SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_19_R2.fq.gz Trimming mode: paired-end Trim Galore version: 0.6.6 Cutadapt version: 3.1 Number of cores used for trimming: 1 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; user defined) Maximum trimming error rate: 0.1 (default) Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp All Read 1 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) All Read 1 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: --outdir /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore --threads 28 Output file will be GZIP compressed This is cutadapt 3.1 with Python 3.8.5 Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_19_R2.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1655.35 s (33 µs/read; 1.80 M reads/minute). === Summary === Total reads processed: 49,611,452 Reads with adapters: 21,264,708 (42.9%) Reads written (passing filters): 49,611,452 (100.0%) Total basepairs processed: 6,250,440,107 bp Quality-trimmed: 1,909,058 bp (0.0%) Total written (filtered): 6,223,480,605 bp (99.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 21264708 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 45.4% C: 10.2% G: 6.3% T: 38.1% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 18951183 12402863.0 0 18951183 2 1500520 3100715.8 0 1500520 3 436592 775178.9 0 436592 4 282984 193794.7 0 282984 5 51132 48448.7 0 51132 6 12327 12112.2 0 12327 7 8936 3028.0 0 8936 8 6950 757.0 0 6950 9 1871 189.3 0 1439 432 10 11241 47.3 1 10289 952 11 133 11.8 1 19 114 12 32 3.0 1 6 26 13 5 0.7 1 1 4 14 2 0.7 1 2 15 4 0.7 1 2 2 16 5 0.7 1 3 2 17 6 0.7 1 2 4 19 5 0.7 1 3 2 21 1 0.7 1 1 22 6 0.7 1 4 2 23 4 0.7 1 0 4 24 3 0.7 1 1 2 25 4 0.7 1 1 3 26 3 0.7 1 2 1 27 5 0.7 1 3 2 28 7 0.7 1 3 4 29 4 0.7 1 2 2 31 3 0.7 1 2 1 32 6 0.7 1 4 2 33 3 0.7 1 1 2 34 5 0.7 1 4 1 35 6 0.7 1 4 2 36 3 0.7 1 3 37 2 0.7 1 1 1 38 3 0.7 1 1 2 39 2 0.7 1 2 40 1 0.7 1 0 1 41 1 0.7 1 1 42 3 0.7 1 3 43 7 0.7 1 5 2 44 4 0.7 1 3 1 45 6 0.7 1 4 2 46 4 0.7 1 2 2 47 2 0.7 1 0 2 49 2 0.7 1 2 50 2 0.7 1 2 52 1 0.7 1 0 1 53 6 0.7 1 3 3 54 3 0.7 1 2 1 55 1 0.7 1 1 56 4 0.7 1 1 3 57 6 0.7 1 6 58 8 0.7 1 5 3 59 2 0.7 1 2 60 3 0.7 1 0 3 61 3 0.7 1 3 62 4 0.7 1 3 1 63 2 0.7 1 1 1 64 2 0.7 1 1 1 65 5 0.7 1 5 66 4 0.7 1 2 2 67 5 0.7 1 4 1 68 6 0.7 1 6 69 1 0.7 1 0 1 70 3 0.7 1 3 71 4 0.7 1 3 1 72 2 0.7 1 2 73 3 0.7 1 3 74 2 0.7 1 2 75 5 0.7 1 5 76 3 0.7 1 3 77 7 0.7 1 4 3 78 3 0.7 1 3 79 3 0.7 1 3 80 5 0.7 1 3 2 81 5 0.7 1 4 1 82 4 0.7 1 3 1 83 2 0.7 1 2 84 1 0.7 1 1 85 3 0.7 1 2 1 86 4 0.7 1 4 87 4 0.7 1 4 88 7 0.7 1 5 2 89 7 0.7 1 5 2 90 8 0.7 1 6 2 91 4 0.7 1 3 1 92 5 0.7 1 5 93 5 0.7 1 4 1 94 4 0.7 1 3 1 95 3 0.7 1 3 96 7 0.7 1 7 97 9 0.7 1 5 4 98 5 0.7 1 3 2 99 11 0.7 1 8 3 100 11 0.7 1 10 1 101 9 0.7 1 4 5 102 15 0.7 1 12 3 103 1 0.7 1 1 104 4 0.7 1 3 1 105 5 0.7 1 4 1 106 7 0.7 1 6 1 107 3 0.7 1 3 108 10 0.7 1 9 1 109 16 0.7 1 12 4 110 12 0.7 1 11 1 111 9 0.7 1 8 1 112 11 0.7 1 11 113 10 0.7 1 7 3 114 9 0.7 1 6 3 115 7 0.7 1 5 2 116 9 0.7 1 8 1 117 9 0.7 1 7 2 118 11 0.7 1 10 1 119 20 0.7 1 17 3 120 7 0.7 1 6 1 121 12 0.7 1 11 1 122 13 0.7 1 12 1 123 12 0.7 1 9 3 124 13 0.7 1 12 1 125 20 0.7 1 16 4 126 14 0.7 1 12 2 127 11 0.7 1 11 128 16 0.7 1 15 1 129 17 0.7 1 15 2 130 17 0.7 1 14 3 131 21 0.7 1 18 3 132 15 0.7 1 11 4 133 23 0.7 1 18 5 134 33 0.7 1 19 14 135 42 0.7 1 19 23 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_19_R2.fq.gz ============================================= 49611452 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 49611452 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 248048 (0.50%)