SUMMARISING RUN PARAMETERS ========================== Input filename: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/16C_32psu_1_S1_L001_R1_001.fastq.gz Trimming mode: single-end Trim Galore version: 0.6.0 Cutadapt version: 2.4 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 before a sequence gets removed: 20 bp Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: --outdir /Volumes/web/metacarcinus/Salmo_Calig/analyses/20190722/TRIM_adapt/FASTQC Output file will be GZIP compressed This is cutadapt 2.4 with Python 3.6.8 Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/16C_32psu_1_S1_L001_R1_001.fastq.gz Processing reads on 1 core in single-end mode ... Finished in 745.76 s (38 us/read; 1.58 M reads/minute). === Summary === Total reads processed: 19,624,894 Reads with adapters: 16,461,713 (83.9%) Reads written (passing filters): 19,624,894 (100.0%) Total basepairs processed: 2,943,734,100 bp Quality-trimmed: 8,161,343 bp (0.3%) Total written (filtered): 2,138,119,098 bp (72.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 16461713 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 29.6% C: 14.5% G: 21.1% T: 34.7% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 1876405 4906223.5 0 1876405 2 285639 1226555.9 0 285639 3 166471 306639.0 0 166471 4 104694 76659.7 0 104694 5 90631 19164.9 0 90631 6 90221 4791.2 0 90221 7 75553 1197.8 0 75553 8 93443 299.5 0 93443 9 94201 74.9 0 93032 1169 10 87809 18.7 1 83198 4611 11 99635 4.7 1 92145 7490 12 94726 1.2 1 88812 5914 13 97394 0.3 1 91137 6257 14 100020 0.3 1 93031 6989 15 103009 0.3 1 96393 6616 16 102618 0.3 1 94905 7713 17 124436 0.3 1 114364 10072 18 107976 0.3 1 101489 6487 19 93413 0.3 1 87422 5991 20 112556 0.3 1 105383 7173 21 124612 0.3 1 116055 8557 22 104064 0.3 1 98066 5998 23 123879 0.3 1 115825 8054 24 114769 0.3 1 105177 9592 25 125576 0.3 1 117036 8540 26 114132 0.3 1 107345 6787 27 127880 0.3 1 118576 9304 28 126438 0.3 1 117548 8890 29 134319 0.3 1 123537 10782 30 144898 0.3 1 136865 8033 31 113550 0.3 1 106291 7259 32 136410 0.3 1 127848 8562 33 133695 0.3 1 124518 9177 34 143757 0.3 1 134451 9306 35 157890 0.3 1 145316 12574 36 132282 0.3 1 123929 8353 37 149188 0.3 1 140073 9115 38 146870 0.3 1 136072 10798 39 172309 0.3 1 159375 12934 40 136570 0.3 1 128574 7996 41 180683 0.3 1 167134 13549 42 139132 0.3 1 127852 11280 43 244330 0.3 1 231176 13154 44 73162 0.3 1 66477 6685 45 161358 0.3 1 150280 11078 46 191244 0.3 1 177928 13316 47 181249 0.3 1 170520 10729 48 141208 0.3 1 129881 11327 49 209170 0.3 1 195203 13967 50 130797 0.3 1 122619 8178 51 161830 0.3 1 151113 10717 52 228270 0.3 1 212080 16190 53 234755 0.3 1 222809 11946 54 127266 0.3 1 118588 8678 55 194077 0.3 1 183800 10277 56 176229 0.3 1 165657 10572 57 215239 0.3 1 203613 11626 58 135465 0.3 1 128771 6694 59 101608 0.3 1 93951 7657 60 209358 0.3 1 197818 11540 61 195964 0.3 1 186497 9467 62 138436 0.3 1 130152 8284 63 180787 0.3 1 170284 10503 64 159166 0.3 1 150739 8427 65 158205 0.3 1 148817 9388 66 190752 0.3 1 179381 11371 67 212991 0.3 1 197325 15666 68 398495 0.3 1 379493 19002 69 144273 0.3 1 135320 8953 70 44631 0.3 1 39323 5308 71 66845 0.3 1 61618 5227 72 147002 0.3 1 138540 8462 73 167373 0.3 1 157828 9545 74 168016 0.3 1 158069 9947 75 167181 0.3 1 157169 10012 76 166317 0.3 1 156562 9755 77 166255 0.3 1 156536 9719 78 159048 0.3 1 149642 9406 79 157934 0.3 1 148379 9555 80 154378 0.3 1 145219 9159 81 154058 0.3 1 144915 9143 82 150711 0.3 1 141779 8932 83 145124 0.3 1 136331 8793 84 142844 0.3 1 134506 8338 85 138019 0.3 1 129804 8215 86 134359 0.3 1 126493 7866 87 130206 0.3 1 122445 7761 88 128131 0.3 1 120526 7605 89 122017 0.3 1 114723 7294 90 121870 0.3 1 114562 7308 91 117180 0.3 1 110087 7093 92 111859 0.3 1 105091 6768 93 105927 0.3 1 99576 6351 94 102547 0.3 1 96466 6081 95 95663 0.3 1 89977 5686 96 91505 0.3 1 85936 5569 97 86471 0.3 1 81209 5262 98 81070 0.3 1 76155 4915 99 79954 0.3 1 74613 5341 100 72882 0.3 1 68442 4440 101 68704 0.3 1 64356 4348 102 63576 0.3 1 59490 4086 103 59368 0.3 1 55615 3753 104 55418 0.3 1 51914 3504 105 49653 0.3 1 46415 3238 106 45561 0.3 1 42651 2910 107 41569 0.3 1 38864 2705 108 39242 0.3 1 36735 2507 109 35181 0.3 1 32884 2297 110 32351 0.3 1 30217 2134 111 29181 0.3 1 27222 1959 112 25447 0.3 1 23718 1729 113 22680 0.3 1 21019 1661 114 19902 0.3 1 18472 1430 115 17153 0.3 1 15867 1286 116 15113 0.3 1 14061 1052 117 13006 0.3 1 12016 990 118 11539 0.3 1 10694 845 119 9431 0.3 1 8642 789 120 7730 0.3 1 7108 622 121 6854 0.3 1 6273 581 122 5610 0.3 1 5167 443 123 4861 0.3 1 4443 418 124 4094 0.3 1 3727 367 125 3465 0.3 1 3160 305 126 2986 0.3 1 2695 291 127 2510 0.3 1 2289 221 128 1832 0.3 1 1674 158 129 1619 0.3 1 1450 169 130 1319 0.3 1 1201 118 131 1116 0.3 1 999 117 132 1063 0.3 1 961 102 133 1337 0.3 1 1208 129 134 1485 0.3 1 1390 95 135 668 0.3 1 615 53 136 381 0.3 1 342 39 137 211 0.3 1 197 14 138 160 0.3 1 144 16 139 121 0.3 1 106 15 140 71 0.3 1 59 12 141 68 0.3 1 57 11 142 52 0.3 1 47 5 143 43 0.3 1 38 5 144 24 0.3 1 22 2 145 53 0.3 1 40 13 146 42 0.3 1 34 8 147 125 0.3 1 106 19 148 83 0.3 1 69 14 149 78 0.3 1 73 5 150 763 0.3 1 673 90 RUN STATISTICS FOR INPUT FILE: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/16C_32psu_1_S1_L001_R1_001.fastq.gz ============================================= 19624894 sequences processed in total Sequences removed because they became shorter than the length cutoff of 20 bp: 8021 (0.0%)