Starting /dee2/code/volunteer_pipeline.sh SRR5423488 current disk space = 3093089308672 free memory = 1562241744 SRR5423488 SRAfilesize 8c889b5e43c7e4eb9701bc6788d28b15 SRR5423488.sra SRR5423488.sra file validated SRR5423488 is single end SRR5423488 is conventional basespace SRR5423488 read1 length is 52 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR5423488_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 32.444 34.0 31.0 34.0 31.0 34.0 2 32.54125 34.0 31.0 34.0 31.0 34.0 3 32.59475 34.0 31.0 34.0 31.0 34.0 4 35.97175 37.0 35.0 37.0 35.0 37.0 5 35.9965 37.0 35.0 37.0 35.0 37.0 6 35.9285 37.0 35.0 37.0 35.0 37.0 7 35.9865 37.0 35.0 37.0 35.0 37.0 8 36.055 37.0 35.0 37.0 35.0 37.0 9 37.78775 39.0 38.0 39.0 35.0 39.0 10 37.50675 39.0 37.0 39.0 35.0 39.0 11 37.56725 39.0 37.0 39.0 35.0 39.0 12 37.611 39.0 37.0 39.0 35.0 39.0 13 37.6005 39.0 37.0 39.0 35.0 39.0 14 38.88825 40.0 38.0 41.0 35.0 41.0 15 39.0235 40.0 38.0 41.0 36.0 41.0 16 39.00925 40.0 38.0 41.0 36.0 41.0 17 38.82925 40.0 38.0 41.0 35.0 41.0 18 38.816 40.0 38.0 41.0 35.0 41.0 19 38.887 40.0 39.0 41.0 35.0 41.0 20 38.95325 40.0 38.0 41.0 35.0 41.0 21 38.8675 40.0 38.0 41.0 35.0 41.0 22 38.85625 40.0 38.0 41.0 35.0 41.0 23 38.94975 40.0 38.0 41.0 36.0 41.0 24 38.87025 40.0 38.0 41.0 35.0 41.0 25 38.8375 40.0 38.0 41.0 35.0 41.0 26 38.7445 40.0 38.0 41.0 35.0 41.0 27 38.6235 40.0 38.0 41.0 35.0 41.0 28 38.7815 40.0 38.0 41.0 35.0 41.0 29 38.7285 40.0 38.0 41.0 35.0 41.0 30 38.6065 40.0 38.0 41.0 34.0 41.0 31 38.6845 40.0 38.0 41.0 35.0 41.0 32 38.683 40.0 38.0 41.0 35.0 41.0 33 38.60575 40.0 38.0 41.0 34.0 41.0 34 38.44125 40.0 38.0 41.0 34.0 41.0 35 38.3485 40.0 38.0 41.0 34.0 41.0 36 38.44875 40.0 38.0 41.0 34.0 41.0 37 38.42975 40.0 38.0 41.0 34.0 41.0 38 38.2965 40.0 38.0 41.0 33.0 41.0 39 38.1175 40.0 38.0 41.0 33.0 41.0 40 37.8935 40.0 37.0 41.0 33.0 41.0 41 38.01175 40.0 37.0 41.0 33.0 41.0 42 37.82975 40.0 37.0 41.0 33.0 41.0 43 37.80175 40.0 37.0 41.0 33.0 41.0 44 37.62375 40.0 37.0 41.0 32.0 41.0 45 37.6685 40.0 37.0 41.0 32.0 41.0 46 37.51975 40.0 37.0 41.0 32.0 41.0 47 37.64975 40.0 37.0 41.0 33.0 41.0 48 37.504 40.0 37.0 41.0 32.0 41.0 49 37.24875 40.0 36.0 41.0 31.0 41.0 50 37.0825 39.0 36.0 41.0 30.0 41.0 51 37.28375 39.0 36.0 41.0 31.0 41.0 52 36.04725 38.0 34.0 40.0 28.0 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 17 1.0 18 0.0 19 2.0 20 1.0 21 3.0 22 3.0 23 4.0 24 7.0 25 10.0 26 10.0 27 20.0 28 23.0 29 50.0 30 40.0 31 42.0 32 97.0 33 101.0 34 154.0 35 171.0 36 275.0 37 415.0 38 724.0 39 1839.0 40 8.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 47.934918648310386 13.74217772215269 4.730913642052566 33.591989987484354 2 22.025 16.3 34.075 27.6 3 18.55 21.349999999999998 27.950000000000003 32.15 4 23.925 28.375 23.375 24.325 5 24.325 33.15 22.0 20.525 6 21.525 31.374999999999996 21.95 25.15 7 16.7 21.625 40.825 20.849999999999998 8 18.35 20.474999999999998 30.0 31.175000000000004 9 18.45 19.900000000000002 32.1 29.549999999999997 10 19.45 36.5 23.075000000000003 20.974999999999998 11 25.624999999999996 25.35 19.475 29.549999999999997 12 23.799999999999997 20.8 25.7 29.7 13 20.05 25.775 28.875 25.3 14 21.3 25.374999999999996 27.224999999999998 26.1 15 21.625 23.75 27.1 27.525 16 23.225 24.9 24.775 27.1 17 22.45 24.7 25.85 27.0 18 22.125 24.775 26.275 26.825 19 22.775000000000002 25.324999999999996 26.375 25.525 20 23.3 25.275 25.474999999999998 25.95 21 22.725 24.625 25.624999999999996 27.025 22 22.175 24.7 25.55 27.575 23 22.825 24.6 25.575 27.0 24 21.9 25.8 25.974999999999998 26.325 25 22.825 24.725 25.324999999999996 27.125 26 22.95 23.9 26.025 27.125 27 21.775 24.175 26.200000000000003 27.85 28 22.425 24.45 26.700000000000003 26.424999999999997 29 21.375 23.925 27.950000000000003 26.75 30 21.925 24.075 27.400000000000002 26.6 31 22.925 24.099999999999998 25.35 27.625 32 23.5 24.525 26.075 25.900000000000002 33 22.1 24.05 26.325 27.525 34 21.45 25.324999999999996 25.85 27.375 35 21.9 25.224999999999998 26.6 26.275 36 22.275 25.374999999999996 25.674999999999997 26.674999999999997 37 23.5 25.05 25.074999999999996 26.375 38 22.775000000000002 24.224999999999998 25.624999999999996 27.375 39 21.875 24.0 25.8 28.325 40 23.150000000000002 25.974999999999998 24.625 26.25 41 22.825 25.15 24.8 27.224999999999998 42 22.775000000000002 23.925 26.35 26.950000000000003 43 22.675 24.6 25.0 27.725 44 21.95 23.775 26.900000000000002 27.375 45 23.575 23.575 24.85 28.000000000000004 46 22.73068267066767 25.656414103525883 24.756189047261813 26.85671417854464 47 22.980745186296573 24.5311327831958 25.056264066016503 27.431857964491122 48 21.930482620655166 24.356089022255563 25.28132033008252 28.432108027006752 49 23.25581395348837 24.8062015503876 25.10627656914228 26.831707926981746 50 22.95573893473368 24.981245311327832 26.281570392598148 25.78144536134033 51 22.650000000000002 24.025 25.724999999999998 27.6 52 22.775000000000002 23.425 25.525 28.275 >>END_MODULE >>Per sequence GC content warn #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 0.0 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 2.0 19 4.0 20 4.0 21 4.0 22 4.0 23 4.0 24 5.0 25 6.0 26 7.5 27 9.0 28 15.5 29 22.0 30 25.5 31 29.0 32 38.5 33 48.0 34 56.5 35 65.0 36 89.5 37 114.0 38 132.0 39 148.5 40 147.0 41 198.0 42 249.0 43 263.0 44 277.0 45 304.5 46 332.0 47 348.5 48 365.0 49 375.5 50 386.0 51 402.5 52 419.0 53 384.0 54 349.0 55 314.5 56 280.0 57 250.5 58 221.0 59 198.0 60 175.0 61 148.0 62 121.0 63 94.5 64 61.0 65 54.0 66 39.5 67 25.0 68 26.5 69 28.0 70 22.5 71 17.0 72 15.0 73 13.0 74 10.0 75 7.0 76 5.5 77 4.0 78 5.0 79 6.0 80 3.5 81 1.0 82 1.0 83 1.0 84 0.5 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 0.125 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 0.025 48 0.025 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 96.72500000000001 #Duplication Level Percentage of deduplicated Percentage of total 1 97.33781338847247 94.15 2 2.145257172395968 4.15 3 0.36185060739209096 1.05 4 0.10338588782631171 0.4 5 0.051692943913155855 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 GTCGCGTATTTAAGTCGTCTGCAAAGGATTCTACCCGCCGCTCGGTGGGAAT 5 0.125 No Hit GATAGAACTCGCACCGAGCTCCAGCTATCCTGAGGGAAACTTCGGAGGGAAC 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 SRR5423488.sra Written 200000 spots for SRR5423488.sra Read 200000 spots for SRR5423488.sra Written 200000 spots for SRR5423488.sra Read 200000 spots for SRR5423488.sra Written 200000 spots for SRR5423488.sra Read 200000 spots for SRR5423488.sra Written 200000 spots for SRR5423488.sra Read 200000 spots for SRR5423488.sra Written 200000 spots for SRR5423488.sra Read 200000 spots for SRR5423488.sra Written 200000 spots for SRR5423488.sra Read 200000 spots for SRR5423488.sra Written 200000 spots for SRR5423488.sra Read 200000 spots for SRR5423488.sra Written 200000 spots for SRR5423488.sra Read 200000 spots for SRR5423488.sra Written 200000 spots for SRR5423488.sra Read 200000 spots for SRR5423488.sra Written 200000 spots for SRR5423488.sra Read 200000 spots for SRR5423488.sra Written 200000 spots for SRR5423488.sra Read 200000 spots for SRR5423488.sra Written 200000 spots for SRR5423488.sra Read 200000 spots for SRR5423488.sra Written 200000 spots for SRR5423488.sra Read 200000 spots for SRR5423488.sra Written 200000 spots for SRR5423488.sra Read 200000 spots for SRR5423488.sra Written 200000 spots for SRR5423488.sra Read 200000 spots for SRR5423488.sra Written 200000 spots for SRR5423488.sra Read 200000 spots for SRR5423488.sra Written 200000 spots for SRR5423488.sra Read 200000 spots for SRR5423488.sra Written 200000 spots for SRR5423488.sra Read 200000 spots for SRR5423488.sra Written 200000 spots for SRR5423488.sra Read 200000 spots for SRR5423488.sra Written 200000 spots for SRR5423488.sra SRR ids: ['SRR5423488.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_27lcx2jl SRR5423488.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]] SRR5423488 file size 703985 SRR5423488 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 SRR5423488 SRR5423488_1.fastq Input file: SRR5423488_1.fastq trimmed: SRR5423488-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 11:05:45 2025 >> started Thu Feb 13 11:05:47 2025 >> done (2.021s) 4000000 reads processed; of these: 225 ( 0.01%) short reads filtered out after trimming by size control 246 ( 0.01%) empty reads filtered out after trimming by size control 3999529 (99.99%) reads available; of these: 71904 ( 1.80%) trimmed reads available after processing 3927625 (98.20%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 8 0.00% 19 7 0.00% 20 0 0.00% 21 0 0.00% 22 3 0.00% 23 4 0.00% 24 6 0.00% 25 7 0.00% 26 10 0.00% 27 16 0.00% 28 24 0.00% 29 33 0.00% 30 25 0.00% 31 30 0.00% 32 55 0.00% 33 55 0.00% 34 45 0.00% 35 35 0.00% 36 67 0.00% 37 75 0.00% 38 87 0.00% 39 111 0.00% 40 131 0.00% 41 168 0.00% 42 170 0.00% 43 253 0.01% 44 321 0.01% 45 687 0.02% 46 962 0.02% 47 1034 0.03% 48 1466 0.04% 49 3154 0.08% 50 7730 0.19% 51 55125 1.38% 52 3927625 98.20% 3999529 reads passed initial QC criterion=sequence-density sequence-density=0.29 sequence-density-rank=1 fanout-score=1.99 fanout-score-rank=24 prefix-density=0.23 prefix-fanout=2.0 sequence=TTCCACATAGTCCAGTAGCGTCCATCATAGTACCCTGGGGACTGGTGGTGCTCGCGGTAGACCCAACCTTTCTCCAACTCGAATTCCAAGCAAGGAACCCACTT criterion=fanout-score sequence-density=0.01 sequence-density-rank=30 fanout-score=13.30 fanout-score-rank=1 prefix-density=0.04 prefix-fanout=3.4 sequence=CTTGGGTCCAAAAAGAGGGGCAGCGCCCCGCCTCCGATTCACGGAATAAGTAAAATAACGTTAAAAGTAGTGGTATTTCACCTTCGCCGAAGCTCCCACTTATCCTACACCTCTCAAGTCATTTCACAAAGTCGGACTAGAGTCAAGCTCAACAGGGTCTTCTTTCCCCGCTGATTCCGCCAAGCCCGTTCCCTTGGCTGTGGTTTCGCTGGATAGTAGACAGGGACAGTGGGAATCTCGTTAATCCATTCATGCGCGTCACTAATTAGATGACGAGGCATTTGGCTACCTTAAGAGAGTCATAGTTACTCCCGCCGTTTACCCGCGCTTGGTTGAATTTCTTCACTTTGACATTCAGAGCACTGGGCAGAAATCACATTGCGTGAGCATCCGCAGGGACCATCGCAATGCTTTGTTTTAATTAAACAGTCGGATTCCCCTTGTCCGTACCAGTTCTGAGTCGACTGTTCGACGCCCGGGGAAGGCCCCCGAAGGG Started job on | Feb 13 11:06:01 Started mapping on | Feb 13 11:06:02 Finished on | Feb 13 11:06:08 Mapping speed, Million of reads per hour | 2399.72 Number of input reads | 3999529 Average input read length | 51 UNIQUE READS: Uniquely mapped reads number | 3204895 Uniquely mapped reads % | 80.13% Average mapped length | 51.85 Number of splices: Total | 398698 Number of splices: Annotated (sjdb) | 394386 Number of splices: GT/AG | 392409 Number of splices: GC/AG | 5688 Number of splices: AT/AC | 224 Number of splices: Non-canonical | 377 Mismatch rate per base, % | 0.30% Deletion rate per base | 0.01% Deletion average length | 1.59 Insertion rate per base | 0.00% Insertion average length | 1.31 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 329871 % of reads mapped to multiple loci | 8.25% Number of reads mapped to too many loci | 441196 % of reads mapped to too many loci | 11.03% 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 464763 464763 464763 N_multimapping 329871 329871 329871 N_noFeature 195106 3166495 207174 N_ambiguous 39311 24 12970 UnstrandedReadsAssigned:2970478 PositiveStrandReadsAssigned:38376 NegativeStrandReadsAssigned:2984751 Dataset is classified negative stranded MeadianReadLen=52 20thPercentileLength=52 echo kmer=47 SRR5423488 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: SRR5423488-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 3,999,529 reads, 3,464,739 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,058 rounds 52401 SRR5423488.ke.tsv 34699 SRR5423488.se.tsv 87100 total ==> SRR5423488.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1919 50 8.70941 Potri.005G024800.1.v4.1 1035 936 0 0 Potri.004G059700.1.v4.1 961 862 2 0.775562 Potri.007G009000.2.v4.1 1416 1317 0 0 Potri.003G141000.2.v4.1 2943 2844 27.468 3.22842 Potri.016G087400.1.v4.1 270 171 104 203.297 Potri.015G069301.1.v4.1 564 465 0 0 Potri.010G195200.1.v4.1 1773 1674 1 0.199682 Potri.012G127500.1.v4.1 977 878 121 46.0665 ==> SRR5423488.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 3 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 76 Potri.001G212900.v4.1 77 Potri.001G182400.v4.1 0 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 6 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 1 SRR5423488 completed mapping pipeline successfully