SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/8C_26psu_1_S9_L002_R1_001.fastq.gz Trimming mode: paired-end Trim Galore version: 0.6.4_dev Cutadapt version: 2.4 Python version: could not detect Number of cores used for trimming: 8 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Using Illumina adapter for trimming (count: 511403). Second best hit was Nextera (count: 1) Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; auto-detected) 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/strigg/analyses/20200427/TG_PE_FASTQS/FastQC --threads 28 Output file will be GZIP compressed This is cutadapt 2.4 with Python 3.7.6 Command line parameters: -j 8 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/8C_26psu_1_S9_L002_R1_001.fastq.gz Processing reads on 8 cores in single-end mode ... Finished in 70.16 s (4 us/read; 15.44 M reads/minute). === Summary === Total reads processed: 18,056,494 Reads with adapters: 13,928,110 (77.1%) Reads written (passing filters): 18,056,494 (100.0%) Total basepairs processed: 2,708,474,100 bp Quality-trimmed: 5,741,117 bp (0.2%) Total written (filtered): 2,137,545,368 bp (78.9%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 13928110 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 30.7% C: 14.8% G: 20.2% T: 34.3% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 2529563 4514123.5 0 2529563 2 355142 1128530.9 0 355142 3 202264 282132.7 0 202264 4 116958 70533.2 0 116958 5 97699 17633.3 0 97699 6 92485 4408.3 0 92485 7 72663 1102.1 0 72663 8 94383 275.5 0 94383 9 92644 68.9 0 91510 1134 10 86522 17.2 1 80894 5628 11 97786 4.3 1 89346 8440 12 93298 1.1 1 86415 6883 13 95771 0.3 1 88325 7446 14 95946 0.3 1 88058 7888 15 101399 0.3 1 93509 7890 16 98158 0.3 1 89606 8552 17 122597 0.3 1 111303 11294 18 101750 0.3 1 94436 7314 19 86831 0.3 1 80395 6436 20 105075 0.3 1 97137 7938 21 118601 0.3 1 108999 9602 22 97228 0.3 1 90470 6758 23 116927 0.3 1 107741 9186 24 105532 0.3 1 95756 9776 25 113828 0.3 1 105061 8767 26 103778 0.3 1 96608 7170 27 117560 0.3 1 107874 9686 28 114336 0.3 1 105504 8832 29 122580 0.3 1 111680 10900 30 130099 0.3 1 121451 8648 31 97669 0.3 1 90483 7186 32 124295 0.3 1 114657 9638 33 112476 0.3 1 103286 9190 34 140784 0.3 1 128812 11972 35 103370 0.3 1 96154 7216 36 134329 0.3 1 122737 11592 37 117550 0.3 1 108946 8604 38 133588 0.3 1 123334 10254 39 130482 0.3 1 119347 11135 40 122686 0.3 1 113961 8725 41 145432 0.3 1 132894 12538 42 118079 0.3 1 107701 10378 43 189764 0.3 1 177939 11825 44 65407 0.3 1 59230 6177 45 132188 0.3 1 122729 9459 46 127290 0.3 1 117848 9442 47 135499 0.3 1 126055 9444 48 126038 0.3 1 116373 9665 49 142407 0.3 1 130956 11451 50 121520 0.3 1 113382 8138 51 130837 0.3 1 121331 9506 52 138254 0.3 1 127263 10991 53 150154 0.3 1 140134 10020 54 113941 0.3 1 105808 8133 55 137202 0.3 1 127382 9820 56 163618 0.3 1 152691 10927 57 113941 0.3 1 104904 9037 58 135543 0.3 1 127222 8321 59 114833 0.3 1 106375 8458 60 134934 0.3 1 125495 9439 61 131069 0.3 1 122212 8857 62 140049 0.3 1 130678 9371 63 118477 0.3 1 109768 8709 64 123661 0.3 1 115672 7989 65 136910 0.3 1 127445 9465 66 142766 0.3 1 132932 9834 67 155161 0.3 1 142407 12754 68 281796 0.3 1 266464 15332 69 68541 0.3 1 62954 5587 70 25774 0.3 1 21904 3870 71 70954 0.3 1 66131 4823 72 107448 0.3 1 100862 6586 73 114621 0.3 1 107221 7400 74 114007 0.3 1 106477 7530 75 113035 0.3 1 105200 7835 76 110785 0.3 1 102896 7889 77 110971 0.3 1 103289 7682 78 105110 0.3 1 97785 7325 79 103881 0.3 1 96578 7303 80 100380 0.3 1 93184 7196 81 99197 0.3 1 92210 6987 82 96750 0.3 1 90051 6699 83 92818 0.3 1 86379 6439 84 91340 0.3 1 84942 6398 85 87669 0.3 1 81553 6116 86 83869 0.3 1 77984 5885 87 80883 0.3 1 75364 5519 88 79450 0.3 1 73820 5630 89 76461 0.3 1 71121 5340 90 75182 0.3 1 69973 5209 91 71175 0.3 1 66391 4784 92 67480 0.3 1 62890 4590 93 64001 0.3 1 59615 4386 94 61685 0.3 1 57457 4228 95 57220 0.3 1 53201 4019 96 54819 0.3 1 51015 3804 97 51023 0.3 1 47551 3472 98 47615 0.3 1 44173 3442 99 45999 0.3 1 42533 3466 100 42439 0.3 1 39454 2985 101 39032 0.3 1 36135 2897 102 36673 0.3 1 33901 2772 103 33569 0.3 1 31176 2393 104 31500 0.3 1 29209 2291 105 28075 0.3 1 26011 2064 106 25509 0.3 1 23615 1894 107 23441 0.3 1 21761 1680 108 21666 0.3 1 19921 1745 109 19354 0.3 1 17847 1507 110 17443 0.3 1 16060 1383 111 15864 0.3 1 14569 1295 112 13943 0.3 1 12833 1110 113 12164 0.3 1 11191 973 114 10656 0.3 1 9783 873 115 9192 0.3 1 8432 760 116 8137 0.3 1 7437 700 117 6646 0.3 1 6079 567 118 6028 0.3 1 5475 553 119 4941 0.3 1 4488 453 120 4276 0.3 1 3914 362 121 3804 0.3 1 3440 364 122 2994 0.3 1 2656 338 123 2568 0.3 1 2298 270 124 2204 0.3 1 2017 187 125 1837 0.3 1 1657 180 126 1524 0.3 1 1357 167 127 1388 0.3 1 1226 162 128 1017 0.3 1 890 127 129 886 0.3 1 773 113 130 713 0.3 1 646 67 131 614 0.3 1 547 67 132 610 0.3 1 554 56 133 738 0.3 1 662 76 134 1198 0.3 1 1126 72 135 479 0.3 1 433 46 136 180 0.3 1 151 29 137 120 0.3 1 102 18 138 100 0.3 1 79 21 139 54 0.3 1 43 11 140 63 0.3 1 49 14 141 34 0.3 1 27 7 142 36 0.3 1 27 9 143 19 0.3 1 17 2 144 13 0.3 1 11 2 145 29 0.3 1 22 7 146 21 0.3 1 18 3 147 72 0.3 1 61 11 148 53 0.3 1 46 7 149 48 0.3 1 42 6 150 601 0.3 1 530 71 RUN STATISTICS FOR INPUT FILE: /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/8C_26psu_1_S9_L002_R1_001.fastq.gz ============================================= 18056494 sequences processed in total