SUMMARISING RUN PARAMETERS ========================== Input filename: /sc/arion/projects/BiNGS/bings_omics/data/bings/2025/bulk_course_data/bulkrna_pipeline/data_rna/raw/fastqs/SRR24071398_2.fastq Trimming mode: paired-end Trim Galore version: 0.6.6 Cutadapt version: 4.9 Python version: 3.12.5 Number of cores used for trimming: 6 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Using Illumina adapter for trimming (count: 316798). Second best hit was Nextera (count: 6) 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 Running FastQC on the data once trimming has completed Output file will be GZIP compressed This is cutadapt 4.9 with Python 3.12.5 Command line parameters: -j 6 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /sc/arion/projects/BiNGS/bings_omics/data/bings/2025/bulk_course_data/bulkrna_pipeline/data_rna/raw/fastqs/SRR24071398_2.fastq Processing single-end reads on 6 cores ... Finished in 294.089 s (7.431 µs/read; 8.07 M reads/minute). === Summary === Total reads processed: 39,573,557 Reads with adapters: 23,338,089 (59.0%) Reads written (passing filters): 39,573,557 (100.0%) Total basepairs processed: 5,936,033,550 bp Quality-trimmed: 86,869,337 bp (1.5%) Total written (filtered): 5,298,712,030 bp (89.3%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 23338089 times Minimum overlap: 1 No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 20.2% C: 35.0% G: 26.7% T: 17.0% none/other: 1.1% Overview of removed sequences length count expect max.err error counts 1 5330487 9893389.2 0 5330487 2 1949132 2473347.3 0 1949132 3 700794 618336.8 0 700794 4 313360 154584.2 0 313360 5 267588 38646.1 0 267588 6 251279 9661.5 0 251279 7 234953 2415.4 0 234953 8 232665 603.8 0 232665 9 247343 151.0 0 245303 2040 10 254141 37.7 1 237159 16982 11 261045 9.4 1 242187 18858 12 262348 2.4 1 243204 19144 13 279158 0.6 1 256191 22967 14 318128 0.6 1 291251 26877 15 231121 0.6 1 215380 15741 16 275026 0.6 1 254176 20850 17 269469 0.6 1 250996 18473 18 222005 0.6 1 207709 14296 19 263442 0.6 1 245776 17666 20 241215 0.6 1 226080 15135 21 254455 0.6 1 238399 16056 22 270172 0.6 1 252038 18134 23 279487 0.6 1 260060 19427 24 289609 0.6 1 268696 20913 25 259753 0.6 1 242918 16835 26 267545 0.6 1 249911 17634 27 260667 0.6 1 243189 17478 28 271862 0.6 1 253075 18787 29 257003 0.6 1 240152 16851 30 327804 0.6 1 304920 22884 31 210267 0.6 1 197992 12275 32 274277 0.6 1 256964 17313 33 247658 0.6 1 233106 14552 34 265222 0.6 1 248451 16771 35 272503 0.6 1 254986 17517 36 268789 0.6 1 251796 16993 37 234251 0.6 1 220754 13497 38 247215 0.6 1 232067 15148 39 231935 0.6 1 218727 13208 40 235054 0.6 1 221096 13958 41 245720 0.6 1 230841 14879 42 264909 0.6 1 248316 16593 43 214982 0.6 1 203358 11624 44 246340 0.6 1 231640 14700 45 215440 0.6 1 203169 12271 46 223283 0.6 1 210181 13102 47 210122 0.6 1 197495 12627 48 206476 0.6 1 193734 12742 49 188515 0.6 1 176924 11591 50 188186 0.6 1 176194 11992 51 175345 0.6 1 165133 10212 52 181247 0.6 1 169484 11763 53 186890 0.6 1 174945 11945 54 185781 0.6 1 174352 11429 55 161158 0.6 1 151817 9341 56 168833 0.6 1 159061 9772 57 146588 0.6 1 138620 7968 58 128026 0.6 1 121240 6786 59 123420 0.6 1 116972 6448 60 120620 0.6 1 114230 6390 61 108654 0.6 1 102898 5756 62 105023 0.6 1 99672 5351 63 120397 0.6 1 114491 5906 64 79145 0.6 1 75508 3637 65 95159 0.6 1 90653 4506 66 84965 0.6 1 81097 3868 67 85743 0.6 1 81586 4157 68 79529 0.6 1 75717 3812 69 67594 0.6 1 64401 3193 70 58980 0.6 1 56187 2793 71 55602 0.6 1 52863 2739 72 53185 0.6 1 50495 2690 73 52528 0.6 1 49604 2924 74 56211 0.6 1 52975 3236 75 74651 0.6 1 63166 11485 76 411301 0.6 1 393344 17957 77 100697 0.6 1 95267 5430 78 31545 0.6 1 29478 2067 79 17058 0.6 1 15852 1206 80 11140 0.6 1 10325 815 81 9208 0.6 1 8536 672 82 7737 0.6 1 7141 596 83 7259 0.6 1 6689 570 84 8426 0.6 1 7812 614 85 8931 0.6 1 8261 670 86 9597 0.6 1 8841 756 87 8821 0.6 1 8169 652 88 7899 0.6 1 7151 748 89 6935 0.6 1 6406 529 90 5395 0.6 1 4932 463 91 4315 0.6 1 3934 381 92 3538 0.6 1 3208 330 93 2997 0.6 1 2710 287 94 2968 0.6 1 2686 282 95 3087 0.6 1 2819 268 96 2823 0.6 1 2494 329 97 2618 0.6 1 2366 252 98 2484 0.6 1 2255 229 99 2213 0.6 1 2043 170 100 2083 0.6 1 1882 201 101 1746 0.6 1 1564 182 102 1528 0.6 1 1348 180 103 1334 0.6 1 1167 167 104 1197 0.6 1 1051 146 105 1096 0.6 1 973 123 106 1097 0.6 1 949 148 107 1160 0.6 1 996 164 108 1096 0.6 1 910 186 109 949 0.6 1 837 112 110 822 0.6 1 731 91 111 740 0.6 1 627 113 112 665 0.6 1 549 116 113 558 0.6 1 456 102 114 619 0.6 1 478 141 115 511 0.6 1 387 124 116 483 0.6 1 409 74 117 470 0.6 1 393 77 118 523 0.6 1 430 93 119 444 0.6 1 340 104 120 368 0.6 1 267 101 121 330 0.6 1 243 87 122 307 0.6 1 218 89 123 275 0.6 1 194 81 124 284 0.6 1 204 80 125 260 0.6 1 191 69 126 232 0.6 1 136 96 127 282 0.6 1 177 105 128 253 0.6 1 177 76 129 238 0.6 1 136 102 130 228 0.6 1 174 54 131 190 0.6 1 128 62 132 171 0.6 1 112 59 133 204 0.6 1 116 88 134 190 0.6 1 100 90 135 167 0.6 1 122 45 136 192 0.6 1 122 70 137 193 0.6 1 116 77 138 167 0.6 1 118 49 139 193 0.6 1 118 75 140 181 0.6 1 110 71 141 246 0.6 1 113 133 142 240 0.6 1 151 89 143 260 0.6 1 174 86 144 317 0.6 1 243 74 145 358 0.6 1 288 70 146 437 0.6 1 355 82 147 672 0.6 1 542 130 148 850 0.6 1 695 155 149 3093 0.6 1 2681 412 150 39124 0.6 1 34140 4984 RUN STATISTICS FOR INPUT FILE: /sc/arion/projects/BiNGS/bings_omics/data/bings/2025/bulk_course_data/bulkrna_pipeline/data_rna/raw/fastqs/SRR24071398_2.fastq ============================================= 39573557 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 39573557 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 348696 (0.88%)