SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/8C_26psu_2_S10_L001_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: 573873). 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/8C_26psu_2_S10_L001_R1_001.fastq.gz Processing reads on 8 cores in single-end mode ... Finished in 66.61 s (4 us/read; 16.65 M reads/minute). === Summary === Total reads processed: 18,482,577 Reads with adapters: 14,846,196 (80.3%) Reads written (passing filters): 18,482,577 (100.0%) Total basepairs processed: 2,772,386,550 bp Quality-trimmed: 5,236,502 bp (0.2%) Total written (filtered): 2,109,664,469 bp (76.1%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 14846196 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 30.0% C: 14.7% G: 20.4% T: 35.0% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 2201281 4620644.2 0 2201281 2 324820 1155161.1 0 324820 3 181187 288790.3 0 181187 4 111024 72197.6 0 111024 5 91444 18049.4 0 91444 6 89339 4512.3 0 89339 7 75499 1128.1 0 75499 8 92079 282.0 0 92079 9 94613 70.5 0 93305 1308 10 87393 17.6 1 82726 4667 11 97272 4.4 1 89821 7451 12 94618 1.1 1 88577 6041 13 94580 0.3 1 88291 6289 14 98608 0.3 1 91401 7207 15 100703 0.3 1 94036 6667 16 100759 0.3 1 93186 7573 17 122345 0.3 1 112475 9870 18 103137 0.3 1 96868 6269 19 89996 0.3 1 84224 5772 20 107642 0.3 1 100714 6928 21 118859 0.3 1 110501 8358 22 101938 0.3 1 96023 5915 23 117604 0.3 1 109853 7751 24 110878 0.3 1 101488 9390 25 118235 0.3 1 110039 8196 26 108371 0.3 1 101787 6584 27 121571 0.3 1 112662 8909 28 119395 0.3 1 110884 8511 29 129888 0.3 1 119161 10727 30 136399 0.3 1 128723 7676 31 101982 0.3 1 95349 6633 32 129923 0.3 1 121526 8397 33 121306 0.3 1 112461 8845 34 134618 0.3 1 125125 9493 35 135522 0.3 1 127399 8123 36 126532 0.3 1 116217 10315 37 132624 0.3 1 124414 8210 38 135436 0.3 1 126589 8847 39 144343 0.3 1 135079 9264 40 131706 0.3 1 123113 8593 41 147103 0.3 1 136472 10631 42 135693 0.3 1 124813 10880 43 208641 0.3 1 197928 10713 44 70084 0.3 1 63748 6336 45 146631 0.3 1 137638 8993 46 134243 0.3 1 125635 8608 47 148092 0.3 1 138684 9408 48 143207 0.3 1 133950 9257 49 157250 0.3 1 146216 11034 50 135654 0.3 1 127338 8316 51 145480 0.3 1 136047 9433 52 151730 0.3 1 141076 10654 53 160594 0.3 1 150536 10058 54 131608 0.3 1 123193 8415 55 153566 0.3 1 143551 10015 56 188903 0.3 1 177823 11080 57 122969 0.3 1 114039 8930 58 155982 0.3 1 147471 8511 59 136864 0.3 1 128026 8838 60 152804 0.3 1 142938 9866 61 149972 0.3 1 141027 8945 62 164460 0.3 1 154790 9670 63 131600 0.3 1 122512 9088 64 147097 0.3 1 138434 8663 65 163813 0.3 1 153627 10186 66 170976 0.3 1 160133 10843 67 181725 0.3 1 167572 14153 68 347424 0.3 1 330644 16780 69 53801 0.3 1 49133 4668 70 21119 0.3 1 17296 3823 71 93829 0.3 1 88082 5747 72 129343 0.3 1 121746 7597 73 137109 0.3 1 128961 8148 74 135639 0.3 1 127288 8351 75 134319 0.3 1 126050 8269 76 133485 0.3 1 125306 8179 77 133818 0.3 1 125641 8177 78 125826 0.3 1 118003 7823 79 124061 0.3 1 116366 7695 80 122381 0.3 1 114907 7474 81 121340 0.3 1 113873 7467 82 118564 0.3 1 111221 7343 83 114400 0.3 1 107282 7118 84 110060 0.3 1 103458 6602 85 107144 0.3 1 100729 6415 86 104597 0.3 1 98129 6468 87 99965 0.3 1 93811 6154 88 99634 0.3 1 93629 6005 89 94213 0.3 1 88311 5902 90 93784 0.3 1 87912 5872 91 88966 0.3 1 83468 5498 92 84640 0.3 1 79309 5331 93 79324 0.3 1 74386 4938 94 77199 0.3 1 72415 4784 95 72155 0.3 1 67634 4521 96 68840 0.3 1 64535 4305 97 64425 0.3 1 60326 4099 98 60153 0.3 1 56199 3954 99 58789 0.3 1 54783 4006 100 53231 0.3 1 49872 3359 101 49747 0.3 1 46474 3273 102 46514 0.3 1 43441 3073 103 42759 0.3 1 39961 2798 104 40408 0.3 1 37725 2683 105 35915 0.3 1 33458 2457 106 33343 0.3 1 31066 2277 107 30056 0.3 1 28019 2037 108 28759 0.3 1 26783 1976 109 25234 0.3 1 23454 1780 110 22936 0.3 1 21306 1630 111 20750 0.3 1 19240 1510 112 17996 0.3 1 16644 1352 113 15908 0.3 1 14749 1159 114 14075 0.3 1 12991 1084 115 12424 0.3 1 11459 965 116 10747 0.3 1 9910 837 117 9113 0.3 1 8333 780 118 8109 0.3 1 7445 664 119 6883 0.3 1 6316 567 120 5713 0.3 1 5209 504 121 5168 0.3 1 4711 457 122 4185 0.3 1 3804 381 123 3552 0.3 1 3218 334 124 3100 0.3 1 2796 304 125 2576 0.3 1 2315 261 126 2168 0.3 1 1937 231 127 1692 0.3 1 1526 166 128 1332 0.3 1 1165 167 129 1229 0.3 1 1107 122 130 923 0.3 1 838 85 131 751 0.3 1 663 88 132 654 0.3 1 579 75 133 679 0.3 1 607 72 134 1033 0.3 1 947 86 135 428 0.3 1 390 38 136 228 0.3 1 207 21 137 170 0.3 1 154 16 138 136 0.3 1 118 18 139 81 0.3 1 70 11 140 68 0.3 1 55 13 141 49 0.3 1 43 6 142 55 0.3 1 47 8 143 45 0.3 1 36 9 144 21 0.3 1 19 2 145 58 0.3 1 54 4 146 122 0.3 1 110 12 147 390 0.3 1 355 35 148 248 0.3 1 225 23 149 170 0.3 1 149 21 150 1709 0.3 1 1353 356 RUN STATISTICS FOR INPUT FILE: /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/8C_26psu_2_S10_L001_R1_001.fastq.gz ============================================= 18482577 sequences processed in total