Starting /dee2/code/volunteer_pipeline.sh SRR522516 current disk space = 1543176826880 free memory = 1606792788 SRR522516 SRAfilesize 4ac8701387b0216c8fddfca6f7bea04d SRR522516.sra SRR522516.sra file validated SRR522516 is single end SRR522516 is conventional basespace SRR522516 read1 length is 43 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR522516_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 43 %GC 47 >>END_MODULE >>Per base sequence quality fail #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 27.677 38.0 2.0 39.0 2.0 40.0 2 29.75625 37.0 17.0 39.0 9.0 40.0 3 29.895 38.0 17.0 39.0 9.0 40.0 4 29.86775 38.0 17.0 39.0 9.0 40.0 5 29.7905 38.0 17.0 39.0 9.0 40.0 6 31.12 38.0 22.0 39.0 14.0 40.0 7 31.03825 38.0 22.0 39.0 14.0 40.0 8 31.013 37.0 22.0 39.0 14.0 40.0 9 30.994 38.0 22.0 39.0 14.0 40.0 10 31.036 37.0 22.0 39.0 14.0 40.0 11 33.71075 38.0 31.0 39.0 25.0 40.0 12 33.546 37.0 31.0 39.0 25.0 40.0 13 33.628 37.0 31.0 39.0 25.0 40.0 14 33.5475 37.0 31.0 39.0 25.0 40.0 15 33.4675 37.0 31.0 39.0 25.0 40.0 16 33.28425 37.0 31.0 39.0 24.0 40.0 17 33.17525 36.0 31.0 39.0 23.0 40.0 18 33.09375 36.0 31.0 39.0 23.0 40.0 19 32.89525 36.0 31.0 39.0 23.0 40.0 20 32.90575 36.0 31.0 39.0 23.0 40.0 21 32.92675 36.0 31.0 39.0 23.0 40.0 22 32.79075 36.0 31.0 39.0 23.0 40.0 23 32.794 36.0 31.0 39.0 23.0 40.0 24 32.6435 36.0 31.0 39.0 23.0 40.0 25 32.4915 36.0 31.0 39.0 23.0 40.0 26 32.38675 36.0 31.0 39.0 20.0 40.0 27 32.106 35.0 31.0 39.0 20.0 40.0 28 31.7895 35.0 31.0 39.0 18.0 40.0 29 31.97475 35.0 31.0 39.0 20.0 40.0 30 31.7755 36.0 31.0 39.0 11.0 40.0 31 31.73925 36.0 31.0 39.0 2.0 40.0 32 31.671 36.0 31.0 39.0 2.0 40.0 33 31.4965 36.0 31.0 39.0 2.0 40.0 34 31.29975 36.0 31.0 39.0 2.0 40.0 35 30.94725 36.0 31.0 39.0 2.0 40.0 36 30.42175 36.0 31.0 39.0 2.0 40.0 37 30.13725 35.0 31.0 39.0 2.0 40.0 38 29.913 35.0 31.0 39.0 2.0 40.0 39 29.7795 35.0 31.0 39.0 2.0 40.0 40 29.39175 35.0 31.0 39.0 2.0 40.0 41 19.622 24.0 2.0 30.0 2.0 33.0 42 19.623 24.0 2.0 30.0 2.0 33.0 43 19.45725 24.0 2.0 30.0 2.0 33.0 >>END_MODULE >>Per tile sequence quality pass #Tile Base Mean 1 1 0.0 1 2 0.0 1 3 0.0 1 4 0.0 1 5 0.0 1 6 0.0 1 7 0.0 1 8 0.0 1 9 0.0 1 10 0.0 1 11 0.0 1 12 0.0 1 13 0.0 1 14 0.0 1 15 0.0 1 16 0.0 1 17 0.0 1 18 0.0 1 19 0.0 1 20 0.0 1 21 0.0 1 22 0.0 1 23 0.0 1 24 0.0 1 25 0.0 1 26 0.0 1 27 0.0 1 28 0.0 1 29 0.0 1 30 0.0 1 31 0.0 1 32 0.0 1 33 0.0 1 34 0.0 1 35 0.0 1 36 0.0 1 37 0.0 1 38 0.0 1 39 0.0 1 40 0.0 1 41 0.0 1 42 0.0 1 43 0.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 194.0 3 0.0 4 1.0 5 0.0 6 1.0 7 6.0 8 8.0 9 4.0 10 3.0 11 6.0 12 9.0 13 17.0 14 21.0 15 15.0 16 17.0 17 31.0 18 42.0 19 40.0 20 47.0 21 62.0 22 79.0 23 77.0 24 106.0 25 152.0 26 190.0 27 174.0 28 79.0 29 61.0 30 101.0 31 115.0 32 119.0 33 135.0 34 194.0 35 278.0 36 323.0 37 413.0 38 541.0 39 339.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 17.469470827679785 30.73270013568521 29.036635006784262 22.761194029850746 2 22.025 33.025 28.125 16.825000000000003 3 28.275 26.924999999999997 18.675 26.125 4 30.475 28.9 20.4 20.225 5 28.325 31.025000000000002 21.2 19.45 6 31.974999999999998 27.575 19.425 21.025 7 28.799999999999997 27.750000000000004 24.875 18.575 8 23.474999999999998 28.575 27.275 20.674999999999997 9 21.725 24.75 34.449999999999996 19.075 10 34.599999999999994 22.2 21.725 21.475 11 25.45 28.325 24.675 21.55 12 27.075 23.400000000000002 29.425 20.1 13 28.849999999999998 24.525 18.3 28.325 14 27.1 27.675 25.374999999999996 19.85 15 26.924999999999997 26.525 26.674999999999997 19.875 16 28.425 25.95 24.125 21.5 17 24.224999999999998 26.1 25.95 23.724999999999998 18 25.4 23.275000000000002 24.275 27.05 19 27.400000000000002 29.25 22.5 20.849999999999998 20 33.825 25.3 23.549999999999997 17.325 21 22.375 27.825 27.750000000000004 22.05 22 22.375 33.525 25.074999999999996 19.025 23 30.5 22.15 27.474999999999998 19.875 24 22.525000000000002 22.1 30.975 24.4 25 15.85 34.300000000000004 24.875 24.975 26 22.25 17.775 36.75 23.225 27 17.474999999999998 17.9 30.275000000000002 34.35 28 14.975 23.95 39.025 22.05 29 17.375 18.325 28.875 35.425000000000004 30 35.8 16.650000000000002 28.175 19.375 31 16.975 17.4 39.0 26.625 32 15.75 29.425 25.900000000000002 28.925 33 23.45 14.325 40.025 22.2 34 31.65 14.025000000000002 30.825000000000003 23.5 35 15.049999999999999 12.275 28.000000000000004 44.675 36 16.525000000000002 11.575000000000001 32.300000000000004 39.6 37 28.849999999999998 12.0 36.625 22.525000000000002 38 14.099999999999998 12.025 44.525 29.349999999999998 39 14.000000000000002 12.725 35.699999999999996 37.574999999999996 40 19.400000000000002 14.2 47.15 19.25 41 14.549999999999999 16.425 42.15 26.875 42 13.325000000000001 18.25 34.0 34.425 43 14.099999999999998 20.875 48.775 16.25 >>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 0.0 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 0.5 21 1.0 22 3.5 23 6.0 24 10.5 25 15.0 26 15.0 27 42.5 28 70.0 29 61.5 30 53.0 31 54.5 32 56.0 33 56.0 34 64.5 35 73.0 36 109.0 37 145.0 38 183.0 39 221.0 40 221.0 41 265.0 42 309.0 43 389.0 44 469.0 45 501.5 46 534.0 47 534.0 48 534.5 49 535.0 50 583.0 51 631.0 52 493.5 53 356.0 54 356.0 55 306.0 56 256.0 57 197.0 58 138.0 59 101.5 60 65.0 61 65.0 62 48.0 63 31.0 64 25.5 65 20.0 66 15.0 67 10.0 68 10.0 69 7.0 70 4.0 71 2.0 72 0.0 73 0.5 74 1.0 75 1.0 76 0.5 77 0.0 78 0.5 79 1.0 80 0.5 81 0.0 82 0.0 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 fail #Base N-Count 1 26.3 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 >>END_MODULE >>Sequence Length Distribution pass #Length Count 43 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 83.275 #Duplication Level Percentage of deduplicated Percentage of total 1 94.14590213149204 78.4 2 3.7526268387871506 6.25 3 0.7805463824677273 1.95 4 0.45031522065445817 1.5 5 0.24016811768237767 1.0 6 0.12008405884118883 0.6 7 0.12008405884118883 0.7000000000000001 8 0.09006304413089163 0.6 9 0.0 0.0 >10 0.24016811768237767 3.325 >50 0.03002101471029721 1.425 >100 0.03002101471029721 4.25 >500 0.0 0.0 >1k 0.0 0.0 >5k 0.0 0.0 >10k+ 0.0 0.0 >>END_MODULE >>Overrepresented sequences fail #Sequence Count Percentage Possible Source TACCTGGTTGATCCTGCCAGTAGTCGTATGCCGTCTTCTGCTT 170 4.25 Illumina Single End Adapter 1 (95% over 21bp) NACCTGGTTGATCCTGCCAGTAGTCGTATGCCGTCTTCTGCTT 57 1.425 Illumina Single End Adapter 1 (95% over 21bp) ATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAA 30 0.75 Illumina Single End Adapter 1 (95% over 24bp) TTTGGATTGAAGGGAGCTCTGATCTCGTATGCCGTCTTCTGCT 26 0.65 Illumina PCR Primer Index 9 (96% over 26bp) CTAACGAACGAACGATTTGAACATCTCGTATGCCGTCTTCTGC 18 0.44999999999999996 RNA PCR Primer, Index 19 (96% over 26bp) AACGAACGAACGATTTGAACATCTCGTATGCCGTCTTCTGCTT 13 0.325 RNA PCR Primer, Index 19 (96% over 28bp) NTTGGATTGAAGGGAGCTCTGATCTCGTATGCCGTCTTCTGCT 13 0.325 Illumina PCR Primer Index 9 (96% over 26bp) CGACACGACTCTCGGCAACGGATCTCGTATGCCGTCTTCTGCT 12 0.3 Illumina PCR Primer Index 9 (96% over 25bp) NTCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAA 11 0.27499999999999997 Illumina Paired End PCR Primer 2 (95% over 24bp) NTAACGAACGAACGATTTGAACATCTCGTATGCCGTCTTCTGC 10 0.25 RNA PCR Primer, Index 19 (96% over 26bp) AACGAACGATTTGAACATCTCGTATGCCGTCTTCTGCTTGAAA 8 0.2 RNA PCR Primer, Index 19 (96% over 29bp) TAACGAACGAACGATTTGAACATCTCGTATGCCGTCTTCTGCT 8 0.2 Illumina PCR Primer Index 7 (96% over 26bp) GGGATTGTAGTTCAATTGGTCAGAGCACCATCTCGTATGCCGT 8 0.2 No Hit CATGATAACTCGACGGATCGCACGGCCCTCGTATGCCGTCTTC 7 0.17500000000000002 No Hit CGGATAACCGTAGTAATTCTAGAGCTAATACGTATCTCGTATG 7 0.17500000000000002 No Hit CACGACTCTCGGCAACGGATATCTATCTCGTATGCCGTCTTCT 7 0.17500000000000002 Illumina PCR Primer Index 2 (95% over 23bp) GACACGACTCTCGGCAACGGATATCTCATCTCGTATGCCGTCT 7 0.17500000000000002 No Hit NATGATAACTCGACGGATCGCACGGCCCTCGTATGCCGTCTTC 6 0.15 No Hit AGGGCTATAGCTCAGTTCGGTAGAGCAACTCGTATGCCGTCTT 6 0.15 No Hit CGACACGACTCTCGGCAACGGATATCATCTCGTATGCCGTCTT 6 0.15 TruSeq Adapter, Index 7 (95% over 22bp) CGACACGACTCTCGGCAACGATCTCGTATGCCGTCTTCTGCTT 6 0.15 Illumina Paired End PCR Primer 2 (96% over 27bp) ACGAACGAACGATTTGAACATCTCGTATGCCGTCTTCTGCTTG 5 0.125 Illumina PCR Primer Index 7 (96% over 28bp) CGACACGACTCTCGGCAACGGATATCTATCTCGTATGCCGTCT 5 0.125 RNA PCR Primer, Index 38 (95% over 21bp) NACGAACGAACGATTTGAACATCTCGTATGCCGTCTTCTGCTT 5 0.125 RNA PCR Primer, Index 19 (96% over 28bp) GAACGAACGATTTGAACATCTCGTATGCCGTCTTCTGCTTGAA 5 0.125 Illumina PCR Primer Index 7 (96% over 28bp) GGGGATGTAGCTCAGATGGTATCTCGTATGCCGTCTTCTGCTT 5 0.125 RNA PCR Primer, Index 34 (96% over 28bp) TCGGATAACCGTAGTAATTCTAGAGCTAATACGTGATCTCGTA 5 0.125 No Hit ATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAACA 5 0.125 Illumina Single End Adapter 1 (95% over 24bp) NGACACGACTCTCGGCAACGGATCTCGTATGCCGTCTTCTGCT 5 0.125 Illumina PCR Primer Index 9 (96% over 25bp) >>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 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TACCTGG 25 1.8344108E-5 49.0 1 ATCCTGC 30 6.73628E-6 36.75 11 GTTGATC 30 6.73628E-6 36.75 7 TGGTTGA 30 6.73628E-6 36.75 5 GGTTGAT 30 6.73628E-6 36.75 6 AGTAGTC 30 6.73628E-6 36.75 19 CCAGTAG 30 6.73628E-6 36.75 17 CCTGCCA 30 6.73628E-6 36.75 13 GTCGTAT 30 6.73628E-6 36.75 23 CAGTAGT 30 6.73628E-6 36.75 18 TGATCCT 30 6.73628E-6 36.75 9 TAGTCGT 30 6.73628E-6 36.75 21 GCCAGTA 30 6.73628E-6 36.75 16 CTGGTTG 30 6.73628E-6 36.75 4 ACCTGGT 30 6.73628E-6 36.75 2 GATCCTG 30 6.73628E-6 36.75 10 AGTCGTA 30 6.73628E-6 36.75 22 TGCCAGT 30 6.73628E-6 36.75 15 TTGATCC 30 6.73628E-6 36.75 8 CTGCCAG 30 6.73628E-6 36.75 14 >>END_MODULE Read 1442334 spots for SRR522516.sra Written 1442334 spots for SRR522516.sra Read 1442334 spots for SRR522516.sra Written 1442334 spots for SRR522516.sra Read 1442334 spots for SRR522516.sra Written 1442334 spots for SRR522516.sra Read 1442334 spots for SRR522516.sra Written 1442334 spots for SRR522516.sra Read 1442334 spots for SRR522516.sra Written 1442334 spots for SRR522516.sra Read 1442334 spots for SRR522516.sra Written 1442334 spots for SRR522516.sra Read 1442334 spots for SRR522516.sra Written 1442334 spots for SRR522516.sra Read 1442334 spots for SRR522516.sra Written 1442334 spots for SRR522516.sra Read 1442334 spots for SRR522516.sra Written 1442334 spots for SRR522516.sra Read 1442334 spots for SRR522516.sra Written 1442334 spots for SRR522516.sra Read 1442334 spots for SRR522516.sra Written 1442334 spots for SRR522516.sra Read 1442334 spots for SRR522516.sra Written 1442334 spots for SRR522516.sra Read 1442334 spots for SRR522516.sra Written 1442334 spots for SRR522516.sra Read 1442334 spots for SRR522516.sra Written 1442334 spots for SRR522516.sra Read 1442334 spots for SRR522516.sra Written 1442334 spots for SRR522516.sra Read 1442334 spots for SRR522516.sra Written 1442334 spots for SRR522516.sra Read 1442334 spots for SRR522516.sra Written 1442334 spots for SRR522516.sra Read 1442338 spots for SRR522516.sra Written 1442338 spots for SRR522516.sra Read 1442334 spots for SRR522516.sra Written 1442334 spots for SRR522516.sra Read 1442334 spots for SRR522516.sra Written 1442334 spots for SRR522516.sra SRR ids: ['SRR522516.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_wiwnupyl SRR522516.sra spots: 28846684 blocks: [[1, 1442334], [1442335, 2884668], [2884669, 4327002], [4327003, 5769336], [5769337, 7211670], [7211671, 8654004], [8654005, 10096338], [10096339, 11538672], [11538673, 12981006], [12981007, 14423340], [14423341, 15865674], [15865675, 17308008], [17308009, 18750342], [18750343, 20192676], [20192677, 21635010], [21635011, 23077344], [23077345, 24519678], [24519679, 25962012], [25962013, 27404346], [27404347, 28846684]] SRR522516 file size 4501774 SRR522516 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 SRR522516 SRR522516_1.fastq Input file: SRR522516_1.fastq trimmed: SRR522516-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 11:13:39 2024 >> started Sat Dec 7 11:13:58 2024 >> done (18.532s) 28846684 reads processed; of these: 30766 ( 0.11%) short reads filtered out after trimming by size control 25944 ( 0.09%) empty reads filtered out after trimming by size control 28789974 (99.80%) reads available; of these: 3948725 (13.72%) trimmed reads available after processing 24841249 (86.28%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 6522 0.02% 19 10858 0.04% 20 17565 0.06% 21 6453 0.02% 22 10912 0.04% 23 21398 0.07% 24 54054 0.19% 25 138048 0.48% 26 47376 0.16% 27 75589 0.26% 28 77841 0.27% 29 315896 1.10% 30 285393 0.99% 31 63317 0.22% 32 50463 0.18% 33 115665 0.40% 34 425113 1.48% 35 633644 2.20% 36 74899 0.26% 37 77702 0.27% 38 123752 0.43% 39 266593 0.93% 40 984085 3.42% 41 35984 0.12% 42 29603 0.10% 43 24841249 86.28% 28789974 reads passed initial QC criterion=sequence-density sequence-density=69.78 sequence-density-rank=1 fanout-score=35.41 fanout-score-rank=1 prefix-density=70.91 prefix-fanout=34.8 sequence=ATCTCGTATGCCGTCTTCTGCTTGAAAAAAA criterion=fanout-score sequence-density=69.78 sequence-density-rank=1 fanout-score=35.41 fanout-score-rank=1 prefix-density=70.91 prefix-fanout=34.8 sequence=ATCTCGTATGCCGTCTTCTGCTTGAAAAAAA Potential 3prime adapter identified. Now checking if in reference sequence Warning: gzbuffer added in zlib v1.2.3.5. Unable to change buffer size from default of 8192. 1 reads; of these: 1 (100.00%) were unpaired; of these: 1 (100.00%) aligned 0 times 0 (0.00%) aligned exactly 1 time 0 (0.00%) aligned >1 times 0.00% overall alignment rate Adapter seq not found in reference. Now shuffling file before clipping skewer v0.2.2 [April 4, 2016] COMMAND LINE: skewer -f sanger -l 18 -t 20 -x ATCTCGTATGCCGTCTTCTGCTTGAAAAAAA -o SRR522516 - Input file: STDIN trimmed: SRR522516-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): ATCTCGTATGCCGTCTTCTGCTTGAAAAAAA -- maximum error ratio allowed (-r): 0.100 -- maximum indel error ratio allowed (-d): 0.030 -- minimum read length allowed after trimming (-l): 18 -- file format (-f): Sanger/Illumina 1.8+ FASTQ -- minimum overlap length for adapter detection (-k): 3 -- number of concurrent threads (-t): 20 Sat Dec 7 11:14:46 2024 >> started Sat Dec 7 11:15:21 2024 >> done (34.685s) 27967403 reads processed; of these: 3512318 (12.56%) short reads filtered out after trimming by size control 1103100 ( 3.94%) empty reads filtered out after trimming by size control 23351985 (83.50%) reads available; of these: 18801989 (80.52%) trimmed reads available after processing 4549996 (19.48%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 786290 3.37% 19 880691 3.77% 20 1054415 4.52% 21 1687833 7.23% 22 1155905 4.95% 23 1517239 6.50% 24 5376263 23.02% 25 1142495 4.89% 26 882794 3.78% 27 815023 3.49% 28 710084 3.04% 29 863731 3.70% 30 636384 2.73% 31 431979 1.85% 32 383598 1.64% 33 342655 1.47% 34 294360 1.26% 35 290088 1.24% 36 180125 0.77% 37 178720 0.77% 38 100973 0.43% 39 99882 0.43% 40 174015 0.75% 41 6620 0.03% 42 5441 0.02% 43 3354382 14.36% criterion=sequence-density sequence-density=12.88 sequence-density-rank=1 fanout-score=4.48 fanout-score-rank=10 prefix-density=13.78 prefix-fanout=4.2 sequence=TCGTATGCCGTCTTCTGCTTGAAAAAA criterion=fanout-score sequence-density=0.01 sequence-density-rank=14 fanout-score=443.51 fanout-score-rank=1 prefix-density=6.43 prefix-fanout=1.0 sequence=TGCCAGTAGTCATATGCTTGTCTCAAAGATTAAGCCATGCATGTGCAAGTATGAACTAATTTGAACTGTGAAACTGCGAATGGCTCATTAAATCAGTTATAGTTTGTTTGATGGTACGTGCTACTCGGATAACCGTAGTAATTCTAGAGCTAATACGTGCAACAAACCCCGACTTCTGG Started job on | Dec 07 11:15:46 Started mapping on | Dec 07 11:15:47 Finished on | Dec 07 11:17:06 Mapping speed, Million of reads per hour | 1101.63 Number of input reads | 24174556 Average input read length | 28 UNIQUE READS: Uniquely mapped reads number | 7711425 Uniquely mapped reads % | 31.90% Average mapped length | 27.03 Number of splices: Total | 171680 Number of splices: Annotated (sjdb) | 41357 Number of splices: GT/AG | 166496 Number of splices: GC/AG | 3283 Number of splices: AT/AC | 32 Number of splices: Non-canonical | 1869 Mismatch rate per base, % | 1.79% Deletion rate per base | 0.00% Deletion average length | 1.40 Insertion rate per base | 0.00% Insertion average length | 1.02 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 3410387 % of reads mapped to multiple loci | 14.11% Number of reads mapped to too many loci | 10564427 % of reads mapped to too many loci | 43.70% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 9.19% % of reads unmapped: other | 1.10% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 13052744 13052744 13052744 N_multimapping 3410387 3410387 3410387 N_noFeature 4429842 4784733 7326019 N_ambiguous 109856 77540 2425 UnstrandedReadsAssigned:3171727 PositiveStrandReadsAssigned:2849152 NegativeStrandReadsAssigned:382981 Dataset is classified positive stranded MeadianReadLen=24 20thPercentileLength=22 echo kmer=19 SRR522516 Starting Kallisto single end mapping to ensembl reference transcriptome. kmer=19 [quant] fragment length distribution is truncated gaussian with mean = 100, sd = 20 [index] k-mer length: 19 [index] number of targets: 52,972 [index] number of k-mers: 65,492,969 [index] number of equivalence classes: 320,172 [quant] running in single-end mode [quant] will process file 1: SRR522516-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 24,174,556 reads, 2,332,335 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,027 rounds 52973 SRR522516.ke.tsv 35125 SRR522516.se.tsv 88098 total ==> SRR522516.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 837 0 0 PNS24247 1044 945 0 0 PNS24249 1928 1829 18.8377 5.73595 PNS24246 1044 945 0 0 PNS24248 1044 945 0 0 PNS24244 1471 1372 6.16225 2.50135 PNS24243 293 194 0 0 KQK14069 1603 1504 7.99291 2.9597 KQK14071 474 375 1.00709 1.49563 ==> SRR522516.se.tsv <== BRADI_1g14170v3 10 BRADI_1g53295v3 4 BRADI_1g59795v3 2 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 26 BRADI_1g74790v3 46 BRADI_1g09890v3 0 BRADI_1g77505v3 8 BRADI_1g48960v3 1 SRR522516 completed mapping pipeline successfully