Starting /dee2/code/volunteer_pipeline.sh SRR5423401 current disk space = 3052214947840 free memory = 1559309540 SRR5423401 SRAfilesize 18ef04a6eeeae65381d09940f1ce0423 SRR5423401.sra SRR5423401.sra file validated SRR5423401 is single end SRR5423401 is conventional basespace SRR5423401 read1 length is 52 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR5423401_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 32.2665 34.0 31.0 34.0 30.0 34.0 2 32.395 34.0 31.0 34.0 30.0 34.0 3 32.4475 34.0 31.0 34.0 30.0 34.0 4 35.85875 37.0 35.0 37.0 35.0 37.0 5 35.81175 37.0 35.0 37.0 33.0 37.0 6 35.89075 37.0 35.0 37.0 35.0 37.0 7 35.903 37.0 35.0 37.0 35.0 37.0 8 35.83075 37.0 35.0 37.0 35.0 37.0 9 37.7145 39.0 37.0 39.0 35.0 39.0 10 37.57475 39.0 37.0 39.0 35.0 39.0 11 37.5215 39.0 37.0 39.0 35.0 39.0 12 37.547 39.0 37.0 39.0 35.0 39.0 13 37.45325 39.0 37.0 39.0 35.0 39.0 14 38.85225 40.0 38.0 41.0 35.0 41.0 15 38.83575 40.0 38.0 41.0 35.0 41.0 16 38.7175 40.0 38.0 41.0 34.0 41.0 17 38.652 40.0 38.0 41.0 34.0 41.0 18 38.68375 40.0 38.0 41.0 34.0 41.0 19 38.6315 40.0 38.0 41.0 34.0 41.0 20 38.699 40.0 38.0 41.0 34.0 41.0 21 38.66775 40.0 38.0 41.0 34.0 41.0 22 38.6955 40.0 38.0 41.0 34.0 41.0 23 38.581 40.0 38.0 41.0 34.0 41.0 24 38.5715 40.0 38.0 41.0 34.0 41.0 25 38.684 40.0 38.0 41.0 34.0 41.0 26 38.45275 40.0 38.0 41.0 34.0 41.0 27 38.255 40.0 38.0 41.0 33.0 41.0 28 38.351 40.0 38.0 41.0 34.0 41.0 29 38.416 40.0 38.0 41.0 34.0 41.0 30 38.4345 40.0 38.0 41.0 34.0 41.0 31 38.473 40.0 38.0 41.0 34.0 41.0 32 38.29775 40.0 38.0 41.0 34.0 41.0 33 38.32675 40.0 38.0 41.0 34.0 41.0 34 38.29475 40.0 38.0 41.0 34.0 41.0 35 38.23625 40.0 38.0 41.0 33.0 41.0 36 38.05025 40.0 38.0 41.0 33.0 41.0 37 38.004 40.0 38.0 41.0 33.0 41.0 38 37.91375 40.0 38.0 41.0 33.0 41.0 39 37.8315 40.0 37.0 41.0 32.0 41.0 40 37.561 40.0 37.0 41.0 32.0 41.0 41 37.742 40.0 37.0 41.0 32.0 41.0 42 37.678 40.0 37.0 41.0 32.0 41.0 43 37.661 40.0 37.0 41.0 31.0 41.0 44 37.5995 40.0 37.0 41.0 31.0 41.0 45 37.479 40.0 37.0 41.0 31.0 41.0 46 37.26575 40.0 36.0 41.0 31.0 41.0 47 37.22875 40.0 36.0 41.0 31.0 41.0 48 37.2705 40.0 36.0 41.0 31.0 41.0 49 37.44625 40.0 37.0 41.0 31.0 41.0 50 37.22675 40.0 36.0 41.0 31.0 41.0 51 36.7555 39.0 35.0 41.0 30.0 41.0 52 35.6725 38.0 34.0 40.0 27.0 41.0 >>END_MODULE >>Per tile sequence quality pass #Tile Base Mean 1208 1 0.0 1208 2 0.0 1208 3 0.0 1208 4 0.0 1208 5 0.0 1208 6 0.0 1208 7 0.0 1208 8 0.0 1208 9 0.0 1208 10 0.0 1208 11 0.0 1208 12 0.0 1208 13 0.0 1208 14 0.0 1208 15 0.0 1208 16 0.0 1208 17 0.0 1208 18 0.0 1208 19 0.0 1208 20 0.0 1208 21 0.0 1208 22 0.0 1208 23 0.0 1208 24 0.0 1208 25 0.0 1208 26 0.0 1208 27 0.0 1208 28 0.0 1208 29 0.0 1208 30 0.0 1208 31 0.0 1208 32 0.0 1208 33 0.0 1208 34 0.0 1208 35 0.0 1208 36 0.0 1208 37 0.0 1208 38 0.0 1208 39 0.0 1208 40 0.0 1208 41 0.0 1208 42 0.0 1208 43 0.0 1208 44 0.0 1208 45 0.0 1208 46 0.0 1208 47 0.0 1208 48 0.0 1208 49 0.0 1208 50 0.0 1208 51 0.0 1208 52 0.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 10 1.0 11 0.0 12 0.0 13 0.0 14 0.0 15 0.0 16 0.0 17 0.0 18 1.0 19 1.0 20 3.0 21 2.0 22 4.0 23 6.0 24 6.0 25 8.0 26 17.0 27 25.0 28 37.0 29 31.0 30 65.0 31 51.0 32 106.0 33 121.0 34 162.0 35 208.0 36 283.0 37 410.0 38 699.0 39 1747.0 40 6.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 28.607214428857713 9.318637274549097 7.515030060120241 54.55911823647295 2 20.9 14.524999999999999 36.6 27.975 3 20.875 16.425 24.25 38.45 4 26.174999999999997 24.85 19.325 29.65 5 25.45 30.8 22.900000000000002 20.849999999999998 6 19.35 32.125 26.900000000000002 21.625 7 15.525 24.175 41.199999999999996 19.1 8 17.025000000000002 21.625 32.25 29.099999999999998 9 17.575 20.3 35.15 26.974999999999998 10 17.375 39.2 23.375 20.05 11 22.6 29.075 21.525 26.8 12 20.95 24.9 27.150000000000002 27.0 13 19.125 27.375 27.950000000000003 25.55 14 19.85 28.675 27.075 24.4 15 21.625 25.624999999999996 28.825 23.925 16 20.65 27.175 26.450000000000003 25.724999999999998 17 21.05 26.974999999999998 26.325 25.650000000000002 18 20.849999999999998 27.775 27.0 24.375 19 19.400000000000002 27.200000000000003 26.474999999999998 26.924999999999997 20 21.45 26.325 25.474999999999998 26.75 21 20.875 26.224999999999998 26.650000000000002 26.25 22 21.55 27.725 24.275 26.450000000000003 23 21.775 28.050000000000004 25.5 24.675 24 22.175 25.95 25.825 26.05 25 22.05 26.275 25.624999999999996 26.05 26 22.525000000000002 27.875 26.6 23.0 27 22.2 26.400000000000002 25.95 25.45 28 21.4 27.025 26.125 25.45 29 20.325 28.9 26.724999999999998 24.05 30 20.974999999999998 26.3 26.275 26.450000000000003 31 20.025000000000002 27.750000000000004 26.075 26.150000000000002 32 20.0 28.349999999999998 26.875 24.775 33 20.825 25.174999999999997 27.775 26.224999999999998 34 21.175 28.025 26.075 24.725 35 21.55 27.825 24.975 25.650000000000002 36 20.674999999999997 28.125 25.3 25.900000000000002 37 20.599999999999998 27.150000000000002 24.175 28.075 38 21.349999999999998 27.875 26.674999999999997 24.099999999999998 39 20.25 25.275 27.725 26.75 40 20.525 26.775 25.4 27.3 41 21.975 28.050000000000004 23.974999999999998 26.0 42 20.575 25.6 27.05 26.775 43 23.150000000000002 26.775 24.425 25.650000000000002 44 22.725 26.625 25.874999999999996 24.775 45 23.724999999999998 27.05 23.575 25.650000000000002 46 23.605901475368842 26.456614153538382 24.081020255063766 25.85646411602901 47 21.9 28.050000000000004 25.525 24.525 48 21.725 26.275 25.674999999999997 26.325 49 21.76088044022011 25.212606303151574 25.26263131565783 27.763881940970485 50 21.380345086271568 26.70667666916729 26.18154538634659 25.731432858214554 51 22.230557639409852 26.081520380095025 24.981245311327832 26.70667666916729 52 21.355338834708675 27.231807951987996 24.756189047261813 26.65666416604151 >>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 0.0 10 0.0 11 0.0 12 0.0 13 0.5 14 1.5 15 2.0 16 2.5 17 3.0 18 3.5 19 4.0 20 7.0 21 10.0 22 12.0 23 14.0 24 11.0 25 8.0 26 15.0 27 22.0 28 27.0 29 32.0 30 36.5 31 41.0 32 62.0 33 83.0 34 96.5 35 110.0 36 138.5 37 167.0 38 198.5 39 230.5 40 231.0 41 256.5 42 282.0 43 296.0 44 310.0 45 309.0 46 308.0 47 332.0 48 356.0 49 334.0 50 312.0 51 319.0 52 326.0 53 326.0 54 326.0 55 280.0 56 234.0 57 199.5 58 165.0 59 159.0 60 153.0 61 131.5 62 110.0 63 82.5 64 50.5 65 46.0 66 38.0 67 30.0 68 21.0 69 12.0 70 10.5 71 9.0 72 7.5 73 6.0 74 3.5 75 1.0 76 0.5 77 0.0 78 0.0 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 0.025 47 0.0 48 0.0 49 0.05 50 0.025 51 0.025 52 0.025 >>END_MODULE >>Sequence Length Distribution pass #Length Count 52 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 86.65 #Duplication Level Percentage of deduplicated Percentage of total 1 92.72937103289094 80.35 2 4.645124062319677 8.05 3 1.154068090017311 3.0 4 0.4039238315060588 1.4000000000000001 5 0.3462204270051933 1.5 6 0.28851702250432776 1.5 7 0.028851702250432775 0.17500000000000002 8 0.1154068090017311 0.8 9 0.17311021350259664 1.35 >10 0.1154068090017311 1.875 >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 33 0.8250000000000001 No Hit CTCGTATTTTCCCCTCTGCCTCGGGTTGTCTCGCGATACCTTCTACAGCTTG 17 0.42500000000000004 No Hit GGGTAAGCTACATAAGCAATAAATTGATTTTCTTCTCCAGCAACGGGCTCGA 14 0.35000000000000003 No Hit CTCCAGCAACGGGCTCGATGTCGTAGCATCGTCCCTTATAACGATCAAGACT 11 0.27499999999999997 No Hit CCTCATTACGAGCTTGTACACATGCTTCTAGAGCTACTCGATTAGCAACGGC 9 0.22499999999999998 No Hit CTTATAACGATCAAGACTGGTAAGCCCGTCGGTCCACACAGTTGTCCATGTA 9 0.22499999999999998 No Hit CCAGCAACGGGCTCGATGTCGTAGCATCGTCCCTTATAACGATCAAGACTGG 9 0.22499999999999998 No Hit CTCATTACGAGCTTGTACACATGCTTCTAGAGCTACTCGATTAGCAACGGCA 9 0.22499999999999998 No Hit CCCGTCGGTCCACACAGTTGTCCATGTACCAGTAGAAGATTCAGCAGCTACT 9 0.22499999999999998 No Hit CCCACTTTTTGGTCTTAAGAATGCTGGTTTTAAGAATGAGTGATTGCCCTTC 9 0.22499999999999998 No Hit CGCAGAAGTAGGAATAATGGCACCAGAAATGATATTGTTTCCATAAAGTAGA 8 0.2 No Hit CTCACGAGCAAGATCACGTCCCTCATTACGAGCTTGTACACATGCTTCTAGA 8 0.2 No Hit GCTCCATTTGCTAGCTTCACGGATAATTTCATTACCCTCACGAGCAAGATCA 8 0.2 No Hit CTCAGCCTGGAATACAATCATAAAGTTAAAAGTACCAGAGATTCCTAGAGGC 8 0.2 No Hit GTAAGCTACATAAGCAATAAATTGATTTTCTTCTCCAGCAACGGGCTCGATG 7 0.17500000000000002 No Hit GTCCCTCATTACGAGCTTGTACACATGCTTCTAGAGCTACTCGATTAGCAAC 6 0.15 No Hit CTCCATTTTATTTTCCCATTGAGGCCGAACCTAAACCTGTGCTCGAGAGATA 6 0.15 No Hit CCTTCTCCGACCCTTACTGCCCAACCTGAGAGCGGACAGCTAATGCGTTCCA 6 0.15 No Hit CACACAGTTGTCCATGTACCAGTAGAAGATTCAGCAGCTACTGCGGCCCCTG 6 0.15 No Hit CTTGACCAAATCTGTAACCTTCATTAGCAGATTCATTTTCTGTGGTTTCCCT 6 0.15 No Hit CTGGAATACAATCATAAAGTTAAAAGTACCAGAGATTCCTAGAGGCATCCCA 6 0.15 No Hit GGGGTAAGCTACATAAGCAATAAATTGATTTTCTTCTCCAGCAACGGGCTCG 6 0.15 No Hit CGATTGGATAAATCAAGAAAACAGCAGTAGCCGCCGCAACAGGAGCTGAATA 6 0.15 No Hit CTCGTACACACTAAGAAAAAAGCCTTATCCATTTACAAAAGTCTTATCCATT 6 0.15 No Hit ATCAAACTAGAGGTTACCAAAGAACCATGCATAGCACTGAATAGGGAGCCGC 6 0.15 No Hit CCACACAGTTGTCCATGTACCAGTAGAAGATTCAGCAGCTACTGCGGCCCCT 5 0.125 No Hit CCCCTCTGCCTCGGGTTGTCTCGCGATACCTTCTACAGCTTGGCCCGCAGCA 5 0.125 No Hit CAGGGCTCCATTTGCTAGCTTCACGGATAATTTCATTACCCTCACGAGCAAG 5 0.125 No Hit CTTCCATACTTCACAAGCAGCAGCTAGTTCAGGGCTCCATTTGCTAGCTTCA 5 0.125 No Hit CCCTGATCAAACTAGAGGTTACCAAAGAACCATGCATAGCACTGAATAGGGA 5 0.125 No Hit CTGCAAAGGATTCTACCCGCCGCTCGGTGGGAATTGTACTTCAAGGCGGCCC 5 0.125 No Hit CAGCAACGGGCTCGATGTCGTAGCATCGTCCCTTATAACGATCAAGACTGGT 5 0.125 No Hit CTGAGTTGGAATCCCATTCTAACTAAGGATTCTTGTGGTTCCGGAGGATCCA 5 0.125 No Hit GCCTCCTCGAGCTCAATCAGCACCTGAGATGCCTCAGTGCATCCAAACATGG 5 0.125 No Hit CCTCTGCCTCGGGTTGTCTCGCGATACCTTCTACAGCTTGGCCCGCAGCAGT 5 0.125 No Hit GTTTCCATAAAGTAGAGATCCAGAAACAGGTTCACGAATACCATCAATGTCT 5 0.125 No Hit AGCACGGTTAATAATATCAGCCCAGGTATTAATTACACGACCTTGACTATCA 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 0.025 0.0 0.0 0.0 0.0 6 0.025 0.0 0.0 0.0 0.0 7 0.025 0.0 0.0 0.0 0.0 8 0.025 0.0 0.0 0.0 0.0 9 0.025 0.0 0.0 0.0 0.0 10 0.025 0.0 0.0 0.0 0.0 11 0.025 0.0 0.0 0.0 0.0 12 0.025 0.0 0.0 0.0 0.0 13 0.025 0.0 0.0 0.0 0.0 14 0.025 0.0 0.0 0.0 0.0 15 0.025 0.0 0.0 0.0 0.0 16 0.025 0.0 0.0 0.0 0.0 17 0.025 0.0 0.0 0.0 0.0 18 0.025 0.0 0.0 0.0 0.0 19 0.025 0.0 0.0 0.0 0.0 20 0.025 0.0 0.0 0.0 0.0 21 0.025 0.0 0.0 0.0 0.0 22 0.025 0.0 0.0 0.0 0.0 23 0.025 0.0 0.0 0.0 0.0 24 0.025 0.0 0.0 0.0 0.0 25 0.025 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 SRR5423401.sra Written 200000 spots for SRR5423401.sra Read 200000 spots for SRR5423401.sra Written 200000 spots for SRR5423401.sra Read 200000 spots for SRR5423401.sra Written 200000 spots for SRR5423401.sra Read 200000 spots for SRR5423401.sra Written 200000 spots for SRR5423401.sra Read 200000 spots for SRR5423401.sra Written 200000 spots for SRR5423401.sra Read 200000 spots for SRR5423401.sra Written 200000 spots for SRR5423401.sra Read 200000 spots for SRR5423401.sra Written 200000 spots for SRR5423401.sra Read 200000 spots for SRR5423401.sra Written 200000 spots for SRR5423401.sra Read 200000 spots for SRR5423401.sra Written 200000 spots for SRR5423401.sra Read 200000 spots for SRR5423401.sra Written 200000 spots for SRR5423401.sra Read 200000 spots for SRR5423401.sra Written 200000 spots for SRR5423401.sra Read 200000 spots for SRR5423401.sra Written 200000 spots for SRR5423401.sra Read 200000 spots for SRR5423401.sra Written 200000 spots for SRR5423401.sra Read 200000 spots for SRR5423401.sra Written 200000 spots for SRR5423401.sra Read 200000 spots for SRR5423401.sra Written 200000 spots for SRR5423401.sra Read 200000 spots for SRR5423401.sra Written 200000 spots for SRR5423401.sra Read 200000 spots for SRR5423401.sra Written 200000 spots for SRR5423401.sra Read 200000 spots for SRR5423401.sra Written 200000 spots for SRR5423401.sra Read 200000 spots for SRR5423401.sra Written 200000 spots for SRR5423401.sra Read 200000 spots for SRR5423401.sra Written 200000 spots for SRR5423401.sra SRR ids: ['SRR5423401.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_vwwwjui1 SRR5423401.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]] SRR5423401 file size 703969 SRR5423401 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 SRR5423401 SRR5423401_1.fastq Input file: SRR5423401_1.fastq trimmed: SRR5423401-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 05:58:38 2025 >> started Thu Feb 13 05:58:40 2025 >> done (1.936s) 4000000 reads processed; of these: 143 ( 0.00%) short reads filtered out after trimming by size control 50 ( 0.00%) empty reads filtered out after trimming by size control 3999807 (100.00%) reads available; of these: 70542 ( 1.76%) trimmed reads available after processing 3929265 (98.24%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 10 0.00% 19 1 0.00% 20 4 0.00% 21 1 0.00% 22 1 0.00% 23 1 0.00% 24 0 0.00% 25 4 0.00% 26 1 0.00% 27 3 0.00% 28 5 0.00% 29 1 0.00% 30 2 0.00% 31 6 0.00% 32 3 0.00% 33 7 0.00% 34 3 0.00% 35 8 0.00% 36 12 0.00% 37 25 0.00% 38 22 0.00% 39 20 0.00% 40 28 0.00% 41 38 0.00% 42 78 0.00% 43 90 0.00% 44 249 0.01% 45 288 0.01% 46 418 0.01% 47 610 0.02% 48 1140 0.03% 49 2700 0.07% 50 8250 0.21% 51 56513 1.41% 52 3929265 98.24% 3999807 reads passed initial QC criterion=sequence-density sequence-density=0.35 sequence-density-rank=1 fanout-score=3.59 fanout-score-rank=12 prefix-density=0.43 prefix-fanout=2.9 sequence=CCATTGCTTGCAATGGAAGTAATGTCATT criterion=fanout-score sequence-density=0.01 sequence-density-rank=30 fanout-score=133.66 fanout-score-rank=1 prefix-density=0.74 prefix-fanout=1.1 sequence=CCCTCTGCCACAAATTTTGACGTAGGCTCTCCCTCTTGGGGAGACCTTAG Started job on | Feb 13 05:58:49 Started mapping on | Feb 13 05:58:49 Finished on | Feb 13 05:58:54 Mapping speed, Million of reads per hour | 2879.86 Number of input reads | 3999807 Average input read length | 51 UNIQUE READS: Uniquely mapped reads number | 3117532 Uniquely mapped reads % | 77.94% Average mapped length | 51.81 Number of splices: Total | 275055 Number of splices: Annotated (sjdb) | 271560 Number of splices: GT/AG | 267203 Number of splices: GC/AG | 6271 Number of splices: AT/AC | 1046 Number of splices: Non-canonical | 535 Mismatch rate per base, % | 0.34% Deletion rate per base | 0.01% Deletion average length | 2.74 Insertion rate per base | 0.00% Insertion average length | 1.34 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 764035 % of reads mapped to multiple loci | 19.10% Number of reads mapped to too many loci | 56641 % of reads mapped to too many loci | 1.42% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.53% % of reads unmapped: other | 0.01% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 118240 118240 118240 N_multimapping 764035 764035 764035 N_noFeature 405008 3076038 435034 N_ambiguous 22857 163 11237 UnstrandedReadsAssigned:2689667 PositiveStrandReadsAssigned:41331 NegativeStrandReadsAssigned:2671261 Dataset is classified negative stranded MeadianReadLen=52 20thPercentileLength=52 echo kmer=47 SRR5423401 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: SRR5423401-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 3,999,807 reads, 3,291,453 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,096 rounds 52401 SRR5423401.ke.tsv 34699 SRR5423401.se.tsv 87100 total ==> SRR5423401.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1919 91 12.6806 Potri.005G024800.1.v4.1 1035 936 3 0.857077 Potri.004G059700.1.v4.1 961 862 2 0.620437 Potri.007G009000.2.v4.1 1416 1317 0 0 Potri.003G141000.2.v4.1 2943 2844 68.3051 6.42241 Potri.016G087400.1.v4.1 270 171 11 17.2017 Potri.015G069301.1.v4.1 564 465 0 0 Potri.010G195200.1.v4.1 1773 1674 1 0.159742 Potri.012G127500.1.v4.1 977 878 6 1.82739 ==> SRR5423401.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 4 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 6 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 0 SRR5423401 completed mapping pipeline successfully