SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_9_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_9_R2.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1536.59 s (31 µs/read; 1.92 M reads/minute). === Summary === Total reads processed: 49,101,606 Reads with adapters: 20,297,822 (41.3%) Reads written (passing filters): 49,101,606 (100.0%) Total basepairs processed: 6,078,278,717 bp Quality-trimmed: 2,099,959 bp (0.0%) Total written (filtered): 6,051,789,039 bp (99.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 20297822 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 45.3% C: 10.1% G: 6.5% T: 38.0% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 17869930 12275401.5 0 17869930 2 1574910 3068850.4 0 1574910 3 427072 767212.6 0 427072 4 296533 191803.1 0 296533 5 70445 47950.8 0 70445 6 17079 11987.7 0 17079 7 12905 2996.9 0 12905 8 9863 749.2 0 9863 9 2451 187.3 0 1954 497 10 15313 46.8 1 14170 1143 11 152 11.7 1 25 127 12 46 2.9 1 12 34 13 10 0.7 1 2 8 14 7 0.7 1 4 3 15 7 0.7 1 3 4 16 6 0.7 1 1 5 17 11 0.7 1 6 5 18 5 0.7 1 4 1 19 8 0.7 1 4 4 20 4 0.7 1 3 1 21 3 0.7 1 2 1 22 2 0.7 1 1 1 23 7 0.7 1 5 2 24 4 0.7 1 3 1 25 7 0.7 1 4 3 26 5 0.7 1 2 3 27 7 0.7 1 4 3 28 8 0.7 1 5 3 29 5 0.7 1 3 2 30 3 0.7 1 2 1 31 4 0.7 1 3 1 32 9 0.7 1 4 5 33 6 0.7 1 3 3 34 4 0.7 1 2 2 35 6 0.7 1 4 2 36 5 0.7 1 3 2 38 2 0.7 1 0 2 39 6 0.7 1 4 2 40 6 0.7 1 4 2 41 7 0.7 1 7 42 4 0.7 1 2 2 43 6 0.7 1 4 2 44 10 0.7 1 5 5 45 5 0.7 1 5 46 4 0.7 1 3 1 47 3 0.7 1 1 2 48 9 0.7 1 7 2 49 5 0.7 1 5 50 2 0.7 1 2 51 10 0.7 1 5 5 52 4 0.7 1 3 1 53 9 0.7 1 6 3 54 9 0.7 1 5 4 55 4 0.7 1 3 1 56 6 0.7 1 5 1 57 11 0.7 1 6 5 58 6 0.7 1 5 1 59 4 0.7 1 4 60 2 0.7 1 1 1 61 6 0.7 1 5 1 62 5 0.7 1 3 2 63 7 0.7 1 5 2 64 11 0.7 1 8 3 65 7 0.7 1 6 1 66 10 0.7 1 7 3 67 5 0.7 1 4 1 68 6 0.7 1 4 2 69 8 0.7 1 7 1 70 1 0.7 1 1 71 3 0.7 1 1 2 72 3 0.7 1 1 2 73 5 0.7 1 3 2 74 2 0.7 1 2 75 6 0.7 1 3 3 76 8 0.7 1 8 77 8 0.7 1 8 78 6 0.7 1 4 2 79 10 0.7 1 6 4 80 12 0.7 1 11 1 81 4 0.7 1 1 3 82 8 0.7 1 6 2 83 11 0.7 1 9 2 84 8 0.7 1 7 1 85 6 0.7 1 4 2 86 10 0.7 1 9 1 87 3 0.7 1 3 88 8 0.7 1 7 1 89 4 0.7 1 4 90 8 0.7 1 6 2 91 4 0.7 1 3 1 92 6 0.7 1 4 2 93 8 0.7 1 6 2 94 8 0.7 1 8 95 18 0.7 1 16 2 96 11 0.7 1 11 97 10 0.7 1 10 98 7 0.7 1 4 3 99 7 0.7 1 6 1 100 9 0.7 1 6 3 101 11 0.7 1 7 4 102 10 0.7 1 10 103 6 0.7 1 5 1 104 10 0.7 1 7 3 105 9 0.7 1 6 3 106 15 0.7 1 13 2 107 10 0.7 1 9 1 108 14 0.7 1 12 2 109 13 0.7 1 11 2 110 14 0.7 1 10 4 111 8 0.7 1 8 112 11 0.7 1 10 1 113 18 0.7 1 15 3 114 14 0.7 1 9 5 115 5 0.7 1 4 1 116 17 0.7 1 14 3 117 10 0.7 1 7 3 118 21 0.7 1 17 4 119 16 0.7 1 15 1 120 23 0.7 1 22 1 121 24 0.7 1 20 4 122 10 0.7 1 9 1 123 9 0.7 1 7 2 124 15 0.7 1 11 4 125 17 0.7 1 14 3 126 20 0.7 1 19 1 127 16 0.7 1 13 3 128 21 0.7 1 20 1 129 20 0.7 1 19 1 130 19 0.7 1 15 4 131 9 0.7 1 8 1 132 21 0.7 1 17 4 133 31 0.7 1 18 13 134 29 0.7 1 19 10 135 43 0.7 1 22 21 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/data/zr3644_9_R2.fq.gz ============================================= 49101606 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 49101606 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 341760 (0.70%)