35 0.0 1207 36 0.0 1207 37 0.0 1207 38 0.0 1207 39 0.0 1207 40 0.0 1207 41 0.0 1207 42 0.0 1207 43 0.0 1207 44 0.0 1207 45 0.0 1207 46 0.0 1207 47 0.0 1207 48 0.0 1207 49 0.0 1207 50 0.0 1207 51 0.0 1207 52 0.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 11 1.0 12 1.0 13 0.0 14 0.0 15 0.0 16 0.0 17 0.0 18 0.0 19 0.0 20 2.0 21 0.0 22 1.0 23 3.0 24 2.0 25 10.0 26 13.0 27 18.0 28 37.0 29 32.0 30 65.0 31 70.0 32 93.0 33 109.0 34 152.0 35 230.0 36 294.0 37 389.0 38 745.0 39 1725.0 40 8.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 38.9571321133116 11.05540235648032 5.164201554274254 44.82326397593382 2 24.224999999999998 13.850000000000001 34.375 27.55 3 21.275 17.45 23.425 37.85 4 25.45 25.85 19.900000000000002 28.799999999999997 5 24.05 31.15 23.674999999999997 21.125 6 19.525000000000002 32.074999999999996 25.4 23.0 7 14.875 23.325000000000003 40.65 21.15 8 17.1 22.900000000000002 31.35 28.65 9 17.925 20.825 33.5 27.750000000000004 10 18.575 37.075 24.45 19.900000000000002 11 23.674999999999997 28.325 20.474999999999998 27.525 12 22.125 25.1 26.075 26.700000000000003 13 20.275000000000002 26.650000000000002 28.4 24.675 14 21.4 27.725 26.075 24.8 15 20.974999999999998 26.700000000000003 26.400000000000002 25.924999999999997 16 21.2 27.175 26.825 24.8 17 22.225 27.250000000000004 25.424999999999997 25.1 18 20.9 28.299999999999997 26.375 24.425 19 21.475 28.575 25.2 24.75 20 20.5 27.625 27.125 24.75 21 21.6 25.35 26.924999999999997 26.125 22 20.599999999999998 29.849999999999998 24.175 25.374999999999996 23 21.175 28.549999999999997 25.724999999999998 24.55 24 21.25 26.3 26.3 26.150000000000002 25 20.849999999999998 26.650000000000002 27.0 25.5 26 22.900000000000002 26.150000000000002 26.150000000000002 24.8 27 21.325 26.674999999999997 27.250000000000004 24.75 28 22.075 27.675 26.650000000000002 23.599999999999998 29 20.375 27.1 27.900000000000002 24.625 30 20.25 25.1 27.650000000000002 27.0 31 21.775 27.3 26.025 24.9 32 20.974999999999998 25.05 27.650000000000002 26.325 33 20.7 26.924999999999997 26.950000000000003 25.424999999999997 34 20.375 26.474999999999998 27.975 25.174999999999997 35 22.0 26.3 26.724999999999998 24.975 36 21.3 25.900000000000002 26.150000000000002 26.650000000000002 37 22.375 25.674999999999997 25.650000000000002 26.3 38 22.175 25.8 25.95 26.075 39 20.875 25.974999999999998 25.974999999999998 27.175 40 21.55 25.724999999999998 25.324999999999996 27.400000000000002 41 21.55 27.05 25.75 25.650000000000002 42 20.45 26.35 27.55 25.650000000000002 43 22.325 26.224999999999998 25.124999999999996 26.325 44 21.625 26.75 26.35 25.275 45 21.45 26.05 25.224999999999998 27.275 46 21.725 27.425 24.85 26.0 47 22.025 26.625 26.05 25.3 48 22.5 26.150000000000002 25.374999999999996 25.974999999999998 49 22.11105552776388 26.338169084542272 25.137568784392194 26.413206603301653 50 23.625 26.75 24.05 25.575 51 23.08654327163582 25.737868934467233 24.287143571785894 26.88844422211106 52 21.75 26.075 26.400000000000002 25.775 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 0.0 1 0.0 2 0.0 3 0.5 4 1.0 5 0.5 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 1.0 15 2.0 16 1.0 17 0.0 18 1.5 19 3.0 20 8.0 21 13.0 22 11.0 23 9.0 24 8.0 25 7.0 26 15.5 27 24.0 28 28.0 29 32.0 30 45.0 31 58.0 32 66.0 33 74.0 34 90.0 35 106.0 36 125.5 37 145.0 38 201.5 39 243.5 40 229.0 41 236.0 42 243.0 43 266.0 44 289.0 45 310.5 46 332.0 47 318.5 48 305.0 49 333.0 50 361.0 51 350.0 52 339.0 53 334.5 54 330.0 55 283.0 56 236.0 57 205.5 58 175.0 59 169.5 60 164.0 61 135.0 62 106.0 63 85.5 64 50.0 65 35.0 66 29.5 67 24.0 68 18.0 69 12.0 70 11.0 71 10.0 72 8.0 73 6.0 74 4.5 75 3.0 76 2.0 77 1.0 78 1.5 79 2.0 80 1.0 81 0.0 82 0.0 83 0.0 84 0.5 85 1.0 86 0.5 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 0.27499999999999997 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 0.05 50 0.0 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 89.25 #Duplication Level Percentage of deduplicated Percentage of total 1 93.8375350140056 83.75 2 3.753501400560224 6.7 3 1.0084033613445378 2.7 4 0.5882352941176471 2.1 5 0.33613445378151263 1.5 6 0.22408963585434172 1.2 7 0.11204481792717086 0.7000000000000001 8 0.028011204481792715 0.2 9 0.0 0.0 >10 0.11204481792717086 1.15 >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 15 0.375 No Hit GGGTAAGCTACATAAGCAATAAATTGATTTTCTTCTCCAGCAACGGGCTCGA 11 0.27499999999999997 No Hit GGGGTAAGCTACATAAGCAATAAATTGATTTTCTTCTCCAGCAACGGGCTCG 10 0.25 No Hit CCCGTCGGTCCACACAGTTGTCCATGTACCAGTAGAAGATTCAGCAGCTACT 10 0.25 No Hit CCTCATTACGAGCTTGTACACATGCTTCTAGAGCTACTCGATTAGCAACGGC 8 0.2 No Hit GTTGTGCTCAGCCTGGAATACAATCATAAAGTTAAAAGTACCAGAGATTCCT 7 0.17500000000000002 No Hit CTCGTACACACTAAGAAAAAAGCCTTATCCATTTACAAAAGTCTTATCCATT 7 0.17500000000000002 No Hit GACCGCATGTGCAGGTAGTGCAAGTGCAGCCAGTACCGCAGTTGCACTTGCC 7 0.17500000000000002 No Hit CTCAGCCTGGAATACAATCATAAAGTTAAAAGTACCAGAGATTCCTAGAGGC 7 0.17500000000000002 No Hit GTCCCTCATTACGAGCTTGTACACATGCTTCTAGAGCTACTCGATTAGCAAC 6 0.15 No Hit CTCGTATTTTCCCCTCTGCCTCGGGTTGTCTCGCGATACCTTCTACAGCTTG 6 0.15 No Hit GTGCTCAGCCTGGAATACAATCATAAAGTTAAAAGTACCAGAGATTCCTAGA 6 0.15 No Hit CTGGAATACAATCATAAAGTTAAAAGTACCAGAGATTCCTAGAGGCATCCCA 6 0.15 No Hit CTCATTACGAGCTTGTACACATGCTTCTAGAGCTACTCGATTAGCAACGGCA 6 0.15 No Hit GCTGGTTTTAAGAATGAGTGATTGCCCTTCTCCGACCCTTACTGCCCAACCT 6 0.15 No Hit CTCCAGCAACGGGCTCGATGTCGTAGCATCGTCCCTTATAACGATCAAGACT 6 0.15 No Hit GTCGTCTGCAAAGGATTCTACCCGCCGCTCGGTGGGAATTGTACTTCAAGGC 6 0.15 No Hit GGGCTCCATTTGCTAGCTTCACGGATAATTTCATTACCCTCACGAGCAAGAT 5 0.125 No Hit CGCAGAAGTAGGAATAATGGCACCAGAAATGATATTGTTTCCATAAAGTAGA 5 0.125 No Hit CCACACAGTTGTCCATGTACCAGTAGAAGATTCAGCAGCTACTGCGGCCCCT 5 0.125 No Hit GCTCAGCCTGGAATACAATCATAAAGTTAAAAGTACCAGAGATTCCTAGAGG 5 0.125 No Hit GTCGCGTATTTAAGTCGTCTGCAAAGGATTCTACCCGCCGCTCGGTGGGAAT 5 0.125 No Hit GTTAATAATATCAGCCCAGGTATTAATTACACGACCTTGACTATCAACTACA 5 0.125 No Hit GCCGCCGCAACAGGAGCTGAATATGCAACAGCAATCCAAGGACGCATACCCA 5 0.125 No Hit CTGCAAAGGATTCTACCCGCCGCTCGGTGGGAATTGTACTTCAAGGCGGCCC 5 0.125 No Hit GTAAGCTACATAAGCAATAAATTGATTTTCTTCTCCAGCAACGGGCTCGATG 5 0.125 No Hit CGATTGGATAAATCAAGAAAACAGCAGTAGCCGCCGCAACAGGAGCTGAATA 5 0.125 No Hit GCCGAATACACCAGCTACGCCTAACATGTGAAATGGGTGCATAAGGATGTTG 5 0.125 No Hit GCTCCATTTGCTAGCTTCACGGATAATTTCATTACCCTCACGAGCAAGATCA 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 0.025 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 SRR5423420.sra Written 200000 spots for SRR5423420.sra Read 200000 spots for SRR5423420.sra Written 200000 spots for SRR5423420.sra Read 200000 spots for SRR5423420.sra Written 200000 spots for SRR5423420.sra Read 200000 spots for SRR5423420.sra Written 200000 spots for SRR5423420.sra Read 200000 spots for SRR5423420.sra Written 200000 spots for SRR5423420.sra Read 200000 spots for SRR5423420.sra Written 200000 spots for SRR5423420.sra Read 200000 spots for SRR5423420.sra Written 200000 spots for SRR5423420.sra Read 200000 spots for SRR5423420.sra Written 200000 spots for SRR5423420.sra Read 200000 spots for SRR5423420.sra Written 200000 spots for SRR5423420.sra Read 200000 spots for SRR5423420.sra Written 200000 spots for SRR5423420.sra Read 200000 spots for SRR5423420.sra Written 200000 spots for SRR5423420.sra Read 200000 spots for SRR5423420.sra Written 200000 spots for SRR5423420.sra Read 200000 spots for SRR5423420.sra Written 200000 spots for SRR5423420.sra Read 200000 spots for SRR5423420.sra Written 200000 spots for SRR5423420.sra Read 200000 spots for SRR5423420.sra Written 200000 spots for SRR5423420.sra Read 200000 spots for SRR5423420.sra Written 200000 spots for SRR5423420.sra Read 200000 spots for SRR5423420.sra Written 200000 spots for SRR5423420.sra Read 200000 spots for SRR5423420.sra Written 200000 spots for SRR5423420.sra Read 200000 spots for SRR5423420.sra Written 200000 spots for SRR5423420.sra Read 200000 spots for SRR5423420.sra Written 200000 spots for SRR5423420.sra SRR ids: ['SRR5423420.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_aig9lgn0 SRR5423420.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]] SRR5423420 file size 703957 SRR5423420 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 SRR5423420 SRR5423420_1.fastq Input file: SRR5423420_1.fastq trimmed: SRR5423420-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 07:53:51 2025 >> started Thu Feb 13 07:58:29 2025 >> done (277.540s) 4000000 reads processed; of these: 163 ( 0.00%) short reads filtered out after trimming by size control 84 ( 0.00%) empty reads filtered out after trimming by size control 3999753 (99.99%) reads available; of these: 72733 ( 1.82%) trimmed reads available after processing 3927020 (98.18%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 12 0.00% 19 9 0.00% 20 4 0.00% 21 0 0.00% 22 0 0.00% 23 0 0.00% 24 0 0.00% 25 1 0.00% 26 2 0.00% 27 2 0.00% 28 4 0.00% 29 3 0.00% 30 4 0.00% 31 0 0.00% 32 11 0.00% 33 7 0.00% 34 12 0.00% 35 7 0.00% 36 17 0.00% 37 20 0.00% 38 30 0.00% 39 27 0.00% 40 35 0.00% 41 53 0.00% 42 77 0.00% 43 88 0.00% 44 187 0.00% 45 230 0.01% 46 348 0.01% 47 637 0.02% 48 1269 0.03% 49 2681 0.07% 50 8692 0.22% 51 58264 1.46% 52 3927020 98.18% 3999753 reads passed initial QC criterion=sequence-density sequence-density=0.45 sequence-density-rank=1 fanout-score=1.99 fanout-score-rank=28 prefix-density=0.46 prefix-fanout=2.0 sequence=TGCTTAATGACCGCATGTGCAGGTAGTGCAAGTGCAGCCAGTACCGCAGTTGCACTTGCCATCGTTCTCAGCTGCTGGCACCTCCATGAC criterion=fanout-score sequence-density=0.01 sequence-density-rank=31 fanout-score=26.93 fanout-score-rank=1 prefix-density=0.31 prefix-fanout=1.2 sequence=CATTTTATTTCTATCTTTCCATACATAACCAAAAAATGGAAAAGATTCTTCAAGAGTCTCGGGTCCTAGAAGTGCATGATAAATACCGCCAAAGCCCAATACTGCAGAGGAAATTAAGTGAAGTACGCCAGATACAAAGTATGGAAAGGTGTCTATGACTTCCCCGCCAGGACCCACCCCCCAACCTAGAGTAGCTAGGTGGGGAAGTAAAATTAATCCTTGTTCATACATTGGCTTCTCCGGTACGAAATGGGCCACTTCAAATAGGTTCATTGCTCCGGCCCAGAATACGATTAATCCAGCATGGGCTACATGAGCTCCCAGCAG Started job on | Feb 13 08:10:00 Started mapping on | Feb 13 08:10:18 Finished on | Feb 13 09:32:23 Mapping speed, Million of reads per hour | 2.92 Number of input reads | 3999753 Average input read length | 51 UNIQUE READS: Uniquely mapped reads number | 3134425 Uniquely mapped reads % | 78.37% Average mapped length | 51.80 Number of splices: Total | 286277 Number of splices: Annotated (sjdb) | 281749 Number of splices: GT/AG | 279761 Number of splices: GC/AG | 5244 Number of splices: AT/AC | 776 Number of splices: Non-canonical | 496 Mismatch rate per base, % | 0.35% Deletion rate per base | 0.01% Deletion average length | 2.23 Insertion rate per base | 0.00% Insertion average length | 1.35 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 710398 % of reads mapped to multiple loci | 17.76% Number of reads mapped to too many loci | 85895 % of reads mapped to too many loci | 2.15% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.71% % of reads unmapped: other | 0.01% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 154930 154930 154930 N_multimapping 710398 710398 710398 N_noFeature 397350 3088895 431584 N_ambiguous 22045 177 10591 UnstrandedReadsAssigned:2715030 PositiveStrandReadsAssigned:45353 NegativeStrandReadsAssigned:2692250 Dataset is classified negative stranded MeadianReadLen=52 20thPercentileLength=52 echo kmer=47 SRR5423420 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: SRR5423420-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 3,999,753 reads, 3,282,236 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,119 rounds 52401 SRR5423420.ke.tsv 34699 SRR5423420.se.tsv 87100 total ==> SRR5423420.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1919 115.787 16.8602 Potri.005G024800.1.v4.1 1035 936 25 7.46344 Potri.004G059700.1.v4.1 961 862 4 1.29667 Potri.007G009000.2.v4.1 1416 1317 0 0 Potri.003G141000.2.v4.1 2943 2844 52.3306 5.14163 Potri.016G087400.1.v4.1 270 171 16 26.1456 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 1.59129 ==> SRR5423420.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 3 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 28 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 SRR5423420 completed mapping pipeline successfully