SUMMARISING RUN PARAMETERS ========================== Input filename: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/8C_26psu_1_S9_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/8C_26psu_1_S9_L001_R1_001.fastq.gz Processing reads on 1 core in single-end mode ... Finished in 734.35 s (40 us/read; 1.48 M reads/minute). === Summary === Total reads processed: 18,172,174 Reads with adapters: 14,009,565 (77.1%) Reads written (passing filters): 18,172,174 (100.0%) Total basepairs processed: 2,725,826,100 bp Quality-trimmed: 5,576,029 bp (0.2%) Total written (filtered): 2,153,538,533 bp (79.0%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 14009565 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 30.7% C: 14.7% G: 20.2% T: 34.4% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 2553382 4543043.5 0 2553382 2 361304 1135760.9 0 361304 3 203451 283940.2 0 203451 4 119346 70985.1 0 119346 5 96383 17746.3 0 96383 6 92443 4436.6 0 92443 7 75722 1109.1 0 75722 8 95119 277.3 0 95119 9 94842 69.3 0 93616 1226 10 89178 17.3 1 84587 4591 11 98839 4.3 1 91164 7675 12 94690 1.1 1 88668 6022 13 96487 0.3 1 90169 6318 14 97956 0.3 1 91158 6798 15 101508 0.3 1 94950 6558 16 99917 0.3 1 92571 7346 17 122129 0.3 1 112362 9767 18 103253 0.3 1 97095 6158 19 88992 0.3 1 83121 5871 20 106240 0.3 1 99305 6935 21 117020 0.3 1 108991 8029 22 99969 0.3 1 94314 5655 23 116939 0.3 1 109185 7754 24 106769 0.3 1 98031 8738 25 115163 0.3 1 107352 7811 26 105376 0.3 1 99072 6304 27 117162 0.3 1 108493 8669 28 115218 0.3 1 107267 7951 29 121831 0.3 1 112202 9629 30 130309 0.3 1 123069 7240 31 100032 0.3 1 93538 6494 32 125002 0.3 1 117224 7778 33 114973 0.3 1 107024 7949 34 140462 0.3 1 130516 9946 35 105315 0.3 1 99186 6129 36 133473 0.3 1 123640 9833 37 118492 0.3 1 111283 7209 38 133856 0.3 1 125329 8527 39 129659 0.3 1 120554 9105 40 124082 0.3 1 117052 7030 41 145782 0.3 1 135364 10418 42 118797 0.3 1 109967 8830 43 194297 0.3 1 184362 9935 44 63920 0.3 1 58531 5389 45 132756 0.3 1 124789 7967 46 128569 0.3 1 120475 8094 47 134969 0.3 1 126850 8119 48 127793 0.3 1 119492 8301 49 141939 0.3 1 132171 9768 50 122730 0.3 1 115608 7122 51 132062 0.3 1 123880 8182 52 137197 0.3 1 127456 9741 53 151575 0.3 1 142793 8782 54 114349 0.3 1 107125 7224 55 137708 0.3 1 129156 8552 56 161649 0.3 1 152383 9266 57 114410 0.3 1 106500 7910 58 137398 0.3 1 130375 7023 59 114545 0.3 1 107545 7000 60 136347 0.3 1 128034 8313 61 131449 0.3 1 123861 7588 62 139001 0.3 1 131253 7748 63 117841 0.3 1 110235 7606 64 124937 0.3 1 117975 6962 65 137827 0.3 1 129558 8269 66 145197 0.3 1 136356 8841 67 156037 0.3 1 144343 11694 68 293703 0.3 1 279898 13805 69 56423 0.3 1 51953 4470 70 20870 0.3 1 17669 3201 71 73391 0.3 1 68872 4519 72 109127 0.3 1 102948 6179 73 115790 0.3 1 109200 6590 74 114108 0.3 1 107376 6732 75 112468 0.3 1 105902 6566 76 111908 0.3 1 105400 6508 77 110508 0.3 1 103945 6563 78 104515 0.3 1 98282 6233 79 103447 0.3 1 97321 6126 80 100314 0.3 1 94349 5965 81 99307 0.3 1 93451 5856 82 96030 0.3 1 90418 5612 83 93920 0.3 1 88302 5618 84 90786 0.3 1 85374 5412 85 87976 0.3 1 82940 5036 86 84575 0.3 1 79489 5086 87 80800 0.3 1 75885 4915 88 79827 0.3 1 75057 4770 89 76306 0.3 1 71788 4518 90 75447 0.3 1 70879 4568 91 70739 0.3 1 66457 4282 92 67827 0.3 1 63701 4126 93 63802 0.3 1 60033 3769 94 61718 0.3 1 57911 3807 95 57339 0.3 1 53808 3531 96 54465 0.3 1 51099 3366 97 51194 0.3 1 48085 3109 98 47800 0.3 1 44777 3023 99 45494 0.3 1 42548 2946 100 41995 0.3 1 39278 2717 101 38874 0.3 1 36431 2443 102 36656 0.3 1 34295 2361 103 33608 0.3 1 31418 2190 104 31440 0.3 1 29409 2031 105 28173 0.3 1 26291 1882 106 25331 0.3 1 23628 1703 107 23358 0.3 1 21803 1555 108 21762 0.3 1 20261 1501 109 19593 0.3 1 18199 1394 110 17697 0.3 1 16476 1221 111 15926 0.3 1 14765 1161 112 13846 0.3 1 12871 975 113 11827 0.3 1 10954 873 114 10902 0.3 1 10102 800 115 9531 0.3 1 8821 710 116 8041 0.3 1 7361 680 117 6932 0.3 1 6371 561 118 5995 0.3 1 5469 526 119 4903 0.3 1 4506 397 120 4372 0.3 1 3973 399 121 3600 0.3 1 3268 332 122 2879 0.3 1 2586 293 123 2449 0.3 1 2225 224 124 2193 0.3 1 1959 234 125 1829 0.3 1 1616 213 126 1642 0.3 1 1488 154 127 1294 0.3 1 1160 134 128 1024 0.3 1 902 122 129 830 0.3 1 734 96 130 651 0.3 1 579 72 131 623 0.3 1 568 55 132 611 0.3 1 554 57 133 770 0.3 1 705 65 134 1146 0.3 1 1081 65 135 448 0.3 1 402 46 136 201 0.3 1 171 30 137 163 0.3 1 138 25 138 82 0.3 1 67 15 139 72 0.3 1 55 17 140 56 0.3 1 42 14 141 36 0.3 1 35 1 142 25 0.3 1 15 10 143 23 0.3 1 18 5 144 8 0.3 1 7 1 145 24 0.3 1 19 5 146 21 0.3 1 20 1 147 76 0.3 1 66 10 148 65 0.3 1 57 8 149 66 0.3 1 57 9 150 608 0.3 1 538 70 RUN STATISTICS FOR INPUT FILE: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/8C_26psu_1_S9_L001_R1_001.fastq.gz ============================================= 18172174 sequences processed in total Sequences removed because they became shorter than the length cutoff of 20 bp: 5180 (0.0%)