Starting /dee2/code/volunteer_pipeline.sh SRR7865988 current disk space = 1523548471296 free memory = 1568543032 SRR7865988 SRAfilesize decff8d52977f8b55870e536e0e1613e SRR7865988.sra SRR7865988.sra file validated SRR7865988 is single end SRR7865988 is conventional basespace SRR7865988 read1 length is 50 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR7865988_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 50 %GC 52 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 32.73475 34.0 31.0 34.0 31.0 34.0 2 31.47525 34.0 31.0 34.0 31.0 34.0 3 32.25975 34.0 31.0 34.0 31.0 34.0 4 36.22225 37.0 37.0 37.0 35.0 37.0 5 36.34275 37.0 37.0 37.0 35.0 37.0 6 36.25875 37.0 37.0 37.0 35.0 37.0 7 36.1995 37.0 37.0 37.0 35.0 37.0 8 36.21775 37.0 37.0 37.0 35.0 37.0 9 37.976 39.0 39.0 39.0 35.0 39.0 10 38.146 39.0 39.0 39.0 37.0 39.0 11 38.185 39.0 39.0 39.0 37.0 39.0 12 38.1145 39.0 39.0 39.0 37.0 39.0 13 38.125 39.0 39.0 39.0 37.0 39.0 14 39.681 41.0 40.0 41.0 37.0 41.0 15 39.644 41.0 40.0 41.0 37.0 41.0 16 39.58075 41.0 40.0 41.0 37.0 41.0 17 39.48975 41.0 39.0 41.0 37.0 41.0 18 39.5025 41.0 40.0 41.0 36.0 41.0 19 39.473 41.0 39.0 41.0 36.0 41.0 20 39.486 41.0 39.0 41.0 37.0 41.0 21 39.33575 41.0 39.0 41.0 36.0 41.0 22 39.2005 41.0 39.0 41.0 36.0 41.0 23 39.133 40.0 39.0 41.0 36.0 41.0 24 39.1165 40.0 39.0 41.0 36.0 41.0 25 38.957 40.0 39.0 41.0 35.0 41.0 26 38.85325 40.0 38.0 41.0 35.0 41.0 27 38.707 40.0 38.0 41.0 35.0 41.0 28 38.4055 40.0 38.0 41.0 34.0 41.0 29 38.30925 40.0 38.0 41.0 34.0 41.0 30 37.62375 40.0 38.0 41.0 32.0 41.0 31 37.867 40.0 38.0 41.0 33.0 41.0 32 37.17875 40.0 37.0 41.0 31.0 41.0 33 37.438 40.0 37.0 41.0 32.0 41.0 34 37.193 40.0 37.0 41.0 31.0 41.0 35 37.546 40.0 37.0 41.0 33.0 41.0 36 37.4535 40.0 37.0 41.0 32.0 41.0 37 37.69 40.0 38.0 41.0 33.0 41.0 38 37.793 40.0 38.0 41.0 33.0 41.0 39 37.79225 40.0 38.0 41.0 33.0 41.0 40 37.605 40.0 37.0 41.0 33.0 41.0 41 37.558 40.0 37.0 41.0 33.0 41.0 42 37.4955 40.0 37.0 41.0 33.0 41.0 43 37.34725 40.0 37.0 41.0 32.0 41.0 44 37.1455 40.0 37.0 41.0 32.0 41.0 45 36.91025 40.0 36.0 41.0 32.0 41.0 46 36.61025 40.0 35.0 41.0 31.0 41.0 47 36.375 40.0 35.0 41.0 31.0 41.0 48 36.2905 39.0 35.0 41.0 31.0 41.0 49 36.13975 39.0 35.0 41.0 31.0 41.0 50 35.781 39.0 35.0 41.0 30.0 41.0 >>END_MODULE >>Per tile sequence quality pass #Tile Base Mean 1101 1 0.0 1101 2 0.0 1101 3 0.0 1101 4 0.0 1101 5 0.0 1101 6 0.0 1101 7 0.0 1101 8 0.0 1101 9 0.0 1101 10 0.0 1101 11 0.0 1101 12 0.0 1101 13 0.0 1101 14 0.0 1101 15 0.0 1101 16 0.0 1101 17 0.0 1101 18 0.0 1101 19 0.0 1101 20 0.0 1101 21 0.0 1101 22 0.0 1101 23 0.0 1101 24 0.0 1101 25 0.0 1101 26 0.0 1101 27 0.0 1101 28 0.0 1101 29 0.0 1101 30 0.0 1101 31 0.0 1101 32 0.0 1101 33 0.0 1101 34 0.0 1101 35 0.0 1101 36 0.0 1101 37 0.0 1101 38 0.0 1101 39 0.0 1101 40 0.0 1101 41 0.0 1101 42 0.0 1101 43 0.0 1101 44 0.0 1101 45 0.0 1101 46 0.0 1101 47 0.0 1101 48 0.0 1101 49 0.0 1101 50 0.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 1.0 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 1.0 13 1.0 14 0.0 15 0.0 16 4.0 17 7.0 18 6.0 19 5.0 20 9.0 21 12.0 22 13.0 23 11.0 24 5.0 25 15.0 26 23.0 27 20.0 28 29.0 29 27.0 30 35.0 31 58.0 32 67.0 33 87.0 34 120.0 35 152.0 36 249.0 37 420.0 38 754.0 39 1869.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 29.37937937937938 11.06106106106106 11.26126126126126 48.2982982982983 2 25.925925925925924 16.837404780667192 28.710270554242186 28.526398739164698 3 26.78169542385596 18.479619904976243 22.255563890972745 32.483120780195044 4 30.8 23.225 17.65 28.325 5 31.424999999999997 26.474999999999998 18.95 23.150000000000002 6 26.525 31.75 19.775000000000002 21.95 7 22.95 20.849999999999998 35.025 21.175 8 23.375 21.95 27.250000000000004 27.425 9 23.025000000000002 21.075 30.125 25.775 10 24.275 33.475 22.6 19.650000000000002 11 27.325 24.6 19.725 28.349999999999998 12 24.525 21.8 24.675 28.999999999999996 13 23.525 24.7 26.450000000000003 25.324999999999996 14 25.324999999999996 25.525 23.599999999999998 25.55 15 26.35 23.45 22.75 27.450000000000003 16 24.9 24.5 24.05 26.55 17 24.5 25.074999999999996 24.8 25.624999999999996 18 24.625 25.124999999999996 23.849999999999998 26.400000000000002 19 26.075 23.825 25.025 25.074999999999996 20 26.75 23.3 24.099999999999998 25.85 21 25.35 24.75 24.3 25.6 22 26.700000000000003 24.224999999999998 24.575 24.5 23 27.35 23.799999999999997 24.2 24.65 24 23.9 24.775 24.6 26.724999999999998 25 25.474999999999998 23.825 24.5 26.200000000000003 26 26.325 24.775 23.575 25.324999999999996 27 27.425 24.325 22.45 25.8 28 27.075 24.125 22.6 26.200000000000003 29 26.625 24.075 23.125 26.174999999999997 30 25.95 24.25 24.2 25.6 31 27.125 23.25 23.674999999999997 25.95 32 26.25 24.4 23.200000000000003 26.150000000000002 33 25.35 23.525 24.45 26.674999999999997 34 27.075 23.175 22.975 26.775 35 27.575 22.925 23.25 26.25 36 25.55 23.375 24.474999999999998 26.6 37 25.575 23.275000000000002 24.275 26.875 38 26.174999999999997 24.15 23.400000000000002 26.275 39 25.650000000000002 23.75 23.375 27.224999999999998 40 25.3 23.825 23.674999999999997 27.200000000000003 41 26.325 23.549999999999997 23.575 26.55 42 26.3 23.95 22.875 26.875 43 25.15 23.925 23.674999999999997 27.250000000000004 44 26.075 23.200000000000003 24.55 26.174999999999997 45 25.15 24.8 23.674999999999997 26.375 46 27.025 23.35 23.200000000000003 26.424999999999997 47 26.924999999999997 22.625 23.125 27.325 48 27.950000000000003 23.7 23.025000000000002 25.324999999999996 49 25.55 22.900000000000002 24.9 26.650000000000002 50 25.15 24.2 23.25 27.400000000000002 >>END_MODULE >>Per sequence GC content fail #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 0.5 12 1.0 13 0.5 14 0.0 15 0.0 16 0.0 17 0.0 18 0.0 19 0.5 20 1.0 21 1.5 22 2.0 23 1.0 24 0.0 25 2.0 26 4.0 27 5.5 28 7.0 29 10.0 30 13.0 31 16.5 32 20.0 33 39.5 34 59.0 35 75.5 36 92.0 37 112.0 38 132.0 39 160.0 40 188.0 41 218.5 42 249.0 43 262.0 44 275.0 45 289.5 46 304.0 47 310.5 48 317.0 49 315.5 50 314.0 51 280.5 52 247.0 53 249.5 54 252.0 55 241.0 56 230.0 57 227.0 58 224.0 59 212.0 60 200.0 61 188.0 62 176.0 63 142.0 64 108.0 65 107.0 66 106.0 67 114.5 68 123.0 69 111.5 70 100.0 71 85.5 72 71.0 73 67.5 74 64.0 75 56.5 76 49.0 77 40.0 78 31.0 79 24.5 80 18.0 81 17.0 82 16.0 83 10.0 84 4.0 85 3.0 86 2.0 87 1.0 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 0.1 2 4.825 3 0.025 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 >>END_MODULE >>Sequence Length Distribution pass #Length Count 50 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 92.425 #Duplication Level Percentage of deduplicated Percentage of total 1 94.3738166080606 87.225 2 4.138490668109278 7.6499999999999995 3 0.8926156342980796 2.475 4 0.4057343792263998 1.5 5 0.054097917230186636 0.25 6 0.054097917230186636 0.3 7 0.054097917230186636 0.35000000000000003 8 0.0 0.0 9 0.0 0.0 >10 0.027048958615093318 0.25 >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 CCGCGATAGTAATTCAACCTAGTACGAGAGGAACCGTTGATTCACACAAT 10 0.25 No Hit CCTGCCAGTAGTCATATGCTTGTCTCAAAGATTAAGCCATGCATGTGCAA 7 0.17500000000000002 No Hit AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCGTACGTAATCTCGTA 7 0.17500000000000002 TruSeq Adapter, Index 22 (97% over 40bp) CTGCCAGTAGTCATATGCTTGTCTCAAAGATTAAGCCATGCATGTGCAAG 6 0.15 No Hit CTTACCAGGTCCAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTT 6 0.15 No Hit CGCGATAGTAATTCAACCTAGTACGAGAGGAACCGTTGATTCACACAATT 5 0.125 No Hit CCTCTAAGAAGCTAGCTGCGGAGGGATGGCTCCGCATAGCTAGTTAGCAG 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 0.175 0.0 0.0 0.0 0.0 2 0.175 0.0 0.0 0.0 0.0 3 0.175 0.0 0.0 0.0 0.0 4 0.175 0.0 0.0 0.0 0.0 5 0.175 0.0 0.0 0.0 0.0 6 0.225 0.0 0.0 0.0 0.0 7 0.225 0.0 0.0 0.0 0.0 8 0.25 0.0 0.0 0.0 0.0 9 0.25 0.0 0.0 0.0 0.0 10 0.275 0.0 0.0 0.0 0.0 11 0.275 0.0 0.0 0.0 0.0 12 0.275 0.0 0.0 0.0 0.0 13 0.275 0.0 0.0 0.0 0.0 14 0.275 0.0 0.0 0.0 0.0 15 0.275 0.0 0.0 0.0 0.0 16 0.275 0.0 0.0 0.0 0.0 17 0.275 0.0 0.0 0.0 0.0 18 0.275 0.0 0.0 0.0 0.0 19 0.275 0.0 0.0 0.0 0.0 20 0.325 0.0 0.0 0.0 0.0 21 0.35 0.0 0.0 0.0 0.0 22 0.35 0.0 0.0 0.0 0.0 23 0.4 0.0 0.0 0.0 0.0 24 0.45 0.0 0.0 0.0 0.0 25 0.475 0.0 0.0 0.0 0.0 26 0.5 0.0 0.0 0.0 0.0 27 0.5 0.0 0.0 0.0 0.0 28 0.525 0.0 0.0 0.0 0.0 29 0.525 0.0 0.0 0.0 0.0 30 0.525 0.0 0.0 0.0 0.0 31 0.525 0.0 0.0 0.0 0.0 32 0.55 0.0 0.0 0.0 0.0 33 0.575 0.0 0.0 0.0 0.0 34 0.575 0.0 0.0 0.0 0.0 35 0.575 0.0 0.0 0.0 0.0 36 0.575 0.0 0.0 0.0 0.0 37 0.575 0.0 0.0 0.0 0.0 38 0.575 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Read 2852243 spots for SRR7865988.sra Written 2852243 spots for SRR7865988.sra Read 2852243 spots for SRR7865988.sra Written 2852243 spots for SRR7865988.sra Read 2852243 spots for SRR7865988.sra Written 2852243 spots for SRR7865988.sra Read 2852243 spots for SRR7865988.sra Written 2852243 spots for SRR7865988.sra Read 2852243 spots for SRR7865988.sra Written 2852243 spots for SRR7865988.sra Read 2852243 spots for SRR7865988.sra Written 2852243 spots for SRR7865988.sra Read 2852243 spots for SRR7865988.sra Written 2852243 spots for SRR7865988.sra Read 2852243 spots for SRR7865988.sra Written 2852243 spots for SRR7865988.sra Read 2852243 spots for SRR7865988.sra Written 2852243 spots for SRR7865988.sra Read 2852243 spots for SRR7865988.sra Written 2852243 spots for SRR7865988.sra Read 2852243 spots for SRR7865988.sra Written 2852243 spots for SRR7865988.sra Read 2852248 spots for SRR7865988.sra Written 2852248 spots for SRR7865988.sra Read 2852243 spots for SRR7865988.sra Written 2852243 spots for SRR7865988.sra Read 2852243 spots for SRR7865988.sra Written 2852243 spots for SRR7865988.sra Read 2852243 spots for SRR7865988.sra Written 2852243 spots for SRR7865988.sra Read 2852243 spots for SRR7865988.sra Written 2852243 spots for SRR7865988.sra Read 2852243 spots for SRR7865988.sra Written 2852243 spots for SRR7865988.sra Read 2852243 spots for SRR7865988.sra Written 2852243 spots for SRR7865988.sra Read 2852243 spots for SRR7865988.sra Written 2852243 spots for SRR7865988.sra Read 2852243 spots for SRR7865988.sra Written 2852243 spots for SRR7865988.sra SRR ids: ['SRR7865988.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_ue8wm8kw SRR7865988.sra spots: 57044865 blocks: [[1, 2852243], [2852244, 5704486], [5704487, 8556729], [8556730, 11408972], [11408973, 14261215], [14261216, 17113458], [17113459, 19965701], [19965702, 22817944], [22817945, 25670187], [25670188, 28522430], [28522431, 31374673], [31374674, 34226916], [34226917, 37079159], [37079160, 39931402], [39931403, 42783645], [42783646, 45635888], [45635889, 48488131], [48488132, 51340374], [51340375, 54192617], [54192618, 57044865]] SRR7865988 file size 9906866 SRR7865988 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 SRR7865988 SRR7865988_1.fastq Input file: SRR7865988_1.fastq trimmed: SRR7865988-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 Tue Dec 10 01:25:48 2024 >> started Tue Dec 10 01:26:27 2024 >> done (38.265s) 57044865 reads processed; of these: 142247 ( 0.25%) short reads filtered out after trimming by size control 148141 ( 0.26%) empty reads filtered out after trimming by size control 56754477 (99.49%) reads available; of these: 3628294 ( 6.39%) trimmed reads available after processing 53126183 (93.61%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 17320 0.03% 19 12357 0.02% 20 14599 0.03% 21 16973 0.03% 22 21722 0.04% 23 30928 0.05% 24 38934 0.07% 25 49552 0.09% 26 47128 0.08% 27 48181 0.08% 28 59462 0.10% 29 79062 0.14% 30 91274 0.16% 31 77592 0.14% 32 75976 0.13% 33 75248 0.13% 34 78103 0.14% 35 82720 0.15% 36 79366 0.14% 37 87661 0.15% 38 101720 0.18% 39 129948 0.23% 40 167615 0.30% 41 242687 0.43% 42 590245 1.04% 43 102143 0.18% 44 189970 0.33% 45 131366 0.23% 46 170335 0.30% 47 210027 0.37% 48 293604 0.52% 49 214476 0.38% 50 53126183 93.61% 56754477 reads passed initial QC criterion=sequence-density sequence-density=0.42 sequence-density-rank=1 fanout-score=2.11 fanout-score-rank=22 prefix-density=0.45 prefix-fanout=2.0 sequence=GTTCAATGGACTTCT criterion=fanout-score sequence-density=0.01 sequence-density-rank=33 fanout-score=174.48 fanout-score-rank=1 prefix-density=0.22 prefix-fanout=6.4 sequence=GCGGCGGCGAACCGCCCCCGTCGCCGCGATCCGAACACTTCACCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGCATTCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCTATATACTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCGTCGCCTAAACGGCGATAGTCCCTCTAAGAAGCTAGCTGCGGAGGGATGGCTCCGCATAGCTAGTTAGCAGGCTGAGGTCTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCATGCACCACCACCCATAGAATCAAGAAAGAGCTCTCAGTCTGTCAATCCTTGCTATGTCTGGACCTGGTAAGT Started job on | Dec 10 01:26:45 Started mapping on | Dec 10 01:26:45 Finished on | Dec 10 01:28:04 Mapping speed, Million of reads per hour | 2586.28 Number of input reads | 56754477 Average input read length | 49 UNIQUE READS: Uniquely mapped reads number | 30432372 Uniquely mapped reads % | 53.62% Average mapped length | 49.02 Number of splices: Total | 3205428 Number of splices: Annotated (sjdb) | 3005637 Number of splices: GT/AG | 3132707 Number of splices: GC/AG | 36001 Number of splices: AT/AC | 1764 Number of splices: Non-canonical | 34956 Mismatch rate per base, % | 0.34% Deletion rate per base | 0.00% Deletion average length | 1.66 Insertion rate per base | 0.01% Insertion average length | 1.09 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 7290148 % of reads mapped to multiple loci | 12.85% Number of reads mapped to too many loci | 17419999 % of reads mapped to too many loci | 30.69% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 2.26% % of reads unmapped: other | 0.58% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 19031957 19031957 19031957 N_multimapping 7290148 7290148 7290148 N_noFeature 1878916 15884784 16091401 N_ambiguous 375725 18829 23176 UnstrandedReadsAssigned:28177731 PositiveStrandReadsAssigned:14528759 NegativeStrandReadsAssigned:14317795 Dataset is classified unstranded MeadianReadLen=50 20thPercentileLength=50 echo kmer=45 SRR7865988 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: 52,972 [index] number of k-mers: 66,720,672 [index] number of equivalence classes: 111,837 [quant] running in single-end mode [quant] will process file 1: SRR7865988-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 56,754,477 reads, 35,206,307 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,173 rounds 52973 SRR7865988.ke.tsv 35125 SRR7865988.se.tsv 88098 total ==> SRR7865988.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 837 2.10394 0.099227 PNS24247 1044 945 55.167 2.30446 PNS24249 1928 1829 438.869 9.47202 PNS24246 1044 945 55.167 2.30446 PNS24248 1044 945 55.167 2.30446 PNS24244 1471 1372 81.526 2.34565 PNS24243 293 194 8 1.62783 KQK14069 1603 1504 1422.93 37.3471 KQK14071 474 375 635.633 66.9108 ==> SRR7865988.se.tsv <== BRADI_1g14170v3 2438 BRADI_1g53295v3 4317 BRADI_1g59795v3 280 BRADI_1g07683v3 0 BRADI_1g00485v3 41 BRADI_1g20270v3 533 BRADI_1g74790v3 1 BRADI_1g09890v3 3 BRADI_1g77505v3 469 BRADI_1g48960v3 16 SRR7865988 completed mapping pipeline successfully