SUMMARISING RUN PARAMETERS ========================== Input filename: /Users/strigg/Desktop/Salmo_Calig/16C_32psu_3_S3_L002_R2_001.fastq.gz Trimming mode: paired-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; 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 5 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 5 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: --outdir /Users/strigg/Desktop/Salmo_Calig/TRIM/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 /Users/strigg/Desktop/Salmo_Calig/16C_32psu_3_S3_L002_R2_001.fastq.gz Processing reads on 1 core in single-end mode ... Finished in 511.55 s (37 us/read; 1.60 M reads/minute). === Summary === Total reads processed: 13,670,957 Reads with adapters: 11,550,197 (84.5%) Reads written (passing filters): 13,670,957 (100.0%) Total basepairs processed: 2,050,643,550 bp Quality-trimmed: 11,580,867 bp (0.6%) Total written (filtered): 1,468,475,211 bp (71.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 11550197 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 28.6% C: 12.3% G: 24.9% T: 34.2% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 1212421 3417739.2 0 1212421 2 191566 854434.8 0 191566 3 121338 213608.7 0 121338 4 68246 53402.2 0 68246 5 66256 13350.5 0 66256 6 60146 3337.6 0 60146 7 46826 834.4 0 46826 8 69191 208.6 0 69191 9 54203 52.2 0 54035 168 10 59001 13.0 1 54514 4487 11 64399 3.3 1 58784 5615 12 63560 0.8 1 57831 5729 13 73714 0.2 1 67412 6302 14 69969 0.2 1 63352 6617 15 54986 0.2 1 50399 4587 16 83002 0.2 1 75869 7133 17 70639 0.2 1 64421 6218 18 61266 0.2 1 56207 5059 19 82751 0.2 1 75847 6904 20 76799 0.2 1 70584 6215 21 67039 0.2 1 61694 5345 22 77648 0.2 1 71294 6354 23 82616 0.2 1 75896 6720 24 82091 0.2 1 75051 7040 25 94761 0.2 1 87866 6895 26 78379 0.2 1 71576 6803 27 86685 0.2 1 79069 7616 28 79766 0.2 1 74088 5678 29 88958 0.2 1 82020 6938 30 87347 0.2 1 80721 6626 31 96436 0.2 1 89116 7320 32 84184 0.2 1 78013 6171 33 99064 0.2 1 91212 7852 34 126286 0.2 1 116784 9502 35 70478 0.2 1 65263 5215 36 102056 0.2 1 93957 8099 37 106427 0.2 1 98476 7951 38 101342 0.2 1 94365 6977 39 95863 0.2 1 89455 6408 40 111287 0.2 1 103069 8218 41 109099 0.2 1 101498 7601 42 114117 0.2 1 106148 7969 43 100632 0.2 1 93666 6966 44 121370 0.2 1 112650 8720 45 132112 0.2 1 122836 9276 46 87481 0.2 1 81280 6201 47 117137 0.2 1 109733 7404 48 116770 0.2 1 109144 7626 49 122930 0.2 1 114503 8427 50 118230 0.2 1 110078 8152 51 151502 0.2 1 141327 10175 52 106392 0.2 1 99321 7071 53 132940 0.2 1 125179 7761 54 95060 0.2 1 89153 5907 55 129755 0.2 1 121823 7932 56 133247 0.2 1 124572 8675 57 128656 0.2 1 121414 7242 58 125177 0.2 1 117960 7217 59 125701 0.2 1 118073 7628 60 133212 0.2 1 125145 8067 61 136943 0.2 1 128912 8031 62 152161 0.2 1 142895 9266 63 197608 0.2 1 187217 10391 64 170164 0.2 1 162758 7406 65 108925 0.2 1 102718 6207 66 119060 0.2 1 112190 6870 67 118638 0.2 1 111538 7100 68 122066 0.2 1 114957 7109 69 121361 0.2 1 113998 7363 70 127330 0.2 1 119753 7577 71 132672 0.2 1 124891 7781 72 129459 0.2 1 121850 7609 73 134714 0.2 1 127048 7666 74 126025 0.2 1 118830 7195 75 121497 0.2 1 114268 7229 76 117925 0.2 1 110905 7020 77 118215 0.2 1 111150 7065 78 114702 0.2 1 108059 6643 79 111977 0.2 1 105512 6465 80 111238 0.2 1 104912 6326 81 110074 0.2 1 103870 6204 82 104747 0.2 1 98712 6035 83 102994 0.2 1 97190 5804 84 97939 0.2 1 92413 5526 85 98027 0.2 1 92612 5415 86 97975 0.2 1 92622 5353 87 99113 0.2 1 93888 5225 88 97377 0.2 1 92204 5173 89 87121 0.2 1 82286 4835 90 84514 0.2 1 79963 4551 91 79415 0.2 1 75190 4225 92 74774 0.2 1 70849 3925 93 72752 0.2 1 68819 3933 94 70292 0.2 1 66493 3799 95 66513 0.2 1 62910 3603 96 64556 0.2 1 61082 3474 97 60915 0.2 1 57800 3115 98 57473 0.2 1 54587 2886 99 57713 0.2 1 54715 2998 100 49481 0.2 1 46774 2707 101 45740 0.2 1 43384 2356 102 41586 0.2 1 39421 2165 103 38173 0.2 1 36099 2074 104 36449 0.2 1 34460 1989 105 32790 0.2 1 31067 1723 106 30381 0.2 1 28796 1585 107 27663 0.2 1 26191 1472 108 25091 0.2 1 23805 1286 109 22776 0.2 1 21667 1109 110 20493 0.2 1 19406 1087 111 19435 0.2 1 18473 962 112 16596 0.2 1 15727 869 113 14532 0.2 1 13752 780 114 12824 0.2 1 12122 702 115 10619 0.2 1 10098 521 116 9188 0.2 1 8686 502 117 7612 0.2 1 7172 440 118 6805 0.2 1 6447 358 119 5613 0.2 1 5287 326 120 4455 0.2 1 4215 240 121 3795 0.2 1 3594 201 122 3385 0.2 1 3227 158 123 2919 0.2 1 2743 176 124 2401 0.2 1 2252 149 125 1949 0.2 1 1858 91 126 1662 0.2 1 1556 106 127 1275 0.2 1 1189 86 128 1017 0.2 1 960 57 129 911 0.2 1 861 50 130 712 0.2 1 666 46 131 583 0.2 1 553 30 132 498 0.2 1 473 25 133 459 0.2 1 441 18 134 540 0.2 1 495 45 135 343 0.2 1 318 25 136 185 0.2 1 166 19 137 142 0.2 1 134 8 138 102 0.2 1 96 6 139 72 0.2 1 71 1 140 56 0.2 1 51 5 141 30 0.2 1 27 3 142 45 0.2 1 39 6 143 48 0.2 1 43 5 144 33 0.2 1 32 1 145 35 0.2 1 32 3 146 81 0.2 1 79 2 147 221 0.2 1 208 13 148 193 0.2 1 178 15 149 78 0.2 1 71 7 150 649 0.2 1 611 38 RUN STATISTICS FOR INPUT FILE: /Users/strigg/Desktop/Salmo_Calig/16C_32psu_3_S3_L002_R2_001.fastq.gz ============================================= 13670957 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 13670957 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 32418 (0.24%)