Starting /dee2/code/volunteer_pipeline.sh SRR5423489 current disk space = 3093167714304 free memory = 1466388088 SRR5423489 SRAfilesize 5dff9523e1d43d2eb5ec79630b32b8cd SRR5423489.sra SRR5423489.sra file validated SRR5423489 is single end SRR5423489 is conventional basespace SRR5423489 read1 length is 52 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR5423489_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 49 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 32.649 34.0 31.0 34.0 31.0 34.0 2 32.6995 34.0 31.0 34.0 31.0 34.0 3 32.73875 34.0 31.0 34.0 31.0 34.0 4 36.16375 37.0 37.0 37.0 35.0 37.0 5 36.18525 37.0 37.0 37.0 35.0 37.0 6 36.123 37.0 36.0 37.0 35.0 37.0 7 36.14425 37.0 36.0 37.0 35.0 37.0 8 36.1155 37.0 36.0 37.0 35.0 37.0 9 37.9685 39.0 38.0 39.0 35.0 39.0 10 37.85725 39.0 38.0 39.0 35.0 39.0 11 37.9755 39.0 38.0 39.0 35.0 39.0 12 37.924 39.0 38.0 39.0 35.0 39.0 13 37.7835 39.0 38.0 39.0 35.0 39.0 14 39.2685 41.0 39.0 41.0 36.0 41.0 15 39.31175 41.0 39.0 41.0 36.0 41.0 16 39.33425 41.0 39.0 41.0 36.0 41.0 17 39.266 40.0 39.0 41.0 36.0 41.0 18 39.153 40.0 39.0 41.0 36.0 41.0 19 39.14625 40.0 39.0 41.0 36.0 41.0 20 38.98475 40.0 39.0 41.0 35.0 41.0 21 39.0235 40.0 39.0 41.0 36.0 41.0 22 39.07725 40.0 39.0 41.0 36.0 41.0 23 39.01325 40.0 39.0 41.0 36.0 41.0 24 39.0635 40.0 39.0 41.0 36.0 41.0 25 39.131 40.0 39.0 41.0 36.0 41.0 26 39.0905 40.0 39.0 41.0 36.0 41.0 27 39.107 40.0 39.0 41.0 36.0 41.0 28 38.91125 40.0 39.0 41.0 35.0 41.0 29 38.82625 40.0 38.0 41.0 35.0 41.0 30 38.853 40.0 39.0 41.0 35.0 41.0 31 38.7695 40.0 38.0 41.0 35.0 41.0 32 38.5985 40.0 38.0 41.0 35.0 41.0 33 38.59675 40.0 38.0 41.0 34.0 41.0 34 38.64575 40.0 38.0 41.0 34.0 41.0 35 38.6415 40.0 38.0 41.0 35.0 41.0 36 38.51125 40.0 38.0 41.0 34.0 41.0 37 38.35525 40.0 38.0 41.0 34.0 41.0 38 38.3525 40.0 38.0 41.0 34.0 41.0 39 38.46675 40.0 38.0 41.0 34.0 41.0 40 38.38025 40.0 38.0 41.0 34.0 41.0 41 38.12925 40.0 38.0 41.0 33.0 41.0 42 38.1605 40.0 38.0 41.0 33.0 41.0 43 38.04025 40.0 38.0 41.0 33.0 41.0 44 37.8715 40.0 38.0 41.0 33.0 41.0 45 36.73 39.0 35.0 41.0 30.0 41.0 46 37.45975 40.0 37.0 41.0 31.0 41.0 47 37.467 40.0 37.0 41.0 32.0 41.0 48 37.6025 40.0 37.0 41.0 32.0 41.0 49 37.57225 40.0 37.0 41.0 32.0 41.0 50 37.2225 40.0 37.0 41.0 31.0 41.0 51 37.2425 40.0 36.0 41.0 31.0 41.0 52 35.72625 38.0 34.0 40.0 27.0 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 9 1.0 10 0.0 11 0.0 12 2.0 13 0.0 14 1.0 15 1.0 16 0.0 17 0.0 18 0.0 19 0.0 20 1.0 21 2.0 22 3.0 23 3.0 24 4.0 25 9.0 26 8.0 27 18.0 28 15.0 29 32.0 30 46.0 31 59.0 32 77.0 33 87.0 34 130.0 35 183.0 36 256.0 37 366.0 38 698.0 39 1993.0 40 5.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 48.38467317806161 13.498622589531681 5.209115952917606 32.90758827948911 2 22.2 15.925 34.4 27.474999999999998 3 18.125 22.225 27.3 32.35 4 24.025 28.849999999999998 24.125 23.0 5 23.825 33.875 22.775000000000002 19.525000000000002 6 19.475 32.4 25.05 23.075000000000003 7 16.0 19.525000000000002 43.425000000000004 21.05 8 17.325 20.65 30.925000000000004 31.1 9 18.6 20.5 31.25 29.65 10 20.599999999999998 35.975 22.900000000000002 20.525 11 24.375 24.575 20.925 30.125 12 22.650000000000002 21.025 25.75 30.575000000000003 13 20.424999999999997 25.674999999999997 28.549999999999997 25.35 14 21.5 24.95 27.375 26.174999999999997 15 20.95 25.15 27.325 26.575 16 23.275000000000002 25.174999999999997 24.825 26.724999999999998 17 23.425 24.0 26.6 25.974999999999998 18 23.65 24.725 25.124999999999996 26.5 19 23.025000000000002 25.900000000000002 25.124999999999996 25.95 20 23.05 25.924999999999997 26.025 25.0 21 22.650000000000002 23.95 27.05 26.35 22 23.025000000000002 24.275 26.1 26.6 23 22.43060765191298 26.131532883220803 25.70642660665166 25.731432858214554 24 20.575 24.2 27.500000000000004 27.725 25 22.5 25.05 26.200000000000003 26.25 26 21.6 23.400000000000002 27.800000000000004 27.200000000000003 27 21.7 24.099999999999998 26.650000000000002 27.55 28 22.6 25.85 24.675 26.875 29 21.4 26.075 25.1 27.425 30 23.75 24.2 25.174999999999997 26.875 31 22.7 24.45 26.424999999999997 26.424999999999997 32 22.5 24.55 26.724999999999998 26.224999999999998 33 22.650000000000002 23.75 26.75 26.85 34 21.4 26.025 24.875 27.700000000000003 35 22.5 24.4 25.775 27.325 36 21.9 25.15 25.95 27.0 37 23.125 25.124999999999996 25.25 26.5 38 21.825 23.45 26.75 27.975 39 22.525000000000002 24.525 26.224999999999998 26.724999999999998 40 22.825 24.8 25.2 27.175 41 22.8 24.0 26.224999999999998 26.974999999999998 42 20.849999999999998 24.425 26.375 28.349999999999998 43 22.875 24.675 25.85 26.6 44 23.225 23.225 26.974999999999998 26.575 45 23.075000000000003 23.825 26.150000000000002 26.950000000000003 46 22.35 25.174999999999997 26.400000000000002 26.075 47 24.25 23.625 26.025 26.1 48 22.255563890972745 24.681170292573142 25.03125781445361 28.032008002000502 49 23.775 24.65 24.625 26.950000000000003 50 22.55563890972743 23.93098274568642 26.6816704176044 26.831707926981746 51 20.655163790947736 24.681170292573142 26.281570392598148 28.382095523880967 52 23.75 23.549999999999997 26.05 26.650000000000002 >>END_MODULE >>Per sequence GC content pass #GC Content Count 0 0.0 1 0.0 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.5 10 1.0 11 0.5 12 0.0 13 0.0 14 0.5 15 1.0 16 0.5 17 0.0 18 1.0 19 2.0 20 1.5 21 1.0 22 3.5 23 6.0 24 5.0 25 4.0 26 6.5 27 9.0 28 16.0 29 23.0 30 27.5 31 32.0 32 47.5 33 63.0 34 65.0 35 67.0 36 85.0 37 103.0 38 125.5 39 167.0 40 186.0 41 205.0 42 224.0 43 258.0 44 292.0 45 336.5 46 381.0 47 379.0 48 377.0 49 373.0 50 369.0 51 358.5 52 348.0 53 362.0 54 376.0 55 349.5 56 323.0 57 264.0 58 205.0 59 181.5 60 158.0 61 132.0 62 106.0 63 84.0 64 51.5 65 41.0 66 34.0 67 27.0 68 23.5 69 20.0 70 17.5 71 15.0 72 12.0 73 9.0 74 10.5 75 12.0 76 7.0 77 2.0 78 3.5 79 5.0 80 2.5 81 0.0 82 0.5 83 1.0 84 0.5 85 0.0 86 0.0 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 0.025 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 0.025 49 0.0 50 0.025 51 0.025 52 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 52 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 96.175 #Duplication Level Percentage of deduplicated Percentage of total 1 96.77670912399272 93.075 2 2.6514166883285677 5.1 3 0.4419027813880946 1.275 4 0.07798284377436965 0.3 5 0.05198856251624642 0.25 6 0.0 0.0 7 0.0 0.0 8 0.0 0.0 9 0.0 0.0 >10 0.0 0.0 >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 GCCGACTTCCCTTGCCTACATTGTTCCATCGACCAGAGGCTGTTCACCTTGG 5 0.125 No Hit CGGCAATCGGACGGCGGGCGCACGCGTCGCATCTAGCCCGGATTCTGACTTA 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 0.025 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 SRR5423489.sra Written 200000 spots for SRR5423489.sra Read 200000 spots for SRR5423489.sra Written 200000 spots for SRR5423489.sra Read 200000 spots for SRR5423489.sra Written 200000 spots for SRR5423489.sra Read 200000 spots for SRR5423489.sra Written 200000 spots for SRR5423489.sra Read 200000 spots for SRR5423489.sra Written 200000 spots for SRR5423489.sra Read 200000 spots for SRR5423489.sra Written 200000 spots for SRR5423489.sra Read 200000 spots for SRR5423489.sra Written 200000 spots for SRR5423489.sra Read 200000 spots for SRR5423489.sra Written 200000 spots for SRR5423489.sra Read 200000 spots for SRR5423489.sra Written 200000 spots for SRR5423489.sra Read 200000 spots for SRR5423489.sra Written 200000 spots for SRR5423489.sra Read 200000 spots for SRR5423489.sra Written 200000 spots for SRR5423489.sra Read 200000 spots for SRR5423489.sra Written 200000 spots for SRR5423489.sra Read 200000 spots for SRR5423489.sra Written 200000 spots for SRR5423489.sra Read 200000 spots for SRR5423489.sra Written 200000 spots for SRR5423489.sra Read 200000 spots for SRR5423489.sra Written 200000 spots for SRR5423489.sra Read 200000 spots for SRR5423489.sra Written 200000 spots for SRR5423489.sra Read 200000 spots for SRR5423489.sra Written 200000 spots for SRR5423489.sra Read 200000 spots for SRR5423489.sra Written 200000 spots for SRR5423489.sra Read 200000 spots for SRR5423489.sra Written 200000 spots for SRR5423489.sra Read 200000 spots for SRR5423489.sra Written 200000 spots for SRR5423489.sra SRR ids: ['SRR5423489.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_uy4msjm9 SRR5423489.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]] SRR5423489 file size 703963 SRR5423489 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 SRR5423489 SRR5423489_1.fastq Input file: SRR5423489_1.fastq trimmed: SRR5423489-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 11:22:34 2025 >> started Thu Feb 13 11:22:36 2025 >> done (1.876s) 4000000 reads processed; of these: 197 ( 0.00%) short reads filtered out after trimming by size control 191 ( 0.00%) empty reads filtered out after trimming by size control 3999612 (99.99%) reads available; of these: 68995 ( 1.73%) trimmed reads available after processing 3930617 (98.27%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 6 0.00% 19 6 0.00% 20 9 0.00% 21 0 0.00% 22 1 0.00% 23 2 0.00% 24 3 0.00% 25 10 0.00% 26 3 0.00% 27 4 0.00% 28 16 0.00% 29 15 0.00% 30 15 0.00% 31 25 0.00% 32 44 0.00% 33 45 0.00% 34 50 0.00% 35 49 0.00% 36 65 0.00% 37 97 0.00% 38 94 0.00% 39 100 0.00% 40 154 0.00% 41 220 0.01% 42 215 0.01% 43 238 0.01% 44 312 0.01% 45 728 0.02% 46 1089 0.03% 47 1139 0.03% 48 1540 0.04% 49 3105 0.08% 50 7694 0.19% 51 51902 1.30% 52 3930617 98.27% 3999612 reads passed initial QC criterion=sequence-density sequence-density=0.29 sequence-density-rank=1 fanout-score=1.99 fanout-score-rank=29 prefix-density=0.24 prefix-fanout=2.0 sequence=TTCCACATAGTCCAGTAGCGTCCATCATAGTACCCTGGGGACTGGTGGTGCTCGCGGTAGACCCAACCTTTCTCCAACTCGAATTCCAAGCAAGGAACCCACTT criterion=fanout-score sequence-density=0.01 sequence-density-rank=31 fanout-score=13.57 fanout-score-rank=1 prefix-density=0.04 prefix-fanout=3.5 sequence=CTTGGGTCCAAAAAGAGGGGCAGCGCCCCGCCTCCGATTCACGGAATAAGTAAAATAACGTTAAAAGTAGTGGTATTTCACCTTCGCCGAAGCTCCCACTTATCCTACACCTCTCAAGTCATTTCACAAAGTCGGACTAGAGTCAAGCTCAACAGGGTCTTCTTTCCCCGCTGATTCCGCCAAGCCCGTTCCCTTGGCTGTGGTTTCGCTGGATAGTAGACAGGGACAGTGGGAATCTCGTTAATCCATTCATGCGCGTCACTAATTAGATGACGAGGCATTTGGCTACCTTAAGAGAGTCATAGTTACTCCCGCCGTTTACCCGCGCTTGGTTGAATTTCTTCACTTTGACATTCAGAGCACTGGGCAGAAATCACATTGCGTGAGCATCCGCAGGGACCATCGCAATGCTTTGTTTTAATTAAACAGTCGGATTCCCCTTGTCCGTACCAGTTCTGAGTCGACTGTTCGACGCCCGGGGAAGGCCCCCGAAGGG Started job on | Feb 13 11:23:47 Started mapping on | Feb 13 11:23:47 Finished on | Feb 13 11:23:53 Mapping speed, Million of reads per hour | 2399.77 Number of input reads | 3999612 Average input read length | 51 UNIQUE READS: Uniquely mapped reads number | 3204871 Uniquely mapped reads % | 80.13% Average mapped length | 51.85 Number of splices: Total | 398722 Number of splices: Annotated (sjdb) | 394398 Number of splices: GT/AG | 392615 Number of splices: GC/AG | 5480 Number of splices: AT/AC | 229 Number of splices: Non-canonical | 398 Mismatch rate per base, % | 0.26% Deletion rate per base | 0.01% Deletion average length | 1.61 Insertion rate per base | 0.00% Insertion average length | 1.29 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 329372 % of reads mapped to multiple loci | 8.24% Number of reads mapped to too many loci | 441454 % of reads mapped to too many loci | 11.04% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 0.59% % of reads unmapped: other | 0.00% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 465369 465369 465369 N_multimapping 329372 329372 329372 N_noFeature 194732 3166405 206907 N_ambiguous 39649 25 13346 UnstrandedReadsAssigned:2970490 PositiveStrandReadsAssigned:38441 NegativeStrandReadsAssigned:2984618 Dataset is classified negative stranded MeadianReadLen=52 20thPercentileLength=52 echo kmer=47 SRR5423489 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: SRR5423489-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 3,999,612 reads, 3,466,510 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,064 rounds 52401 SRR5423489.ke.tsv 34699 SRR5423489.se.tsv 87100 total ==> SRR5423489.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1919 65 11.3164 Potri.005G024800.1.v4.1 1035 936 6 2.14164 Potri.004G059700.1.v4.1 961 862 7 2.71307 Potri.007G009000.2.v4.1 1416 1317 0 0 Potri.003G141000.2.v4.1 2943 2844 38.6797 4.54385 Potri.016G087400.1.v4.1 270 171 95 185.608 Potri.015G069301.1.v4.1 564 465 0 0 Potri.010G195200.1.v4.1 1773 1674 0 0 Potri.012G127500.1.v4.1 977 878 111 42.2375 ==> SRR5423489.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 1 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 62 Potri.001G212900.v4.1 80 Potri.001G182400.v4.1 0 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 8 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 0 SRR5423489 completed mapping pipeline successfully