Starting /dee2/code/volunteer_pipeline.sh SRR6322416 current disk space = 1543391059968 free memory = 1605264196 SRR6322416 SRAfilesize e7a1770608e981b85e3a928ea4e007c6 SRR6322416.sra SRR6322416.sra file validated SRR6322416 is single end SRR6322416 is conventional basespace SRR6322416 read1 length is 50 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR6322416_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 50 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 32.42725 33.0 33.0 34.0 32.0 34.0 2 32.507 33.0 33.0 34.0 31.0 34.0 3 32.561 33.0 33.0 34.0 31.0 34.0 4 32.42275 34.0 33.0 34.0 31.0 34.0 5 32.42575 33.0 33.0 34.0 31.0 34.0 6 35.97975 38.0 36.0 38.0 31.0 38.0 7 36.4785 38.0 37.0 38.0 34.0 38.0 8 36.53925 38.0 38.0 38.0 34.0 38.0 9 36.60375 38.0 38.0 38.0 34.0 38.0 10 36.607 38.0 38.0 38.0 34.0 38.0 11 36.61725 38.0 38.0 38.0 34.0 38.0 12 36.67075 38.0 38.0 38.0 34.0 38.0 13 36.7125 38.0 38.0 38.0 35.0 38.0 14 36.794 38.0 38.0 38.0 34.0 38.0 15 36.76625 38.0 38.0 38.0 34.0 38.0 16 36.72675 38.0 38.0 38.0 34.0 38.0 17 36.84075 38.0 38.0 38.0 35.0 38.0 18 36.73775 38.0 38.0 38.0 34.0 38.0 19 36.7985 38.0 38.0 38.0 34.0 38.0 20 36.569 38.0 38.0 38.0 34.0 38.0 21 36.69925 38.0 38.0 38.0 34.0 38.0 22 36.65725 38.0 38.0 38.0 34.0 38.0 23 36.72875 38.0 38.0 38.0 34.0 38.0 24 36.6845 38.0 38.0 38.0 34.0 38.0 25 36.60475 38.0 38.0 38.0 34.0 38.0 26 36.639 38.0 38.0 38.0 34.0 38.0 27 36.61775 38.0 38.0 38.0 34.0 38.0 28 36.657 38.0 38.0 38.0 34.0 38.0 29 36.6795 38.0 38.0 38.0 34.0 38.0 30 36.7205 38.0 38.0 38.0 34.0 38.0 31 36.6835 38.0 38.0 38.0 34.0 38.0 32 36.614 38.0 38.0 38.0 34.0 38.0 33 36.66225 38.0 38.0 38.0 34.0 38.0 34 36.55 38.0 38.0 38.0 34.0 38.0 35 36.538 38.0 38.0 38.0 34.0 38.0 36 36.49925 38.0 38.0 38.0 34.0 38.0 37 36.4315 38.0 38.0 38.0 34.0 38.0 38 36.44575 38.0 38.0 38.0 34.0 38.0 39 36.53725 38.0 38.0 38.0 34.0 38.0 40 36.53275 38.0 38.0 38.0 34.0 38.0 41 36.40475 38.0 38.0 38.0 34.0 38.0 42 36.473 38.0 38.0 38.0 34.0 38.0 43 36.5735 38.0 38.0 38.0 34.0 38.0 44 36.447 38.0 38.0 38.0 34.0 38.0 45 36.45675 38.0 38.0 38.0 34.0 38.0 46 36.38875 38.0 38.0 38.0 34.0 38.0 47 36.38525 38.0 38.0 38.0 34.0 38.0 48 36.3305 38.0 38.0 38.0 34.0 38.0 49 36.2425 38.0 38.0 38.0 34.0 38.0 50 36.129 38.0 38.0 38.0 33.0 38.0 >>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 1.0 11 0.0 12 0.0 13 0.0 14 1.0 15 1.0 16 0.0 17 0.0 18 2.0 19 1.0 20 0.0 21 1.0 22 1.0 23 6.0 24 9.0 25 10.0 26 19.0 27 25.0 28 36.0 29 30.0 30 70.0 31 84.0 32 121.0 33 133.0 34 180.0 35 287.0 36 559.0 37 2422.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 37.23324127542054 15.967863419533016 7.732864674868189 39.066030630178254 2 23.95 21.375 35.949999999999996 18.725 3 20.825 25.575 22.575 31.025000000000002 4 27.150000000000002 32.25 18.525 22.075 5 24.912456228114056 31.96598299149575 22.536268134067033 20.58529264632316 6 20.625 30.125 23.275000000000002 25.974999999999998 7 19.775000000000002 15.65 39.725 24.85 8 22.05 18.15 26.200000000000003 33.6 9 20.0 17.0 30.175 32.824999999999996 10 24.0 31.874999999999996 21.75 22.375 11 29.075 19.55 18.625 32.75 12 28.525 15.825 23.025000000000002 32.625 13 22.175 21.8 26.924999999999997 29.099999999999998 14 23.65 24.75 26.424999999999997 25.174999999999997 15 23.575 23.799999999999997 25.275 27.35 16 25.25 23.075000000000003 25.575 26.1 17 24.55 24.2 25.05 26.200000000000003 18 23.075000000000003 24.725 26.6 25.6 19 24.075 24.975 24.675 26.275 20 24.2 24.575 25.575 25.650000000000002 21 24.625 24.725 25.825 24.825 22 24.375 24.775 24.175 26.674999999999997 23 22.875 24.425 27.05 25.650000000000002 24 24.45 23.825 25.6 26.125 25 25.1 22.925 24.474999999999998 27.500000000000004 26 23.525 24.75 26.700000000000003 25.025 27 24.45 22.75 26.35 26.450000000000003 28 25.05 23.599999999999998 24.925 26.424999999999997 29 23.45 24.875 26.150000000000002 25.525 30 24.0 24.349999999999998 25.85 25.8 31 24.224999999999998 23.5 25.1 27.175 32 23.225 24.4 26.625 25.75 33 23.175 23.674999999999997 26.400000000000002 26.75 34 24.175 24.15 25.75 25.924999999999997 35 23.175 25.0 26.5 25.324999999999996 36 23.674999999999997 23.549999999999997 24.975 27.800000000000004 37 23.45 24.525 25.275 26.75 38 24.65 23.724999999999998 24.575 27.05 39 23.474999999999998 23.799999999999997 25.5 27.224999999999998 40 23.95598899724931 25.18129532383096 24.8062015503876 26.056514128532132 41 24.275 25.124999999999996 25.474999999999998 25.124999999999996 42 23.9 23.75 24.75 27.6 43 23.575 24.125 25.3 27.0 44 24.9 24.474999999999998 26.900000000000002 23.724999999999998 45 24.95 23.674999999999997 24.6 26.775 46 23.525 24.5 24.975 27.0 47 22.275 23.375 28.349999999999998 26.0 48 23.45 23.150000000000002 26.825 26.575 49 23.625 25.05 24.5 26.825 50 23.724999999999998 23.3 26.625 26.35 >>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 0.0 19 0.0 20 0.0 21 1.5 22 3.0 23 3.5 24 4.0 25 7.0 26 10.0 27 12.5 28 15.0 29 16.0 30 17.0 31 26.0 32 35.0 33 53.5 34 72.0 35 97.0 36 122.0 37 146.0 38 170.0 39 191.0 40 212.0 41 226.5 42 241.0 43 278.5 44 316.0 45 316.5 46 317.0 47 322.0 48 327.0 49 320.0 50 313.0 51 314.0 52 315.0 53 301.5 54 288.0 55 261.5 56 235.0 57 209.0 58 183.0 59 170.5 60 158.0 61 145.5 62 133.0 63 123.5 64 114.0 65 93.5 66 73.0 67 79.5 68 86.0 69 78.0 70 70.0 71 64.0 72 58.0 73 49.0 74 40.0 75 32.5 76 25.0 77 20.0 78 15.0 79 19.0 80 23.0 81 13.5 82 4.0 83 4.0 84 4.0 85 2.5 86 1.0 87 1.0 88 1.0 89 0.5 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 0.42500000000000004 2 0.0 3 0.0 4 0.0 5 0.05 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 0.025 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 93.45 #Duplication Level Percentage of deduplicated Percentage of total 1 95.61262707330123 89.35 2 3.0230069555912253 5.65 3 0.8560727661851256 2.4 4 0.32102728731942215 1.2 5 0.08025682182985554 0.375 6 0.026752273943285176 0.15 7 0.0 0.0 8 0.026752273943285176 0.2 9 0.0 0.0 >10 0.05350454788657035 0.675 >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 GTCAACGCGAGCTGATGACTCGCGCTTACTAGGCATTCCTCGTTGAAGAC 16 0.4 No Hit GGCAATTTCAAGCACTCTTTGACTCTCTTTTCAAAGTCCTTTTCATCTTT 11 0.27499999999999997 No Hit CTTCACTCTCCGCCTTCTTTAAAACGACATAGTTTTGTGGTATGATTAAC 8 0.2 No Hit AGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGC 6 0.15 No Hit GCCAAACTCCCCACCTGACAATGTCTTCCGCCCGGATCGGCCCGGTCAGA 5 0.125 No Hit GGCAGGCGTGCCCTCGACCGGGTGGCCTCGGGCGCAACTTGCGTTCAAAG 5 0.125 No Hit GTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGCATTCCTCGTTGAA 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 >>END_MODULE >>Kmer Content pass >>END_MODULE Read 804613 spots for SRR6322416.sra Written 804613 spots for SRR6322416.sra Read 804613 spots for SRR6322416.sra Written 804613 spots for SRR6322416.sra Read 804613 spots for SRR6322416.sra Written 804613 spots for SRR6322416.sra Read 804613 spots for SRR6322416.sra Written 804613 spots for SRR6322416.sra Read 804613 spots for SRR6322416.sra Written 804613 spots for SRR6322416.sra Read 804613 spots for SRR6322416.sra Written 804613 spots for SRR6322416.sra Read 804613 spots for SRR6322416.sra Written 804613 spots for SRR6322416.sra Read 804613 spots for SRR6322416.sra Written 804613 spots for SRR6322416.sra Read 804622 spots for SRR6322416.sra Written 804622 spots for SRR6322416.sra Read 804613 spots for SRR6322416.sra Written 804613 spots for SRR6322416.sra Read 804613 spots for SRR6322416.sra Written 804613 spots for SRR6322416.sra Read 804613 spots for SRR6322416.sra Written 804613 spots for SRR6322416.sra Read 804613 spots for SRR6322416.sra Written 804613 spots for SRR6322416.sra Read 804613 spots for SRR6322416.sra Written 804613 spots for SRR6322416.sra Read 804613 spots for SRR6322416.sra Written 804613 spots for SRR6322416.sra Read 804613 spots for SRR6322416.sra Written 804613 spots for SRR6322416.sra Read 804613 spots for SRR6322416.sra Written 804613 spots for SRR6322416.sra Read 804613 spots for SRR6322416.sra Written 804613 spots for SRR6322416.sra Read 804613 spots for SRR6322416.sra Written 804613 spots for SRR6322416.sra Read 804613 spots for SRR6322416.sra Written 804613 spots for SRR6322416.sra SRR ids: ['SRR6322416.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_b_vx84a0 SRR6322416.sra spots: 16092269 blocks: [[1, 804613], [804614, 1609226], [1609227, 2413839], [2413840, 3218452], [3218453, 4023065], [4023066, 4827678], [4827679, 5632291], [5632292, 6436904], [6436905, 7241517], [7241518, 8046130], [8046131, 8850743], [8850744, 9655356], [9655357, 10459969], [10459970, 11264582], [11264583, 12069195], [12069196, 12873808], [12873809, 13678421], [13678422, 14483034], [14483035, 15287647], [15287648, 16092269]] SRR6322416 file size 2794131 SRR6322416 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 SRR6322416 SRR6322416_1.fastq Input file: SRR6322416_1.fastq trimmed: SRR6322416-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 Sat Dec 7 10:34:31 2024 >> started Sat Dec 7 10:34:46 2024 >> done (14.795s) 16092269 reads processed; of these: 4335 ( 0.03%) short reads filtered out after trimming by size control 8425 ( 0.05%) empty reads filtered out after trimming by size control 16079509 (99.92%) reads available; of these: 232662 ( 1.45%) trimmed reads available after processing 15846847 (98.55%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 237 0.00% 19 240 0.00% 20 250 0.00% 21 312 0.00% 22 387 0.00% 23 462 0.00% 24 526 0.00% 25 680 0.00% 26 707 0.00% 27 710 0.00% 28 806 0.01% 29 857 0.01% 30 952 0.01% 31 1054 0.01% 32 1233 0.01% 33 1432 0.01% 34 1657 0.01% 35 1955 0.01% 36 2267 0.01% 37 2707 0.02% 38 3181 0.02% 39 3764 0.02% 40 4609 0.03% 41 5523 0.03% 42 7203 0.04% 43 8839 0.05% 44 11102 0.07% 45 14925 0.09% 46 20516 0.13% 47 28163 0.18% 48 43542 0.27% 49 61864 0.38% 50 15846847 98.55% 16079509 reads passed initial QC criterion=sequence-density sequence-density=0.66 sequence-density-rank=1 fanout-score=2.01 fanout-score-rank=24 prefix-density=0.66 prefix-fanout=2.0 sequence=TTTGGCTTTGGC criterion=fanout-score sequence-density=0.05 sequence-density-rank=21 fanout-score=42.36 fanout-score-rank=1 prefix-density=0.29 prefix-fanout=7.1 sequence=CTGCTGCTGCCGCCGCCACCACACGGGTGCTACTTCTTGTTCGCGCCCCTGCTGCAGTTGTCTCTCATCTTGTTGTTGATGTGGGCACGGCTGCTCCGGCTGAACCGACCATGGTTTCTCCTGCGCCATGCCCTGGCTACATCTAGTCTCTCGCTGTGCAATGGTGGTGCTAGC Started job on | Dec 07 10:34:57 Started mapping on | Dec 07 10:34:57 Finished on | Dec 07 10:35:15 Mapping speed, Million of reads per hour | 3215.90 Number of input reads | 16079509 Average input read length | 49 UNIQUE READS: Uniquely mapped reads number | 12349908 Uniquely mapped reads % | 76.81% Average mapped length | 49.85 Number of splices: Total | 1905849 Number of splices: Annotated (sjdb) | 1817603 Number of splices: GT/AG | 1874132 Number of splices: GC/AG | 25131 Number of splices: AT/AC | 1306 Number of splices: Non-canonical | 5280 Mismatch rate per base, % | 0.18% Deletion rate per base | 0.01% Deletion average length | 1.62 Insertion rate per base | 0.00% Insertion average length | 1.42 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 1594018 % of reads mapped to multiple loci | 9.91% Number of reads mapped to too many loci | 2029687 % of reads mapped to too many loci | 12.62% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 0.49% % of reads unmapped: other | 0.16% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 2135583 2135583 2135583 N_multimapping 1594018 1594018 1594018 N_noFeature 798508 12104240 908628 N_ambiguous 149654 841 13858 UnstrandedReadsAssigned:11401746 PositiveStrandReadsAssigned:244827 NegativeStrandReadsAssigned:11427422 Dataset is classified negative stranded MeadianReadLen=50 20thPercentileLength=50 echo kmer=45 SRR6322416 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: SRR6322416-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 16,079,509 reads, 12,510,008 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,187 rounds 52973 SRR6322416.ke.tsv 35125 SRR6322416.se.tsv 88098 total ==> SRR6322416.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 837 76.8736 11.3343 PNS24247 1044 945 24.2761 3.17021 PNS24249 1928 1829 136.074 9.1813 PNS24246 1044 945 24.2761 3.17021 PNS24248 1044 945 24.2761 3.17021 PNS24244 1471 1372 61.2238 5.50691 PNS24243 293 194 0 0 KQK14069 1603 1504 103.542 8.49595 KQK14071 474 375 23.8878 7.86115 ==> SRR6322416.se.tsv <== BRADI_1g14170v3 160 BRADI_1g53295v3 156 BRADI_1g59795v3 203 BRADI_1g07683v3 0 BRADI_1g00485v3 2 BRADI_1g20270v3 761 BRADI_1g74790v3 2 BRADI_1g09890v3 0 BRADI_1g77505v3 272 BRADI_1g48960v3 1 SRR6322416 completed mapping pipeline successfully