SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/16C_32psu_1_S1_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: 635901). Second best hit was smallRNA (count: 1) 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_L001_R1_001.fastq.gz Processing reads on 8 cores in single-end mode ... Finished in 69.59 s (4 us/read; 16.92 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: /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/16C_32psu_1_S1_L001_R1_001.fastq.gz ============================================= 19624894 sequences processed in total