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 (>> /mnt/owl/nightingales/C_virginica/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/20180410_trimgalore_trim14bp_Cvirginica_MBD/zr2096_10_s1_R1.fastq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /mnt/owl/nightingales/C_virginica/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 14 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 14 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /home/sam/20180410_trimgalore_trim14bp_Cvirginica_MBD/20180410_fastqc_trimgalore_trim14bp_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 /mnt/owl/nightingales/C_virginica/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 /mnt/owl/nightingales/C_virginica/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 375.71 s (21 us/read; 2.83 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: /mnt/owl/nightingales/C_virginica/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/20180410_trimgalore_trim14bp_Cvirginica_MBD/zr2096_10_s1_R2.fastq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /mnt/owl/nightingales/C_virginica/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 14 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 14 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /home/sam/20180410_trimgalore_trim14bp_Cvirginica_MBD/20180410_fastqc_trimgalore_trim14bp_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 /mnt/owl/nightingales/C_virginica/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 /mnt/owl/nightingales/C_virginica/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 342.15 s (19 us/read; 3.11 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: /mnt/owl/nightingales/C_virginica/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): 181256 (1.02%) >>> 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/20180410_trimgalore_trim14bp_Cvirginica_MBD/zr2096_1_s1_R1.fastq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /mnt/owl/nightingales/C_virginica/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 14 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 14 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /home/sam/20180410_trimgalore_trim14bp_Cvirginica_MBD/20180410_fastqc_trimgalore_trim14bp_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 /mnt/owl/nightingales/C_virginica/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 /mnt/owl/nightingales/C_virginica/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 531.61 s (18 us/read; 3.27 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: /mnt/owl/nightingales/C_virginica/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/20180410_trimgalore_trim14bp_Cvirginica_MBD/zr2096_1_s1_R2.fastq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /mnt/owl/nightingales/C_virginica/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 14 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 14 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /home/sam/20180410_trimgalore_trim14bp_Cvirginica_MBD/20180410_fastqc_trimgalore_trim14bp_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 /mnt/owl/nightingales/C_virginica/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 /mnt/owl/nightingales/C_virginica/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 506.50 s (17 us/read; 3.43 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: /mnt/owl/nightingales/C_virginica/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): 213145 (0.74%) >>> 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/20180410_trimgalore_trim14bp_Cvirginica_MBD/zr2096_2_s1_R1.fastq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /mnt/owl/nightingales/C_virginica/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 14 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 14 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /home/sam/20180410_trimgalore_trim14bp_Cvirginica_MBD/20180410_fastqc_trimgalore_trim14bp_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 /mnt/owl/nightingales/C_virginica/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 /mnt/owl/nightingales/C_virginica/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 554.67 s (18 us/read; 3.33 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: /mnt/owl/nightingales/C_virginica/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/20180410_trimgalore_trim14bp_Cvirginica_MBD/zr2096_2_s1_R2.fastq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /mnt/owl/nightingales/C_virginica/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 14 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 14 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /home/sam/20180410_trimgalore_trim14bp_Cvirginica_MBD/20180410_fastqc_trimgalore_trim14bp_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 /mnt/owl/nightingales/C_virginica/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 /mnt/owl/nightingales/C_virginica/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 523.49 s (17 us/read; 3.53 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: /mnt/owl/nightingales/C_virginica/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): 221380 (0.72%) >>> 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/20180410_trimgalore_trim14bp_Cvirginica_MBD/zr2096_3_s1_R1.fastq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /mnt/owl/nightingales/C_virginica/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 14 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 14 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /home/sam/20180410_trimgalore_trim14bp_Cvirginica_MBD/20180410_fastqc_trimgalore_trim14bp_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 /mnt/owl/nightingales/C_virginica/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 /mnt/owl/nightingales/C_virginica/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 542.22 s (18 us/read; 3.31 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: /mnt/owl/nightingales/C_virginica/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/20180410_trimgalore_trim14bp_Cvirginica_MBD/zr2096_3_s1_R2.fastq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /mnt/owl/nightingales/C_virginica/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 14 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 14 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /home/sam/20180410_trimgalore_trim14bp_Cvirginica_MBD/20180410_fastqc_trimgalore_trim14bp_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 /mnt/owl/nightingales/C_virginica/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 /mnt/owl/nightingales/C_virginica/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 513.04 s (17 us/read; 3.50 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: /mnt/owl/nightingales/C_virginica/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): 174967 (0.59%) >>> 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/20180410_trimgalore_trim14bp_Cvirginica_MBD/zr2096_4_s1_R1.fastq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /mnt/owl/nightingales/C_virginica/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 14 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 14 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /home/sam/20180410_trimgalore_trim14bp_Cvirginica_MBD/20180410_fastqc_trimgalore_trim14bp_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 /mnt/owl/nightingales/C_virginica/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 /mnt/owl/nightingales/C_virginica/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 434.29 s (18 us/read; 3.36 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: /mnt/owl/nightingales/C_virginica/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/20180410_trimgalore_trim14bp_Cvirginica_MBD/zr2096_4_s1_R2.fastq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /mnt/owl/nightingales/C_virginica/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 14 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 14 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /home/sam/20180410_trimgalore_trim14bp_Cvirginica_MBD/20180410_fastqc_trimgalore_trim14bp_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 /mnt/owl/nightingales/C_virginica/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 /mnt/owl/nightingales/C_virginica/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 409.58 s (17 us/read; 3.57 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: /mnt/owl/nightingales/C_virginica/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): 176698 (0.73%) >>> 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/20180410_trimgalore_trim14bp_Cvirginica_MBD/zr2096_5_s1_R1.fastq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /mnt/owl/nightingales/C_virginica/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 14 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 14 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /home/sam/20180410_trimgalore_trim14bp_Cvirginica_MBD/20180410_fastqc_trimgalore_trim14bp_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 /mnt/owl/nightingales/C_virginica/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 /mnt/owl/nightingales/C_virginica/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 591.51 s (19 us/read; 3.22 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: /mnt/owl/nightingales/C_virginica/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/20180410_trimgalore_trim14bp_Cvirginica_MBD/zr2096_5_s1_R2.fastq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /mnt/owl/nightingales/C_virginica/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 14 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 14 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /home/sam/20180410_trimgalore_trim14bp_Cvirginica_MBD/20180410_fastqc_trimgalore_trim14bp_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 /mnt/owl/nightingales/C_virginica/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 /mnt/owl/nightingales/C_virginica/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 563.29 s (18 us/read; 3.38 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: /mnt/owl/nightingales/C_virginica/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): 148997 (0.47%) >>> 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/20180410_trimgalore_trim14bp_Cvirginica_MBD/zr2096_6_s1_R1.fastq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /mnt/owl/nightingales/C_virginica/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 14 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 14 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /home/sam/20180410_trimgalore_trim14bp_Cvirginica_MBD/20180410_fastqc_trimgalore_trim14bp_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 /mnt/owl/nightingales/C_virginica/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 /mnt/owl/nightingales/C_virginica/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 433.07 s (18 us/read; 3.36 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: /mnt/owl/nightingales/C_virginica/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/20180410_trimgalore_trim14bp_Cvirginica_MBD/zr2096_6_s1_R2.fastq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /mnt/owl/nightingales/C_virginica/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 14 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 14 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /home/sam/20180410_trimgalore_trim14bp_Cvirginica_MBD/20180410_fastqc_trimgalore_trim14bp_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 /mnt/owl/nightingales/C_virginica/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 /mnt/owl/nightingales/C_virginica/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 407.37 s (17 us/read; 3.57 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: /mnt/owl/nightingales/C_virginica/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): 157171 (0.65%) >>> 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/20180410_trimgalore_trim14bp_Cvirginica_MBD/zr2096_7_s1_R1.fastq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /mnt/owl/nightingales/C_virginica/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 14 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 14 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /home/sam/20180410_trimgalore_trim14bp_Cvirginica_MBD/20180410_fastqc_trimgalore_trim14bp_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 /mnt/owl/nightingales/C_virginica/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 /mnt/owl/nightingales/C_virginica/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 547.99 s (19 us/read; 3.23 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: /mnt/owl/nightingales/C_virginica/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/20180410_trimgalore_trim14bp_Cvirginica_MBD/zr2096_7_s1_R2.fastq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /mnt/owl/nightingales/C_virginica/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 14 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 14 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /home/sam/20180410_trimgalore_trim14bp_Cvirginica_MBD/20180410_fastqc_trimgalore_trim14bp_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 /mnt/owl/nightingales/C_virginica/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 /mnt/owl/nightingales/C_virginica/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 510.27 s (17 us/read; 3.47 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: /mnt/owl/nightingales/C_virginica/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): 138575 (0.47%) >>> 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/20180410_trimgalore_trim14bp_Cvirginica_MBD/zr2096_8_s1_R1.fastq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /mnt/owl/nightingales/C_virginica/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 14 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 14 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /home/sam/20180410_trimgalore_trim14bp_Cvirginica_MBD/20180410_fastqc_trimgalore_trim14bp_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 /mnt/owl/nightingales/C_virginica/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 /mnt/owl/nightingales/C_virginica/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 541.07 s (18 us/read; 3.30 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: /mnt/owl/nightingales/C_virginica/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/20180410_trimgalore_trim14bp_Cvirginica_MBD/zr2096_8_s1_R2.fastq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /mnt/owl/nightingales/C_virginica/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 14 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 14 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /home/sam/20180410_trimgalore_trim14bp_Cvirginica_MBD/20180410_fastqc_trimgalore_trim14bp_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 /mnt/owl/nightingales/C_virginica/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 /mnt/owl/nightingales/C_virginica/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 511.70 s (17 us/read; 3.49 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: /mnt/owl/nightingales/C_virginica/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): 142299 (0.48%) >>> 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/20180410_trimgalore_trim14bp_Cvirginica_MBD/zr2096_9_s1_R1.fastq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /mnt/owl/nightingales/C_virginica/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 14 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 14 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /home/sam/20180410_trimgalore_trim14bp_Cvirginica_MBD/20180410_fastqc_trimgalore_trim14bp_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 /mnt/owl/nightingales/C_virginica/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 /mnt/owl/nightingales/C_virginica/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 637.56 s (20 us/read; 3.07 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: /mnt/owl/nightingales/C_virginica/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/20180410_trimgalore_trim14bp_Cvirginica_MBD/zr2096_9_s1_R2.fastq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /mnt/owl/nightingales/C_virginica/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 14 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 14 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /home/sam/20180410_trimgalore_trim14bp_Cvirginica_MBD/20180410_fastqc_trimgalore_trim14bp_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 /mnt/owl/nightingales/C_virginica/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 /mnt/owl/nightingales/C_virginica/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 597.84 s (18 us/read; 3.28 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: /mnt/owl/nightingales/C_virginica/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): 545499 (1.67%) >>> 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 ====================================================================================================