Starting /dee2/code/volunteer_pipeline.sh SRR5423411 current disk space = 3052640620544 free memory = 1582242184 SRR5423411 SRAfilesize 0992a91903bf535a479a47e16bd4fdc4 SRR5423411.sra SRR5423411.sra file validated SRR5423411 is single end SRR5423411 is conventional basespace SRR5423411 read1 length is 52 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR5423411_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 32.352 34.0 31.0 34.0 30.0 34.0 2 32.52975 34.0 31.0 34.0 30.0 34.0 3 32.59125 34.0 31.0 34.0 31.0 34.0 4 35.98675 37.0 35.0 37.0 35.0 37.0 5 35.874 37.0 35.0 37.0 35.0 37.0 6 35.99325 37.0 35.0 37.0 35.0 37.0 7 36.01775 37.0 35.0 37.0 35.0 37.0 8 35.97775 37.0 35.0 37.0 35.0 37.0 9 37.71325 39.0 38.0 39.0 35.0 39.0 10 37.66375 39.0 37.0 39.0 35.0 39.0 11 37.70425 39.0 38.0 39.0 35.0 39.0 12 37.67425 39.0 37.0 39.0 35.0 39.0 13 37.61325 39.0 37.0 39.0 35.0 39.0 14 38.9815 40.0 38.0 41.0 36.0 41.0 15 38.90975 40.0 38.0 41.0 35.0 41.0 16 38.874 40.0 38.0 41.0 35.0 41.0 17 38.88875 40.0 38.0 41.0 35.0 41.0 18 38.9115 40.0 38.0 41.0 36.0 41.0 19 38.981 40.0 38.0 41.0 35.0 41.0 20 38.7875 40.0 38.0 41.0 34.0 41.0 21 38.894 40.0 38.0 41.0 35.0 41.0 22 38.85825 40.0 38.0 41.0 35.0 41.0 23 38.8405 40.0 38.0 41.0 35.0 41.0 24 38.651 40.0 38.0 41.0 34.0 41.0 25 38.71325 40.0 38.0 41.0 35.0 41.0 26 38.4595 40.0 38.0 41.0 34.0 41.0 27 38.41175 40.0 38.0 41.0 34.0 41.0 28 38.383 40.0 38.0 41.0 34.0 41.0 29 38.20925 40.0 38.0 41.0 33.0 41.0 30 38.1105 40.0 38.0 41.0 33.0 41.0 31 38.1305 40.0 38.0 41.0 33.0 41.0 32 38.22675 40.0 38.0 41.0 34.0 41.0 33 38.1535 40.0 38.0 41.0 33.0 41.0 34 37.79675 40.0 38.0 41.0 32.0 41.0 35 37.752 40.0 38.0 41.0 32.0 41.0 36 37.90875 40.0 38.0 41.0 33.0 41.0 37 37.7385 40.0 38.0 41.0 32.0 41.0 38 37.83 40.0 38.0 41.0 33.0 41.0 39 37.64875 40.0 38.0 41.0 31.0 41.0 40 37.63075 40.0 37.0 41.0 32.0 41.0 41 37.619 40.0 37.0 41.0 32.0 41.0 42 37.47975 40.0 37.0 41.0 31.0 41.0 43 37.36275 40.0 37.0 41.0 31.0 41.0 44 37.3985 40.0 37.0 41.0 31.0 41.0 45 37.2695 40.0 37.0 41.0 31.0 41.0 46 37.2625 40.0 37.0 41.0 31.0 41.0 47 36.9795 40.0 36.0 41.0 30.0 41.0 48 36.91 40.0 36.0 41.0 30.0 41.0 49 36.9565 39.0 36.0 41.0 30.0 41.0 50 36.619 39.0 35.0 41.0 30.0 41.0 51 36.571 39.0 36.0 41.0 28.0 41.0 52 34.6215 38.0 33.0 40.0 24.0 41.0 >>END_MODULE >>Per tile sequence quality pass #Tile Base Mean 1302 1 0.0 1302 2 0.0 1302 3 0.0 1302 4 0.0 1302 5 0.0 1302 6 0.0 1302 7 0.0 1302 8 0.0 1302 9 0.0 1302 10 0.0 1302 11 0.0 1302 12 0.0 1302 13 0.0 1302 14 0.0 1302 15 0.0 1302 16 0.0 1302 17 0.0 1302 18 0.0 1302 19 0.0 1302 20 0.0 1302 21 0.0 1302 22 0.0 1302 23 0.0 1302 24 0.0 1302 25 0.0 1302 26 0.0 1302 27 0.0 1302 28 0.0 1302 29 0.0 1302 30 0.0 1302 31 0.0 1302 32 0.0 1302 33 0.0 1302 34 0.0 1302 35 0.0 1302 36 0.0 1302 37 0.0 1302 38 0.0 1302 39 0.0 1302 40 0.0 1302 41 0.0 1302 42 0.0 1302 43 0.0 1302 44 0.0 1302 45 0.0 1302 46 0.0 1302 47 0.0 1302 48 0.0 1302 49 0.0 1302 50 0.0 1302 51 0.0 1302 52 0.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 21 8.0 22 5.0 23 19.0 24 10.0 25 16.0 26 22.0 27 25.0 28 33.0 29 43.0 30 47.0 31 71.0 32 101.0 33 114.0 34 118.0 35 221.0 36 273.0 37 402.0 38 695.0 39 1772.0 40 5.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 29.526671675432002 9.691960931630353 7.337841222138743 53.4435261707989 2 20.95 13.15 38.324999999999996 27.575 3 20.974999999999998 16.375 22.75 39.900000000000006 4 26.025 24.5 19.925 29.549999999999997 5 25.35 29.975 24.65 20.025000000000002 6 18.85 33.225 26.1 21.825 7 15.55 24.55 39.574999999999996 20.325 8 18.85 22.925 29.349999999999998 28.875 9 18.275 21.75 33.300000000000004 26.674999999999997 10 16.55 38.574999999999996 24.75 20.125 11 23.125 28.799999999999997 21.375 26.700000000000003 12 20.599999999999998 23.200000000000003 27.150000000000002 29.049999999999997 13 19.400000000000002 28.000000000000004 27.950000000000003 24.65 14 20.275000000000002 27.650000000000002 27.450000000000003 24.625 15 21.85 25.8 27.474999999999998 24.875 16 21.675 27.975 26.5 23.849999999999998 17 20.674999999999997 27.725 27.075 24.525 18 21.55 27.700000000000003 26.150000000000002 24.6 19 21.125 27.525 25.775 25.575 20 21.925 27.425 25.25 25.4 21 20.95 25.900000000000002 27.3 25.85 22 21.5 28.425 25.35 24.725 23 23.1 28.175 24.775 23.95 24 21.625 26.75 25.924999999999997 25.7 25 20.825 27.675 26.325 25.174999999999997 26 22.35 26.075 26.575 25.0 27 20.1 26.875 26.8 26.224999999999998 28 21.0 27.775 26.224999999999998 25.0 29 20.9 27.975 26.900000000000002 24.224999999999998 30 20.45 25.324999999999996 27.0 27.224999999999998 31 19.950000000000003 29.275000000000002 26.1 24.675 32 21.475 27.125 26.900000000000002 24.5 33 21.5 25.974999999999998 27.075 25.45 34 20.225 26.625 26.625 26.525 35 21.175 26.825 25.55 26.450000000000003 36 20.474999999999998 27.0 25.7 26.825 37 22.2 25.724999999999998 25.55 26.525 38 21.75 26.224999999999998 25.5 26.525 39 21.6 26.575 25.374999999999996 26.450000000000003 40 21.825 25.95 25.1 27.125 41 21.175 27.400000000000002 25.3 26.125 42 20.375 25.75 25.974999999999998 27.900000000000002 43 22.075 28.1 23.575 26.25 44 22.775000000000002 26.950000000000003 25.674999999999997 24.6 45 21.525 26.775 26.775 24.925 46 24.2 26.3 24.025 25.474999999999998 47 24.675 27.05 23.825 24.45 48 22.125 25.474999999999998 26.400000000000002 26.0 49 21.825 24.9 25.525 27.750000000000004 50 23.1 27.025 24.4 25.474999999999998 51 22.475 25.624999999999996 24.9 27.0 52 21.075 27.875 25.5 25.55 >>END_MODULE >>Per sequence GC content pass #GC Content Count 0 0.0 1 0.5 2 1.0 3 0.5 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10 0.0 11 0.5 12 1.0 13 0.5 14 0.5 15 1.0 16 1.0 17 1.0 18 3.5 19 6.0 20 9.0 21 12.0 22 9.5 23 7.0 24 9.5 25 12.0 26 16.5 27 21.0 28 28.5 29 36.0 30 39.5 31 43.0 32 54.5 33 66.0 34 89.5 35 113.0 36 133.5 37 154.0 38 189.0 39 222.0 40 220.0 41 245.0 42 270.0 43 306.5 44 343.0 45 339.0 46 335.0 47 340.5 48 346.0 49 330.0 50 314.0 51 323.5 52 333.0 53 324.5 54 316.0 55 272.0 56 228.0 57 204.5 58 181.0 59 158.5 60 136.0 61 130.5 62 125.0 63 87.5 64 45.0 65 40.0 66 36.5 67 33.0 68 22.0 69 11.0 70 7.5 71 4.0 72 5.0 73 6.0 74 5.0 75 4.0 76 4.0 77 4.0 78 2.5 79 1.0 80 0.5 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 0.5 90 1.0 91 0.5 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 0.17500000000000002 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 87.55 #Duplication Level Percentage of deduplicated Percentage of total 1 93.0039977155911 81.425 2 4.340376927470017 7.6 3 1.227869788692176 3.225 4 0.5425471159337522 1.9 5 0.34266133637921187 1.5 6 0.1142204454597373 0.6 7 0.1142204454597373 0.7000000000000001 8 0.028555111364934323 0.2 9 0.028555111364934323 0.22499999999999998 >10 0.2569960022844089 2.625 >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 CTCATTACGAGCTTGTACACATGCTTCTAGAGCTACTCGATTAGCAACGGCA 13 0.325 No Hit CTCGTATTTTCCCCTCTGCCTCGGGTTGTCTCGCGATACCTTCTACAGCTTG 12 0.3 No Hit CTCCAGCAACGGGCTCGATGTCGTAGCATCGTCCCTTATAACGATCAAGACT 12 0.3 No Hit CCCGTCGGTCCACACAGTTGTCCATGTACCAGTAGAAGATTCAGCAGCTACT 11 0.27499999999999997 No Hit GGGTAAGCTACATAAGCAATAAATTGATTTTCTTCTCCAGCAACGGGCTCGA 11 0.27499999999999997 No Hit CTCGTACACACTAAGAAAAAAGCCTTATCCATTTACAAAAGTCTTATCCATT 11 0.27499999999999997 No Hit CTGGAATACAATCATAAAGTTAAAAGTACCAGAGATTCCTAGAGGCATCCCA 10 0.25 No Hit GGGGTAAGCTACATAAGCAATAAATTGATTTTCTTCTCCAGCAACGGGCTCG 10 0.25 No Hit CGCAGAAGTAGGAATAATGGCACCAGAAATGATATTGTTTCCATAAAGTAGA 9 0.22499999999999998 No Hit CTCAGCCTGGAATACAATCATAAAGTTAAAAGTACCAGAGATTCCTAGAGGC 8 0.2 No Hit CTCACGAGCAAGATCACGTCCCTCATTACGAGCTTGTACACATGCTTCTAGA 7 0.17500000000000002 No Hit CAGAGATTCCTAGAGGCATCCCATCCGAAAAACTTCCTTGACCGATTGGATA 7 0.17500000000000002 No Hit CCTCATTACGAGCTTGTACACATGCTTCTAGAGCTACTCGATTAGCAACGGC 7 0.17500000000000002 No Hit GTGCATAAGGATGTTGTGCTCAGCCTGGAATACAATCATAAAGTTAAAAGTA 7 0.17500000000000002 No Hit CCACACAGTTGTCCATGTACCAGTAGAAGATTCAGCAGCTACTGCGGCCCCT 6 0.15 No Hit CCCTGATCAAACTAGAGGTTACCAAAGAACCATGCATAGCACTGAATAGGGA 6 0.15 No Hit GTCCTAGAAGTGCATGATAAATACCGCCAAAGCCCAATACTGCAGAGGAAAT 6 0.15 No Hit AGCACGGTTAATAATATCAGCCCAGGTATTAATTACACGACCTTGACTATCA 6 0.15 No Hit GTCCCTCATTACGAGCTTGTACACATGCTTCTAGAGCTACTCGATTAGCAAC 5 0.125 No Hit GTCCATGTACCAGTAGAAGATTCAGCAGCTACTGCGGCCCCTGCTTCCTCGG 5 0.125 No Hit CTCATAAGGACCGCCGTTGTATAACCATTCATCAACGGATGCCGCTTCCCAT 5 0.125 No Hit GTCCCTTATAACGATCAAGACTGGTAAGCCCGTCGGTCCACACAGTTGTCCA 5 0.125 No Hit CCAGCAACGGGCTCGATGTCGTAGCATCGTCCCTTATAACGATCAAGACTGG 5 0.125 No Hit CTGAGTTGGAATCCCATTCTAACTAAGGATTCTTGTGGTTCCGGAGGATCCA 5 0.125 No Hit GCTGGTTTTAAGAATGAGTGATTGCCCTTCTCCGACCCTTACTGCCCAACCT 5 0.125 No Hit CGCCGAATACACCAGCTACGCCTAACATGTGAAATGGGTGCATAAGGATGTT 5 0.125 No Hit CCTCTGCCTCGGGTTGTCTCGCGATACCTTCTACAGCTTGGCCCGCAGCAGT 5 0.125 No Hit GTCCACACAGTTGTCCATGTACCAGTAGAAGATTCAGCAGCTACTGCGGCCC 5 0.125 No Hit ATCAAACTAGAGGTTACCAAAGAACCATGCATAGCACTGAATAGGGAGCCGC 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 0.0 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 SRR5423411.sra Written 200000 spots for SRR5423411.sra Read 200000 spots for SRR5423411.sra Written 200000 spots for SRR5423411.sra Read 200000 spots for SRR5423411.sra Written 200000 spots for SRR5423411.sra Read 200000 spots for SRR5423411.sra Written 200000 spots for SRR5423411.sra Read 200000 spots for SRR5423411.sra Written 200000 spots for SRR5423411.sra Read 200000 spots for SRR5423411.sra Written 200000 spots for SRR5423411.sra Read 200000 spots for SRR5423411.sra Written 200000 spots for SRR5423411.sra Read 200000 spots for SRR5423411.sra Written 200000 spots for SRR5423411.sra Read 200000 spots for SRR5423411.sra Written 200000 spots for SRR5423411.sra Read 200000 spots for SRR5423411.sra Written 200000 spots for SRR5423411.sra Read 200000 spots for SRR5423411.sra Written 200000 spots for SRR5423411.sra Read 200000 spots for SRR5423411.sra Written 200000 spots for SRR5423411.sra Read 200000 spots for SRR5423411.sra Written 200000 spots for SRR5423411.sra Read 200000 spots for SRR5423411.sra Written 200000 spots for SRR5423411.sra Read 200000 spots for SRR5423411.sra Written 200000 spots for SRR5423411.sra Read 200000 spots for SRR5423411.sra Written 200000 spots for SRR5423411.sra Read 200000 spots for SRR5423411.sra Written 200000 spots for SRR5423411.sra Read 200000 spots for SRR5423411.sra Written 200000 spots for SRR5423411.sra Read 200000 spots for SRR5423411.sra Written 200000 spots for SRR5423411.sra Read 200000 spots for SRR5423411.sra Written 200000 spots for SRR5423411.sra SRR ids: ['SRR5423411.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_rguoc67j SRR5423411.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]] SRR5423411 file size 703949 SRR5423411 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 SRR5423411 SRR5423411_1.fastq Input file: SRR5423411_1.fastq trimmed: SRR5423411-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 07:52:50 2025 >> started Thu Feb 13 08:02:15 2025 >> done (564.623s) 4000000 reads processed; of these: 131 ( 0.00%) short reads filtered out after trimming by size control 60 ( 0.00%) empty reads filtered out after trimming by size control 3999809 (100.00%) reads available; of these: 82328 ( 2.06%) trimmed reads available after processing 3917481 (97.94%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 3 0.00% 19 4 0.00% 20 5 0.00% 21 2 0.00% 22 1 0.00% 23 1 0.00% 24 2 0.00% 25 4 0.00% 26 1 0.00% 27 2 0.00% 28 2 0.00% 29 0 0.00% 30 5 0.00% 31 9 0.00% 32 9 0.00% 33 8 0.00% 34 6 0.00% 35 22 0.00% 36 25 0.00% 37 21 0.00% 38 23 0.00% 39 37 0.00% 40 45 0.00% 41 64 0.00% 42 96 0.00% 43 139 0.00% 44 374 0.01% 45 451 0.01% 46 464 0.01% 47 682 0.02% 48 1300 0.03% 49 3382 0.08% 50 9668 0.24% 51 65471 1.64% 52 3917481 97.94% 3999809 reads passed initial QC criterion=sequence-density sequence-density=0.50 sequence-density-rank=1 fanout-score=1.96 fanout-score-rank=22 prefix-density=0.51 prefix-fanout=1.9 sequence=TGAGATGCCTCAGTGCATCCAAACATGGGTAG criterion=fanout-score sequence-density=0.02 sequence-density-rank=26 fanout-score=25.81 fanout-score-rank=1 prefix-density=0.37 prefix-fanout=1.1 sequence=CATTTTATTTCTATCTTTCCATACATAACCAAAAAATGGAAAAGATTCTTCAAGAGTCTCGGGTCCTAGAAGTGCATGATAAATACCGCCAAAGCCCAATACTGCAGAGGAAATTAAGTGAAGTACGCCAGATACAAAGTATGGAAAGGTGTCTATGACTTCCCCGCCAGGACCCACCCCCCAACCTAGAGTAGCTAGGTGGGGAAGTAAAATTAATCCTTGTTCATACATTGGCTTCTCCGGTACGAAATGGGCCACTTCAAATAGGTTCATTGCTCCGGCCCAGAATACGATTAATCCAGCATGGGCTACATGAGCTCCCAGCAGTTTACCGGATAAATTGATAAGTCGGGCATTCCCGGCCCACCAAGCGAAACCTGTGGT Started job on | Feb 13 08:04:53 Started mapping on | Feb 13 08:05:02 Finished on | Feb 13 08:14:08 Mapping speed, Million of reads per hour | 26.37 Number of input reads | 3999809 Average input read length | 51 UNIQUE READS: Uniquely mapped reads number | 3117345 Uniquely mapped reads % | 77.94% Average mapped length | 51.81 Number of splices: Total | 277118 Number of splices: Annotated (sjdb) | 273637 Number of splices: GT/AG | 269346 Number of splices: GC/AG | 6234 Number of splices: AT/AC | 1043 Number of splices: Non-canonical | 495 Mismatch rate per base, % | 0.32% Deletion rate per base | 0.01% Deletion average length | 2.74 Insertion rate per base | 0.00% Insertion average length | 1.32 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 766132 % of reads mapped to multiple loci | 19.15% Number of reads mapped to too many loci | 55194 % of reads mapped to too many loci | 1.38% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.52% % of reads unmapped: other | 0.01% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 116332 116332 116332 N_multimapping 766132 766132 766132 N_noFeature 404315 3077123 433366 N_ambiguous 22333 159 11012 UnstrandedReadsAssigned:2690697 PositiveStrandReadsAssigned:40063 NegativeStrandReadsAssigned:2672967 Dataset is classified negative stranded MeadianReadLen=52 20thPercentileLength=52 echo kmer=47 SRR5423411 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: SRR5423411-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 3,999,809 reads, 3,292,409 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,057 rounds 52401 SRR5423411.ke.tsv 34699 SRR5423411.se.tsv 87100 total ==> SRR5423411.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1919 63 8.82031 Potri.005G024800.1.v4.1 1035 936 3 0.86112 Potri.004G059700.1.v4.1 961 862 4 1.24673 Potri.007G009000.2.v4.1 1416 1317 0 0 Potri.003G141000.2.v4.1 2943 2844 65.5515 6.19258 Potri.016G087400.1.v4.1 270 171 14 21.9963 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 3 0.918005 ==> SRR5423411.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 3 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 22 Potri.001G212900.v4.1 1 Potri.001G182400.v4.1 1 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 6 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 0 SRR5423411 completed mapping pipeline successfully