No quality encoding type selected. Assuming that the data provided uses Sanger encoded Phred scores (default) Path to Cutadapt set as: 'cutadapt' (default) Cutadapt seems to be working fine (tested command 'cutadapt --version') AUTO-DETECTING ADAPTER TYPE =========================== Attempting to auto-detect adapter type from the first 1 million sequences of the first file (>> /home/sam/Downloads/zr2096/Raw_data/zr2096_10_s1_R1.fastq.gz <<) Found perfect matches for the following adapter sequences: Adapter type Count Sequence Sequences analysed Percentage smallRNA 4020 TGGAATTCTCGG 1000000 0.40 Illumina 0 AGATCGGAAGAGC 1000000 0.00 Nextera 0 CTGTCTCTTATA 1000000 0.00 Using smallRNA adapter for trimming (count: 4020). Second best hit was Illumina (count: 0) Reducing length cutoff to 18bp for small RNA-Seq reads because a cutoff of 20bp may remove some short species of small RNAs if they had been trimmed by 1,2 or 3bp Setting the Illumina smallRNA 5' adapter as adapter 2: 'GATCGTCGGACT' Writing report to '/home/sam/Downloads/20180411_trimgalore_10bp_Cvirginica_MBD/zr2096_10_s1_R1.fastq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /home/sam/Downloads/zr2096/Raw_data/zr2096_10_s1_R1.fastq.gz Trimming mode: paired-end Trim Galore version: 0.4.4_dev Cutadapt version: 1.16 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'TGGAATTCTCGG' (Illumina small RNA adapter; auto-detected) Maximum trimming error rate: 0.1 (default) Optional adapter 2 sequence (only used for read 2 of paired-end files): 'GATCGTCGGACT' Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length for both reads before a sequence pair gets removed: 18 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 ~/Downloads/20180411_trimgalore_10bp_Cvirginica_MBD/20180411_fastqc_trim_10bp_Cvirginica_MBD --threads 18' Output file(s) will be GZIP compressed Writing final adapter and quality trimmed output to zr2096_10_s1_R1_trimmed.fq.gz >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'TGGAATTCTCGG' from file /home/sam/Downloads/zr2096/Raw_data/zr2096_10_s1_R1.fastq.gz <<< 10000000 sequences processed This is cutadapt 1.16 with Python 2.7.12 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a TGGAATTCTCGG /home/sam/Downloads/zr2096/Raw_data/zr2096_10_s1_R1.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 344.94 s (19 us/read; 3.08 M reads/minute). === Summary === Total reads processed: 17,717,127 Reads with adapters: 8,066,766 (45.5%) Reads written (passing filters): 17,717,127 (100.0%) Total basepairs processed: 1,619,391,518 bp Quality-trimmed: 7,953,221 bp (0.5%) Total written (filtered): 1,596,548,832 bp (98.6%) === Adapter 1 === Sequence: TGGAATTCTCGG; Type: regular 3'; Length: 12; Trimmed: 8066766 times. No. of allowed errors: 0-9 bp: 0; 10-12 bp: 1 Bases preceding removed adapters: A: 26.9% C: 6.0% G: 21.7% T: 45.2% none/other: 0.1% Overview of removed sequences length count expect max.err error counts 1 6836099 4429281.8 0 6836099 2 785279 1107320.4 0 785279 3 280553 276830.1 0 280553 4 50900 69207.5 0 50900 5 19406 17301.9 0 19406 6 6096 4325.5 0 6096 7 3109 1081.4 0 3109 8 231 270.3 0 231 9 424 67.6 0 390 34 10 319 16.9 1 160 159 11 279 4.2 1 160 119 12 156 1.1 1 71 85 13 298 1.1 1 157 141 14 152 1.1 1 49 103 15 245 1.1 1 136 109 16 179 1.1 1 109 70 17 230 1.1 1 155 75 18 561 1.1 1 381 180 19 507 1.1 1 378 129 20 136 1.1 1 65 71 21 137 1.1 1 67 70 22 415 1.1 1 272 143 23 452 1.1 1 283 169 24 430 1.1 1 316 114 25 576 1.1 1 414 162 26 538 1.1 1 376 162 27 893 1.1 1 688 205 28 353 1.1 1 240 113 29 464 1.1 1 321 143 30 610 1.1 1 397 213 31 556 1.1 1 388 168 32 820 1.1 1 565 255 33 603 1.1 1 449 154 34 728 1.1 1 555 173 35 741 1.1 1 564 177 36 882 1.1 1 684 198 37 1416 1.1 1 1143 273 38 513 1.1 1 363 150 39 535 1.1 1 379 156 40 590 1.1 1 415 175 41 417 1.1 1 285 132 42 360 1.1 1 255 105 43 639 1.1 1 492 147 44 378 1.1 1 289 89 45 552 1.1 1 415 137 46 974 1.1 1 695 279 47 1020 1.1 1 707 313 48 623 1.1 1 398 225 49 689 1.1 1 509 180 50 675 1.1 1 507 168 51 395 1.1 1 290 105 52 745 1.1 1 569 176 53 945 1.1 1 704 241 54 1060 1.1 1 844 216 55 1798 1.1 1 1454 344 56 1255 1.1 1 990 265 57 878 1.1 1 668 210 58 614 1.1 1 449 165 59 856 1.1 1 668 188 60 1283 1.1 1 1030 253 61 1817 1.1 1 1389 428 62 429 1.1 1 314 115 63 552 1.1 1 432 120 64 1073 1.1 1 826 247 65 1173 1.1 1 884 289 66 1534 1.1 1 1164 370 67 2018 1.1 1 1575 443 68 3376 1.1 1 2743 633 69 1972 1.1 1 1592 380 70 2167 1.1 1 1814 353 71 3104 1.1 1 2698 406 72 4968 1.1 1 4397 571 73 4402 1.1 1 3871 531 74 2816 1.1 1 2417 399 75 1918 1.1 1 1560 358 76 1595 1.1 1 1177 418 77 1719 1.1 1 1226 493 78 1925 1.1 1 1302 623 79 1864 1.1 1 1265 599 80 1778 1.1 1 1246 532 81 1534 1.1 1 1090 444 82 852 1.1 1 582 270 83 513 1.1 1 345 168 84 478 1.1 1 324 154 85 536 1.1 1 347 189 86 545 1.1 1 354 191 87 476 1.1 1 293 183 88 436 1.1 1 284 152 89 404 1.1 1 261 143 90 409 1.1 1 267 142 91 440 1.1 1 283 157 92 414 1.1 1 257 157 93 357 1.1 1 250 107 94 408 1.1 1 262 146 95 365 1.1 1 243 122 96 385 1.1 1 237 148 97 479 1.1 1 307 172 98 462 1.1 1 298 164 99 664 1.1 1 428 236 100 842 1.1 1 560 282 RUN STATISTICS FOR INPUT FILE: /home/sam/Downloads/zr2096/Raw_data/zr2096_10_s1_R1.fastq.gz ============================================= 17717127 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Writing report to '/home/sam/Downloads/20180411_trimgalore_10bp_Cvirginica_MBD/zr2096_10_s1_R2.fastq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /home/sam/Downloads/zr2096/Raw_data/zr2096_10_s1_R2.fastq.gz Trimming mode: paired-end Trim Galore version: 0.4.4_dev Cutadapt version: 1.16 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'TGGAATTCTCGG' (Illumina small RNA adapter; auto-detected) Maximum trimming error rate: 0.1 (default) Optional adapter 2 sequence (only used for read 2 of paired-end files): 'GATCGTCGGACT' Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length for both reads before a sequence pair gets removed: 18 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 ~/Downloads/20180411_trimgalore_10bp_Cvirginica_MBD/20180411_fastqc_trim_10bp_Cvirginica_MBD --threads 18' Output file(s) will be GZIP compressed Writing final adapter and quality trimmed output to zr2096_10_s1_R2_trimmed.fq.gz >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'GATCGTCGGACT' from file /home/sam/Downloads/zr2096/Raw_data/zr2096_10_s1_R2.fastq.gz <<< 10000000 sequences processed This is cutadapt 1.16 with Python 2.7.12 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a GATCGTCGGACT /home/sam/Downloads/zr2096/Raw_data/zr2096_10_s1_R2.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 319.52 s (18 us/read; 3.33 M reads/minute). === Summary === Total reads processed: 17,717,127 Reads with adapters: 3,640,439 (20.5%) Reads written (passing filters): 17,717,127 (100.0%) Total basepairs processed: 1,619,992,471 bp Quality-trimmed: 7,309,137 bp (0.5%) Total written (filtered): 1,605,021,321 bp (99.1%) === Adapter 1 === Sequence: GATCGTCGGACT; Type: regular 3'; Length: 12; Trimmed: 3640439 times. No. of allowed errors: 0-9 bp: 0; 10-12 bp: 1 Bases preceding removed adapters: A: 22.8% C: 14.1% G: 32.1% T: 30.8% none/other: 0.1% Overview of removed sequences length count expect max.err error counts 1 2646925 4429281.8 0 2646925 2 648480 1107320.4 0 648480 3 279757 276830.1 0 279757 4 10277 69207.5 0 10277 5 6428 17301.9 0 6428 6 2905 4325.5 0 2905 7 259 1081.4 0 259 8 192 270.3 0 192 9 207 67.6 0 48 159 10 392 16.9 1 80 312 11 202 4.2 1 90 112 12 54 1.1 1 20 34 13 116 1.1 1 59 57 14 354 1.1 1 191 163 15 65 1.1 1 26 39 16 70 1.1 1 38 32 17 209 1.1 1 127 82 18 249 1.1 1 137 112 19 201 1.1 1 110 91 20 309 1.1 1 183 126 21 369 1.1 1 231 138 22 116 1.1 1 52 64 23 96 1.1 1 46 50 24 361 1.1 1 215 146 25 490 1.1 1 312 178 26 155 1.1 1 82 73 27 428 1.1 1 283 145 28 193 1.1 1 109 84 29 297 1.1 1 182 115 30 1375 1.1 1 937 438 31 145 1.1 1 71 74 32 93 1.1 1 35 58 33 177 1.1 1 88 89 34 273 1.1 1 150 123 35 442 1.1 1 302 140 36 788 1.1 1 579 209 37 275 1.1 1 183 92 38 205 1.1 1 126 79 39 484 1.1 1 337 147 40 325 1.1 1 239 86 41 131 1.1 1 77 54 42 326 1.1 1 206 120 43 570 1.1 1 381 189 44 84 1.1 1 51 33 45 291 1.1 1 189 102 46 440 1.1 1 337 103 47 82 1.1 1 43 39 48 217 1.1 1 134 83 49 260 1.1 1 154 106 50 246 1.1 1 147 99 51 314 1.1 1 197 117 52 311 1.1 1 201 110 53 395 1.1 1 250 145 54 592 1.1 1 406 186 55 718 1.1 1 496 222 56 667 1.1 1 465 202 57 510 1.1 1 343 167 58 618 1.1 1 385 233 59 567 1.1 1 396 171 60 971 1.1 1 629 342 61 945 1.1 1 653 292 62 936 1.1 1 636 300 63 1294 1.1 1 960 334 64 2281 1.1 1 1867 414 65 1784 1.1 1 1430 354 66 1036 1.1 1 737 299 67 901 1.1 1 574 327 68 892 1.1 1 535 357 69 495 1.1 1 298 197 70 457 1.1 1 257 200 71 507 1.1 1 282 225 72 501 1.1 1 281 220 73 489 1.1 1 277 212 74 546 1.1 1 307 239 75 583 1.1 1 323 260 76 751 1.1 1 416 335 77 941 1.1 1 491 450 78 1213 1.1 1 669 544 79 1126 1.1 1 608 518 80 1054 1.1 1 575 479 81 907 1.1 1 510 397 82 521 1.1 1 278 243 83 384 1.1 1 201 183 84 335 1.1 1 193 142 85 348 1.1 1 198 150 86 415 1.1 1 234 181 87 403 1.1 1 218 185 88 335 1.1 1 170 165 89 309 1.1 1 159 150 90 324 1.1 1 179 145 91 315 1.1 1 167 148 92 258 1.1 1 146 112 93 255 1.1 1 138 117 94 282 1.1 1 143 139 95 302 1.1 1 150 152 96 305 1.1 1 143 162 97 384 1.1 1 196 188 98 449 1.1 1 236 213 99 757 1.1 1 388 369 100 1071 1.1 1 577 494 RUN STATISTICS FOR INPUT FILE: /home/sam/Downloads/zr2096/Raw_data/zr2096_10_s1_R2.fastq.gz ============================================= 17717127 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Validate paired-end files zr2096_10_s1_R1_trimmed.fq.gz and zr2096_10_s1_R2_trimmed.fq.gz file_1: zr2096_10_s1_R1_trimmed.fq.gz, file_2: zr2096_10_s1_R2_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: zr2096_10_s1_R1_trimmed.fq.gz and zr2096_10_s1_R2_trimmed.fq.gz <<<<< Writing validated paired-end read 1 reads to zr2096_10_s1_R1_val_1.fq.gz Writing validated paired-end read 2 reads to zr2096_10_s1_R2_val_2.fq.gz Total number of sequences analysed: 17717127 Number of sequence pairs removed because at least one read was shorter than the length cutoff (18 bp): 268244 (1.51%) >>> Now running FastQC on the validated data zr2096_10_s1_R1_val_1.fq.gz<<< Started analysis of zr2096_10_s1_R1_val_1.fq.gz Approx 5% complete for zr2096_10_s1_R1_val_1.fq.gz Approx 10% complete for zr2096_10_s1_R1_val_1.fq.gz Approx 15% complete for zr2096_10_s1_R1_val_1.fq.gz Approx 20% complete for zr2096_10_s1_R1_val_1.fq.gz Approx 25% complete for zr2096_10_s1_R1_val_1.fq.gz Approx 30% complete for zr2096_10_s1_R1_val_1.fq.gz Approx 35% complete for zr2096_10_s1_R1_val_1.fq.gz Approx 40% complete for zr2096_10_s1_R1_val_1.fq.gz Approx 45% complete for zr2096_10_s1_R1_val_1.fq.gz Approx 50% complete for zr2096_10_s1_R1_val_1.fq.gz Approx 55% complete for zr2096_10_s1_R1_val_1.fq.gz Approx 60% complete for zr2096_10_s1_R1_val_1.fq.gz Approx 65% complete for zr2096_10_s1_R1_val_1.fq.gz Approx 70% complete for zr2096_10_s1_R1_val_1.fq.gz Approx 75% complete for zr2096_10_s1_R1_val_1.fq.gz Approx 80% complete for zr2096_10_s1_R1_val_1.fq.gz Approx 85% complete for zr2096_10_s1_R1_val_1.fq.gz Approx 90% complete for zr2096_10_s1_R1_val_1.fq.gz Approx 95% complete for zr2096_10_s1_R1_val_1.fq.gz >>> Now running FastQC on the validated data zr2096_10_s1_R2_val_2.fq.gz<<< Started analysis of zr2096_10_s1_R2_val_2.fq.gz Approx 5% complete for zr2096_10_s1_R2_val_2.fq.gz Approx 10% complete for zr2096_10_s1_R2_val_2.fq.gz Approx 15% complete for zr2096_10_s1_R2_val_2.fq.gz Approx 20% complete for zr2096_10_s1_R2_val_2.fq.gz Approx 25% complete for zr2096_10_s1_R2_val_2.fq.gz Approx 30% complete for zr2096_10_s1_R2_val_2.fq.gz Approx 35% complete for zr2096_10_s1_R2_val_2.fq.gz Approx 40% complete for zr2096_10_s1_R2_val_2.fq.gz Approx 45% complete for zr2096_10_s1_R2_val_2.fq.gz Approx 50% complete for zr2096_10_s1_R2_val_2.fq.gz Approx 55% complete for zr2096_10_s1_R2_val_2.fq.gz Approx 60% complete for zr2096_10_s1_R2_val_2.fq.gz Approx 65% complete for zr2096_10_s1_R2_val_2.fq.gz Approx 70% complete for zr2096_10_s1_R2_val_2.fq.gz Approx 75% complete for zr2096_10_s1_R2_val_2.fq.gz Approx 80% complete for zr2096_10_s1_R2_val_2.fq.gz Approx 85% complete for zr2096_10_s1_R2_val_2.fq.gz Approx 90% complete for zr2096_10_s1_R2_val_2.fq.gz Approx 95% complete for zr2096_10_s1_R2_val_2.fq.gz Deleting both intermediate output files zr2096_10_s1_R1_trimmed.fq.gz and zr2096_10_s1_R2_trimmed.fq.gz ==================================================================================================== Writing report to '/home/sam/Downloads/20180411_trimgalore_10bp_Cvirginica_MBD/zr2096_1_s1_R1.fastq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /home/sam/Downloads/zr2096/Raw_data/zr2096_1_s1_R1.fastq.gz Trimming mode: paired-end Trim Galore version: 0.4.4_dev Cutadapt version: 1.16 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'TGGAATTCTCGG' (Illumina small RNA adapter; auto-detected) Maximum trimming error rate: 0.1 (default) Optional adapter 2 sequence (only used for read 2 of paired-end files): 'GATCGTCGGACT' Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length for both reads before a sequence pair gets removed: 18 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 ~/Downloads/20180411_trimgalore_10bp_Cvirginica_MBD/20180411_fastqc_trim_10bp_Cvirginica_MBD --threads 18' Output file(s) will be GZIP compressed Writing final adapter and quality trimmed output to zr2096_1_s1_R1_trimmed.fq.gz >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'TGGAATTCTCGG' from file /home/sam/Downloads/zr2096/Raw_data/zr2096_1_s1_R1.fastq.gz <<< 10000000 sequences processed 20000000 sequences processed This is cutadapt 1.16 with Python 2.7.12 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a TGGAATTCTCGG /home/sam/Downloads/zr2096/Raw_data/zr2096_1_s1_R1.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 535.85 s (18 us/read; 3.25 M reads/minute). === Summary === Total reads processed: 28,982,766 Reads with adapters: 12,553,900 (43.3%) Reads written (passing filters): 28,982,766 (100.0%) Total basepairs processed: 2,652,423,020 bp Quality-trimmed: 11,158,723 bp (0.4%) Total written (filtered): 2,625,957,959 bp (99.0%) === Adapter 1 === Sequence: TGGAATTCTCGG; Type: regular 3'; Length: 12; Trimmed: 12553900 times. No. of allowed errors: 0-9 bp: 0; 10-12 bp: 1 Bases preceding removed adapters: A: 24.8% C: 6.4% G: 22.8% T: 45.9% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 10658399 7245691.5 0 10658399 2 1276010 1811422.9 0 1276010 3 507213 452855.7 0 507213 4 75615 113213.9 0 75615 5 24781 28303.5 0 24781 6 7188 7075.9 0 7188 7 2888 1769.0 0 2888 8 30 442.2 0 30 9 26 110.6 0 7 19 10 90 27.6 1 0 90 11 44 6.9 1 0 44 12 26 1.7 1 0 26 13 24 1.7 1 0 24 14 23 1.7 1 0 23 15 21 1.7 1 0 21 16 22 1.7 1 0 22 17 24 1.7 1 0 24 18 25 1.7 1 0 25 19 18 1.7 1 0 18 20 13 1.7 1 0 13 21 19 1.7 1 0 19 22 19 1.7 1 0 19 23 23 1.7 1 0 23 24 13 1.7 1 0 13 25 22 1.7 1 0 22 26 27 1.7 1 0 27 27 12 1.7 1 0 12 28 24 1.7 1 0 24 29 16 1.7 1 0 16 30 36 1.7 1 0 36 31 18 1.7 1 0 18 32 21 1.7 1 0 21 33 14 1.7 1 0 14 34 24 1.7 1 0 24 35 24 1.7 1 0 24 36 25 1.7 1 0 25 37 23 1.7 1 0 23 38 25 1.7 1 0 25 39 15 1.7 1 0 15 40 19 1.7 1 0 19 41 21 1.7 1 0 21 42 30 1.7 1 0 30 43 20 1.7 1 0 20 44 29 1.7 1 0 29 45 16 1.7 1 0 16 46 24 1.7 1 0 24 47 14 1.7 1 0 14 48 21 1.7 1 0 21 49 23 1.7 1 0 23 50 15 1.7 1 0 15 51 28 1.7 1 0 28 52 16 1.7 1 0 16 53 18 1.7 1 0 18 54 21 1.7 1 0 21 55 19 1.7 1 0 19 56 16 1.7 1 0 16 57 24 1.7 1 0 24 58 13 1.7 1 0 13 59 19 1.7 1 1 18 60 19 1.7 1 0 19 61 18 1.7 1 0 18 62 25 1.7 1 1 24 63 12 1.7 1 0 12 64 18 1.7 1 0 18 65 21 1.7 1 0 21 66 15 1.7 1 0 15 67 24 1.7 1 0 24 68 8 1.7 1 0 8 69 18 1.7 1 0 18 70 19 1.7 1 0 19 71 18 1.7 1 0 18 72 18 1.7 1 0 18 73 23 1.7 1 0 23 74 15 1.7 1 0 15 75 14 1.7 1 0 14 76 12 1.7 1 0 12 77 20 1.7 1 0 20 78 12 1.7 1 0 12 79 15 1.7 1 0 15 80 18 1.7 1 0 18 81 21 1.7 1 0 21 82 15 1.7 1 0 15 83 21 1.7 1 0 21 84 11 1.7 1 0 11 85 11 1.7 1 0 11 86 14 1.7 1 0 14 87 23 1.7 1 0 23 88 15 1.7 1 0 15 89 12 1.7 1 0 12 90 9 1.7 1 0 9 91 12 1.7 1 0 12 92 12 1.7 1 0 12 93 9 1.7 1 0 9 94 11 1.7 1 0 11 95 12 1.7 1 0 12 96 9 1.7 1 0 9 97 13 1.7 1 0 13 98 11 1.7 1 0 11 99 7 1.7 1 0 7 100 4 1.7 1 0 4 RUN STATISTICS FOR INPUT FILE: /home/sam/Downloads/zr2096/Raw_data/zr2096_1_s1_R1.fastq.gz ============================================= 28982766 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Writing report to '/home/sam/Downloads/20180411_trimgalore_10bp_Cvirginica_MBD/zr2096_1_s1_R2.fastq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /home/sam/Downloads/zr2096/Raw_data/zr2096_1_s1_R2.fastq.gz Trimming mode: paired-end Trim Galore version: 0.4.4_dev Cutadapt version: 1.16 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'TGGAATTCTCGG' (Illumina small RNA adapter; auto-detected) Maximum trimming error rate: 0.1 (default) Optional adapter 2 sequence (only used for read 2 of paired-end files): 'GATCGTCGGACT' Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length for both reads before a sequence pair gets removed: 18 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 ~/Downloads/20180411_trimgalore_10bp_Cvirginica_MBD/20180411_fastqc_trim_10bp_Cvirginica_MBD --threads 18' Output file(s) will be GZIP compressed Writing final adapter and quality trimmed output to zr2096_1_s1_R2_trimmed.fq.gz >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'GATCGTCGGACT' from file /home/sam/Downloads/zr2096/Raw_data/zr2096_1_s1_R2.fastq.gz <<< 10000000 sequences processed 20000000 sequences processed This is cutadapt 1.16 with Python 2.7.12 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a GATCGTCGGACT /home/sam/Downloads/zr2096/Raw_data/zr2096_1_s1_R2.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 511.08 s (18 us/read; 3.40 M reads/minute). === Summary === Total reads processed: 28,982,766 Reads with adapters: 6,081,102 (21.0%) Reads written (passing filters): 28,982,766 (100.0%) Total basepairs processed: 2,650,680,530 bp Quality-trimmed: 12,111,002 bp (0.5%) Total written (filtered): 2,630,377,175 bp (99.2%) === Adapter 1 === Sequence: GATCGTCGGACT; Type: regular 3'; Length: 12; Trimmed: 6081102 times. No. of allowed errors: 0-9 bp: 0; 10-12 bp: 1 Bases preceding removed adapters: A: 20.0% C: 18.5% G: 33.6% T: 27.8% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 4531715 7245691.5 0 4531715 2 1086759 1811422.9 0 1086759 3 419635 452855.7 0 419635 4 17753 113213.9 0 17753 5 14526 28303.5 0 14526 6 8480 7075.9 0 8480 7 575 1769.0 0 575 8 342 442.2 0 342 9 431 110.6 0 135 296 10 443 27.6 1 2 441 11 61 6.9 1 0 61 12 5 1.7 1 1 4 13 3 1.7 1 0 3 14 10 1.7 1 0 10 15 5 1.7 1 0 5 16 2 1.7 1 0 2 17 3 1.7 1 0 3 18 3 1.7 1 0 3 19 5 1.7 1 0 5 20 5 1.7 1 0 5 21 2 1.7 1 0 2 22 5 1.7 1 0 5 23 13 1.7 1 0 13 24 3 1.7 1 0 3 25 6 1.7 1 0 6 26 3 1.7 1 0 3 27 13 1.7 1 0 13 28 15 1.7 1 0 15 29 7 1.7 1 0 7 30 6 1.7 1 0 6 31 3 1.7 1 0 3 32 5 1.7 1 0 5 33 9 1.7 1 0 9 34 11 1.7 1 1 10 35 3 1.7 1 0 3 36 6 1.7 1 0 6 37 6 1.7 1 0 6 38 7 1.7 1 0 7 39 5 1.7 1 0 5 40 4 1.7 1 0 4 41 4 1.7 1 0 4 42 6 1.7 1 0 6 43 5 1.7 1 0 5 44 3 1.7 1 0 3 45 10 1.7 1 0 10 46 8 1.7 1 0 8 47 6 1.7 1 0 6 48 5 1.7 1 0 5 49 9 1.7 1 0 9 50 5 1.7 1 0 5 51 4 1.7 1 0 4 52 5 1.7 1 0 5 53 7 1.7 1 0 7 54 4 1.7 1 0 4 55 2 1.7 1 0 2 56 2 1.7 1 0 2 57 1 1.7 1 0 1 58 1 1.7 1 0 1 59 6 1.7 1 0 6 60 5 1.7 1 1 4 61 3 1.7 1 0 3 62 4 1.7 1 0 4 63 5 1.7 1 0 5 64 2 1.7 1 0 2 65 8 1.7 1 0 8 66 4 1.7 1 0 4 67 2 1.7 1 0 2 68 3 1.7 1 0 3 69 3 1.7 1 0 3 70 5 1.7 1 0 5 71 4 1.7 1 0 4 72 6 1.7 1 0 6 73 6 1.7 1 0 6 74 3 1.7 1 0 3 75 1 1.7 1 0 1 76 4 1.7 1 0 4 77 2 1.7 1 0 2 78 3 1.7 1 0 3 79 2 1.7 1 0 2 80 1 1.7 1 0 1 82 2 1.7 1 0 2 83 5 1.7 1 0 5 84 2 1.7 1 0 2 85 1 1.7 1 0 1 86 4 1.7 1 0 4 87 3 1.7 1 0 3 88 3 1.7 1 0 3 89 2 1.7 1 0 2 90 4 1.7 1 0 4 91 4 1.7 1 0 4 92 2 1.7 1 0 2 93 1 1.7 1 0 1 94 3 1.7 1 0 3 95 3 1.7 1 0 3 96 1 1.7 1 0 1 RUN STATISTICS FOR INPUT FILE: /home/sam/Downloads/zr2096/Raw_data/zr2096_1_s1_R2.fastq.gz ============================================= 28982766 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Validate paired-end files zr2096_1_s1_R1_trimmed.fq.gz and zr2096_1_s1_R2_trimmed.fq.gz file_1: zr2096_1_s1_R1_trimmed.fq.gz, file_2: zr2096_1_s1_R2_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: zr2096_1_s1_R1_trimmed.fq.gz and zr2096_1_s1_R2_trimmed.fq.gz <<<<< Writing validated paired-end read 1 reads to zr2096_1_s1_R1_val_1.fq.gz Writing validated paired-end read 2 reads to zr2096_1_s1_R2_val_2.fq.gz Total number of sequences analysed: 28982766 Number of sequence pairs removed because at least one read was shorter than the length cutoff (18 bp): 379420 (1.31%) >>> Now running FastQC on the validated data zr2096_1_s1_R1_val_1.fq.gz<<< Started analysis of zr2096_1_s1_R1_val_1.fq.gz Approx 5% complete for zr2096_1_s1_R1_val_1.fq.gz Approx 10% complete for zr2096_1_s1_R1_val_1.fq.gz Approx 15% complete for zr2096_1_s1_R1_val_1.fq.gz Approx 20% complete for zr2096_1_s1_R1_val_1.fq.gz Approx 25% complete for zr2096_1_s1_R1_val_1.fq.gz Approx 30% complete for zr2096_1_s1_R1_val_1.fq.gz Approx 35% complete for zr2096_1_s1_R1_val_1.fq.gz Approx 40% complete for zr2096_1_s1_R1_val_1.fq.gz Approx 45% complete for zr2096_1_s1_R1_val_1.fq.gz Approx 50% complete for zr2096_1_s1_R1_val_1.fq.gz Approx 55% complete for zr2096_1_s1_R1_val_1.fq.gz Approx 60% complete for zr2096_1_s1_R1_val_1.fq.gz Approx 65% complete for zr2096_1_s1_R1_val_1.fq.gz Approx 70% complete for zr2096_1_s1_R1_val_1.fq.gz Approx 75% complete for zr2096_1_s1_R1_val_1.fq.gz Approx 80% complete for zr2096_1_s1_R1_val_1.fq.gz Approx 85% complete for zr2096_1_s1_R1_val_1.fq.gz Approx 90% complete for zr2096_1_s1_R1_val_1.fq.gz Approx 95% complete for zr2096_1_s1_R1_val_1.fq.gz >>> Now running FastQC on the validated data zr2096_1_s1_R2_val_2.fq.gz<<< Started analysis of zr2096_1_s1_R2_val_2.fq.gz Approx 5% complete for zr2096_1_s1_R2_val_2.fq.gz Approx 10% complete for zr2096_1_s1_R2_val_2.fq.gz Approx 15% complete for zr2096_1_s1_R2_val_2.fq.gz Approx 20% complete for zr2096_1_s1_R2_val_2.fq.gz Approx 25% complete for zr2096_1_s1_R2_val_2.fq.gz Approx 30% complete for zr2096_1_s1_R2_val_2.fq.gz Approx 35% complete for zr2096_1_s1_R2_val_2.fq.gz Approx 40% complete for zr2096_1_s1_R2_val_2.fq.gz Approx 45% complete for zr2096_1_s1_R2_val_2.fq.gz Approx 50% complete for zr2096_1_s1_R2_val_2.fq.gz Approx 55% complete for zr2096_1_s1_R2_val_2.fq.gz Approx 60% complete for zr2096_1_s1_R2_val_2.fq.gz Approx 65% complete for zr2096_1_s1_R2_val_2.fq.gz Approx 70% complete for zr2096_1_s1_R2_val_2.fq.gz Approx 75% complete for zr2096_1_s1_R2_val_2.fq.gz Approx 80% complete for zr2096_1_s1_R2_val_2.fq.gz Approx 85% complete for zr2096_1_s1_R2_val_2.fq.gz Approx 90% complete for zr2096_1_s1_R2_val_2.fq.gz Approx 95% complete for zr2096_1_s1_R2_val_2.fq.gz Deleting both intermediate output files zr2096_1_s1_R1_trimmed.fq.gz and zr2096_1_s1_R2_trimmed.fq.gz ==================================================================================================== Writing report to '/home/sam/Downloads/20180411_trimgalore_10bp_Cvirginica_MBD/zr2096_2_s1_R1.fastq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /home/sam/Downloads/zr2096/Raw_data/zr2096_2_s1_R1.fastq.gz Trimming mode: paired-end Trim Galore version: 0.4.4_dev Cutadapt version: 1.16 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'TGGAATTCTCGG' (Illumina small RNA adapter; auto-detected) Maximum trimming error rate: 0.1 (default) Optional adapter 2 sequence (only used for read 2 of paired-end files): 'GATCGTCGGACT' Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length for both reads before a sequence pair gets removed: 18 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 ~/Downloads/20180411_trimgalore_10bp_Cvirginica_MBD/20180411_fastqc_trim_10bp_Cvirginica_MBD --threads 18' Output file(s) will be GZIP compressed Writing final adapter and quality trimmed output to zr2096_2_s1_R1_trimmed.fq.gz >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'TGGAATTCTCGG' from file /home/sam/Downloads/zr2096/Raw_data/zr2096_2_s1_R1.fastq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed This is cutadapt 1.16 with Python 2.7.12 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a TGGAATTCTCGG /home/sam/Downloads/zr2096/Raw_data/zr2096_2_s1_R1.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 560.17 s (18 us/read; 3.30 M reads/minute). === Summary === Total reads processed: 30,798,582 Reads with adapters: 13,311,629 (43.2%) Reads written (passing filters): 30,798,582 (100.0%) Total basepairs processed: 2,667,762,176 bp Quality-trimmed: 8,816,864 bp (0.3%) Total written (filtered): 2,642,064,564 bp (99.0%) === Adapter 1 === Sequence: TGGAATTCTCGG; Type: regular 3'; Length: 12; Trimmed: 13311629 times. No. of allowed errors: 0-9 bp: 0; 10-12 bp: 1 Bases preceding removed adapters: A: 25.0% C: 6.6% G: 25.5% T: 42.9% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 10904738 7699645.5 0 10904738 2 1590759 1924911.4 0 1590759 3 664944 481227.8 0 664944 4 98584 120307.0 0 98584 5 35292 30076.7 0 35292 6 10391 7519.2 0 10391 7 3699 1879.8 0 3699 8 76 469.9 0 76 9 64 117.5 0 13 51 10 127 29.4 1 0 127 11 83 7.3 1 1 82 12 47 1.8 1 0 47 13 47 1.8 1 0 47 14 85 1.8 1 0 85 15 45 1.8 1 0 45 16 32 1.8 1 0 32 17 32 1.8 1 1 31 18 56 1.8 1 0 56 19 37 1.8 1 0 37 20 40 1.8 1 0 40 21 45 1.8 1 0 45 22 44 1.8 1 0 44 23 59 1.8 1 0 59 24 44 1.8 1 0 44 25 41 1.8 1 0 41 26 52 1.8 1 0 52 27 43 1.8 1 1 42 28 35 1.8 1 0 35 29 28 1.8 1 0 28 30 42 1.8 1 0 42 31 37 1.8 1 0 37 32 32 1.8 1 0 32 33 45 1.8 1 0 45 34 40 1.8 1 0 40 35 50 1.8 1 0 50 36 33 1.8 1 0 33 37 40 1.8 1 0 40 38 34 1.8 1 0 34 39 50 1.8 1 0 50 40 38 1.8 1 0 38 41 28 1.8 1 0 28 42 52 1.8 1 0 52 43 38 1.8 1 0 38 44 34 1.8 1 0 34 45 36 1.8 1 0 36 46 28 1.8 1 0 28 47 28 1.8 1 0 28 48 34 1.8 1 0 34 49 57 1.8 1 0 57 50 61 1.8 1 0 61 51 37 1.8 1 0 37 52 36 1.8 1 0 36 53 41 1.8 1 0 41 54 42 1.8 1 0 42 55 42 1.8 1 0 42 56 27 1.8 1 0 27 57 51 1.8 1 0 51 58 31 1.8 1 0 31 59 28 1.8 1 0 28 60 38 1.8 1 0 38 61 33 1.8 1 0 33 62 22 1.8 1 0 22 63 26 1.8 1 0 26 64 24 1.8 1 0 24 65 27 1.8 1 0 27 66 24 1.8 1 0 24 67 29 1.8 1 1 28 68 15 1.8 1 0 15 69 29 1.8 1 0 29 70 16 1.8 1 0 16 71 23 1.8 1 0 23 72 20 1.8 1 0 20 73 23 1.8 1 0 23 74 33 1.8 1 0 33 75 12 1.8 1 0 12 76 37 1.8 1 0 37 77 28 1.8 1 0 28 78 27 1.8 1 0 27 79 21 1.8 1 0 21 80 13 1.8 1 0 13 81 19 1.8 1 0 19 82 17 1.8 1 0 17 83 17 1.8 1 0 17 84 25 1.8 1 0 25 85 19 1.8 1 0 19 86 26 1.8 1 0 26 87 29 1.8 1 0 29 88 25 1.8 1 0 25 89 21 1.8 1 0 21 90 16 1.8 1 0 16 91 23 1.8 1 0 23 92 23 1.8 1 0 23 93 20 1.8 1 0 20 94 17 1.8 1 0 17 95 13 1.8 1 0 13 96 13 1.8 1 0 13 97 20 1.8 1 0 20 98 16 1.8 1 0 16 99 7 1.8 1 0 7 100 2 1.8 1 0 2 RUN STATISTICS FOR INPUT FILE: /home/sam/Downloads/zr2096/Raw_data/zr2096_2_s1_R1.fastq.gz ============================================= 30798582 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Writing report to '/home/sam/Downloads/20180411_trimgalore_10bp_Cvirginica_MBD/zr2096_2_s1_R2.fastq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /home/sam/Downloads/zr2096/Raw_data/zr2096_2_s1_R2.fastq.gz Trimming mode: paired-end Trim Galore version: 0.4.4_dev Cutadapt version: 1.16 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'TGGAATTCTCGG' (Illumina small RNA adapter; auto-detected) Maximum trimming error rate: 0.1 (default) Optional adapter 2 sequence (only used for read 2 of paired-end files): 'GATCGTCGGACT' Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length for both reads before a sequence pair gets removed: 18 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 ~/Downloads/20180411_trimgalore_10bp_Cvirginica_MBD/20180411_fastqc_trim_10bp_Cvirginica_MBD --threads 18' Output file(s) will be GZIP compressed Writing final adapter and quality trimmed output to zr2096_2_s1_R2_trimmed.fq.gz >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'GATCGTCGGACT' from file /home/sam/Downloads/zr2096/Raw_data/zr2096_2_s1_R2.fastq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed This is cutadapt 1.16 with Python 2.7.12 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a GATCGTCGGACT /home/sam/Downloads/zr2096/Raw_data/zr2096_2_s1_R2.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 535.07 s (17 us/read; 3.45 M reads/minute). === Summary === Total reads processed: 30,798,582 Reads with adapters: 7,597,858 (24.7%) Reads written (passing filters): 30,798,582 (100.0%) Total basepairs processed: 2,666,689,257 bp Quality-trimmed: 9,450,051 bp (0.4%) Total written (filtered): 2,647,320,826 bp (99.3%) === Adapter 1 === Sequence: GATCGTCGGACT; Type: regular 3'; Length: 12; Trimmed: 7597858 times. No. of allowed errors: 0-9 bp: 0; 10-12 bp: 1 Bases preceding removed adapters: A: 21.7% C: 14.3% G: 35.6% T: 28.5% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 5888183 7699645.5 0 5888183 2 1196023 1924911.4 0 1196023 3 476916 481227.8 0 476916 4 16920 120307.0 0 16920 5 12402 30076.7 0 12402 6 5297 7519.2 0 5297 7 477 1879.8 0 477 8 240 469.9 0 240 9 279 117.5 0 37 242 10 309 29.4 1 6 303 11 96 7.3 1 0 96 12 8 1.8 1 0 8 13 6 1.8 1 0 6 14 8 1.8 1 0 8 15 7 1.8 1 0 7 16 8 1.8 1 0 8 17 5 1.8 1 0 5 18 9 1.8 1 0 9 19 13 1.8 1 0 13 20 9 1.8 1 0 9 21 10 1.8 1 0 10 22 9 1.8 1 0 9 23 18 1.8 1 0 18 24 5 1.8 1 1 4 25 14 1.8 1 0 14 26 8 1.8 1 0 8 27 47 1.8 1 0 47 28 15 1.8 1 0 15 29 9 1.8 1 0 9 30 5 1.8 1 0 5 31 7 1.8 1 0 7 32 9 1.8 1 0 9 33 12 1.8 1 0 12 34 8 1.8 1 0 8 35 8 1.8 1 0 8 36 10 1.8 1 0 10 37 10 1.8 1 0 10 38 5 1.8 1 0 5 39 12 1.8 1 0 12 40 8 1.8 1 0 8 41 5 1.8 1 0 5 42 9 1.8 1 0 9 43 7 1.8 1 0 7 44 11 1.8 1 0 11 45 10 1.8 1 0 10 46 18 1.8 1 0 18 47 14 1.8 1 0 14 48 10 1.8 1 0 10 49 6 1.8 1 0 6 50 17 1.8 1 0 17 51 10 1.8 1 0 10 52 12 1.8 1 0 12 53 18 1.8 1 0 18 54 11 1.8 1 0 11 55 12 1.8 1 0 12 56 10 1.8 1 0 10 57 2 1.8 1 0 2 58 3 1.8 1 0 3 59 10 1.8 1 0 10 60 4 1.8 1 0 4 61 10 1.8 1 0 10 62 11 1.8 1 0 11 63 13 1.8 1 0 13 64 10 1.8 1 0 10 65 12 1.8 1 0 12 66 9 1.8 1 0 9 67 10 1.8 1 0 10 68 5 1.8 1 0 5 69 2 1.8 1 0 2 70 9 1.8 1 0 9 71 5 1.8 1 0 5 72 7 1.8 1 0 7 73 5 1.8 1 0 5 74 14 1.8 1 0 14 75 6 1.8 1 0 6 76 6 1.8 1 0 6 77 3 1.8 1 0 3 78 3 1.8 1 0 3 79 8 1.8 1 0 8 80 4 1.8 1 0 4 81 5 1.8 1 0 5 82 4 1.8 1 0 4 83 4 1.8 1 0 4 84 3 1.8 1 0 3 85 5 1.8 1 0 5 86 2 1.8 1 0 2 87 3 1.8 1 0 3 88 4 1.8 1 0 4 89 4 1.8 1 0 4 90 1 1.8 1 0 1 91 5 1.8 1 0 5 92 2 1.8 1 0 2 93 2 1.8 1 0 2 94 4 1.8 1 0 4 95 4 1.8 1 0 4 96 3 1.8 1 1 2 97 3 1.8 1 0 3 98 3 1.8 1 0 3 100 2 1.8 1 0 2 RUN STATISTICS FOR INPUT FILE: /home/sam/Downloads/zr2096/Raw_data/zr2096_2_s1_R2.fastq.gz ============================================= 30798582 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Validate paired-end files zr2096_2_s1_R1_trimmed.fq.gz and zr2096_2_s1_R2_trimmed.fq.gz file_1: zr2096_2_s1_R1_trimmed.fq.gz, file_2: zr2096_2_s1_R2_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: zr2096_2_s1_R1_trimmed.fq.gz and zr2096_2_s1_R2_trimmed.fq.gz <<<<< Writing validated paired-end read 1 reads to zr2096_2_s1_R1_val_1.fq.gz Writing validated paired-end read 2 reads to zr2096_2_s1_R2_val_2.fq.gz Total number of sequences analysed: 30798582 Number of sequence pairs removed because at least one read was shorter than the length cutoff (18 bp): 472976 (1.54%) >>> Now running FastQC on the validated data zr2096_2_s1_R1_val_1.fq.gz<<< Started analysis of zr2096_2_s1_R1_val_1.fq.gz Approx 5% complete for zr2096_2_s1_R1_val_1.fq.gz Approx 10% complete for zr2096_2_s1_R1_val_1.fq.gz Approx 15% complete for zr2096_2_s1_R1_val_1.fq.gz Approx 20% complete for zr2096_2_s1_R1_val_1.fq.gz Approx 25% complete for zr2096_2_s1_R1_val_1.fq.gz Approx 30% complete for zr2096_2_s1_R1_val_1.fq.gz Approx 35% complete for zr2096_2_s1_R1_val_1.fq.gz Approx 40% complete for zr2096_2_s1_R1_val_1.fq.gz Approx 45% complete for zr2096_2_s1_R1_val_1.fq.gz Approx 50% complete for zr2096_2_s1_R1_val_1.fq.gz Approx 55% complete for zr2096_2_s1_R1_val_1.fq.gz Approx 60% complete for zr2096_2_s1_R1_val_1.fq.gz Approx 65% complete for zr2096_2_s1_R1_val_1.fq.gz Approx 70% complete for zr2096_2_s1_R1_val_1.fq.gz Approx 75% complete for zr2096_2_s1_R1_val_1.fq.gz Approx 80% complete for zr2096_2_s1_R1_val_1.fq.gz Approx 85% complete for zr2096_2_s1_R1_val_1.fq.gz Approx 90% complete for zr2096_2_s1_R1_val_1.fq.gz Approx 95% complete for zr2096_2_s1_R1_val_1.fq.gz >>> Now running FastQC on the validated data zr2096_2_s1_R2_val_2.fq.gz<<< Started analysis of zr2096_2_s1_R2_val_2.fq.gz Approx 5% complete for zr2096_2_s1_R2_val_2.fq.gz Approx 10% complete for zr2096_2_s1_R2_val_2.fq.gz Approx 15% complete for zr2096_2_s1_R2_val_2.fq.gz Approx 20% complete for zr2096_2_s1_R2_val_2.fq.gz Approx 25% complete for zr2096_2_s1_R2_val_2.fq.gz Approx 30% complete for zr2096_2_s1_R2_val_2.fq.gz Approx 35% complete for zr2096_2_s1_R2_val_2.fq.gz Approx 40% complete for zr2096_2_s1_R2_val_2.fq.gz Approx 45% complete for zr2096_2_s1_R2_val_2.fq.gz Approx 50% complete for zr2096_2_s1_R2_val_2.fq.gz Approx 55% complete for zr2096_2_s1_R2_val_2.fq.gz Approx 60% complete for zr2096_2_s1_R2_val_2.fq.gz Approx 65% complete for zr2096_2_s1_R2_val_2.fq.gz Approx 70% complete for zr2096_2_s1_R2_val_2.fq.gz Approx 75% complete for zr2096_2_s1_R2_val_2.fq.gz Approx 80% complete for zr2096_2_s1_R2_val_2.fq.gz Approx 85% complete for zr2096_2_s1_R2_val_2.fq.gz Approx 90% complete for zr2096_2_s1_R2_val_2.fq.gz Approx 95% complete for zr2096_2_s1_R2_val_2.fq.gz Deleting both intermediate output files zr2096_2_s1_R1_trimmed.fq.gz and zr2096_2_s1_R2_trimmed.fq.gz ==================================================================================================== Writing report to '/home/sam/Downloads/20180411_trimgalore_10bp_Cvirginica_MBD/zr2096_3_s1_R1.fastq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /home/sam/Downloads/zr2096/Raw_data/zr2096_3_s1_R1.fastq.gz Trimming mode: paired-end Trim Galore version: 0.4.4_dev Cutadapt version: 1.16 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'TGGAATTCTCGG' (Illumina small RNA adapter; auto-detected) Maximum trimming error rate: 0.1 (default) Optional adapter 2 sequence (only used for read 2 of paired-end files): 'GATCGTCGGACT' Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length for both reads before a sequence pair gets removed: 18 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 ~/Downloads/20180411_trimgalore_10bp_Cvirginica_MBD/20180411_fastqc_trim_10bp_Cvirginica_MBD --threads 18' Output file(s) will be GZIP compressed Writing final adapter and quality trimmed output to zr2096_3_s1_R1_trimmed.fq.gz >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'TGGAATTCTCGG' from file /home/sam/Downloads/zr2096/Raw_data/zr2096_3_s1_R1.fastq.gz <<< 10000000 sequences processed 20000000 sequences processed This is cutadapt 1.16 with Python 2.7.12 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a TGGAATTCTCGG /home/sam/Downloads/zr2096/Raw_data/zr2096_3_s1_R1.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 553.52 s (19 us/read; 3.24 M reads/minute). === Summary === Total reads processed: 29,892,002 Reads with adapters: 13,088,943 (43.8%) Reads written (passing filters): 29,892,002 (100.0%) Total basepairs processed: 2,698,353,334 bp Quality-trimmed: 8,120,692 bp (0.3%) Total written (filtered): 2,674,123,947 bp (99.1%) === Adapter 1 === Sequence: TGGAATTCTCGG; Type: regular 3'; Length: 12; Trimmed: 13088943 times. No. of allowed errors: 0-9 bp: 0; 10-12 bp: 1 Bases preceding removed adapters: A: 27.1% C: 6.8% G: 22.4% T: 43.7% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 11066739 7473000.5 0 11066739 2 1369931 1868250.1 0 1369931 3 522764 467062.5 0 522764 4 82767 116765.6 0 82767 5 30112 29191.4 0 30112 6 8805 7297.9 0 8805 7 3969 1824.5 0 3969 8 96 456.1 0 96 9 69 114.0 0 12 57 10 158 28.5 1 1 157 11 106 7.1 1 0 106 12 56 1.8 1 0 56 13 57 1.8 1 0 57 14 100 1.8 1 0 100 15 40 1.8 1 0 40 16 41 1.8 1 0 41 17 37 1.8 1 0 37 18 60 1.8 1 0 60 19 44 1.8 1 0 44 20 47 1.8 1 0 47 21 45 1.8 1 1 44 22 45 1.8 1 0 45 23 64 1.8 1 2 62 24 38 1.8 1 0 38 25 53 1.8 1 0 53 26 68 1.8 1 0 68 27 45 1.8 1 0 45 28 60 1.8 1 0 60 29 46 1.8 1 0 46 30 71 1.8 1 0 71 31 41 1.8 1 0 41 32 47 1.8 1 0 47 33 50 1.8 1 0 50 34 40 1.8 1 0 40 35 49 1.8 1 0 49 36 37 1.8 1 0 37 37 35 1.8 1 0 35 38 43 1.8 1 0 43 39 52 1.8 1 0 52 40 43 1.8 1 0 43 41 58 1.8 1 0 58 42 55 1.8 1 0 55 43 40 1.8 1 0 40 44 36 1.8 1 0 36 45 33 1.8 1 0 33 46 48 1.8 1 0 48 47 37 1.8 1 0 37 48 42 1.8 1 0 42 49 42 1.8 1 0 42 50 40 1.8 1 0 40 51 37 1.8 1 1 36 52 46 1.8 1 0 46 53 37 1.8 1 0 37 54 45 1.8 1 0 45 55 43 1.8 1 1 42 56 38 1.8 1 0 38 57 38 1.8 1 0 38 58 41 1.8 1 0 41 59 36 1.8 1 0 36 60 44 1.8 1 1 43 61 32 1.8 1 0 32 62 33 1.8 1 0 33 63 31 1.8 1 0 31 64 52 1.8 1 0 52 65 27 1.8 1 0 27 66 37 1.8 1 0 37 67 31 1.8 1 0 31 68 24 1.8 1 0 24 69 45 1.8 1 0 45 70 33 1.8 1 0 33 71 36 1.8 1 0 36 72 34 1.8 1 0 34 73 32 1.8 1 0 32 74 39 1.8 1 0 39 75 32 1.8 1 0 32 76 20 1.8 1 0 20 77 34 1.8 1 0 34 78 34 1.8 1 0 34 79 31 1.8 1 0 31 80 27 1.8 1 0 27 81 22 1.8 1 0 22 82 25 1.8 1 0 25 83 42 1.8 1 0 42 84 32 1.8 1 0 32 85 24 1.8 1 0 24 86 32 1.8 1 1 31 87 44 1.8 1 0 44 88 32 1.8 1 0 32 89 16 1.8 1 0 16 90 25 1.8 1 0 25 91 32 1.8 1 0 32 92 22 1.8 1 0 22 93 28 1.8 1 0 28 94 22 1.8 1 0 22 95 7 1.8 1 0 7 96 24 1.8 1 0 24 97 16 1.8 1 0 16 98 20 1.8 1 1 19 99 7 1.8 1 0 7 100 1 1.8 1 0 1 RUN STATISTICS FOR INPUT FILE: /home/sam/Downloads/zr2096/Raw_data/zr2096_3_s1_R1.fastq.gz ============================================= 29892002 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Writing report to '/home/sam/Downloads/20180411_trimgalore_10bp_Cvirginica_MBD/zr2096_3_s1_R2.fastq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /home/sam/Downloads/zr2096/Raw_data/zr2096_3_s1_R2.fastq.gz Trimming mode: paired-end Trim Galore version: 0.4.4_dev Cutadapt version: 1.16 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'TGGAATTCTCGG' (Illumina small RNA adapter; auto-detected) Maximum trimming error rate: 0.1 (default) Optional adapter 2 sequence (only used for read 2 of paired-end files): 'GATCGTCGGACT' Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length for both reads before a sequence pair gets removed: 18 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 ~/Downloads/20180411_trimgalore_10bp_Cvirginica_MBD/20180411_fastqc_trim_10bp_Cvirginica_MBD --threads 18' Output file(s) will be GZIP compressed Writing final adapter and quality trimmed output to zr2096_3_s1_R2_trimmed.fq.gz >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'GATCGTCGGACT' from file /home/sam/Downloads/zr2096/Raw_data/zr2096_3_s1_R2.fastq.gz <<< 10000000 sequences processed 20000000 sequences processed This is cutadapt 1.16 with Python 2.7.12 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a GATCGTCGGACT /home/sam/Downloads/zr2096/Raw_data/zr2096_3_s1_R2.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 519.95 s (17 us/read; 3.45 M reads/minute). === Summary === Total reads processed: 29,892,002 Reads with adapters: 6,569,375 (22.0%) Reads written (passing filters): 29,892,002 (100.0%) Total basepairs processed: 2,696,736,157 bp Quality-trimmed: 9,005,435 bp (0.3%) Total written (filtered): 2,678,973,518 bp (99.3%) === Adapter 1 === Sequence: GATCGTCGGACT; Type: regular 3'; Length: 12; Trimmed: 6569375 times. No. of allowed errors: 0-9 bp: 0; 10-12 bp: 1 Bases preceding removed adapters: A: 22.4% C: 15.5% G: 33.6% T: 28.4% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 4997725 7473000.5 0 4997725 2 1065489 1868250.1 0 1065489 3 469883 467062.5 0 469883 4 16657 116765.6 0 16657 5 12123 29191.4 0 12123 6 5013 7297.9 0 5013 7 246 1824.5 0 246 8 256 456.1 0 256 9 348 114.0 0 46 302 10 509 28.5 1 4 505 11 134 7.1 1 0 134 12 13 1.8 1 0 13 13 10 1.8 1 0 10 14 13 1.8 1 0 13 15 5 1.8 1 1 4 16 8 1.8 1 0 8 17 9 1.8 1 0 9 18 13 1.8 1 0 13 19 21 1.8 1 0 21 20 9 1.8 1 0 9 21 11 1.8 1 0 11 22 17 1.8 1 0 17 23 17 1.8 1 0 17 24 10 1.8 1 0 10 25 8 1.8 1 0 8 26 17 1.8 1 0 17 27 66 1.8 1 0 66 28 16 1.8 1 0 16 29 8 1.8 1 0 8 30 12 1.8 1 0 12 31 7 1.8 1 0 7 32 16 1.8 1 0 16 33 12 1.8 1 0 12 34 12 1.8 1 0 12 35 13 1.8 1 0 13 36 18 1.8 1 0 18 37 9 1.8 1 0 9 38 12 1.8 1 0 12 39 18 1.8 1 0 18 40 9 1.8 1 0 9 41 8 1.8 1 0 8 42 16 1.8 1 0 16 43 14 1.8 1 0 14 44 13 1.8 1 0 13 45 16 1.8 1 0 16 46 23 1.8 1 0 23 47 18 1.8 1 0 18 48 24 1.8 1 0 24 49 12 1.8 1 0 12 50 15 1.8 1 0 15 51 10 1.8 1 0 10 52 15 1.8 1 0 15 53 10 1.8 1 0 10 54 10 1.8 1 0 10 55 7 1.8 1 0 7 56 12 1.8 1 0 12 57 3 1.8 1 0 3 58 14 1.8 1 0 14 59 5 1.8 1 0 5 60 13 1.8 1 0 13 61 10 1.8 1 0 10 62 13 1.8 1 0 13 63 19 1.8 1 0 19 64 15 1.8 1 0 15 65 10 1.8 1 0 10 66 19 1.8 1 0 19 67 13 1.8 1 0 13 68 8 1.8 1 0 8 69 11 1.8 1 0 11 70 8 1.8 1 0 8 71 13 1.8 1 0 13 72 13 1.8 1 0 13 73 11 1.8 1 0 11 74 13 1.8 1 0 13 75 7 1.8 1 0 7 76 18 1.8 1 0 18 77 4 1.8 1 0 4 78 5 1.8 1 0 5 79 11 1.8 1 0 11 80 9 1.8 1 0 9 81 5 1.8 1 0 5 82 6 1.8 1 0 6 83 9 1.8 1 0 9 84 9 1.8 1 0 9 85 6 1.8 1 0 6 86 3 1.8 1 0 3 87 1 1.8 1 0 1 88 2 1.8 1 0 2 89 6 1.8 1 0 6 90 2 1.8 1 0 2 91 11 1.8 1 0 11 92 6 1.8 1 0 6 93 5 1.8 1 0 5 94 6 1.8 1 0 6 95 5 1.8 1 0 5 96 7 1.8 1 0 7 97 2 1.8 1 0 2 98 1 1.8 1 0 1 99 3 1.8 1 0 3 RUN STATISTICS FOR INPUT FILE: /home/sam/Downloads/zr2096/Raw_data/zr2096_3_s1_R2.fastq.gz ============================================= 29892002 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Validate paired-end files zr2096_3_s1_R1_trimmed.fq.gz and zr2096_3_s1_R2_trimmed.fq.gz file_1: zr2096_3_s1_R1_trimmed.fq.gz, file_2: zr2096_3_s1_R2_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: zr2096_3_s1_R1_trimmed.fq.gz and zr2096_3_s1_R2_trimmed.fq.gz <<<<< Writing validated paired-end read 1 reads to zr2096_3_s1_R1_val_1.fq.gz Writing validated paired-end read 2 reads to zr2096_3_s1_R2_val_2.fq.gz Total number of sequences analysed: 29892002 Number of sequence pairs removed because at least one read was shorter than the length cutoff (18 bp): 343249 (1.15%) >>> Now running FastQC on the validated data zr2096_3_s1_R1_val_1.fq.gz<<< Started analysis of zr2096_3_s1_R1_val_1.fq.gz Approx 5% complete for zr2096_3_s1_R1_val_1.fq.gz Approx 10% complete for zr2096_3_s1_R1_val_1.fq.gz Approx 15% complete for zr2096_3_s1_R1_val_1.fq.gz Approx 20% complete for zr2096_3_s1_R1_val_1.fq.gz Approx 25% complete for zr2096_3_s1_R1_val_1.fq.gz Approx 30% complete for zr2096_3_s1_R1_val_1.fq.gz Approx 35% complete for zr2096_3_s1_R1_val_1.fq.gz Approx 40% complete for zr2096_3_s1_R1_val_1.fq.gz Approx 45% complete for zr2096_3_s1_R1_val_1.fq.gz Approx 50% complete for zr2096_3_s1_R1_val_1.fq.gz Approx 55% complete for zr2096_3_s1_R1_val_1.fq.gz Approx 60% complete for zr2096_3_s1_R1_val_1.fq.gz Approx 65% complete for zr2096_3_s1_R1_val_1.fq.gz Approx 70% complete for zr2096_3_s1_R1_val_1.fq.gz Approx 75% complete for zr2096_3_s1_R1_val_1.fq.gz Approx 80% complete for zr2096_3_s1_R1_val_1.fq.gz Approx 85% complete for zr2096_3_s1_R1_val_1.fq.gz Approx 90% complete for zr2096_3_s1_R1_val_1.fq.gz Approx 95% complete for zr2096_3_s1_R1_val_1.fq.gz >>> Now running FastQC on the validated data zr2096_3_s1_R2_val_2.fq.gz<<< Started analysis of zr2096_3_s1_R2_val_2.fq.gz Approx 5% complete for zr2096_3_s1_R2_val_2.fq.gz Approx 10% complete for zr2096_3_s1_R2_val_2.fq.gz Approx 15% complete for zr2096_3_s1_R2_val_2.fq.gz Approx 20% complete for zr2096_3_s1_R2_val_2.fq.gz Approx 25% complete for zr2096_3_s1_R2_val_2.fq.gz Approx 30% complete for zr2096_3_s1_R2_val_2.fq.gz Approx 35% complete for zr2096_3_s1_R2_val_2.fq.gz Approx 40% complete for zr2096_3_s1_R2_val_2.fq.gz Approx 45% complete for zr2096_3_s1_R2_val_2.fq.gz Approx 50% complete for zr2096_3_s1_R2_val_2.fq.gz Approx 55% complete for zr2096_3_s1_R2_val_2.fq.gz Approx 60% complete for zr2096_3_s1_R2_val_2.fq.gz Approx 65% complete for zr2096_3_s1_R2_val_2.fq.gz Approx 70% complete for zr2096_3_s1_R2_val_2.fq.gz Approx 75% complete for zr2096_3_s1_R2_val_2.fq.gz Approx 80% complete for zr2096_3_s1_R2_val_2.fq.gz Approx 85% complete for zr2096_3_s1_R2_val_2.fq.gz Approx 90% complete for zr2096_3_s1_R2_val_2.fq.gz Approx 95% complete for zr2096_3_s1_R2_val_2.fq.gz Deleting both intermediate output files zr2096_3_s1_R1_trimmed.fq.gz and zr2096_3_s1_R2_trimmed.fq.gz ==================================================================================================== Writing report to '/home/sam/Downloads/20180411_trimgalore_10bp_Cvirginica_MBD/zr2096_4_s1_R1.fastq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /home/sam/Downloads/zr2096/Raw_data/zr2096_4_s1_R1.fastq.gz Trimming mode: paired-end Trim Galore version: 0.4.4_dev Cutadapt version: 1.16 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'TGGAATTCTCGG' (Illumina small RNA adapter; auto-detected) Maximum trimming error rate: 0.1 (default) Optional adapter 2 sequence (only used for read 2 of paired-end files): 'GATCGTCGGACT' Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length for both reads before a sequence pair gets removed: 18 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 ~/Downloads/20180411_trimgalore_10bp_Cvirginica_MBD/20180411_fastqc_trim_10bp_Cvirginica_MBD --threads 18' Output file(s) will be GZIP compressed Writing final adapter and quality trimmed output to zr2096_4_s1_R1_trimmed.fq.gz >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'TGGAATTCTCGG' from file /home/sam/Downloads/zr2096/Raw_data/zr2096_4_s1_R1.fastq.gz <<< 10000000 sequences processed 20000000 sequences processed This is cutadapt 1.16 with Python 2.7.12 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a TGGAATTCTCGG /home/sam/Downloads/zr2096/Raw_data/zr2096_4_s1_R1.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 449.87 s (18 us/read; 3.25 M reads/minute). === Summary === Total reads processed: 24,341,968 Reads with adapters: 10,689,983 (43.9%) Reads written (passing filters): 24,341,968 (100.0%) Total basepairs processed: 2,140,220,885 bp Quality-trimmed: 6,722,337 bp (0.3%) Total written (filtered): 2,120,093,942 bp (99.1%) === Adapter 1 === Sequence: TGGAATTCTCGG; Type: regular 3'; Length: 12; Trimmed: 10689983 times. No. of allowed errors: 0-9 bp: 0; 10-12 bp: 1 Bases preceding removed adapters: A: 26.6% C: 6.7% G: 23.7% T: 43.1% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 8852591 6085492.0 0 8852591 2 1242097 1521373.0 0 1242097 3 476517 380343.2 0 476517 4 75989 95085.8 0 75989 5 29444 23771.5 0 29444 6 7498 5942.9 0 7498 7 3157 1485.7 0 3157 8 64 371.4 0 64 9 52 92.9 0 11 41 10 119 23.2 1 1 118 11 84 5.8 1 0 84 12 35 1.5 1 0 35 13 40 1.5 1 0 40 14 48 1.5 1 0 48 15 30 1.5 1 0 30 16 29 1.5 1 0 29 17 27 1.5 1 1 26 18 37 1.5 1 0 37 19 18 1.5 1 0 18 20 22 1.5 1 0 22 21 26 1.5 1 0 26 22 43 1.5 1 0 43 23 35 1.5 1 0 35 24 31 1.5 1 0 31 25 29 1.5 1 0 29 26 38 1.5 1 0 38 27 31 1.5 1 0 31 28 42 1.5 1 0 42 29 32 1.5 1 0 32 30 40 1.5 1 0 40 31 44 1.5 1 0 44 32 29 1.5 1 0 29 33 25 1.5 1 0 25 34 36 1.5 1 0 36 35 36 1.5 1 0 36 36 40 1.5 1 0 40 37 24 1.5 1 0 24 38 28 1.5 1 0 28 39 31 1.5 1 1 30 40 46 1.5 1 0 46 41 32 1.5 1 0 32 42 41 1.5 1 0 41 43 43 1.5 1 0 43 44 24 1.5 1 0 24 45 32 1.5 1 0 32 46 28 1.5 1 0 28 47 34 1.5 1 0 34 48 40 1.5 1 0 40 49 39 1.5 1 0 39 50 33 1.5 1 0 33 51 30 1.5 1 0 30 52 38 1.5 1 0 38 53 30 1.5 1 0 30 54 30 1.5 1 1 29 55 21 1.5 1 0 21 56 33 1.5 1 0 33 57 28 1.5 1 0 28 58 26 1.5 1 0 26 59 26 1.5 1 0 26 60 27 1.5 1 0 27 61 26 1.5 1 0 26 62 30 1.5 1 0 30 63 13 1.5 1 0 13 64 29 1.5 1 0 29 65 16 1.5 1 0 16 66 16 1.5 1 0 16 67 21 1.5 1 0 21 68 13 1.5 1 0 13 69 31 1.5 1 0 31 70 21 1.5 1 0 21 71 18 1.5 1 0 18 72 21 1.5 1 0 21 73 26 1.5 1 0 26 74 27 1.5 1 0 27 75 27 1.5 1 0 27 76 21 1.5 1 0 21 77 25 1.5 1 0 25 78 19 1.5 1 0 19 79 23 1.5 1 0 23 80 17 1.5 1 0 17 81 22 1.5 1 0 22 82 24 1.5 1 0 24 83 13 1.5 1 0 13 84 20 1.5 1 0 20 85 19 1.5 1 0 19 86 28 1.5 1 0 28 87 26 1.5 1 0 26 88 17 1.5 1 0 17 89 15 1.5 1 0 15 90 12 1.5 1 0 12 91 17 1.5 1 0 17 92 21 1.5 1 0 21 93 11 1.5 1 0 11 94 17 1.5 1 0 17 95 17 1.5 1 0 17 96 10 1.5 1 0 10 97 11 1.5 1 0 11 98 14 1.5 1 0 14 99 7 1.5 1 0 7 100 3 1.5 1 0 3 RUN STATISTICS FOR INPUT FILE: /home/sam/Downloads/zr2096/Raw_data/zr2096_4_s1_R1.fastq.gz ============================================= 24341968 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Writing report to '/home/sam/Downloads/20180411_trimgalore_10bp_Cvirginica_MBD/zr2096_4_s1_R2.fastq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /home/sam/Downloads/zr2096/Raw_data/zr2096_4_s1_R2.fastq.gz Trimming mode: paired-end Trim Galore version: 0.4.4_dev Cutadapt version: 1.16 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'TGGAATTCTCGG' (Illumina small RNA adapter; auto-detected) Maximum trimming error rate: 0.1 (default) Optional adapter 2 sequence (only used for read 2 of paired-end files): 'GATCGTCGGACT' Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length for both reads before a sequence pair gets removed: 18 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 ~/Downloads/20180411_trimgalore_10bp_Cvirginica_MBD/20180411_fastqc_trim_10bp_Cvirginica_MBD --threads 18' Output file(s) will be GZIP compressed Writing final adapter and quality trimmed output to zr2096_4_s1_R2_trimmed.fq.gz >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'GATCGTCGGACT' from file /home/sam/Downloads/zr2096/Raw_data/zr2096_4_s1_R2.fastq.gz <<< 10000000 sequences processed 20000000 sequences processed This is cutadapt 1.16 with Python 2.7.12 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a GATCGTCGGACT /home/sam/Downloads/zr2096/Raw_data/zr2096_4_s1_R2.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 414.69 s (17 us/read; 3.52 M reads/minute). === Summary === Total reads processed: 24,341,968 Reads with adapters: 5,730,058 (23.5%) Reads written (passing filters): 24,341,968 (100.0%) Total basepairs processed: 2,138,379,836 bp Quality-trimmed: 7,229,586 bp (0.3%) Total written (filtered): 2,123,664,226 bp (99.3%) === Adapter 1 === Sequence: GATCGTCGGACT; Type: regular 3'; Length: 12; Trimmed: 5730058 times. No. of allowed errors: 0-9 bp: 0; 10-12 bp: 1 Bases preceding removed adapters: A: 23.1% C: 12.5% G: 34.6% T: 29.8% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 4437637 6085492.0 0 4437637 2 894680 1521373.0 0 894680 3 373576 380343.2 0 373576 4 11988 95085.8 0 11988 5 7986 23771.5 0 7986 6 2794 5942.9 0 2794 7 175 1485.7 0 175 8 175 371.4 0 175 9 222 92.9 0 33 189 10 243 23.2 1 4 239 11 65 5.8 1 1 64 12 8 1.5 1 0 8 13 5 1.5 1 0 5 14 3 1.5 1 0 3 15 2 1.5 1 0 2 16 6 1.5 1 0 6 17 8 1.5 1 0 8 18 8 1.5 1 0 8 19 13 1.5 1 0 13 20 8 1.5 1 0 8 21 3 1.5 1 0 3 22 2 1.5 1 0 2 23 9 1.5 1 0 9 24 6 1.5 1 0 6 25 7 1.5 1 0 7 26 12 1.5 1 0 12 27 23 1.5 1 1 22 28 11 1.5 1 0 11 29 11 1.5 1 0 11 30 2 1.5 1 0 2 31 2 1.5 1 0 2 32 11 1.5 1 0 11 33 2 1.5 1 0 2 34 7 1.5 1 0 7 35 7 1.5 1 0 7 36 4 1.5 1 0 4 37 4 1.5 1 0 4 38 4 1.5 1 0 4 39 5 1.5 1 0 5 40 4 1.5 1 0 4 41 3 1.5 1 0 3 42 5 1.5 1 0 5 43 3 1.5 1 0 3 44 6 1.5 1 0 6 45 10 1.5 1 0 10 46 13 1.5 1 0 13 47 18 1.5 1 0 18 48 4 1.5 1 0 4 49 6 1.5 1 0 6 50 13 1.5 1 0 13 51 12 1.5 1 0 12 52 9 1.5 1 0 9 53 14 1.5 1 0 14 54 1 1.5 1 0 1 55 11 1.5 1 0 11 56 4 1.5 1 0 4 57 6 1.5 1 0 6 58 2 1.5 1 0 2 59 5 1.5 1 0 5 60 2 1.5 1 0 2 61 4 1.5 1 0 4 62 4 1.5 1 0 4 63 6 1.5 1 0 6 64 4 1.5 1 0 4 65 4 1.5 1 0 4 66 2 1.5 1 0 2 67 7 1.5 1 1 6 68 1 1.5 1 0 1 69 7 1.5 1 0 7 70 4 1.5 1 0 4 71 6 1.5 1 0 6 72 2 1.5 1 0 2 73 12 1.5 1 0 12 74 2 1.5 1 0 2 75 6 1.5 1 0 6 76 11 1.5 1 0 11 77 2 1.5 1 0 2 78 6 1.5 1 0 6 79 3 1.5 1 0 3 80 7 1.5 1 0 7 81 6 1.5 1 0 6 82 7 1.5 1 0 7 83 6 1.5 1 0 6 84 5 1.5 1 0 5 85 5 1.5 1 0 5 86 6 1.5 1 0 6 87 4 1.5 1 0 4 88 5 1.5 1 0 5 89 4 1.5 1 0 4 90 7 1.5 1 0 7 91 1 1.5 1 0 1 92 2 1.5 1 0 2 93 1 1.5 1 0 1 94 3 1.5 1 0 3 95 3 1.5 1 0 3 96 3 1.5 1 0 3 97 3 1.5 1 0 3 98 2 1.5 1 0 2 RUN STATISTICS FOR INPUT FILE: /home/sam/Downloads/zr2096/Raw_data/zr2096_4_s1_R2.fastq.gz ============================================= 24341968 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Validate paired-end files zr2096_4_s1_R1_trimmed.fq.gz and zr2096_4_s1_R2_trimmed.fq.gz file_1: zr2096_4_s1_R1_trimmed.fq.gz, file_2: zr2096_4_s1_R2_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: zr2096_4_s1_R1_trimmed.fq.gz and zr2096_4_s1_R2_trimmed.fq.gz <<<<< Writing validated paired-end read 1 reads to zr2096_4_s1_R1_val_1.fq.gz Writing validated paired-end read 2 reads to zr2096_4_s1_R2_val_2.fq.gz Total number of sequences analysed: 24341968 Number of sequence pairs removed because at least one read was shorter than the length cutoff (18 bp): 371452 (1.53%) >>> Now running FastQC on the validated data zr2096_4_s1_R1_val_1.fq.gz<<< Started analysis of zr2096_4_s1_R1_val_1.fq.gz Approx 5% complete for zr2096_4_s1_R1_val_1.fq.gz Approx 10% complete for zr2096_4_s1_R1_val_1.fq.gz Approx 15% complete for zr2096_4_s1_R1_val_1.fq.gz Approx 20% complete for zr2096_4_s1_R1_val_1.fq.gz Approx 25% complete for zr2096_4_s1_R1_val_1.fq.gz Approx 30% complete for zr2096_4_s1_R1_val_1.fq.gz Approx 35% complete for zr2096_4_s1_R1_val_1.fq.gz Approx 40% complete for zr2096_4_s1_R1_val_1.fq.gz Approx 45% complete for zr2096_4_s1_R1_val_1.fq.gz Approx 50% complete for zr2096_4_s1_R1_val_1.fq.gz Approx 55% complete for zr2096_4_s1_R1_val_1.fq.gz Approx 60% complete for zr2096_4_s1_R1_val_1.fq.gz Approx 65% complete for zr2096_4_s1_R1_val_1.fq.gz Approx 70% complete for zr2096_4_s1_R1_val_1.fq.gz Approx 75% complete for zr2096_4_s1_R1_val_1.fq.gz Approx 80% complete for zr2096_4_s1_R1_val_1.fq.gz Approx 85% complete for zr2096_4_s1_R1_val_1.fq.gz Approx 90% complete for zr2096_4_s1_R1_val_1.fq.gz Approx 95% complete for zr2096_4_s1_R1_val_1.fq.gz >>> Now running FastQC on the validated data zr2096_4_s1_R2_val_2.fq.gz<<< Started analysis of zr2096_4_s1_R2_val_2.fq.gz Approx 5% complete for zr2096_4_s1_R2_val_2.fq.gz Approx 10% complete for zr2096_4_s1_R2_val_2.fq.gz Approx 15% complete for zr2096_4_s1_R2_val_2.fq.gz Approx 20% complete for zr2096_4_s1_R2_val_2.fq.gz Approx 25% complete for zr2096_4_s1_R2_val_2.fq.gz Approx 30% complete for zr2096_4_s1_R2_val_2.fq.gz Approx 35% complete for zr2096_4_s1_R2_val_2.fq.gz Approx 40% complete for zr2096_4_s1_R2_val_2.fq.gz Approx 45% complete for zr2096_4_s1_R2_val_2.fq.gz Approx 50% complete for zr2096_4_s1_R2_val_2.fq.gz Approx 55% complete for zr2096_4_s1_R2_val_2.fq.gz Approx 60% complete for zr2096_4_s1_R2_val_2.fq.gz Approx 65% complete for zr2096_4_s1_R2_val_2.fq.gz Approx 70% complete for zr2096_4_s1_R2_val_2.fq.gz Approx 75% complete for zr2096_4_s1_R2_val_2.fq.gz Approx 80% complete for zr2096_4_s1_R2_val_2.fq.gz Approx 85% complete for zr2096_4_s1_R2_val_2.fq.gz Approx 90% complete for zr2096_4_s1_R2_val_2.fq.gz Approx 95% complete for zr2096_4_s1_R2_val_2.fq.gz Deleting both intermediate output files zr2096_4_s1_R1_trimmed.fq.gz and zr2096_4_s1_R2_trimmed.fq.gz ==================================================================================================== Writing report to '/home/sam/Downloads/20180411_trimgalore_10bp_Cvirginica_MBD/zr2096_5_s1_R1.fastq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /home/sam/Downloads/zr2096/Raw_data/zr2096_5_s1_R1.fastq.gz Trimming mode: paired-end Trim Galore version: 0.4.4_dev Cutadapt version: 1.16 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'TGGAATTCTCGG' (Illumina small RNA adapter; auto-detected) Maximum trimming error rate: 0.1 (default) Optional adapter 2 sequence (only used for read 2 of paired-end files): 'GATCGTCGGACT' Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length for both reads before a sequence pair gets removed: 18 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 ~/Downloads/20180411_trimgalore_10bp_Cvirginica_MBD/20180411_fastqc_trim_10bp_Cvirginica_MBD --threads 18' Output file(s) will be GZIP compressed Writing final adapter and quality trimmed output to zr2096_5_s1_R1_trimmed.fq.gz >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'TGGAATTCTCGG' from file /home/sam/Downloads/zr2096/Raw_data/zr2096_5_s1_R1.fastq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed This is cutadapt 1.16 with Python 2.7.12 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a TGGAATTCTCGG /home/sam/Downloads/zr2096/Raw_data/zr2096_5_s1_R1.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 582.61 s (18 us/read; 3.27 M reads/minute). === Summary === Total reads processed: 31,778,715 Reads with adapters: 14,444,625 (45.5%) Reads written (passing filters): 31,778,715 (100.0%) Total basepairs processed: 2,881,909,346 bp Quality-trimmed: 9,171,799 bp (0.3%) Total written (filtered): 2,854,903,402 bp (99.1%) === Adapter 1 === Sequence: TGGAATTCTCGG; Type: regular 3'; Length: 12; Trimmed: 14444625 times. No. of allowed errors: 0-9 bp: 0; 10-12 bp: 1 Bases preceding removed adapters: A: 27.1% C: 6.0% G: 22.2% T: 44.8% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 12146141 7944678.8 0 12146141 2 1572510 1986169.7 0 1572510 3 579698 496542.4 0 579698 4 91296 124135.6 0 91296 5 36238 31033.9 0 36238 6 10602 7758.5 0 10602 7 4501 1939.6 0 4501 8 92 484.9 0 92 9 78 121.2 0 15 63 10 162 30.3 1 0 162 11 104 7.6 1 0 104 12 42 1.9 1 0 42 13 62 1.9 1 0 62 14 71 1.9 1 1 70 15 41 1.9 1 0 41 16 40 1.9 1 0 40 17 37 1.9 1 0 37 18 45 1.9 1 0 45 19 28 1.9 1 0 28 20 32 1.9 1 0 32 21 37 1.9 1 0 37 22 48 1.9 1 0 48 23 50 1.9 1 0 50 24 53 1.9 1 0 53 25 40 1.9 1 1 39 26 70 1.9 1 1 69 27 59 1.9 1 0 59 28 34 1.9 1 0 34 29 46 1.9 1 0 46 30 49 1.9 1 0 49 31 38 1.9 1 0 38 32 38 1.9 1 0 38 33 42 1.9 1 0 42 34 44 1.9 1 0 44 35 42 1.9 1 0 42 36 47 1.9 1 0 47 37 37 1.9 1 0 37 38 35 1.9 1 0 35 39 40 1.9 1 0 40 40 41 1.9 1 0 41 41 48 1.9 1 0 48 42 55 1.9 1 0 55 43 49 1.9 1 0 49 44 35 1.9 1 0 35 45 44 1.9 1 0 44 46 43 1.9 1 0 43 47 47 1.9 1 0 47 48 44 1.9 1 0 44 49 46 1.9 1 0 46 50 34 1.9 1 0 34 51 40 1.9 1 0 40 52 58 1.9 1 1 57 53 27 1.9 1 0 27 54 39 1.9 1 0 39 55 37 1.9 1 0 37 56 48 1.9 1 0 48 57 42 1.9 1 0 42 58 36 1.9 1 0 36 59 42 1.9 1 0 42 60 59 1.9 1 1 58 61 45 1.9 1 0 45 62 35 1.9 1 0 35 63 31 1.9 1 0 31 64 32 1.9 1 0 32 65 25 1.9 1 0 25 66 23 1.9 1 0 23 67 35 1.9 1 0 35 68 28 1.9 1 1 27 69 47 1.9 1 0 47 70 27 1.9 1 0 27 71 29 1.9 1 0 29 72 28 1.9 1 0 28 73 22 1.9 1 0 22 74 30 1.9 1 0 30 75 21 1.9 1 0 21 76 20 1.9 1 0 20 77 33 1.9 1 0 33 78 23 1.9 1 0 23 79 35 1.9 1 0 35 80 29 1.9 1 0 29 81 29 1.9 1 0 29 82 32 1.9 1 0 32 83 31 1.9 1 0 31 84 32 1.9 1 0 32 85 27 1.9 1 0 27 86 24 1.9 1 0 24 87 24 1.9 1 0 24 88 29 1.9 1 0 29 89 21 1.9 1 0 21 90 27 1.9 1 0 27 91 25 1.9 1 1 24 92 23 1.9 1 0 23 93 22 1.9 1 0 22 94 22 1.9 1 0 22 95 12 1.9 1 0 12 96 10 1.9 1 0 10 97 15 1.9 1 0 15 98 23 1.9 1 0 23 99 13 1.9 1 0 13 100 3 1.9 1 0 3 RUN STATISTICS FOR INPUT FILE: /home/sam/Downloads/zr2096/Raw_data/zr2096_5_s1_R1.fastq.gz ============================================= 31778715 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Writing report to '/home/sam/Downloads/20180411_trimgalore_10bp_Cvirginica_MBD/zr2096_5_s1_R2.fastq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /home/sam/Downloads/zr2096/Raw_data/zr2096_5_s1_R2.fastq.gz Trimming mode: paired-end Trim Galore version: 0.4.4_dev Cutadapt version: 1.16 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'TGGAATTCTCGG' (Illumina small RNA adapter; auto-detected) Maximum trimming error rate: 0.1 (default) Optional adapter 2 sequence (only used for read 2 of paired-end files): 'GATCGTCGGACT' Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length for both reads before a sequence pair gets removed: 18 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 ~/Downloads/20180411_trimgalore_10bp_Cvirginica_MBD/20180411_fastqc_trim_10bp_Cvirginica_MBD --threads 18' Output file(s) will be GZIP compressed Writing final adapter and quality trimmed output to zr2096_5_s1_R2_trimmed.fq.gz >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'GATCGTCGGACT' from file /home/sam/Downloads/zr2096/Raw_data/zr2096_5_s1_R2.fastq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed This is cutadapt 1.16 with Python 2.7.12 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a GATCGTCGGACT /home/sam/Downloads/zr2096/Raw_data/zr2096_5_s1_R2.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 547.82 s (17 us/read; 3.48 M reads/minute). === Summary === Total reads processed: 31,778,715 Reads with adapters: 6,846,951 (21.5%) Reads written (passing filters): 31,778,715 (100.0%) Total basepairs processed: 2,877,311,782 bp Quality-trimmed: 9,863,732 bp (0.3%) Total written (filtered): 2,858,374,133 bp (99.3%) === Adapter 1 === Sequence: GATCGTCGGACT; Type: regular 3'; Length: 12; Trimmed: 6846951 times. No. of allowed errors: 0-9 bp: 0; 10-12 bp: 1 Bases preceding removed adapters: A: 22.3% C: 13.4% G: 33.2% T: 31.1% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 5229812 7944678.8 0 5229812 2 1095891 1986169.7 0 1095891 3 489213 496542.4 0 489213 4 15569 124135.6 0 15569 5 10559 31033.9 0 10559 6 4110 7758.5 0 4110 7 221 1939.6 0 221 8 231 484.9 0 231 9 248 121.2 0 46 202 10 275 30.3 1 1 274 11 71 7.6 1 0 71 12 10 1.9 1 0 10 13 11 1.9 1 0 11 14 15 1.9 1 0 15 15 10 1.9 1 0 10 16 13 1.9 1 0 13 17 7 1.9 1 0 7 18 10 1.9 1 0 10 19 9 1.9 1 0 9 20 10 1.9 1 0 10 21 11 1.9 1 0 11 22 12 1.9 1 0 12 23 18 1.9 1 0 18 24 11 1.9 1 0 11 25 7 1.9 1 0 7 26 13 1.9 1 0 13 27 32 1.9 1 0 32 28 18 1.9 1 0 18 29 7 1.9 1 0 7 30 9 1.9 1 0 9 31 10 1.9 1 0 10 32 11 1.9 1 0 11 33 5 1.9 1 0 5 34 15 1.9 1 0 15 35 10 1.9 1 0 10 36 6 1.9 1 0 6 37 4 1.9 1 0 4 38 10 1.9 1 0 10 39 9 1.9 1 0 9 40 11 1.9 1 0 11 41 12 1.9 1 0 12 42 11 1.9 1 0 11 43 6 1.9 1 0 6 44 10 1.9 1 0 10 45 15 1.9 1 0 15 46 10 1.9 1 0 10 47 14 1.9 1 0 14 48 6 1.9 1 0 6 49 7 1.9 1 0 7 50 8 1.9 1 0 8 51 14 1.9 1 0 14 52 16 1.9 1 1 15 53 15 1.9 1 0 15 54 12 1.9 1 0 12 55 10 1.9 1 0 10 56 6 1.9 1 0 6 57 8 1.9 1 0 8 58 9 1.9 1 0 9 59 3 1.9 1 0 3 60 4 1.9 1 0 4 61 10 1.9 1 0 10 62 5 1.9 1 0 5 63 10 1.9 1 0 10 64 6 1.9 1 1 5 65 11 1.9 1 0 11 66 7 1.9 1 0 7 67 1 1.9 1 0 1 68 8 1.9 1 0 8 69 6 1.9 1 0 6 70 12 1.9 1 0 12 71 5 1.9 1 0 5 72 6 1.9 1 0 6 73 4 1.9 1 0 4 74 8 1.9 1 0 8 75 9 1.9 1 0 9 76 8 1.9 1 0 8 77 10 1.9 1 0 10 78 5 1.9 1 0 5 79 3 1.9 1 0 3 80 4 1.9 1 0 4 81 7 1.9 1 0 7 82 7 1.9 1 0 7 83 14 1.9 1 0 14 84 10 1.9 1 0 10 85 6 1.9 1 0 6 86 3 1.9 1 0 3 87 3 1.9 1 0 3 88 4 1.9 1 0 4 89 5 1.9 1 0 5 90 5 1.9 1 0 5 91 5 1.9 1 0 5 92 3 1.9 1 0 3 93 2 1.9 1 0 2 94 4 1.9 1 0 4 95 6 1.9 1 0 6 96 4 1.9 1 0 4 97 4 1.9 1 0 4 98 1 1.9 1 0 1 RUN STATISTICS FOR INPUT FILE: /home/sam/Downloads/zr2096/Raw_data/zr2096_5_s1_R2.fastq.gz ============================================= 31778715 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Validate paired-end files zr2096_5_s1_R1_trimmed.fq.gz and zr2096_5_s1_R2_trimmed.fq.gz file_1: zr2096_5_s1_R1_trimmed.fq.gz, file_2: zr2096_5_s1_R2_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: zr2096_5_s1_R1_trimmed.fq.gz and zr2096_5_s1_R2_trimmed.fq.gz <<<<< Writing validated paired-end read 1 reads to zr2096_5_s1_R1_val_1.fq.gz Writing validated paired-end read 2 reads to zr2096_5_s1_R2_val_2.fq.gz Total number of sequences analysed: 31778715 Number of sequence pairs removed because at least one read was shorter than the length cutoff (18 bp): 275434 (0.87%) >>> Now running FastQC on the validated data zr2096_5_s1_R1_val_1.fq.gz<<< Started analysis of zr2096_5_s1_R1_val_1.fq.gz Approx 5% complete for zr2096_5_s1_R1_val_1.fq.gz Approx 10% complete for zr2096_5_s1_R1_val_1.fq.gz Approx 15% complete for zr2096_5_s1_R1_val_1.fq.gz Approx 20% complete for zr2096_5_s1_R1_val_1.fq.gz Approx 25% complete for zr2096_5_s1_R1_val_1.fq.gz Approx 30% complete for zr2096_5_s1_R1_val_1.fq.gz Approx 35% complete for zr2096_5_s1_R1_val_1.fq.gz Approx 40% complete for zr2096_5_s1_R1_val_1.fq.gz Approx 45% complete for zr2096_5_s1_R1_val_1.fq.gz Approx 50% complete for zr2096_5_s1_R1_val_1.fq.gz Approx 55% complete for zr2096_5_s1_R1_val_1.fq.gz Approx 60% complete for zr2096_5_s1_R1_val_1.fq.gz Approx 65% complete for zr2096_5_s1_R1_val_1.fq.gz Approx 70% complete for zr2096_5_s1_R1_val_1.fq.gz Approx 75% complete for zr2096_5_s1_R1_val_1.fq.gz Approx 80% complete for zr2096_5_s1_R1_val_1.fq.gz Approx 85% complete for zr2096_5_s1_R1_val_1.fq.gz Approx 90% complete for zr2096_5_s1_R1_val_1.fq.gz Approx 95% complete for zr2096_5_s1_R1_val_1.fq.gz >>> Now running FastQC on the validated data zr2096_5_s1_R2_val_2.fq.gz<<< Started analysis of zr2096_5_s1_R2_val_2.fq.gz Approx 5% complete for zr2096_5_s1_R2_val_2.fq.gz Approx 10% complete for zr2096_5_s1_R2_val_2.fq.gz Approx 15% complete for zr2096_5_s1_R2_val_2.fq.gz Approx 20% complete for zr2096_5_s1_R2_val_2.fq.gz Approx 25% complete for zr2096_5_s1_R2_val_2.fq.gz Approx 30% complete for zr2096_5_s1_R2_val_2.fq.gz Approx 35% complete for zr2096_5_s1_R2_val_2.fq.gz Approx 40% complete for zr2096_5_s1_R2_val_2.fq.gz Approx 45% complete for zr2096_5_s1_R2_val_2.fq.gz Approx 50% complete for zr2096_5_s1_R2_val_2.fq.gz Approx 55% complete for zr2096_5_s1_R2_val_2.fq.gz Approx 60% complete for zr2096_5_s1_R2_val_2.fq.gz Approx 65% complete for zr2096_5_s1_R2_val_2.fq.gz Approx 70% complete for zr2096_5_s1_R2_val_2.fq.gz Approx 75% complete for zr2096_5_s1_R2_val_2.fq.gz Approx 80% complete for zr2096_5_s1_R2_val_2.fq.gz Approx 85% complete for zr2096_5_s1_R2_val_2.fq.gz Approx 90% complete for zr2096_5_s1_R2_val_2.fq.gz Approx 95% complete for zr2096_5_s1_R2_val_2.fq.gz Deleting both intermediate output files zr2096_5_s1_R1_trimmed.fq.gz and zr2096_5_s1_R2_trimmed.fq.gz ==================================================================================================== Writing report to '/home/sam/Downloads/20180411_trimgalore_10bp_Cvirginica_MBD/zr2096_6_s1_R1.fastq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /home/sam/Downloads/zr2096/Raw_data/zr2096_6_s1_R1.fastq.gz Trimming mode: paired-end Trim Galore version: 0.4.4_dev Cutadapt version: 1.16 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'TGGAATTCTCGG' (Illumina small RNA adapter; auto-detected) Maximum trimming error rate: 0.1 (default) Optional adapter 2 sequence (only used for read 2 of paired-end files): 'GATCGTCGGACT' Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length for both reads before a sequence pair gets removed: 18 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 ~/Downloads/20180411_trimgalore_10bp_Cvirginica_MBD/20180411_fastqc_trim_10bp_Cvirginica_MBD --threads 18' Output file(s) will be GZIP compressed Writing final adapter and quality trimmed output to zr2096_6_s1_R1_trimmed.fq.gz >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'TGGAATTCTCGG' from file /home/sam/Downloads/zr2096/Raw_data/zr2096_6_s1_R1.fastq.gz <<< 10000000 sequences processed 20000000 sequences processed This is cutadapt 1.16 with Python 2.7.12 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a TGGAATTCTCGG /home/sam/Downloads/zr2096/Raw_data/zr2096_6_s1_R1.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 445.61 s (18 us/read; 3.26 M reads/minute). === Summary === Total reads processed: 24,237,290 Reads with adapters: 10,903,318 (45.0%) Reads written (passing filters): 24,237,290 (100.0%) Total basepairs processed: 2,142,776,317 bp Quality-trimmed: 6,660,811 bp (0.3%) Total written (filtered): 2,122,519,922 bp (99.1%) === Adapter 1 === Sequence: TGGAATTCTCGG; Type: regular 3'; Length: 12; Trimmed: 10903318 times. No. of allowed errors: 0-9 bp: 0; 10-12 bp: 1 Bases preceding removed adapters: A: 26.6% C: 6.1% G: 23.4% T: 43.8% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 9087937 6059322.5 0 9087937 2 1227972 1514830.6 0 1227972 3 467659 378707.7 0 467659 4 75619 94676.9 0 75619 5 30315 23669.2 0 30315 6 7702 5917.3 0 7702 7 3275 1479.3 0 3275 8 61 369.8 0 61 9 59 92.5 0 5 54 10 132 23.1 1 2 130 11 70 5.8 1 0 70 12 47 1.4 1 0 47 13 28 1.4 1 0 28 14 62 1.4 1 0 62 15 27 1.4 1 0 27 16 36 1.4 1 0 36 17 26 1.4 1 0 26 18 45 1.4 1 1 44 19 32 1.4 1 0 32 20 21 1.4 1 0 21 21 44 1.4 1 1 43 22 42 1.4 1 0 42 23 47 1.4 1 0 47 24 28 1.4 1 0 28 25 31 1.4 1 0 31 26 42 1.4 1 0 42 27 31 1.4 1 0 31 28 38 1.4 1 0 38 29 23 1.4 1 0 23 30 43 1.4 1 0 43 31 43 1.4 1 1 42 32 47 1.4 1 0 47 33 36 1.4 1 0 36 34 46 1.4 1 0 46 35 23 1.4 1 0 23 36 30 1.4 1 1 29 37 30 1.4 1 0 30 38 28 1.4 1 0 28 39 33 1.4 1 3 30 40 43 1.4 1 0 43 41 36 1.4 1 0 36 42 57 1.4 1 1 56 43 27 1.4 1 0 27 44 38 1.4 1 0 38 45 33 1.4 1 0 33 46 25 1.4 1 0 25 47 29 1.4 1 0 29 48 53 1.4 1 0 53 49 40 1.4 1 0 40 50 39 1.4 1 0 39 51 27 1.4 1 0 27 52 37 1.4 1 0 37 53 26 1.4 1 0 26 54 30 1.4 1 0 30 55 30 1.4 1 0 30 56 25 1.4 1 0 25 57 30 1.4 1 0 30 58 35 1.4 1 0 35 59 25 1.4 1 0 25 60 30 1.4 1 0 30 61 19 1.4 1 0 19 62 22 1.4 1 0 22 63 24 1.4 1 0 24 64 13 1.4 1 0 13 65 36 1.4 1 0 36 66 23 1.4 1 0 23 67 23 1.4 1 0 23 68 21 1.4 1 0 21 69 33 1.4 1 0 33 70 21 1.4 1 0 21 71 21 1.4 1 0 21 72 27 1.4 1 0 27 73 14 1.4 1 0 14 74 34 1.4 1 0 34 75 21 1.4 1 0 21 76 21 1.4 1 0 21 77 22 1.4 1 0 22 78 22 1.4 1 0 22 79 27 1.4 1 0 27 80 27 1.4 1 0 27 81 21 1.4 1 0 21 82 29 1.4 1 0 29 83 17 1.4 1 0 17 84 25 1.4 1 0 25 85 14 1.4 1 0 14 86 21 1.4 1 0 21 87 18 1.4 1 0 18 88 26 1.4 1 0 26 89 17 1.4 1 0 17 90 15 1.4 1 0 15 91 14 1.4 1 0 14 92 12 1.4 1 0 12 93 15 1.4 1 0 15 94 15 1.4 1 0 15 95 13 1.4 1 0 13 96 11 1.4 1 0 11 97 22 1.4 1 0 22 98 11 1.4 1 0 11 99 5 1.4 1 0 5 100 1 1.4 1 0 1 RUN STATISTICS FOR INPUT FILE: /home/sam/Downloads/zr2096/Raw_data/zr2096_6_s1_R1.fastq.gz ============================================= 24237290 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Writing report to '/home/sam/Downloads/20180411_trimgalore_10bp_Cvirginica_MBD/zr2096_6_s1_R2.fastq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /home/sam/Downloads/zr2096/Raw_data/zr2096_6_s1_R2.fastq.gz Trimming mode: paired-end Trim Galore version: 0.4.4_dev Cutadapt version: 1.16 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'TGGAATTCTCGG' (Illumina small RNA adapter; auto-detected) Maximum trimming error rate: 0.1 (default) Optional adapter 2 sequence (only used for read 2 of paired-end files): 'GATCGTCGGACT' Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length for both reads before a sequence pair gets removed: 18 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 ~/Downloads/20180411_trimgalore_10bp_Cvirginica_MBD/20180411_fastqc_trim_10bp_Cvirginica_MBD --threads 18' Output file(s) will be GZIP compressed Writing final adapter and quality trimmed output to zr2096_6_s1_R2_trimmed.fq.gz >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'GATCGTCGGACT' from file /home/sam/Downloads/zr2096/Raw_data/zr2096_6_s1_R2.fastq.gz <<< 10000000 sequences processed 20000000 sequences processed This is cutadapt 1.16 with Python 2.7.12 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a GATCGTCGGACT /home/sam/Downloads/zr2096/Raw_data/zr2096_6_s1_R2.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 412.81 s (17 us/read; 3.52 M reads/minute). === Summary === Total reads processed: 24,237,290 Reads with adapters: 5,603,158 (23.1%) Reads written (passing filters): 24,237,290 (100.0%) Total basepairs processed: 2,140,665,258 bp Quality-trimmed: 7,420,892 bp (0.3%) Total written (filtered): 2,125,867,555 bp (99.3%) === Adapter 1 === Sequence: GATCGTCGGACT; Type: regular 3'; Length: 12; Trimmed: 5603158 times. No. of allowed errors: 0-9 bp: 0; 10-12 bp: 1 Bases preceding removed adapters: A: 23.3% C: 13.4% G: 34.3% T: 29.0% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 4305035 6059322.5 0 4305035 2 895820 1514830.6 0 895820 3 376833 378707.7 0 376833 4 12244 94676.9 0 12244 5 8415 23669.2 0 8415 6 3206 5917.3 0 3206 7 186 1479.3 0 186 8 162 369.8 0 162 9 239 92.5 0 31 208 10 291 23.1 1 9 282 11 84 5.8 1 1 83 12 5 1.4 1 0 5 13 6 1.4 1 0 6 14 5 1.4 1 0 5 15 7 1.4 1 0 7 16 7 1.4 1 0 7 17 8 1.4 1 0 8 18 10 1.4 1 0 10 19 12 1.4 1 0 12 20 2 1.4 1 0 2 21 6 1.4 1 0 6 22 14 1.4 1 0 14 23 17 1.4 1 0 17 24 8 1.4 1 0 8 25 6 1.4 1 0 6 26 10 1.4 1 0 10 27 25 1.4 1 0 25 28 8 1.4 1 0 8 29 8 1.4 1 0 8 30 10 1.4 1 0 10 31 11 1.4 1 0 11 32 8 1.4 1 0 8 33 5 1.4 1 0 5 34 7 1.4 1 0 7 35 13 1.4 1 0 13 36 16 1.4 1 0 16 37 9 1.4 1 0 9 38 10 1.4 1 0 10 39 13 1.4 1 0 13 40 6 1.4 1 0 6 41 8 1.4 1 1 7 42 7 1.4 1 0 7 43 6 1.4 1 0 6 44 7 1.4 1 0 7 45 15 1.4 1 0 15 46 18 1.4 1 0 18 47 9 1.4 1 0 9 48 7 1.4 1 0 7 49 8 1.4 1 0 8 50 11 1.4 1 0 11 51 13 1.4 1 0 13 52 11 1.4 1 0 11 53 16 1.4 1 0 16 54 10 1.4 1 0 10 55 7 1.4 1 0 7 56 7 1.4 1 0 7 57 6 1.4 1 0 6 58 7 1.4 1 0 7 59 5 1.4 1 0 5 60 6 1.4 1 0 6 61 5 1.4 1 0 5 62 5 1.4 1 0 5 63 19 1.4 1 0 19 64 14 1.4 1 0 14 65 7 1.4 1 0 7 66 7 1.4 1 0 7 67 1 1.4 1 0 1 68 3 1.4 1 0 3 69 5 1.4 1 0 5 70 9 1.4 1 0 9 71 4 1.4 1 0 4 72 5 1.4 1 0 5 73 8 1.4 1 0 8 74 6 1.4 1 0 6 75 5 1.4 1 0 5 76 2 1.4 1 0 2 77 2 1.4 1 0 2 78 7 1.4 1 0 7 79 4 1.4 1 0 4 80 6 1.4 1 0 6 81 3 1.4 1 0 3 82 2 1.4 1 0 2 83 3 1.4 1 0 3 84 3 1.4 1 0 3 85 7 1.4 1 0 7 86 4 1.4 1 0 4 87 3 1.4 1 0 3 88 4 1.4 1 0 4 89 4 1.4 1 0 4 90 2 1.4 1 0 2 91 3 1.4 1 0 3 92 3 1.4 1 0 3 93 3 1.4 1 0 3 94 2 1.4 1 0 2 95 8 1.4 1 0 8 96 4 1.4 1 0 4 97 1 1.4 1 0 1 98 2 1.4 1 0 2 99 1 1.4 1 0 1 100 1 1.4 1 0 1 RUN STATISTICS FOR INPUT FILE: /home/sam/Downloads/zr2096/Raw_data/zr2096_6_s1_R2.fastq.gz ============================================= 24237290 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Validate paired-end files zr2096_6_s1_R1_trimmed.fq.gz and zr2096_6_s1_R2_trimmed.fq.gz file_1: zr2096_6_s1_R1_trimmed.fq.gz, file_2: zr2096_6_s1_R2_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: zr2096_6_s1_R1_trimmed.fq.gz and zr2096_6_s1_R2_trimmed.fq.gz <<<<< Writing validated paired-end read 1 reads to zr2096_6_s1_R1_val_1.fq.gz Writing validated paired-end read 2 reads to zr2096_6_s1_R2_val_2.fq.gz Total number of sequences analysed: 24237290 Number of sequence pairs removed because at least one read was shorter than the length cutoff (18 bp): 327797 (1.35%) >>> Now running FastQC on the validated data zr2096_6_s1_R1_val_1.fq.gz<<< Started analysis of zr2096_6_s1_R1_val_1.fq.gz Approx 5% complete for zr2096_6_s1_R1_val_1.fq.gz Approx 10% complete for zr2096_6_s1_R1_val_1.fq.gz Approx 15% complete for zr2096_6_s1_R1_val_1.fq.gz Approx 20% complete for zr2096_6_s1_R1_val_1.fq.gz Approx 25% complete for zr2096_6_s1_R1_val_1.fq.gz Approx 30% complete for zr2096_6_s1_R1_val_1.fq.gz Approx 35% complete for zr2096_6_s1_R1_val_1.fq.gz Approx 40% complete for zr2096_6_s1_R1_val_1.fq.gz Approx 45% complete for zr2096_6_s1_R1_val_1.fq.gz Approx 50% complete for zr2096_6_s1_R1_val_1.fq.gz Approx 55% complete for zr2096_6_s1_R1_val_1.fq.gz Approx 60% complete for zr2096_6_s1_R1_val_1.fq.gz Approx 65% complete for zr2096_6_s1_R1_val_1.fq.gz Approx 70% complete for zr2096_6_s1_R1_val_1.fq.gz Approx 75% complete for zr2096_6_s1_R1_val_1.fq.gz Approx 80% complete for zr2096_6_s1_R1_val_1.fq.gz Approx 85% complete for zr2096_6_s1_R1_val_1.fq.gz Approx 90% complete for zr2096_6_s1_R1_val_1.fq.gz Approx 95% complete for zr2096_6_s1_R1_val_1.fq.gz >>> Now running FastQC on the validated data zr2096_6_s1_R2_val_2.fq.gz<<< Started analysis of zr2096_6_s1_R2_val_2.fq.gz Approx 5% complete for zr2096_6_s1_R2_val_2.fq.gz Approx 10% complete for zr2096_6_s1_R2_val_2.fq.gz Approx 15% complete for zr2096_6_s1_R2_val_2.fq.gz Approx 20% complete for zr2096_6_s1_R2_val_2.fq.gz Approx 25% complete for zr2096_6_s1_R2_val_2.fq.gz Approx 30% complete for zr2096_6_s1_R2_val_2.fq.gz Approx 35% complete for zr2096_6_s1_R2_val_2.fq.gz Approx 40% complete for zr2096_6_s1_R2_val_2.fq.gz Approx 45% complete for zr2096_6_s1_R2_val_2.fq.gz Approx 50% complete for zr2096_6_s1_R2_val_2.fq.gz Approx 55% complete for zr2096_6_s1_R2_val_2.fq.gz Approx 60% complete for zr2096_6_s1_R2_val_2.fq.gz Approx 65% complete for zr2096_6_s1_R2_val_2.fq.gz Approx 70% complete for zr2096_6_s1_R2_val_2.fq.gz Approx 75% complete for zr2096_6_s1_R2_val_2.fq.gz Approx 80% complete for zr2096_6_s1_R2_val_2.fq.gz Approx 85% complete for zr2096_6_s1_R2_val_2.fq.gz Approx 90% complete for zr2096_6_s1_R2_val_2.fq.gz Approx 95% complete for zr2096_6_s1_R2_val_2.fq.gz Deleting both intermediate output files zr2096_6_s1_R1_trimmed.fq.gz and zr2096_6_s1_R2_trimmed.fq.gz ==================================================================================================== Writing report to '/home/sam/Downloads/20180411_trimgalore_10bp_Cvirginica_MBD/zr2096_7_s1_R1.fastq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /home/sam/Downloads/zr2096/Raw_data/zr2096_7_s1_R1.fastq.gz Trimming mode: paired-end Trim Galore version: 0.4.4_dev Cutadapt version: 1.16 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'TGGAATTCTCGG' (Illumina small RNA adapter; auto-detected) Maximum trimming error rate: 0.1 (default) Optional adapter 2 sequence (only used for read 2 of paired-end files): 'GATCGTCGGACT' Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length for both reads before a sequence pair gets removed: 18 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 ~/Downloads/20180411_trimgalore_10bp_Cvirginica_MBD/20180411_fastqc_trim_10bp_Cvirginica_MBD --threads 18' Output file(s) will be GZIP compressed Writing final adapter and quality trimmed output to zr2096_7_s1_R1_trimmed.fq.gz >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'TGGAATTCTCGG' from file /home/sam/Downloads/zr2096/Raw_data/zr2096_7_s1_R1.fastq.gz <<< 10000000 sequences processed 20000000 sequences processed This is cutadapt 1.16 with Python 2.7.12 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a TGGAATTCTCGG /home/sam/Downloads/zr2096/Raw_data/zr2096_7_s1_R1.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 549.70 s (19 us/read; 3.22 M reads/minute). === Summary === Total reads processed: 29,534,746 Reads with adapters: 13,300,837 (45.0%) Reads written (passing filters): 29,534,746 (100.0%) Total basepairs processed: 2,711,811,528 bp Quality-trimmed: 8,678,708 bp (0.3%) Total written (filtered): 2,686,940,853 bp (99.1%) === Adapter 1 === Sequence: TGGAATTCTCGG; Type: regular 3'; Length: 12; Trimmed: 13300837 times. No. of allowed errors: 0-9 bp: 0; 10-12 bp: 1 Bases preceding removed adapters: A: 28.0% C: 6.4% G: 21.3% T: 44.3% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 11345362 7383686.5 0 11345362 2 1348726 1845921.6 0 1348726 3 476512 461480.4 0 476512 4 81590 115370.1 0 81590 5 31877 28842.5 0 31877 6 9281 7210.6 0 9281 7 4185 1802.7 0 4185 8 72 450.7 0 72 9 56 112.7 0 10 46 10 135 28.2 1 1 134 11 78 7.0 1 0 78 12 49 1.8 1 0 49 13 55 1.8 1 0 55 14 81 1.8 1 0 81 15 34 1.8 1 0 34 16 33 1.8 1 0 33 17 47 1.8 1 0 47 18 48 1.8 1 0 48 19 37 1.8 1 0 37 20 31 1.8 1 0 31 21 35 1.8 1 0 35 22 41 1.8 1 0 41 23 59 1.8 1 1 58 24 34 1.8 1 0 34 25 30 1.8 1 1 29 26 57 1.8 1 0 57 27 46 1.8 1 0 46 28 47 1.8 1 1 46 29 37 1.8 1 0 37 30 53 1.8 1 0 53 31 39 1.8 1 0 39 32 46 1.8 1 0 46 33 43 1.8 1 0 43 34 45 1.8 1 0 45 35 35 1.8 1 0 35 36 33 1.8 1 0 33 37 27 1.8 1 0 27 38 31 1.8 1 0 31 39 34 1.8 1 0 34 40 38 1.8 1 0 38 41 32 1.8 1 0 32 42 60 1.8 1 0 60 43 35 1.8 1 0 35 44 29 1.8 1 0 29 45 34 1.8 1 0 34 46 21 1.8 1 0 21 47 32 1.8 1 0 32 48 43 1.8 1 0 43 49 46 1.8 1 0 46 50 48 1.8 1 0 48 51 33 1.8 1 0 33 52 32 1.8 1 0 32 53 33 1.8 1 0 33 54 45 1.8 1 0 45 55 51 1.8 1 0 51 56 32 1.8 1 0 32 57 39 1.8 1 0 39 58 38 1.8 1 0 38 59 32 1.8 1 0 32 60 37 1.8 1 0 37 61 22 1.8 1 0 22 62 36 1.8 1 0 36 63 33 1.8 1 0 33 64 34 1.8 1 0 34 65 41 1.8 1 0 41 66 36 1.8 1 0 36 67 33 1.8 1 1 32 68 28 1.8 1 0 28 69 25 1.8 1 0 25 70 19 1.8 1 0 19 71 33 1.8 1 0 33 72 21 1.8 1 0 21 73 20 1.8 1 0 20 74 28 1.8 1 1 27 75 25 1.8 1 0 25 76 30 1.8 1 0 30 77 25 1.8 1 0 25 78 35 1.8 1 0 35 79 31 1.8 1 0 31 80 34 1.8 1 0 34 81 22 1.8 1 0 22 82 22 1.8 1 0 22 83 29 1.8 1 0 29 84 27 1.8 1 0 27 85 21 1.8 1 0 21 86 27 1.8 1 0 27 87 29 1.8 1 0 29 88 18 1.8 1 0 18 89 17 1.8 1 0 17 90 25 1.8 1 0 25 91 21 1.8 1 0 21 92 19 1.8 1 0 19 93 18 1.8 1 0 18 94 16 1.8 1 0 16 95 15 1.8 1 0 15 96 19 1.8 1 0 19 97 19 1.8 1 0 19 98 19 1.8 1 0 19 99 11 1.8 1 0 11 100 3 1.8 1 0 3 RUN STATISTICS FOR INPUT FILE: /home/sam/Downloads/zr2096/Raw_data/zr2096_7_s1_R1.fastq.gz ============================================= 29534746 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Writing report to '/home/sam/Downloads/20180411_trimgalore_10bp_Cvirginica_MBD/zr2096_7_s1_R2.fastq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /home/sam/Downloads/zr2096/Raw_data/zr2096_7_s1_R2.fastq.gz Trimming mode: paired-end Trim Galore version: 0.4.4_dev Cutadapt version: 1.16 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'TGGAATTCTCGG' (Illumina small RNA adapter; auto-detected) Maximum trimming error rate: 0.1 (default) Optional adapter 2 sequence (only used for read 2 of paired-end files): 'GATCGTCGGACT' Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length for both reads before a sequence pair gets removed: 18 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 ~/Downloads/20180411_trimgalore_10bp_Cvirginica_MBD/20180411_fastqc_trim_10bp_Cvirginica_MBD --threads 18' Output file(s) will be GZIP compressed Writing final adapter and quality trimmed output to zr2096_7_s1_R2_trimmed.fq.gz >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'GATCGTCGGACT' from file /home/sam/Downloads/zr2096/Raw_data/zr2096_7_s1_R2.fastq.gz <<< 10000000 sequences processed 20000000 sequences processed This is cutadapt 1.16 with Python 2.7.12 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a GATCGTCGGACT /home/sam/Downloads/zr2096/Raw_data/zr2096_7_s1_R2.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 512.70 s (17 us/read; 3.46 M reads/minute). === Summary === Total reads processed: 29,534,746 Reads with adapters: 5,991,787 (20.3%) Reads written (passing filters): 29,534,746 (100.0%) Total basepairs processed: 2,711,789,087 bp Quality-trimmed: 8,555,178 bp (0.3%) Total written (filtered): 2,695,158,789 bp (99.4%) === Adapter 1 === Sequence: GATCGTCGGACT; Type: regular 3'; Length: 12; Trimmed: 5991787 times. No. of allowed errors: 0-9 bp: 0; 10-12 bp: 1 Bases preceding removed adapters: A: 23.4% C: 13.8% G: 32.0% T: 30.8% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 4490237 7383686.5 0 4490237 2 1005906 1845921.6 0 1005906 3 465034 461480.4 0 465034 4 14918 115370.1 0 14918 5 9836 28842.5 0 9836 6 4113 7210.6 0 4113 7 197 1802.7 0 197 8 200 450.7 0 200 9 237 112.7 0 29 208 10 321 28.2 1 7 314 11 78 7.0 1 0 78 12 8 1.8 1 0 8 13 4 1.8 1 0 4 14 8 1.8 1 0 8 15 6 1.8 1 0 6 16 8 1.8 1 0 8 17 5 1.8 1 0 5 18 13 1.8 1 0 13 19 19 1.8 1 0 19 20 7 1.8 1 0 7 21 7 1.8 1 0 7 22 9 1.8 1 0 9 23 8 1.8 1 0 8 24 5 1.8 1 0 5 25 9 1.8 1 0 9 26 13 1.8 1 0 13 27 23 1.8 1 0 23 28 26 1.8 1 0 26 29 11 1.8 1 0 11 30 9 1.8 1 0 9 31 8 1.8 1 0 8 32 9 1.8 1 0 9 33 11 1.8 1 0 11 34 15 1.8 1 0 15 35 2 1.8 1 0 2 36 15 1.8 1 0 15 37 2 1.8 1 0 2 38 13 1.8 1 0 13 39 10 1.8 1 0 10 40 12 1.8 1 0 12 41 2 1.8 1 0 2 42 4 1.8 1 0 4 43 10 1.8 1 0 10 44 12 1.8 1 0 12 45 10 1.8 1 0 10 46 3 1.8 1 0 3 47 15 1.8 1 0 15 48 12 1.8 1 0 12 49 9 1.8 1 0 9 50 17 1.8 1 0 17 51 14 1.8 1 0 14 52 6 1.8 1 0 6 53 9 1.8 1 0 9 54 10 1.8 1 0 10 55 10 1.8 1 0 10 56 11 1.8 1 0 11 57 8 1.8 1 0 8 58 5 1.8 1 0 5 59 5 1.8 1 0 5 60 6 1.8 1 0 6 61 7 1.8 1 0 7 62 9 1.8 1 0 9 63 11 1.8 1 0 11 64 8 1.8 1 0 8 65 5 1.8 1 0 5 66 4 1.8 1 0 4 67 8 1.8 1 0 8 68 6 1.8 1 0 6 69 6 1.8 1 0 6 70 10 1.8 1 0 10 71 7 1.8 1 0 7 72 9 1.8 1 0 9 73 6 1.8 1 0 6 74 5 1.8 1 0 5 75 6 1.8 1 0 6 76 7 1.8 1 0 7 77 10 1.8 1 0 10 78 9 1.8 1 0 9 79 7 1.8 1 0 7 80 1 1.8 1 0 1 81 10 1.8 1 0 10 82 5 1.8 1 0 5 83 10 1.8 1 0 10 84 7 1.8 1 0 7 85 3 1.8 1 0 3 86 5 1.8 1 0 5 87 5 1.8 1 0 5 88 5 1.8 1 0 5 89 5 1.8 1 0 5 90 3 1.8 1 0 3 91 4 1.8 1 0 4 92 4 1.8 1 0 4 93 4 1.8 1 0 4 94 10 1.8 1 0 10 95 4 1.8 1 0 4 96 6 1.8 1 0 6 97 3 1.8 1 0 3 98 2 1.8 1 0 2 99 1 1.8 1 0 1 RUN STATISTICS FOR INPUT FILE: /home/sam/Downloads/zr2096/Raw_data/zr2096_7_s1_R2.fastq.gz ============================================= 29534746 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Validate paired-end files zr2096_7_s1_R1_trimmed.fq.gz and zr2096_7_s1_R2_trimmed.fq.gz file_1: zr2096_7_s1_R1_trimmed.fq.gz, file_2: zr2096_7_s1_R2_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: zr2096_7_s1_R1_trimmed.fq.gz and zr2096_7_s1_R2_trimmed.fq.gz <<<<< Writing validated paired-end read 1 reads to zr2096_7_s1_R1_val_1.fq.gz Writing validated paired-end read 2 reads to zr2096_7_s1_R2_val_2.fq.gz Total number of sequences analysed: 29534746 Number of sequence pairs removed because at least one read was shorter than the length cutoff (18 bp): 261111 (0.88%) >>> Now running FastQC on the validated data zr2096_7_s1_R1_val_1.fq.gz<<< Started analysis of zr2096_7_s1_R1_val_1.fq.gz Approx 5% complete for zr2096_7_s1_R1_val_1.fq.gz Approx 10% complete for zr2096_7_s1_R1_val_1.fq.gz Approx 15% complete for zr2096_7_s1_R1_val_1.fq.gz Approx 20% complete for zr2096_7_s1_R1_val_1.fq.gz Approx 25% complete for zr2096_7_s1_R1_val_1.fq.gz Approx 30% complete for zr2096_7_s1_R1_val_1.fq.gz Approx 35% complete for zr2096_7_s1_R1_val_1.fq.gz Approx 40% complete for zr2096_7_s1_R1_val_1.fq.gz Approx 45% complete for zr2096_7_s1_R1_val_1.fq.gz Approx 50% complete for zr2096_7_s1_R1_val_1.fq.gz Approx 55% complete for zr2096_7_s1_R1_val_1.fq.gz Approx 60% complete for zr2096_7_s1_R1_val_1.fq.gz Approx 65% complete for zr2096_7_s1_R1_val_1.fq.gz Approx 70% complete for zr2096_7_s1_R1_val_1.fq.gz Approx 75% complete for zr2096_7_s1_R1_val_1.fq.gz Approx 80% complete for zr2096_7_s1_R1_val_1.fq.gz Approx 85% complete for zr2096_7_s1_R1_val_1.fq.gz Approx 90% complete for zr2096_7_s1_R1_val_1.fq.gz Approx 95% complete for zr2096_7_s1_R1_val_1.fq.gz >>> Now running FastQC on the validated data zr2096_7_s1_R2_val_2.fq.gz<<< Started analysis of zr2096_7_s1_R2_val_2.fq.gz Approx 5% complete for zr2096_7_s1_R2_val_2.fq.gz Approx 10% complete for zr2096_7_s1_R2_val_2.fq.gz Approx 15% complete for zr2096_7_s1_R2_val_2.fq.gz Approx 20% complete for zr2096_7_s1_R2_val_2.fq.gz Approx 25% complete for zr2096_7_s1_R2_val_2.fq.gz Approx 30% complete for zr2096_7_s1_R2_val_2.fq.gz Approx 35% complete for zr2096_7_s1_R2_val_2.fq.gz Approx 40% complete for zr2096_7_s1_R2_val_2.fq.gz Approx 45% complete for zr2096_7_s1_R2_val_2.fq.gz Approx 50% complete for zr2096_7_s1_R2_val_2.fq.gz Approx 55% complete for zr2096_7_s1_R2_val_2.fq.gz Approx 60% complete for zr2096_7_s1_R2_val_2.fq.gz Approx 65% complete for zr2096_7_s1_R2_val_2.fq.gz Approx 70% complete for zr2096_7_s1_R2_val_2.fq.gz Approx 75% complete for zr2096_7_s1_R2_val_2.fq.gz Approx 80% complete for zr2096_7_s1_R2_val_2.fq.gz Approx 85% complete for zr2096_7_s1_R2_val_2.fq.gz Approx 90% complete for zr2096_7_s1_R2_val_2.fq.gz Approx 95% complete for zr2096_7_s1_R2_val_2.fq.gz Deleting both intermediate output files zr2096_7_s1_R1_trimmed.fq.gz and zr2096_7_s1_R2_trimmed.fq.gz ==================================================================================================== Writing report to '/home/sam/Downloads/20180411_trimgalore_10bp_Cvirginica_MBD/zr2096_8_s1_R1.fastq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /home/sam/Downloads/zr2096/Raw_data/zr2096_8_s1_R1.fastq.gz Trimming mode: paired-end Trim Galore version: 0.4.4_dev Cutadapt version: 1.16 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'TGGAATTCTCGG' (Illumina small RNA adapter; auto-detected) Maximum trimming error rate: 0.1 (default) Optional adapter 2 sequence (only used for read 2 of paired-end files): 'GATCGTCGGACT' Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length for both reads before a sequence pair gets removed: 18 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 ~/Downloads/20180411_trimgalore_10bp_Cvirginica_MBD/20180411_fastqc_trim_10bp_Cvirginica_MBD --threads 18' Output file(s) will be GZIP compressed Writing final adapter and quality trimmed output to zr2096_8_s1_R1_trimmed.fq.gz >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'TGGAATTCTCGG' from file /home/sam/Downloads/zr2096/Raw_data/zr2096_8_s1_R1.fastq.gz <<< 10000000 sequences processed 20000000 sequences processed This is cutadapt 1.16 with Python 2.7.12 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a TGGAATTCTCGG /home/sam/Downloads/zr2096/Raw_data/zr2096_8_s1_R1.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 547.55 s (18 us/read; 3.26 M reads/minute). === Summary === Total reads processed: 29,761,837 Reads with adapters: 13,441,159 (45.2%) Reads written (passing filters): 29,761,837 (100.0%) Total basepairs processed: 2,707,315,822 bp Quality-trimmed: 8,285,086 bp (0.3%) Total written (filtered): 2,682,461,698 bp (99.1%) === Adapter 1 === Sequence: TGGAATTCTCGG; Type: regular 3'; Length: 12; Trimmed: 13441159 times. No. of allowed errors: 0-9 bp: 0; 10-12 bp: 1 Bases preceding removed adapters: A: 26.8% C: 6.3% G: 22.4% T: 44.5% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 11303071 7440459.2 0 11303071 2 1459012 1860114.8 0 1459012 3 547133 465028.7 0 547133 4 82671 116257.2 0 82671 5 31711 29064.3 0 31711 6 10548 7266.1 0 10548 7 4205 1816.5 0 4205 8 81 454.1 0 81 9 68 113.5 0 6 62 10 113 28.4 1 1 112 11 73 7.1 1 0 73 12 40 1.8 1 0 40 13 42 1.8 1 0 42 14 60 1.8 1 0 60 15 25 1.8 1 0 25 16 31 1.8 1 0 31 17 29 1.8 1 0 29 18 41 1.8 1 1 40 19 25 1.8 1 0 25 20 29 1.8 1 0 29 21 31 1.8 1 0 31 22 41 1.8 1 0 41 23 41 1.8 1 0 41 24 34 1.8 1 0 34 25 35 1.8 1 0 35 26 43 1.8 1 1 42 27 33 1.8 1 0 33 28 34 1.8 1 0 34 29 27 1.8 1 0 27 30 44 1.8 1 0 44 31 33 1.8 1 0 33 32 34 1.8 1 1 33 33 38 1.8 1 1 37 34 41 1.8 1 0 41 35 38 1.8 1 0 38 36 26 1.8 1 0 26 37 36 1.8 1 0 36 38 31 1.8 1 0 31 39 42 1.8 1 0 42 40 39 1.8 1 0 39 41 27 1.8 1 0 27 42 44 1.8 1 0 44 43 31 1.8 1 0 31 44 25 1.8 1 0 25 45 47 1.8 1 0 47 46 32 1.8 1 0 32 47 30 1.8 1 0 30 48 32 1.8 1 0 32 49 31 1.8 1 0 31 50 29 1.8 1 1 28 51 40 1.8 1 0 40 52 22 1.8 1 0 22 53 20 1.8 1 0 20 54 32 1.8 1 0 32 55 31 1.8 1 0 31 56 35 1.8 1 0 35 57 27 1.8 1 0 27 58 29 1.8 1 0 29 59 26 1.8 1 2 24 60 38 1.8 1 1 37 61 16 1.8 1 0 16 62 34 1.8 1 0 34 63 18 1.8 1 0 18 64 23 1.8 1 0 23 65 31 1.8 1 0 31 66 19 1.8 1 0 19 67 19 1.8 1 0 19 68 18 1.8 1 0 18 69 18 1.8 1 1 17 70 28 1.8 1 0 28 71 32 1.8 1 0 32 72 28 1.8 1 0 28 73 22 1.8 1 0 22 74 26 1.8 1 0 26 75 16 1.8 1 0 16 76 24 1.8 1 0 24 77 26 1.8 1 0 26 78 13 1.8 1 0 13 79 38 1.8 1 1 37 80 14 1.8 1 0 14 81 17 1.8 1 0 17 82 23 1.8 1 0 23 83 21 1.8 1 0 21 84 22 1.8 1 0 22 85 21 1.8 1 0 21 86 21 1.8 1 0 21 87 21 1.8 1 0 21 88 19 1.8 1 0 19 89 21 1.8 1 0 21 90 19 1.8 1 0 19 91 16 1.8 1 0 16 92 24 1.8 1 0 24 93 13 1.8 1 0 13 94 22 1.8 1 0 22 95 12 1.8 1 0 12 96 10 1.8 1 0 10 97 16 1.8 1 0 16 98 13 1.8 1 0 13 99 8 1.8 1 0 8 RUN STATISTICS FOR INPUT FILE: /home/sam/Downloads/zr2096/Raw_data/zr2096_8_s1_R1.fastq.gz ============================================= 29761837 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Writing report to '/home/sam/Downloads/20180411_trimgalore_10bp_Cvirginica_MBD/zr2096_8_s1_R2.fastq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /home/sam/Downloads/zr2096/Raw_data/zr2096_8_s1_R2.fastq.gz Trimming mode: paired-end Trim Galore version: 0.4.4_dev Cutadapt version: 1.16 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'TGGAATTCTCGG' (Illumina small RNA adapter; auto-detected) Maximum trimming error rate: 0.1 (default) Optional adapter 2 sequence (only used for read 2 of paired-end files): 'GATCGTCGGACT' Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length for both reads before a sequence pair gets removed: 18 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 ~/Downloads/20180411_trimgalore_10bp_Cvirginica_MBD/20180411_fastqc_trim_10bp_Cvirginica_MBD --threads 18' Output file(s) will be GZIP compressed Writing final adapter and quality trimmed output to zr2096_8_s1_R2_trimmed.fq.gz >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'GATCGTCGGACT' from file /home/sam/Downloads/zr2096/Raw_data/zr2096_8_s1_R2.fastq.gz <<< 10000000 sequences processed 20000000 sequences processed This is cutadapt 1.16 with Python 2.7.12 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a GATCGTCGGACT /home/sam/Downloads/zr2096/Raw_data/zr2096_8_s1_R2.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 517.69 s (17 us/read; 3.45 M reads/minute). === Summary === Total reads processed: 29,761,837 Reads with adapters: 6,230,529 (20.9%) Reads written (passing filters): 29,761,837 (100.0%) Total basepairs processed: 2,705,142,381 bp Quality-trimmed: 9,093,824 bp (0.3%) Total written (filtered): 2,687,730,288 bp (99.4%) === Adapter 1 === Sequence: GATCGTCGGACT; Type: regular 3'; Length: 12; Trimmed: 6230529 times. No. of allowed errors: 0-9 bp: 0; 10-12 bp: 1 Bases preceding removed adapters: A: 22.5% C: 13.9% G: 32.7% T: 30.9% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 4708845 7440459.2 0 4708845 2 1035200 1860114.8 0 1035200 3 454845 465028.7 0 454845 4 15837 116257.2 0 15837 5 10378 29064.3 0 10378 6 3993 7266.1 0 3993 7 162 1816.5 0 162 8 166 454.1 0 166 9 234 113.5 0 36 198 10 238 28.4 1 2 236 11 62 7.1 1 0 62 12 8 1.8 1 0 8 13 1 1.8 1 0 1 14 2 1.8 1 0 2 15 9 1.8 1 0 9 16 5 1.8 1 0 5 17 3 1.8 1 0 3 18 7 1.8 1 0 7 19 11 1.8 1 0 11 20 5 1.8 1 0 5 21 2 1.8 1 0 2 22 14 1.8 1 0 14 23 11 1.8 1 0 11 24 5 1.8 1 0 5 25 11 1.8 1 0 11 26 7 1.8 1 0 7 27 14 1.8 1 0 14 28 12 1.8 1 0 12 29 12 1.8 1 0 12 30 11 1.8 1 0 11 31 6 1.8 1 0 6 32 2 1.8 1 0 2 33 6 1.8 1 0 6 34 15 1.8 1 0 15 35 12 1.8 1 0 12 36 12 1.8 1 0 12 37 10 1.8 1 0 10 38 11 1.8 1 0 11 39 4 1.8 1 0 4 40 11 1.8 1 0 11 41 6 1.8 1 0 6 42 2 1.8 1 0 2 43 4 1.8 1 0 4 44 10 1.8 1 1 9 45 15 1.8 1 0 15 46 13 1.8 1 0 13 47 12 1.8 1 0 12 48 6 1.8 1 0 6 49 8 1.8 1 0 8 50 8 1.8 1 0 8 51 15 1.8 1 0 15 52 7 1.8 1 0 7 53 13 1.8 1 0 13 54 7 1.8 1 0 7 55 7 1.8 1 0 7 56 4 1.8 1 0 4 57 10 1.8 1 0 10 58 4 1.8 1 0 4 59 7 1.8 1 0 7 60 8 1.8 1 0 8 61 3 1.8 1 0 3 62 6 1.8 1 0 6 63 3 1.8 1 0 3 64 7 1.8 1 0 7 65 7 1.8 1 0 7 66 7 1.8 1 0 7 67 5 1.8 1 0 5 68 1 1.8 1 0 1 69 2 1.8 1 0 2 70 7 1.8 1 0 7 71 5 1.8 1 0 5 72 5 1.8 1 0 5 73 5 1.8 1 0 5 74 5 1.8 1 0 5 75 4 1.8 1 0 4 76 9 1.8 1 0 9 77 7 1.8 1 0 7 78 7 1.8 1 0 7 79 3 1.8 1 0 3 80 5 1.8 1 0 5 81 6 1.8 1 0 6 82 3 1.8 1 0 3 83 4 1.8 1 0 4 84 6 1.8 1 0 6 85 4 1.8 1 0 4 86 3 1.8 1 0 3 87 1 1.8 1 0 1 88 4 1.8 1 0 4 89 3 1.8 1 0 3 90 3 1.8 1 0 3 91 3 1.8 1 0 3 92 5 1.8 1 0 5 93 4 1.8 1 0 4 94 1 1.8 1 0 1 95 3 1.8 1 0 3 96 2 1.8 1 0 2 97 3 1.8 1 0 3 98 2 1.8 1 0 2 99 1 1.8 1 1 RUN STATISTICS FOR INPUT FILE: /home/sam/Downloads/zr2096/Raw_data/zr2096_8_s1_R2.fastq.gz ============================================= 29761837 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Validate paired-end files zr2096_8_s1_R1_trimmed.fq.gz and zr2096_8_s1_R2_trimmed.fq.gz file_1: zr2096_8_s1_R1_trimmed.fq.gz, file_2: zr2096_8_s1_R2_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: zr2096_8_s1_R1_trimmed.fq.gz and zr2096_8_s1_R2_trimmed.fq.gz <<<<< Writing validated paired-end read 1 reads to zr2096_8_s1_R1_val_1.fq.gz Writing validated paired-end read 2 reads to zr2096_8_s1_R2_val_2.fq.gz Total number of sequences analysed: 29761837 Number of sequence pairs removed because at least one read was shorter than the length cutoff (18 bp): 278619 (0.94%) >>> Now running FastQC on the validated data zr2096_8_s1_R1_val_1.fq.gz<<< Started analysis of zr2096_8_s1_R1_val_1.fq.gz Approx 5% complete for zr2096_8_s1_R1_val_1.fq.gz Approx 10% complete for zr2096_8_s1_R1_val_1.fq.gz Approx 15% complete for zr2096_8_s1_R1_val_1.fq.gz Approx 20% complete for zr2096_8_s1_R1_val_1.fq.gz Approx 25% complete for zr2096_8_s1_R1_val_1.fq.gz Approx 30% complete for zr2096_8_s1_R1_val_1.fq.gz Approx 35% complete for zr2096_8_s1_R1_val_1.fq.gz Approx 40% complete for zr2096_8_s1_R1_val_1.fq.gz Approx 45% complete for zr2096_8_s1_R1_val_1.fq.gz Approx 50% complete for zr2096_8_s1_R1_val_1.fq.gz Approx 55% complete for zr2096_8_s1_R1_val_1.fq.gz Approx 60% complete for zr2096_8_s1_R1_val_1.fq.gz Approx 65% complete for zr2096_8_s1_R1_val_1.fq.gz Approx 70% complete for zr2096_8_s1_R1_val_1.fq.gz Approx 75% complete for zr2096_8_s1_R1_val_1.fq.gz Approx 80% complete for zr2096_8_s1_R1_val_1.fq.gz Approx 85% complete for zr2096_8_s1_R1_val_1.fq.gz Approx 90% complete for zr2096_8_s1_R1_val_1.fq.gz Approx 95% complete for zr2096_8_s1_R1_val_1.fq.gz >>> Now running FastQC on the validated data zr2096_8_s1_R2_val_2.fq.gz<<< Started analysis of zr2096_8_s1_R2_val_2.fq.gz Approx 5% complete for zr2096_8_s1_R2_val_2.fq.gz Approx 10% complete for zr2096_8_s1_R2_val_2.fq.gz Approx 15% complete for zr2096_8_s1_R2_val_2.fq.gz Approx 20% complete for zr2096_8_s1_R2_val_2.fq.gz Approx 25% complete for zr2096_8_s1_R2_val_2.fq.gz Approx 30% complete for zr2096_8_s1_R2_val_2.fq.gz Approx 35% complete for zr2096_8_s1_R2_val_2.fq.gz Approx 40% complete for zr2096_8_s1_R2_val_2.fq.gz Approx 45% complete for zr2096_8_s1_R2_val_2.fq.gz Approx 50% complete for zr2096_8_s1_R2_val_2.fq.gz Approx 55% complete for zr2096_8_s1_R2_val_2.fq.gz Approx 60% complete for zr2096_8_s1_R2_val_2.fq.gz Approx 65% complete for zr2096_8_s1_R2_val_2.fq.gz Approx 70% complete for zr2096_8_s1_R2_val_2.fq.gz Approx 75% complete for zr2096_8_s1_R2_val_2.fq.gz Approx 80% complete for zr2096_8_s1_R2_val_2.fq.gz Approx 85% complete for zr2096_8_s1_R2_val_2.fq.gz Approx 90% complete for zr2096_8_s1_R2_val_2.fq.gz Approx 95% complete for zr2096_8_s1_R2_val_2.fq.gz Deleting both intermediate output files zr2096_8_s1_R1_trimmed.fq.gz and zr2096_8_s1_R2_trimmed.fq.gz ==================================================================================================== Writing report to '/home/sam/Downloads/20180411_trimgalore_10bp_Cvirginica_MBD/zr2096_9_s1_R1.fastq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /home/sam/Downloads/zr2096/Raw_data/zr2096_9_s1_R1.fastq.gz Trimming mode: paired-end Trim Galore version: 0.4.4_dev Cutadapt version: 1.16 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'TGGAATTCTCGG' (Illumina small RNA adapter; auto-detected) Maximum trimming error rate: 0.1 (default) Optional adapter 2 sequence (only used for read 2 of paired-end files): 'GATCGTCGGACT' Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length for both reads before a sequence pair gets removed: 18 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 ~/Downloads/20180411_trimgalore_10bp_Cvirginica_MBD/20180411_fastqc_trim_10bp_Cvirginica_MBD --threads 18' Output file(s) will be GZIP compressed Writing final adapter and quality trimmed output to zr2096_9_s1_R1_trimmed.fq.gz >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'TGGAATTCTCGG' from file /home/sam/Downloads/zr2096/Raw_data/zr2096_9_s1_R1.fastq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed This is cutadapt 1.16 with Python 2.7.12 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a TGGAATTCTCGG /home/sam/Downloads/zr2096/Raw_data/zr2096_9_s1_R1.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 635.85 s (19 us/read; 3.08 M reads/minute). === Summary === Total reads processed: 32,636,231 Reads with adapters: 15,181,617 (46.5%) Reads written (passing filters): 32,636,231 (100.0%) Total basepairs processed: 2,952,817,074 bp Quality-trimmed: 17,135,297 bp (0.6%) Total written (filtered): 2,891,237,315 bp (97.9%) === Adapter 1 === Sequence: TGGAATTCTCGG; Type: regular 3'; Length: 12; Trimmed: 15181617 times. No. of allowed errors: 0-9 bp: 0; 10-12 bp: 1 Bases preceding removed adapters: A: 26.0% C: 6.0% G: 22.4% T: 45.5% none/other: 0.2% Overview of removed sequences length count expect max.err error counts 1 12610638 8159057.8 0 12610638 2 1442340 2039764.4 0 1442340 3 531582 509941.1 0 531582 4 95137 127485.3 0 95137 5 35022 31871.3 0 35022 6 11761 7967.8 0 11761 7 6641 1992.0 0 6641 8 1081 498.0 0 1081 9 2380 124.5 0 2305 75 10 1336 31.1 1 897 439 11 1745 7.8 1 1391 354 12 464 1.9 1 241 223 13 1464 1.9 1 1054 410 14 508 1.9 1 228 280 15 1090 1.9 1 796 294 16 962 1.9 1 711 251 17 1476 1.9 1 1169 307 18 3269 1.9 1 2621 648 19 3998 1.9 1 3572 426 20 423 1.9 1 252 171 21 493 1.9 1 318 175 22 2707 1.9 1 2170 537 23 2340 1.9 1 1750 590 24 2586 1.9 1 2161 425 25 3670 1.9 1 3027 643 26 3551 1.9 1 2959 592 27 6851 1.9 1 6173 678 28 1153 1.9 1 772 381 29 2511 1.9 1 2048 463 30 2927 1.9 1 2245 682 31 3450 1.9 1 2950 500 32 4151 1.9 1 3421 730 33 3883 1.9 1 3329 554 34 5455 1.9 1 4701 754 35 4551 1.9 1 3668 883 36 15556 1.9 1 14504 1052 37 5218 1.9 1 4226 992 38 1382 1.9 1 968 414 39 2005 1.9 1 1538 467 40 2134 1.9 1 1678 456 41 3177 1.9 1 2743 434 42 2756 1.9 1 2374 382 43 2439 1.9 1 1907 532 44 5256 1.9 1 4860 396 45 3203 1.9 1 2660 543 46 7760 1.9 1 6708 1052 47 3548 1.9 1 2577 971 48 2942 1.9 1 2300 642 49 4983 1.9 1 4301 682 50 2454 1.9 1 1884 570 51 2575 1.9 1 2199 376 52 4678 1.9 1 4039 639 53 5046 1.9 1 4260 786 54 5081 1.9 1 4280 801 55 10370 1.9 1 9056 1314 56 8327 1.9 1 7346 981 57 3350 1.9 1 2716 634 58 3749 1.9 1 3200 549 59 4206 1.9 1 3503 703 60 10467 1.9 1 9588 879 61 5606 1.9 1 4394 1212 62 1447 1.9 1 1057 390 63 3144 1.9 1 2726 418 64 5419 1.9 1 4605 814 65 5300 1.9 1 4334 966 66 7570 1.9 1 6299 1271 67 9742 1.9 1 8095 1647 68 19843 1.9 1 17495 2348 69 8801 1.9 1 7537 1264 70 10433 1.9 1 9064 1369 71 19008 1.9 1 17361 1647 72 28936 1.9 1 26955 1981 73 24996 1.9 1 23010 1986 74 15927 1.9 1 14436 1491 75 10243 1.9 1 8965 1278 76 7940 1.9 1 6579 1361 77 7489 1.9 1 5918 1571 78 7812 1.9 1 5946 1866 79 7893 1.9 1 5904 1989 80 7580 1.9 1 5724 1856 81 6541 1.9 1 4992 1549 82 3574 1.9 1 2676 898 83 1916 1.9 1 1402 514 84 1792 1.9 1 1292 500 85 1878 1.9 1 1305 573 86 2019 1.9 1 1473 546 87 1878 1.9 1 1336 542 88 1652 1.9 1 1159 493 89 1526 1.9 1 1090 436 90 1545 1.9 1 1095 450 91 1490 1.9 1 1019 471 92 1360 1.9 1 965 395 93 1277 1.9 1 935 342 94 1308 1.9 1 909 399 95 1273 1.9 1 856 417 96 1326 1.9 1 913 413 97 1583 1.9 1 1056 527 98 1441 1.9 1 969 472 99 2067 1.9 1 1410 657 100 2784 1.9 1 1990 794 RUN STATISTICS FOR INPUT FILE: /home/sam/Downloads/zr2096/Raw_data/zr2096_9_s1_R1.fastq.gz ============================================= 32636231 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Writing report to '/home/sam/Downloads/20180411_trimgalore_10bp_Cvirginica_MBD/zr2096_9_s1_R2.fastq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /home/sam/Downloads/zr2096/Raw_data/zr2096_9_s1_R2.fastq.gz Trimming mode: paired-end Trim Galore version: 0.4.4_dev Cutadapt version: 1.16 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'TGGAATTCTCGG' (Illumina small RNA adapter; auto-detected) Maximum trimming error rate: 0.1 (default) Optional adapter 2 sequence (only used for read 2 of paired-end files): 'GATCGTCGGACT' Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length for both reads before a sequence pair gets removed: 18 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 ~/Downloads/20180411_trimgalore_10bp_Cvirginica_MBD/20180411_fastqc_trim_10bp_Cvirginica_MBD --threads 18' Output file(s) will be GZIP compressed Writing final adapter and quality trimmed output to zr2096_9_s1_R2_trimmed.fq.gz >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'GATCGTCGGACT' from file /home/sam/Downloads/zr2096/Raw_data/zr2096_9_s1_R2.fastq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed This is cutadapt 1.16 with Python 2.7.12 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a GATCGTCGGACT /home/sam/Downloads/zr2096/Raw_data/zr2096_9_s1_R2.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 590.96 s (18 us/read; 3.31 M reads/minute). === Summary === Total reads processed: 32,636,231 Reads with adapters: 6,933,718 (21.2%) Reads written (passing filters): 32,636,231 (100.0%) Total basepairs processed: 2,953,164,569 bp Quality-trimmed: 15,971,942 bp (0.5%) Total written (filtered): 2,909,626,875 bp (98.5%) === Adapter 1 === Sequence: GATCGTCGGACT; Type: regular 3'; Length: 12; Trimmed: 6933718 times. No. of allowed errors: 0-9 bp: 0; 10-12 bp: 1 Bases preceding removed adapters: A: 21.9% C: 15.5% G: 32.2% T: 30.2% none/other: 0.3% Overview of removed sequences length count expect max.err error counts 1 4900033 8159057.8 0 4900033 2 1191999 2039764.4 0 1191999 3 470362 509941.1 0 470362 4 21023 127485.3 0 21023 5 12967 31871.3 0 12967 6 7282 7967.8 0 7282 7 1811 1992.0 0 1811 8 435 498.0 0 435 9 481 124.5 0 198 283 10 1434 31.1 1 782 652 11 1674 7.8 1 1367 307 12 213 1.9 1 106 107 13 694 1.9 1 511 183 14 2537 1.9 1 1999 538 15 316 1.9 1 164 152 16 213 1.9 1 97 116 17 1642 1.9 1 1247 395 18 1903 1.9 1 1461 442 19 1281 1.9 1 921 360 20 3271 1.9 1 2708 563 21 3897 1.9 1 3346 551 22 468 1.9 1 255 213 23 387 1.9 1 228 159 24 3004 1.9 1 2368 636 25 5277 1.9 1 4575 702 26 648 1.9 1 405 243 27 5067 1.9 1 4503 564 28 938 1.9 1 574 364 29 2100 1.9 1 1610 490 30 13896 1.9 1 12017 1879 31 647 1.9 1 314 333 32 345 1.9 1 176 169 33 698 1.9 1 395 303 34 1142 1.9 1 653 489 35 3037 1.9 1 2327 710 36 9549 1.9 1 8468 1081 37 3124 1.9 1 2736 388 38 1105 1.9 1 759 346 39 4549 1.9 1 3948 601 40 4610 1.9 1 4139 471 41 654 1.9 1 426 228 42 2179 1.9 1 1700 479 43 6444 1.9 1 5773 671 44 562 1.9 1 400 162 45 2238 1.9 1 1894 344 46 6367 1.9 1 5909 458 47 390 1.9 1 259 131 48 1800 1.9 1 1528 272 49 2601 1.9 1 2186 415 50 1731 1.9 1 1354 377 51 2961 1.9 1 2546 415 52 2473 1.9 1 2039 434 53 3086 1.9 1 2521 565 54 3482 1.9 1 2740 742 55 6328 1.9 1 5447 881 56 5780 1.9 1 4872 908 57 3575 1.9 1 2861 714 58 4364 1.9 1 3506 858 59 3677 1.9 1 2728 949 60 7389 1.9 1 6051 1338 61 6585 1.9 1 5394 1191 62 6101 1.9 1 4946 1155 63 9196 1.9 1 7785 1411 64 28226 1.9 1 26305 1921 65 25732 1.9 1 24150 1582 66 14246 1.9 1 13037 1209 67 9091 1.9 1 7832 1259 68 7572 1.9 1 6223 1349 69 3523 1.9 1 2800 723 70 2859 1.9 1 2152 707 71 2576 1.9 1 1839 737 72 2588 1.9 1 1806 782 73 2465 1.9 1 1682 783 74 2652 1.9 1 1780 872 75 2849 1.9 1 1849 1000 76 3382 1.9 1 2131 1251 77 4110 1.9 1 2610 1500 78 4963 1.9 1 3113 1850 79 4818 1.9 1 3134 1684 80 4781 1.9 1 3026 1755 81 4149 1.9 1 2674 1475 82 2282 1.9 1 1452 830 83 1393 1.9 1 884 509 84 1336 1.9 1 836 500 85 1386 1.9 1 855 531 86 1574 1.9 1 1033 541 87 1509 1.9 1 996 513 88 1306 1.9 1 831 475 89 1136 1.9 1 753 383 90 1152 1.9 1 716 436 91 1120 1.9 1 671 449 92 1002 1.9 1 606 396 93 932 1.9 1 556 376 94 965 1.9 1 599 366 95 972 1.9 1 581 391 96 1081 1.9 1 649 432 97 1225 1.9 1 747 478 98 1239 1.9 1 691 548 99 2175 1.9 1 1245 930 100 3329 1.9 1 2050 1279 RUN STATISTICS FOR INPUT FILE: /home/sam/Downloads/zr2096/Raw_data/zr2096_9_s1_R2.fastq.gz ============================================= 32636231 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Validate paired-end files zr2096_9_s1_R1_trimmed.fq.gz and zr2096_9_s1_R2_trimmed.fq.gz file_1: zr2096_9_s1_R1_trimmed.fq.gz, file_2: zr2096_9_s1_R2_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: zr2096_9_s1_R1_trimmed.fq.gz and zr2096_9_s1_R2_trimmed.fq.gz <<<<< Writing validated paired-end read 1 reads to zr2096_9_s1_R1_val_1.fq.gz Writing validated paired-end read 2 reads to zr2096_9_s1_R2_val_2.fq.gz Total number of sequences analysed: 32636231 Number of sequence pairs removed because at least one read was shorter than the length cutoff (18 bp): 788690 (2.42%) >>> Now running FastQC on the validated data zr2096_9_s1_R1_val_1.fq.gz<<< Started analysis of zr2096_9_s1_R1_val_1.fq.gz Approx 5% complete for zr2096_9_s1_R1_val_1.fq.gz Approx 10% complete for zr2096_9_s1_R1_val_1.fq.gz Approx 15% complete for zr2096_9_s1_R1_val_1.fq.gz Approx 20% complete for zr2096_9_s1_R1_val_1.fq.gz Approx 25% complete for zr2096_9_s1_R1_val_1.fq.gz Approx 30% complete for zr2096_9_s1_R1_val_1.fq.gz Approx 35% complete for zr2096_9_s1_R1_val_1.fq.gz Approx 40% complete for zr2096_9_s1_R1_val_1.fq.gz Approx 45% complete for zr2096_9_s1_R1_val_1.fq.gz Approx 50% complete for zr2096_9_s1_R1_val_1.fq.gz Approx 55% complete for zr2096_9_s1_R1_val_1.fq.gz Approx 60% complete for zr2096_9_s1_R1_val_1.fq.gz Approx 65% complete for zr2096_9_s1_R1_val_1.fq.gz Approx 70% complete for zr2096_9_s1_R1_val_1.fq.gz Approx 75% complete for zr2096_9_s1_R1_val_1.fq.gz Approx 80% complete for zr2096_9_s1_R1_val_1.fq.gz Approx 85% complete for zr2096_9_s1_R1_val_1.fq.gz Approx 90% complete for zr2096_9_s1_R1_val_1.fq.gz Approx 95% complete for zr2096_9_s1_R1_val_1.fq.gz >>> Now running FastQC on the validated data zr2096_9_s1_R2_val_2.fq.gz<<< Started analysis of zr2096_9_s1_R2_val_2.fq.gz Approx 5% complete for zr2096_9_s1_R2_val_2.fq.gz Approx 10% complete for zr2096_9_s1_R2_val_2.fq.gz Approx 15% complete for zr2096_9_s1_R2_val_2.fq.gz Approx 20% complete for zr2096_9_s1_R2_val_2.fq.gz Approx 25% complete for zr2096_9_s1_R2_val_2.fq.gz Approx 30% complete for zr2096_9_s1_R2_val_2.fq.gz Approx 35% complete for zr2096_9_s1_R2_val_2.fq.gz Approx 40% complete for zr2096_9_s1_R2_val_2.fq.gz Approx 45% complete for zr2096_9_s1_R2_val_2.fq.gz Approx 50% complete for zr2096_9_s1_R2_val_2.fq.gz Approx 55% complete for zr2096_9_s1_R2_val_2.fq.gz Approx 60% complete for zr2096_9_s1_R2_val_2.fq.gz Approx 65% complete for zr2096_9_s1_R2_val_2.fq.gz Approx 70% complete for zr2096_9_s1_R2_val_2.fq.gz Approx 75% complete for zr2096_9_s1_R2_val_2.fq.gz Approx 80% complete for zr2096_9_s1_R2_val_2.fq.gz Approx 85% complete for zr2096_9_s1_R2_val_2.fq.gz Approx 90% complete for zr2096_9_s1_R2_val_2.fq.gz Approx 95% complete for zr2096_9_s1_R2_val_2.fq.gz Deleting both intermediate output files zr2096_9_s1_R1_trimmed.fq.gz and zr2096_9_s1_R2_trimmed.fq.gz ====================================================================================================