Starting /dee2/code/volunteer_pipeline.sh SRR2962699 current disk space = 3058761039872 free memory = 1152230992 SRR2962699 SRAfilesize dc242e8a6390d9af16b7722f0073af6b SRR2962699.sra SRR2962699.sra file validated SRR2962699 is single end SRR2962699 is conventional basespace SRR2962699 read1 length is 46 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR2962699_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 46 %GC 43 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.4835 37.0 37.0 37.0 35.0 37.0 2 36.20575 37.0 37.0 37.0 35.0 37.0 3 36.2975 37.0 37.0 37.0 35.0 37.0 4 36.20675 37.0 37.0 37.0 35.0 37.0 5 36.295 37.0 37.0 37.0 35.0 37.0 6 38.1085 39.0 39.0 39.0 35.0 39.0 7 38.02775 39.0 39.0 39.0 35.0 39.0 8 38.03925 39.0 39.0 39.0 35.0 39.0 9 38.10225 39.0 39.0 39.0 37.0 39.0 10 38.08775 39.0 39.0 39.0 35.0 39.0 11 39.5835 41.0 40.0 41.0 37.0 41.0 12 39.48825 41.0 40.0 41.0 37.0 41.0 13 39.544 41.0 40.0 41.0 37.0 41.0 14 39.4545 41.0 40.0 41.0 36.0 41.0 15 39.42675 41.0 39.0 41.0 36.0 41.0 16 39.39125 41.0 39.0 41.0 36.0 41.0 17 39.36475 41.0 39.0 41.0 36.0 41.0 18 39.57375 41.0 39.0 41.0 37.0 41.0 19 39.75325 41.0 40.0 41.0 38.0 41.0 20 39.75525 41.0 40.0 41.0 38.0 41.0 21 39.9175 41.0 40.0 41.0 38.0 41.0 22 39.7025 41.0 40.0 41.0 37.0 41.0 23 39.43475 41.0 40.0 41.0 37.0 41.0 24 39.5625 41.0 40.0 41.0 37.0 41.0 25 39.66625 41.0 40.0 41.0 37.0 41.0 26 39.771 41.0 40.0 41.0 38.0 41.0 27 40.18525 41.0 40.0 41.0 39.0 41.0 28 39.9865 41.0 40.0 41.0 39.0 41.0 29 39.10375 40.0 39.0 41.0 37.0 41.0 30 39.08175 40.0 39.0 40.0 37.0 41.0 31 39.4915 40.0 40.0 41.0 38.0 41.0 32 39.8225 41.0 40.0 41.0 38.0 41.0 33 40.1195 41.0 40.0 41.0 39.0 41.0 34 40.42 41.0 41.0 41.0 40.0 41.0 35 40.17675 41.0 40.0 41.0 39.0 41.0 36 39.22925 40.0 39.0 41.0 37.0 41.0 37 39.06725 40.0 39.0 40.0 37.0 41.0 38 39.7065 40.0 40.0 41.0 38.0 41.0 39 40.334 41.0 40.0 41.0 39.0 41.0 40 40.1935 41.0 40.0 41.0 39.0 41.0 41 40.07325 41.0 40.0 41.0 39.0 41.0 42 39.9855 41.0 40.0 41.0 38.0 41.0 43 39.9985 41.0 40.0 41.0 38.0 41.0 44 39.9365 41.0 40.0 41.0 38.0 41.0 45 40.25975 41.0 41.0 41.0 40.0 41.0 46 39.75525 41.0 40.0 41.0 38.0 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 >>END_MODULE >>Per sequence quality scores pass #Quality Count 15 2.0 16 0.0 17 2.0 18 0.0 19 0.0 20 1.0 21 1.0 22 1.0 23 0.0 24 4.0 25 4.0 26 1.0 27 3.0 28 6.0 29 12.0 30 14.0 31 19.0 32 25.0 33 46.0 34 56.0 35 91.0 36 113.0 37 170.0 38 292.0 39 1084.0 40 2053.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 27.975 20.025000000000002 31.0 21.0 2 18.425 35.05 30.3 16.225 3 20.150000000000002 30.2 31.45 18.2 4 20.724999999999998 28.125 35.575 15.575 5 19.625 24.625 36.05 19.7 6 21.349999999999998 27.875 33.625 17.150000000000002 7 22.0 27.025 34.675 16.3 8 22.875 31.25 29.425 16.45 9 20.724999999999998 31.775 29.875 17.625 10 21.075 29.225 34.25 15.45 11 19.975 29.775000000000002 32.574999999999996 17.675 12 19.6 32.675 31.874999999999996 15.85 13 20.05 30.875000000000004 32.15 16.925 14 20.025000000000002 31.225 32.25 16.5 15 19.950000000000003 30.5 33.525 16.025 16 16.7 32.775 33.25 17.275 17 13.8 28.1 34.55 23.549999999999997 18 4.375 65.35 16.900000000000002 13.375 19 0.05 40.150000000000006 0.7250000000000001 59.075 20 0.27499999999999997 59.35 2.175 38.2 21 2.075 38.125 59.425 0.375 22 59.3 0.17500000000000002 40.2 0.325 23 38.224999999999994 2.025 59.150000000000006 0.6 24 0.27499999999999997 59.0 38.425 2.3 25 0.42500000000000004 38.15 2.275 59.150000000000006 26 0.22499999999999998 0.15 59.45 40.175 27 2.1 0.05 38.45 59.4 28 59.075 0.1 2.45 38.375 29 38.224999999999994 1.95 59.475 0.35000000000000003 30 0.3 58.875 40.25 0.575 31 2.15 38.05 59.425 0.375 32 59.199999999999996 0.05 38.475 2.275 33 38.175 0.025 0.5 61.3 34 2.1 0.025 0.775 97.1 35 59.0 0.15 2.55 38.3 36 38.5 0.2 59.150000000000006 2.15 37 0.125 0.5 40.275 59.099999999999994 38 0.17500000000000002 0.5 61.075 38.25 39 0.125 0.5499999999999999 97.225 2.1 40 0.25 0.625 40.2 58.925000000000004 41 2.0 0.75 59.099999999999994 38.15 42 58.975 0.8250000000000001 38.224999999999994 1.975 43 38.1 0.95 2.075 58.875 44 0.125 1.0 60.824999999999996 38.05 45 1.925 1.0999999999999999 96.925 0.05 46 58.85 3.0 38.15 0.0 >>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 0.0 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 1.0 28 2.0 29 8.0 30 14.0 31 14.0 32 24.5 33 35.0 34 71.0 35 107.0 36 197.5 37 288.0 38 391.5 39 495.0 40 539.0 41 583.0 42 663.0 43 743.0 44 743.0 45 671.0 46 599.0 47 575.0 48 551.0 49 450.0 50 349.0 51 250.5 52 152.0 53 103.5 54 55.0 55 39.5 56 24.0 57 24.0 58 13.5 59 3.0 60 1.5 61 0.0 62 0.0 63 0.0 64 0.0 65 0.0 66 0.0 67 0.0 68 0.0 69 0.0 70 0.0 71 0.0 72 0.0 73 0.0 74 0.0 75 0.0 76 0.0 77 0.0 78 0.0 79 0.0 80 0.0 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 pass #Base N-Count 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 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 >>END_MODULE >>Sequence Length Distribution pass #Length Count 46 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 83.75 #Duplication Level Percentage of deduplicated Percentage of total 1 90.71641791044776 75.97500000000001 2 5.970149253731343 10.0 3 1.761194029850746 4.425 4 0.6268656716417911 2.1 5 0.2985074626865672 1.25 6 0.1791044776119403 0.8999999999999999 7 0.05970149253731343 0.35000000000000003 8 0.029850746268656716 0.2 9 0.08955223880597014 0.675 >10 0.26865671641791045 4.125 >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 fail #Sequence Count Percentage Possible Source GTGATTGAATGAAAAATACATGTACTCGTATGCCGTCTTCTGCTTG 41 1.0250000000000001 TruSeq Adapter, Index 23 (95% over 24bp) GGCTCCTGATCCAGTTACACATGTACTCGTATGCCGTCTTCTGCTT 28 0.7000000000000001 TruSeq Adapter, Index 22 (95% over 24bp) TATGCTTGGAAACTTGAACATGTACTCGTATGCCGTCTTCTGCTTG 22 0.5499999999999999 TruSeq Adapter, Index 22 (96% over 25bp) TAATATTGCTATAAGAAACATGTACTCGTATGCCGTCTTCTGCTTG 16 0.4 TruSeq Adapter, Index 22 (96% over 25bp) GCCTCCTCAAATCCTTTACATGTACTCGTATGCCGTCTTCTGCTTG 16 0.4 TruSeq Adapter, Index 23 (95% over 24bp) TGCCAACACATGTACTCGTATGCCGTCTTCTGCTTGAAAAAAAAAA 11 0.27499999999999997 TruSeq Adapter, Index 22 (96% over 25bp) CCTGGATGAAAAACTTCACATGTACTCGTATGCCGTCTTCTGCTTG 11 0.27499999999999997 TruSeq Adapter, Index 20 (95% over 24bp) TTTTCAGGATCATTTCCACATGTACTCGTATGCCGTCTTCTGCTTG 10 0.25 TruSeq Adapter, Index 22 (96% over 25bp) AGTGAATAATAAGAAGCACATGTACTCGTATGCCGTCTTCTGCTTG 10 0.25 TruSeq Adapter, Index 20 (95% over 24bp) TGCTGAAATTGAGCTGCACATGTACTCGTATGCCGTCTTCTGCTTG 9 0.22499999999999998 TruSeq Adapter, Index 22 (96% over 25bp) GTGATTGAATGAAAAATGACATGTACTCGTATGCCGTCTTCTGCTT 9 0.22499999999999998 TruSeq Adapter, Index 20 (95% over 23bp) GAATTATGTATCTTTAAACATGTACTCGTATGCCGTCTTCTGCTTG 9 0.22499999999999998 TruSeq Adapter, Index 22 (96% over 25bp) TTGTCCAAGATAATGTCACATGTACTCGTATGCCGTCTTCTGCTTG 8 0.2 TruSeq Adapter, Index 22 (96% over 25bp) TTTGTATAATGGTGCTTACATGTACTCGTATGCCGTCTTCTGCTTG 7 0.17500000000000002 TruSeq Adapter, Index 22 (96% over 25bp) AAATGAAGCACCAGTTCAACATGTACTCGTATGCCGTCTTCTGCTT 7 0.17500000000000002 TruSeq Adapter, Index 23 (95% over 23bp) CGGGCATACATACACACACATGTACTCGTATGCCGTCTTCTGCTTG 6 0.15 TruSeq Adapter, Index 22 (96% over 25bp) GAATTATGAAAATAGTCACATGTACTCGTATGCCGTCTTCTGCTTG 6 0.15 TruSeq Adapter, Index 22 (96% over 25bp) TGAAATAAACGTTTCCTACATGTACTCGTATGCCGTCTTCTGCTTG 6 0.15 TruSeq Adapter, Index 23 (95% over 24bp) GCAGTAATGGAAGGAAATACATGTACTCGTATGCCGTCTTCTGCTT 6 0.15 TruSeq Adapter, Index 23 (95% over 23bp) CAGTTTTATTATGCTCGCACATGTACTCGTATGCCGTCTTCTGCTT 6 0.15 TruSeq Adapter, Index 20 (95% over 23bp) TGTTTTGAAATGATAATACATGTACTCGTATGCCGTCTTCTGCTTG 6 0.15 TruSeq Adapter, Index 22 (96% over 25bp) CGTGTATTGCAATCTTCACATGTACTCGTATGCCGTCTTCTGCTTG 5 0.125 TruSeq Adapter, Index 20 (95% over 24bp) TATGCTTGGAAACTTGACATGTACTCGTATGCCGTCTTCTGCTTGA 5 0.125 TruSeq Adapter, Index 22 (96% over 25bp) CTATGCTACTTTCTTTCACATGTACTCGTATGCCGTCTTCTGCTTG 5 0.125 TruSeq Adapter, Index 22 (96% over 25bp) GTTAAATTGCCAGACCGCACATGTACTCGTATGCCGTCTTCTGCTT 5 0.125 TruSeq Adapter, Index 22 (95% over 24bp) GCCTCCTCAAATCCTTTCACATGTACTCGTATGCCGTCTTCTGCTT 5 0.125 TruSeq Adapter, Index 22 (95% over 24bp) TATGGTGCTTGGATAATTACATGTACTCGTATGCCGTCTTCTGCTT 5 0.125 TruSeq Adapter, Index 22 (95% over 24bp) TAAATGACTAGAATAATACATGTACTCGTATGCCGTCTTCTGCTTG 5 0.125 TruSeq Adapter, Index 22 (96% over 25bp) TCGCTAACTGGGTATTATACATGTACTCGTATGCCGTCTTCTGCTT 5 0.125 TruSeq Adapter, Index 23 (95% over 23bp) TTGTCCAAGATAATGTCTACATGTACTCGTATGCCGTCTTCTGCTT 5 0.125 TruSeq Adapter, Index 23 (95% over 23bp) GACTGTCAAGCAAAAACACATGTACTCGTATGCCGTCTTCTGCTTG 5 0.125 TruSeq Adapter, Index 20 (95% over 24bp) >>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 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GGACATG 20 0.00111172 40.000004 16 CTGCTTG 230 0.0 38.26087 40 GACATGT 45 3.495188E-8 35.555553 17 AAACATG 25 0.0033271667 32.0 16 AACATGT 55 2.0439438E-7 29.090908 17 TTACATG 60 4.3841465E-7 26.666668 17 GTACATG 30 0.008119183 26.666668 17 GCACATG 30 0.008119183 26.666668 16 CTACATG 30 0.008119183 26.666668 16 TACATGT 150 0.0 22.666666 18 ACTCGTA 400 0.0 22.0 24 GTATGCC 400 0.0 22.0 28 ACATGTA 400 0.0 22.0 18 TGCCGTC 400 0.0 22.0 31 GTACTCG 400 0.0 22.0 22 TATGCCG 400 0.0 22.0 29 CCGTCTT 400 0.0 22.0 33 ATGCCGT 400 0.0 22.0 30 GTCTTCT 400 0.0 22.0 35 CGTATGC 400 0.0 22.0 27 >>END_MODULE Read 240829 spots for SRR2962699.sra Written 240829 spots for SRR2962699.sra Read 240829 spots for SRR2962699.sra Written 240829 spots for SRR2962699.sra Read 240829 spots for SRR2962699.sra Written 240829 spots for SRR2962699.sra Read 240829 spots for SRR2962699.sra Written 240829 spots for SRR2962699.sra Read 240829 spots for SRR2962699.sra Written 240829 spots for SRR2962699.sra Read 240829 spots for SRR2962699.sra Written 240829 spots for SRR2962699.sra Read 240829 spots for SRR2962699.sra Written 240829 spots for SRR2962699.sra Read 240829 spots for SRR2962699.sra Written 240829 spots for SRR2962699.sra Read 240829 spots for SRR2962699.sra Written 240829 spots for SRR2962699.sra Read 240829 spots for SRR2962699.sra Written 240829 spots for SRR2962699.sra Read 240829 spots for SRR2962699.sra Written 240829 spots for SRR2962699.sra Read 240829 spots for SRR2962699.sra Written 240829 spots for SRR2962699.sra Read 240829 spots for SRR2962699.sra Written 240829 spots for SRR2962699.sra Read 240829 spots for SRR2962699.sra Written 240829 spots for SRR2962699.sra Read 240829 spots for SRR2962699.sra Written 240829 spots for SRR2962699.sra Read 240833 spots for SRR2962699.sra Written 240833 spots for SRR2962699.sra Read 240829 spots for SRR2962699.sra Written 240829 spots for SRR2962699.sra Read 240829 spots for SRR2962699.sra Written 240829 spots for SRR2962699.sra Read 240829 spots for SRR2962699.sra Written 240829 spots for SRR2962699.sra Read 240829 spots for SRR2962699.sra Written 240829 spots for SRR2962699.sra SRR ids: ['SRR2962699.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_4nej62u_ SRR2962699.sra spots: 4816584 blocks: [[1, 240829], [240830, 481658], [481659, 722487], [722488, 963316], [963317, 1204145], [1204146, 1444974], [1444975, 1685803], [1685804, 1926632], [1926633, 2167461], [2167462, 2408290], [2408291, 2649119], [2649120, 2889948], [2889949, 3130777], [3130778, 3371606], [3371607, 3612435], [3612436, 3853264], [3853265, 4094093], [4094094, 4334922], [4334923, 4575751], [4575752, 4816584]] SRR2962699 file size 735002 SRR2962699 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 SRR2962699 SRR2962699_1.fastq Input file: SRR2962699_1.fastq trimmed: SRR2962699-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 Mon Feb 10 12:13:58 2025 >> started Mon Feb 10 12:14:00 2025 >> done (2.123s) 4816584 reads processed; of these: 2085 ( 0.04%) short reads filtered out after trimming by size control 13 ( 0.00%) empty reads filtered out after trimming by size control 4814486 (99.96%) reads available; of these: 69245 ( 1.44%) trimmed reads available after processing 4745241 (98.56%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 2090 0.04% 19 810 0.02% 20 962 0.02% 21 1743 0.04% 22 1189 0.02% 23 432 0.01% 24 479 0.01% 25 1414 0.03% 26 784 0.02% 27 872 0.02% 28 1143 0.02% 29 634 0.01% 30 471 0.01% 31 440 0.01% 32 294 0.01% 33 379 0.01% 34 2080 0.04% 35 1133 0.02% 36 1258 0.03% 37 803 0.02% 38 977 0.02% 39 6672 0.14% 40 4360 0.09% 41 3079 0.06% 42 2853 0.06% 43 3968 0.08% 44 4895 0.10% 45 23031 0.48% 46 4745241 98.56% 4814486 reads passed initial QC criterion=sequence-density sequence-density=99.63 sequence-density-rank=1 fanout-score=40.20 fanout-score-rank=1 prefix-density=99.60 prefix-fanout=40.2 sequence=ACATGTACTCGTATGCCGTCTTCTGCTTGAAAAA criterion=fanout-score sequence-density=99.63 sequence-density-rank=1 fanout-score=40.20 fanout-score-rank=1 prefix-density=99.60 prefix-fanout=40.2 sequence=ACATGTACTCGTATGCCGTCTTCTGCTTGAAAAA 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 ACATGTACTCGTATGCCGTCTTCTGCTTGAAAAA -o SRR2962699 - Input file: STDIN trimmed: SRR2962699-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): ACATGTACTCGTATGCCGTCTTCTGCTTGAAAAA -- 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 Mon Feb 10 12:14:08 2025 >> started Mon Feb 10 12:14:11 2025 >> done (2.898s) 4718196 reads processed; of these: 2875597 (60.95%) short reads filtered out after trimming by size control 636 ( 0.01%) empty reads filtered out after trimming by size control 1841963 (39.04%) reads available; of these: 1837958 (99.78%) trimmed reads available after processing 4005 ( 0.22%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 1831886 99.45% 19 3087 0.17% 20 1812 0.10% 21 1481 0.08% 22 813 0.04% 23 710 0.04% 24 452 0.02% 25 247 0.01% 26 185 0.01% 27 99 0.01% 28 54 0.00% 29 27 0.00% 30 15 0.00% 31 30 0.00% 32 65 0.00% 33 78 0.00% 34 99 0.01% 35 81 0.00% 36 505 0.03% 37 152 0.01% 38 2 0.00% 39 0 0.00% 40 0 0.00% 41 3 0.00% 42 3 0.00% 43 1 0.00% 44 2 0.00% 45 5 0.00% 46 69 0.00% criterion=sequence-density sequence-density=4.95 sequence-density-rank=1 fanout-score=40.16 fanout-score-rank=1 prefix-density=4.95 prefix-fanout=40.2 sequence=ACATGTACTCGTATGCCGTCTTCTGCTTGAAAAA criterion=fanout-score sequence-density=4.95 sequence-density-rank=1 fanout-score=40.16 fanout-score-rank=1 prefix-density=4.95 prefix-fanout=40.2 sequence=ACATGTACTCGTATGCCGTCTTCTGCTTGAAAAA Started job on | Feb 10 12:14:19 Started mapping on | Feb 10 12:14:20 Finished on | Feb 10 12:14:55 Mapping speed, Million of reads per hour | 199.36 Number of input reads | 1938253 Average input read length | 19 UNIQUE READS: Uniquely mapped reads number | 1442303 Uniquely mapped reads % | 74.41% Average mapped length | 17.99 Number of splices: Total | 14599 Number of splices: Annotated (sjdb) | 14366 Number of splices: GT/AG | 14410 Number of splices: GC/AG | 149 Number of splices: AT/AC | 33 Number of splices: Non-canonical | 7 Mismatch rate per base, % | 0.01% Deletion rate per base | 0.00% Deletion average length | 0.00 Insertion rate per base | 0.00% Insertion average length | 0.00 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 378525 % of reads mapped to multiple loci | 19.53% Number of reads mapped to too many loci | 14048 % of reads mapped to too many loci | 0.72% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 5.01% % of reads unmapped: other | 0.32% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 117425 117425 117425 N_multimapping 378525 378525 378525 N_noFeature 134919 308433 1256988 N_ambiguous 16543 3218 1548 UnstrandedReadsAssigned:1290841 PositiveStrandReadsAssigned:1130652 NegativeStrandReadsAssigned:183767 Dataset is classified positive stranded MeadianReadLen=18 20thPercentileLength=18 echo kmer=19 SRR2962699 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: 52,400 [index] number of k-mers: 59,590,899 [index] number of equivalence classes: 293,668 [quant] running in single-end mode [quant] will process file 1: SRR2962699-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 1,938,253 reads, 14,029 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 627 rounds 52401 SRR2962699.ke.tsv 34699 SRR2962699.se.tsv 87100 total ==> SRR2962699.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1919 3 138.444 Potri.005G024800.1.v4.1 1035 936 0 0 Potri.004G059700.1.v4.1 961 862 0 0 Potri.007G009000.2.v4.1 1416 1317 0 0 Potri.003G141000.2.v4.1 2943 2844 0 0 Potri.016G087400.1.v4.1 270 171 0 0 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 3 302.589 ==> SRR2962699.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 1 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 100 Potri.001G212900.v4.1 0 Potri.001G182400.v4.1 0 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 0 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 3 SRR2962699 completed mapping pipeline successfully