SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/16C_32psu_1_S1_L002_R2_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: 628232). Second best hit was Nextera (count: 0) 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/16C_32psu_1_S1_L002_R2_001.fastq.gz Processing reads on 8 cores in single-end mode ... Finished in 73.76 s (4 us/read; 15.92 M reads/minute). === Summary === Total reads processed: 19,571,235 Reads with adapters: 16,271,535 (83.1%) Reads written (passing filters): 19,571,235 (100.0%) Total basepairs processed: 2,935,685,250 bp Quality-trimmed: 14,968,782 bp (0.5%) Total written (filtered): 2,137,866,393 bp (72.8%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 16271535 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 28.4% C: 12.6% G: 25.1% T: 33.9% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 1934443 4892808.8 0 1934443 2 292006 1223202.2 0 292006 3 180981 305800.5 0 180981 4 103045 76450.1 0 103045 5 98608 19112.5 0 98608 6 87562 4778.1 0 87562 7 69739 1194.5 0 69739 8 101138 298.6 0 101138 9 80590 74.7 0 80291 299 10 87083 18.7 1 80903 6180 11 94744 4.7 1 86859 7885 12 93509 1.2 1 85833 7676 13 107672 0.3 1 99050 8622 14 100767 0.3 1 91771 8996 15 81145 0.3 1 74763 6382 16 119727 0.3 1 109867 9860 17 101003 0.3 1 92682 8321 18 90163 0.3 1 83122 7041 19 118403 0.3 1 108874 9529 20 111750 0.3 1 103085 8665 21 98369 0.3 1 90814 7555 22 111808 0.3 1 103242 8566 23 118255 0.3 1 109009 9246 24 118284 0.3 1 108899 9385 25 134913 0.3 1 125516 9397 26 111710 0.3 1 102736 8974 27 124043 0.3 1 113612 10431 28 113048 0.3 1 105567 7481 29 126854 0.3 1 117529 9325 30 124172 0.3 1 115653 8519 31 138567 0.3 1 128798 9769 32 118532 0.3 1 110581 7951 33 139520 0.3 1 129113 10407 34 182115 0.3 1 169415 12700 35 97650 0.3 1 90702 6948 36 141232 0.3 1 130648 10584 37 151183 0.3 1 140571 10612 38 140794 0.3 1 131792 9002 39 135094 0.3 1 126791 8303 40 155470 0.3 1 144881 10589 41 152110 0.3 1 142307 9803 42 156034 0.3 1 145893 10141 43 140408 0.3 1 131398 9010 44 166488 0.3 1 155279 11209 45 176759 0.3 1 165212 11547 46 127616 0.3 1 119430 8186 47 162788 0.3 1 153156 9632 48 159821 0.3 1 150024 9797 49 167515 0.3 1 156791 10724 50 162854 0.3 1 152416 10438 51 201852 0.3 1 189155 12697 52 145803 0.3 1 136773 9030 53 181599 0.3 1 171435 10164 54 132563 0.3 1 124771 7792 55 175847 0.3 1 165921 9926 56 182238 0.3 1 170952 11286 57 175759 0.3 1 166454 9305 58 168899 0.3 1 159768 9131 59 170487 0.3 1 160788 9699 60 179591 0.3 1 169442 10149 61 183203 0.3 1 173168 10035 62 201509 0.3 1 189650 11859 63 267932 0.3 1 254493 13439 64 223354 0.3 1 213922 9432 65 145944 0.3 1 138249 7695 66 160488 0.3 1 151671 8817 67 160429 0.3 1 151245 9184 68 163626 0.3 1 154620 9006 69 162388 0.3 1 153192 9196 70 171183 0.3 1 161721 9462 71 179954 0.3 1 170347 9607 72 173057 0.3 1 163544 9513 73 181347 0.3 1 171665 9682 74 168687 0.3 1 159362 9325 75 161354 0.3 1 152554 8800 76 158086 0.3 1 149538 8548 77 158408 0.3 1 149654 8754 78 152524 0.3 1 144195 8329 79 148468 0.3 1 140463 8005 80 146791 0.3 1 138965 7826 81 146914 0.3 1 138951 7963 82 140738 0.3 1 133245 7493 83 136720 0.3 1 129557 7163 84 133340 0.3 1 126399 6941 85 131509 0.3 1 124949 6560 86 131725 0.3 1 125074 6651 87 132992 0.3 1 126515 6477 88 130544 0.3 1 124131 6413 89 118247 0.3 1 112246 6001 90 114880 0.3 1 109042 5838 91 108202 0.3 1 102767 5435 92 102465 0.3 1 97298 5167 93 99313 0.3 1 94369 4944 94 96247 0.3 1 91557 4690 95 90355 0.3 1 85764 4591 96 86105 0.3 1 81859 4246 97 80863 0.3 1 77002 3861 98 76806 0.3 1 73205 3601 99 77725 0.3 1 74014 3711 100 71514 0.3 1 68090 3424 101 67122 0.3 1 63869 3253 102 62547 0.3 1 59630 2917 103 55990 0.3 1 53291 2699 104 53130 0.3 1 50496 2634 105 47112 0.3 1 44737 2375 106 43436 0.3 1 41396 2040 107 39313 0.3 1 37430 1883 108 36083 0.3 1 34294 1789 109 32958 0.3 1 31374 1584 110 30549 0.3 1 29023 1526 111 28680 0.3 1 27349 1331 112 25012 0.3 1 23754 1258 113 21932 0.3 1 20848 1084 114 19318 0.3 1 18424 894 115 16367 0.3 1 15528 839 116 14214 0.3 1 13511 703 117 11890 0.3 1 11258 632 118 10558 0.3 1 10008 550 119 8964 0.3 1 8531 433 120 7160 0.3 1 6810 350 121 6260 0.3 1 5925 335 122 5526 0.3 1 5261 265 123 4601 0.3 1 4388 213 124 3924 0.3 1 3711 213 125 3337 0.3 1 3153 184 126 2851 0.3 1 2683 168 127 2269 0.3 1 2147 122 128 1715 0.3 1 1615 100 129 1527 0.3 1 1454 73 130 1240 0.3 1 1181 59 131 1038 0.3 1 985 53 132 992 0.3 1 936 56 133 1237 0.3 1 1180 57 134 1424 0.3 1 1372 52 135 637 0.3 1 603 34 136 325 0.3 1 316 9 137 239 0.3 1 218 21 138 165 0.3 1 161 4 139 114 0.3 1 104 10 140 92 0.3 1 87 5 141 71 0.3 1 68 3 142 32 0.3 1 29 3 143 33 0.3 1 28 5 144 26 0.3 1 21 5 145 62 0.3 1 60 2 146 42 0.3 1 41 1 147 127 0.3 1 113 14 148 65 0.3 1 60 5 149 42 0.3 1 37 5 150 529 0.3 1 500 29 RUN STATISTICS FOR INPUT FILE: /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/16C_32psu_1_S1_L002_R2_001.fastq.gz ============================================= 19571235 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 19571235 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 259958 (1.33%)