Starting /dee2/code/volunteer_pipeline.sh SRR5423384 current disk space = 3049246457856 free memory = 1576282732 SRR5423384 SRAfilesize 9fef1d8aee7093d36bcc02f9a4e8118b SRR5423384.sra SRR5423384.sra file validated SRR5423384 is single end SRR5423384 is conventional basespace SRR5423384 read1 length is 52 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR5423384_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 32.2155 34.0 31.0 34.0 30.0 34.0 2 32.26975 34.0 31.0 34.0 30.0 34.0 3 32.34975 34.0 31.0 34.0 30.0 34.0 4 35.74825 37.0 35.0 37.0 33.0 37.0 5 35.788 37.0 35.0 37.0 33.0 37.0 6 35.8275 37.0 35.0 37.0 35.0 37.0 7 35.708 37.0 35.0 37.0 35.0 37.0 8 35.6035 37.0 35.0 37.0 33.0 37.0 9 37.24625 39.0 37.0 39.0 34.0 39.0 10 37.24225 39.0 37.0 39.0 33.0 39.0 11 37.28575 39.0 37.0 39.0 33.0 39.0 12 37.396 39.0 37.0 39.0 34.0 39.0 13 37.316 39.0 37.0 39.0 34.0 39.0 14 38.68 40.0 38.0 41.0 34.0 41.0 15 38.48675 40.0 38.0 41.0 33.0 41.0 16 38.5735 40.0 38.0 41.0 34.0 41.0 17 38.6145 40.0 38.0 41.0 34.0 41.0 18 38.559 40.0 38.0 41.0 34.0 41.0 19 38.45975 40.0 38.0 41.0 34.0 41.0 20 38.53125 40.0 38.0 41.0 34.0 41.0 21 38.54825 40.0 38.0 41.0 34.0 41.0 22 38.483 40.0 38.0 41.0 34.0 41.0 23 38.57 40.0 38.0 41.0 34.0 41.0 24 38.45425 40.0 38.0 41.0 34.0 41.0 25 38.5045 40.0 38.0 41.0 34.0 41.0 26 38.4745 40.0 38.0 41.0 34.0 41.0 27 38.4575 40.0 38.0 41.0 34.0 41.0 28 38.323 40.0 38.0 41.0 33.0 41.0 29 38.41425 40.0 38.0 41.0 34.0 41.0 30 38.226 40.0 38.0 41.0 33.0 41.0 31 38.29275 40.0 38.0 41.0 34.0 41.0 32 38.18875 40.0 38.0 41.0 33.0 41.0 33 38.30775 40.0 38.0 41.0 34.0 41.0 34 38.16775 40.0 38.0 41.0 33.0 41.0 35 38.05175 40.0 37.0 41.0 33.0 41.0 36 38.053 40.0 37.0 41.0 33.0 41.0 37 38.07125 40.0 37.0 41.0 33.0 41.0 38 38.00325 40.0 37.0 41.0 33.0 41.0 39 37.92575 40.0 37.0 41.0 33.0 41.0 40 37.73725 40.0 37.0 41.0 32.0 41.0 41 37.9265 40.0 37.0 41.0 33.0 41.0 42 37.73375 40.0 37.0 41.0 32.0 41.0 43 37.70275 40.0 37.0 41.0 32.0 41.0 44 37.61825 40.0 37.0 41.0 32.0 41.0 45 37.5925 40.0 37.0 41.0 32.0 41.0 46 37.36475 40.0 36.0 41.0 32.0 41.0 47 37.2155 39.0 36.0 41.0 31.0 41.0 48 37.286 39.0 36.0 41.0 31.0 41.0 49 37.2785 39.0 36.0 41.0 31.0 41.0 50 37.33225 39.0 36.0 41.0 31.0 41.0 51 37.286 39.0 36.0 41.0 31.0 41.0 52 36.12725 38.0 34.0 40.0 29.0 41.0 >>END_MODULE >>Per tile sequence quality pass #Tile Base Mean 1310 1 0.0 1310 2 0.0 1310 3 0.0 1310 4 0.0 1310 5 0.0 1310 6 0.0 1310 7 0.0 1310 8 0.0 1310 9 0.0 1310 10 0.0 1310 11 0.0 1310 12 0.0 1310 13 0.0 1310 14 0.0 1310 15 0.0 1310 16 0.0 1310 17 0.0 1310 18 0.0 1310 19 0.0 1310 20 0.0 1310 21 0.0 1310 22 0.0 1310 23 0.0 1310 24 0.0 1310 25 0.0 1310 26 0.0 1310 27 0.0 1310 28 0.0 1310 29 0.0 1310 30 0.0 1310 31 0.0 1310 32 0.0 1310 33 0.0 1310 34 0.0 1310 35 0.0 1310 36 0.0 1310 37 0.0 1310 38 0.0 1310 39 0.0 1310 40 0.0 1310 41 0.0 1310 42 0.0 1310 43 0.0 1310 44 0.0 1310 45 0.0 1310 46 0.0 1310 47 0.0 1310 48 0.0 1310 49 0.0 1310 50 0.0 1310 51 0.0 1310 52 0.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 11 1.0 12 0.0 13 1.0 14 0.0 15 1.0 16 0.0 17 0.0 18 0.0 19 0.0 20 1.0 21 4.0 22 1.0 23 1.0 24 2.0 25 7.0 26 15.0 27 17.0 28 26.0 29 46.0 30 62.0 31 82.0 32 88.0 33 145.0 34 191.0 35 217.0 36 291.0 37 435.0 38 708.0 39 1653.0 40 5.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 43.598095715359555 14.131796542219996 5.537459283387622 36.73264845903282 2 20.125 15.075 36.55 28.249999999999996 3 19.7 19.75 26.25 34.300000000000004 4 25.124999999999996 27.275 21.175 26.424999999999997 5 24.6 33.275 23.150000000000002 18.975 6 19.825 36.05 22.575 21.55 7 14.75 25.75 40.325 19.175 8 17.875 23.525 29.575000000000003 29.025000000000002 9 18.575 21.075 32.300000000000004 28.050000000000004 10 19.950000000000003 38.0 24.525 17.525 11 23.150000000000002 29.45 21.275 26.125 12 21.925 24.95 25.074999999999996 28.050000000000004 13 20.525 28.65 26.650000000000002 24.175 14 20.0 29.025000000000002 28.225 22.75 15 22.075 26.724999999999998 25.45 25.75 16 21.375 26.924999999999997 26.400000000000002 25.3 17 20.9 27.250000000000004 27.250000000000004 24.6 18 21.175 26.55 25.900000000000002 26.375 19 21.15 28.325 25.624999999999996 24.9 20 20.75 26.6 27.575 25.074999999999996 21 21.405351337834457 26.70667666916729 25.6064016004001 26.281570392598148 22 21.7 27.075 26.400000000000002 24.825 23 21.775 27.800000000000004 25.124999999999996 25.3 24 21.875 25.5 27.500000000000004 25.124999999999996 25 21.7 28.025 24.425 25.85 26 22.425 26.924999999999997 25.474999999999998 25.174999999999997 27 20.7 26.674999999999997 25.5 27.125 28 21.725 27.450000000000003 26.05 24.775 29 20.424999999999997 26.950000000000003 27.0 25.624999999999996 30 20.125 25.85 25.55 28.475 31 21.349999999999998 27.725 26.075 24.85 32 20.4 27.55 25.724999999999998 26.325 33 20.674999999999997 26.0 27.05 26.275 34 20.45 26.974999999999998 26.5 26.075 35 20.474999999999998 28.025 24.7 26.8 36 22.25 27.85 23.724999999999998 26.174999999999997 37 21.775 26.400000000000002 25.6 26.224999999999998 38 21.075 26.25 25.8 26.875 39 21.85 25.85 25.1 27.200000000000003 40 21.65 28.075 24.6 25.674999999999997 41 21.65 28.075 24.975 25.3 42 20.5 25.525 26.85 27.125 43 21.224999999999998 28.599999999999998 25.15 25.025 44 22.325 27.525 25.775 24.375 45 22.5 25.3 25.15 27.05 46 23.25 27.125 23.7 25.924999999999997 47 22.675 27.35 25.575 24.4 48 21.575 26.775 25.05 26.6 49 21.780445111277817 27.556889222305575 24.131032758189548 26.531632908227053 50 22.05551387846962 27.231807951987996 25.656414103525883 25.056264066016503 51 22.825 26.474999999999998 23.875 26.825 52 22.375 27.650000000000002 24.224999999999998 25.75 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 6.0 1 4.5 2 3.0 3 2.5 4 2.0 5 1.5 6 1.0 7 1.5 8 2.0 9 1.0 10 0.0 11 0.5 12 1.0 13 1.0 14 1.5 15 2.0 16 2.5 17 3.0 18 5.5 19 8.0 20 9.0 21 10.0 22 13.0 23 16.0 24 20.0 25 24.0 26 27.0 27 30.0 28 36.0 29 42.0 30 44.0 31 46.0 32 69.5 33 93.0 34 116.5 35 140.0 36 146.5 37 153.0 38 170.0 39 205.5 40 224.0 41 241.0 42 258.0 43 270.5 44 283.0 45 295.0 46 307.0 47 295.0 48 283.0 49 311.5 50 340.0 51 345.5 52 351.0 53 330.0 54 309.0 55 267.0 56 225.0 57 212.5 58 200.0 59 174.5 60 149.0 61 131.0 62 113.0 63 95.5 64 56.5 65 35.0 66 33.5 67 32.0 68 24.0 69 16.0 70 12.0 71 8.0 72 8.0 73 8.0 74 6.0 75 4.0 76 4.0 77 4.0 78 3.0 79 2.0 80 1.5 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 pass #Base N-Count 1 0.22499999999999998 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 0.025 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 0.025 50 0.025 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 87.775 #Duplication Level Percentage of deduplicated Percentage of total 1 92.28140131016804 81.0 2 5.326117915123897 9.35 3 0.8829393335232129 2.325 4 0.6550840216462547 2.3 5 0.3417829678154372 1.5 6 0.19937339789233835 1.05 7 0.11392765593847907 0.7000000000000001 8 0.05696382796923954 0.4 9 0.02848191398461977 0.22499999999999998 >10 0.11392765593847907 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 16 0.4 No Hit GCCCGTCGGTCCACACAGTTGTCCATGTACCAGTAGAAGATTCAGCAGCTAC 10 0.25 No Hit GTCCCTTATAACGATCAAGACTGGTAAGCCCGTCGGTCCACACAGTTGTCCA 10 0.25 No Hit GCCAGACTAAGCAATAAAGTACCTCGTATTTTCCCCTCTGCCTCGGGTTGTC 10 0.25 No Hit CTCGTATTTTCCCCTCTGCCTCGGGTTGTCTCGCGATACCTTCTACAGCTTG 9 0.22499999999999998 No Hit GTTAATAATATCAGCCCAGGTATTAATTACACGACCTTGACTATCAACTACA 8 0.2 No Hit GGGGTAAGCTACATAAGCAATAAATTGATTTTCTTCTCCAGCAACGGGCTCG 8 0.2 No Hit GCACTGAATAGGGAGCCGCCGAATACACCAGCTACGCCTAACATGTGAAATG 7 0.17500000000000002 No Hit CTCCAGCAACGGGCTCGATGTCGTAGCATCGTCCCTTATAACGATCAAGACT 7 0.17500000000000002 No Hit GCTCCATTTGCTAGCTTCACGGATAATTTCATTACCCTCACGAGCAAGATCA 7 0.17500000000000002 No Hit GCCGCTTCCCATATTGGGTAAAAGTGCAACCCTATAGCCGCAGAAGTAGGAA 7 0.17500000000000002 No Hit GCTCAGCCTGGAATACAATCATAAAGTTAAAAGTACCAGAGATTCCTAGAGG 6 0.15 No Hit GGTTAATAATATCAGCCCAGGTATTAATTACACGACCTTGACTATCAACTAC 6 0.15 No Hit GGTGCATAAGGATGTTGTGCTCAGCCTGGAATACAATCATAAAGTTAAAAGT 6 0.15 No Hit CCGCATTTCGCTAAAGGGTTGAAGGAGGATAGTGCATCAAGCTGTTCGCAAG 6 0.15 No Hit AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 6 0.15 No Hit GCCGAATACACCAGCTACGCCTAACATGTGAAATGGGTGCATAAGGATGTTG 6 0.15 No Hit AGCACGGTTAATAATATCAGCCCAGGTATTAATTACACGACCTTGACTATCA 6 0.15 No Hit CAGAGATTCCTAGAGGCATCCCATCCGAAAAACTTCCTTGACCGATTGGATA 5 0.125 No Hit CTCGACGATGCCAGCAGTGTAGCTGCTTCCCTTCTTGACACACTGGGTCTTG 5 0.125 No Hit CCCAGGTATTAATTACACGACCTTGACTATCAACTACAGATTGGTTGAAATT 5 0.125 No Hit GTCAGCAGAGAGGCCAGCAGTGTCCCAGCCGTAGTCACCAGGGAACTCACCA 5 0.125 No Hit CTGCAAAGGATTCTACCCGCCGCTCGGTGGGAATTGTACTTCAAGGCGGCCC 5 0.125 No Hit GTGCTCAGCCTGGAATACAATCATAAAGTTAAAAGTACCAGAGATTCCTAGA 5 0.125 No Hit CTTATAACGATCAAGACTGGTAAGCCCGTCGGTCCACACAGTTGTCCATGTA 5 0.125 No Hit CCAGCAACGGGCTCGATGTCGTAGCATCGTCCCTTATAACGATCAAGACTGG 5 0.125 No Hit GCTGGTTTTAAGAATGAGTGATTGCCCTTCTCCGACCCTTACTGCCCAACCT 5 0.125 No Hit GCACGGTTAATAATATCAGCCCAGGTATTAATTACACGACCTTGACTATCAA 5 0.125 No Hit GGGTAAGCTACATAAGCAATAAATTGATTTTCTTCTCCAGCAACGGGCTCGA 5 0.125 No Hit GTGCATAAGGATGTTGTGCTCAGCCTGGAATACAATCATAAAGTTAAAAGTA 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 SRR5423384.sra Written 200000 spots for SRR5423384.sra Read 200000 spots for SRR5423384.sra Written 200000 spots for SRR5423384.sra Read 200000 spots for SRR5423384.sra Written 200000 spots for SRR5423384.sra Read 200000 spots for SRR5423384.sra Written 200000 spots for SRR5423384.sra Read 200000 spots for SRR5423384.sra Written 200000 spots for SRR5423384.sra Read 200000 spots for SRR5423384.sra Written 200000 spots for SRR5423384.sra Read 200000 spots for SRR5423384.sra Written 200000 spots for SRR5423384.sra Read 200000 spots for SRR5423384.sra Written 200000 spots for SRR5423384.sra Read 200000 spots for SRR5423384.sra Written 200000 spots for SRR5423384.sra Read 200000 spots for SRR5423384.sra Written 200000 spots for SRR5423384.sra Read 200000 spots for SRR5423384.sra Written 200000 spots for SRR5423384.sra Read 200000 spots for SRR5423384.sra Written 200000 spots for SRR5423384.sra Read 200000 spots for SRR5423384.sra Written 200000 spots for SRR5423384.sra Read 200000 spots for SRR5423384.sra Written 200000 spots for SRR5423384.sra Read 200000 spots for SRR5423384.sra Written 200000 spots for SRR5423384.sra Read 200000 spots for SRR5423384.sra Written 200000 spots for SRR5423384.sra Read 200000 spots for SRR5423384.sra Written 200000 spots for SRR5423384.sra Read 200000 spots for SRR5423384.sra Written 200000 spots for SRR5423384.sra Read 200000 spots for SRR5423384.sra Written 200000 spots for SRR5423384.sra Read 200000 spots for SRR5423384.sra Written 200000 spots for SRR5423384.sra SRR ids: ['SRR5423384.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_jjsksz_x SRR5423384.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]] SRR5423384 file size 703963 SRR5423384 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 SRR5423384 SRR5423384_1.fastq Input file: SRR5423384_1.fastq trimmed: SRR5423384-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 08:21:41 2025 >> started Wed Feb 12 08:21:43 2025 >> done (1.988s) 4000000 reads processed; of these: 94 ( 0.00%) short reads filtered out after trimming by size control 898 ( 0.02%) empty reads filtered out after trimming by size control 3999008 (99.98%) reads available; of these: 77938 ( 1.95%) trimmed reads available after processing 3921070 (98.05%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 17 0.00% 19 7 0.00% 20 8 0.00% 21 2 0.00% 22 4 0.00% 23 4 0.00% 24 5 0.00% 25 5 0.00% 26 6 0.00% 27 1 0.00% 28 4 0.00% 29 6 0.00% 30 5 0.00% 31 11 0.00% 32 12 0.00% 33 15 0.00% 34 18 0.00% 35 10 0.00% 36 35 0.00% 37 37 0.00% 38 48 0.00% 39 49 0.00% 40 83 0.00% 41 95 0.00% 42 124 0.00% 43 182 0.00% 44 257 0.01% 45 365 0.01% 46 491 0.01% 47 836 0.02% 48 1430 0.04% 49 3068 0.08% 50 9380 0.23% 51 61318 1.53% 52 3921070 98.05% 3999008 reads passed initial QC criterion=sequence-density sequence-density=0.38 sequence-density-rank=1 fanout-score=1.89 fanout-score-rank=28 prefix-density=0.35 prefix-fanout=1.9 sequence=TGGCACCGGCCCGTAATCCTTCCACTGCCAGGAGCGGGAGGTGATCGCTGCTCTGTGAGACCAGCCTCACGCTGTGCCCTCCCCTCTAGGAGCCACGACACC criterion=fanout-score sequence-density=0.01 sequence-density-rank=42 fanout-score=25.10 fanout-score-rank=1 prefix-density=0.07 prefix-fanout=1.8 sequence=TGGGCCGAGTTTAATTTAATTGCAATTCAATTACGAGAATGAACATTAATTAGTGGATTACAACGTATCCATTGCTTGGAATTCAAATTTAATCTCCTTCCATACTTCACAAGCAGCAGCTAGTTCAGGGCTCCATTTGCTAGCTTCACGGATAATTTCATTACCCTCACGAGCAAGATCACGTCCCTCATTACGAGCTTGTACACATGCTTCTAGAGCTACTCGATTAGCAACGGCACCGGGTGCATTTCCCCAAGGGTGCCCTAAAGTTCCTCCACCGAATTGTAGTACGGAATCATCTCCAAAGATCTCGGTCAGAGCAGGCATATGCCAAACGTGAATACCCCCCGAAGCCACGGGTAGAACACCCGGTAGAGAGACCCAATCTTGAGTGAAATAAATACCGCGGCTTCGATCTTTTTCAACAAAATCATCACGCAGTAAATCAACAAAACCCAAAGTTATGTCTCTTTCCCCTTCAAGTTTACCTACTACGGTACCAGAGTGAATA Started job on | Feb 12 08:21:56 Started mapping on | Feb 12 08:21:56 Finished on | Feb 12 08:22:01 Mapping speed, Million of reads per hour | 2879.29 Number of input reads | 3999008 Average input read length | 51 UNIQUE READS: Uniquely mapped reads number | 3006078 Uniquely mapped reads % | 75.17% Average mapped length | 51.80 Number of splices: Total | 257931 Number of splices: Annotated (sjdb) | 254633 Number of splices: GT/AG | 250189 Number of splices: GC/AG | 6219 Number of splices: AT/AC | 846 Number of splices: Non-canonical | 677 Mismatch rate per base, % | 0.35% Deletion rate per base | 0.01% Deletion average length | 2.29 Insertion rate per base | 0.00% Insertion average length | 1.32 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 841355 % of reads mapped to multiple loci | 21.04% Number of reads mapped to too many loci | 74708 % of reads mapped to too many loci | 1.87% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.80% % of reads unmapped: other | 0.12% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 151575 151575 151575 N_multimapping 841355 841355 841355 N_noFeature 455922 2935064 516018 N_ambiguous 22126 171 11051 UnstrandedReadsAssigned:2528030 PositiveStrandReadsAssigned:70843 NegativeStrandReadsAssigned:2479009 Dataset is classified negative stranded MeadianReadLen=52 20thPercentileLength=52 echo kmer=47 SRR5423384 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: SRR5423384-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 3,999,008 reads, 3,157,294 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,052 rounds 52401 SRR5423384.ke.tsv 34699 SRR5423384.se.tsv 87100 total ==> SRR5423384.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1919 77 10.6853 Potri.005G024800.1.v4.1 1035 936 2 0.569017 Potri.004G059700.1.v4.1 961 862 3 0.926798 Potri.007G009000.2.v4.1 1416 1317 0 0 Potri.003G141000.2.v4.1 2943 2844 71.3303 6.67906 Potri.016G087400.1.v4.1 270 171 9 14.0158 Potri.015G069301.1.v4.1 564 465 0 0 Potri.010G195200.1.v4.1 1773 1674 1 0.15908 Potri.012G127500.1.v4.1 977 878 5 1.51651 ==> SRR5423384.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 6 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 25 Potri.001G212900.v4.1 3 Potri.001G182400.v4.1 0 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 5 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 1 SRR5423384 completed mapping pipeline successfully