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 (>> 2112_lane1_ACAGTG.fastq.gz <<) Found perfect matches for the following adapter sequences: Adapter type Count Sequence Sequences analysed Percentage Illumina 43268 AGATCGGAAGAGC 1000000 4.33 Nextera 0 CTGTCTCTTATA 1000000 0.00 smallRNA 0 TGGAATTCTCGG 1000000 0.00 Using Illumina adapter for trimming (count: 43268). Second best hit was Nextera (count: 0) Writing report to '/home/sam/analyses/20180911_virginica_oil_trimgalore_01/2112_lane1_ACAGTG.fastq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: 2112_lane1_ACAGTG.fastq.gz Trimming mode: single-end Trim Galore version: 0.4.4_dev Cutadapt version: 1.9.1 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; auto-detected) Maximum trimming error rate: 0.1 (default) Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length before a sequence gets removed: 20 bp Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /home/sam/analyses/20180911_virginica_oil_trimgalore_01/20180911_virginica_oil_trimmed_fastqc --threads 16' Output file(s) will be GZIP compressed Writing final adapter and quality trimmed output to 2112_lane1_ACAGTG_trimmed.fq.gz >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file 2112_lane1_ACAGTG.fastq.gz <<< 10000000 sequences processed This is cutadapt 1.9.1 with Python 2.7.12 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC 2112_lane1_ACAGTG.fastq.gz Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 397.25 s (23 us/read; 2.62 M reads/minute). === Summary === Total reads processed: 17,327,210 Reads with adapters: 10,263,059 (59.2%) Reads written (passing filters): 17,327,210 (100.0%) Total basepairs processed: 1,750,048,210 bp Quality-trimmed: 185,921,084 bp (10.6%) Total written (filtered): 1,261,527,856 bp (72.1%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 10263059 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 28.4% C: 14.1% G: 6.2% T: 13.4% none/other: 38.0% Overview of removed sequences length count expect max.err error counts 1 4187128 4331802.5 0 4187128 2 454105 1082950.6 0 454105 3 173887 270737.7 0 173887 4 132573 67684.4 0 132573 5 112014 16921.1 0 112014 6 112058 4230.3 0 112058 7 118966 1057.6 0 118966 8 75644 264.4 0 75644 9 82132 66.1 0 81258 874 10 91566 16.5 1 90662 904 11 49449 4.1 1 48579 870 12 74402 1.0 1 73557 845 13 54356 0.3 1 53474 882 14 54152 0.3 1 53335 817 15 51633 0.3 1 50745 888 16 45761 0.3 1 44877 884 17 50139 0.3 1 48938 1201 18 49514 0.3 1 48856 658 19 20534 0.3 1 20080 454 20 33290 0.3 1 32710 580 21 29372 0.3 1 28697 675 22 33080 0.3 1 32419 661 23 19223 0.3 1 18693 530 24 21075 0.3 1 20530 545 25 21912 0.3 1 21297 615 26 18258 0.3 1 16907 1351 27 19242 0.3 1 17472 1770 28 22623 0.3 1 19941 2682 29 13645 0.3 1 12102 1543 30 17134 0.3 1 15866 1268 31 8771 0.3 1 7489 1282 32 15705 0.3 1 11988 3717 33 11427 0.3 1 7518 3909 34 11995 0.3 1 9523 2472 35 8576 0.3 1 6341 2235 36 14389 0.3 1 7992 6397 37 11073 0.3 1 7217 3856 38 10008 0.3 1 8264 1744 39 4031 0.3 1 2275 1756 40 8813 0.3 1 5164 3649 41 7361 0.3 1 2676 4685 42 8430 0.3 1 3157 5273 43 5950 0.3 1 3071 2879 44 4902 0.3 1 2756 2146 45 4218 0.3 1 2813 1405 46 4226 0.3 1 2704 1522 47 3516 0.3 1 1742 1774 48 3322 0.3 1 1428 1894 49 3799 0.3 1 1840 1959 50 4609 0.3 1 1432 3177 51 5145 0.3 1 1432 3713 52 5288 0.3 1 1634 3654 53 3974 0.3 1 1619 2355 54 4262 0.3 1 522 3740 55 4224 0.3 1 812 3412 56 5448 0.3 1 816 4632 57 8442 0.3 1 1008 7434 58 8455 0.3 1 857 7598 59 5746 0.3 1 910 4836 60 9462 0.3 1 529 8933 61 12883 0.3 1 591 12292 62 34190 0.3 1 673 33517 63 60413 0.3 1 1245 59168 64 20284 0.3 1 1108 19176 65 25390 0.3 1 305 25085 66 57515 0.3 1 449 57066 67 203411 0.3 1 694 202717 68 453643 0.3 1 1657 451986 69 1544843 0.3 1 2603 1542240 70 698942 0.3 1 5353 693589 71 251952 0.3 1 1270 250682 72 90056 0.3 1 392 89664 73 25840 0.3 1 109 25731 74 13657 0.3 1 61 13596 75 7878 0.3 1 44 7834 76 6202 0.3 1 49 6153 77 8053 0.3 1 48 8005 78 8207 0.3 1 47 8160 79 7538 0.3 1 57 7481 80 6582 0.3 1 19 6563 81 5978 0.3 1 16 5962 82 5811 0.3 1 12 5799 83 5628 0.3 1 13 5615 84 5305 0.3 1 15 5290 85 5343 0.3 1 17 5326 86 5444 0.3 1 29 5415 87 5906 0.3 1 18 5888 88 5690 0.3 1 25 5665 89 5649 0.3 1 40 5609 90 6103 0.3 1 16 6087 91 6211 0.3 1 2 6209 92 6664 0.3 1 13 6651 93 6982 0.3 1 4 6978 94 7732 0.3 1 11 7721 95 7979 0.3 1 4 7975 96 9450 0.3 1 2 9448 97 10273 0.3 1 1 10272 98 11315 0.3 1 2 11313 99 13205 0.3 1 1 13204 100 26252 0.3 1 2 26250 101 108226 0.3 1 4 108222 RUN STATISTICS FOR INPUT FILE: 2112_lane1_ACAGTG.fastq.gz ============================================= 17327210 sequences processed in total Sequences removed because they became shorter than the length cutoff of 20 bp: 3919105 (22.6%) >>> Now running FastQC on the data <<< Started analysis of 2112_lane1_ACAGTG_trimmed.fq.gz Approx 5% complete for 2112_lane1_ACAGTG_trimmed.fq.gz Approx 10% complete for 2112_lane1_ACAGTG_trimmed.fq.gz Approx 15% complete for 2112_lane1_ACAGTG_trimmed.fq.gz Approx 20% complete for 2112_lane1_ACAGTG_trimmed.fq.gz Approx 25% complete for 2112_lane1_ACAGTG_trimmed.fq.gz Approx 30% complete for 2112_lane1_ACAGTG_trimmed.fq.gz Approx 35% complete for 2112_lane1_ACAGTG_trimmed.fq.gz Approx 40% complete for 2112_lane1_ACAGTG_trimmed.fq.gz Approx 45% complete for 2112_lane1_ACAGTG_trimmed.fq.gz Approx 50% complete for 2112_lane1_ACAGTG_trimmed.fq.gz Approx 55% complete for 2112_lane1_ACAGTG_trimmed.fq.gz Approx 60% complete for 2112_lane1_ACAGTG_trimmed.fq.gz Approx 65% complete for 2112_lane1_ACAGTG_trimmed.fq.gz Approx 70% complete for 2112_lane1_ACAGTG_trimmed.fq.gz Approx 75% complete for 2112_lane1_ACAGTG_trimmed.fq.gz Approx 80% complete for 2112_lane1_ACAGTG_trimmed.fq.gz Approx 85% complete for 2112_lane1_ACAGTG_trimmed.fq.gz Approx 90% complete for 2112_lane1_ACAGTG_trimmed.fq.gz Approx 95% complete for 2112_lane1_ACAGTG_trimmed.fq.gz Writing report to '/home/sam/analyses/20180911_virginica_oil_trimgalore_01/2112_lane1_ATCACG.fastq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: 2112_lane1_ATCACG.fastq.gz Trimming mode: single-end Trim Galore version: 0.4.4_dev Cutadapt version: 1.9.1 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; auto-detected) Maximum trimming error rate: 0.1 (default) Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length before a sequence gets removed: 20 bp Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /home/sam/analyses/20180911_virginica_oil_trimgalore_01/20180911_virginica_oil_trimmed_fastqc --threads 16' Output file(s) will be GZIP compressed Writing final adapter and quality trimmed output to 2112_lane1_ATCACG_trimmed.fq.gz >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file 2112_lane1_ATCACG.fastq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed This is cutadapt 1.9.1 with Python 2.7.12 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC 2112_lane1_ATCACG.fastq.gz Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 749.44 s (22 us/read; 2.67 M reads/minute). === Summary === Total reads processed: 33,409,414 Reads with adapters: 17,611,436 (52.7%) Reads written (passing filters): 33,409,414 (100.0%) Total basepairs processed: 3,374,350,814 bp Quality-trimmed: 220,159,975 bp (6.5%) Total written (filtered): 2,847,951,372 bp (84.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 17611436 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 36.3% C: 16.1% G: 7.6% T: 18.9% none/other: 21.1% Overview of removed sequences length count expect max.err error counts 1 10442109 8352353.5 0 10442109 2 858531 2088088.4 0 858531 3 323059 522022.1 0 323059 4 208999 130505.5 0 208999 5 156468 32626.4 0 156468 6 150095 8156.6 0 150095 7 150683 2039.1 0 150683 8 112087 509.8 0 112087 9 121119 127.4 0 119789 1330 10 120185 31.9 1 118496 1689 11 82522 8.0 1 80895 1627 12 102396 2.0 1 100840 1556 13 83339 0.5 1 81773 1566 14 80199 0.5 1 78593 1606 15 80591 0.5 1 78931 1660 16 71183 0.5 1 69586 1597 17 78307 0.5 1 76360 1947 18 77111 0.5 1 75828 1283 19 37842 0.5 1 36894 948 20 53140 0.5 1 51938 1202 21 48734 0.5 1 47537 1197 22 51325 0.5 1 50222 1103 23 35379 0.5 1 34409 970 24 35467 0.5 1 34472 995 25 36003 0.5 1 34999 1004 26 29489 0.5 1 27823 1666 27 30967 0.5 1 28456 2511 28 35485 0.5 1 31877 3608 29 22082 0.5 1 19860 2222 30 27130 0.5 1 25572 1558 31 12798 0.5 1 11146 1652 32 21740 0.5 1 16029 5711 33 20199 0.5 1 13434 6765 34 19003 0.5 1 13472 5531 35 14389 0.5 1 11153 3236 36 11969 0.5 1 10095 1874 37 13574 0.5 1 8671 4903 38 13729 0.5 1 9035 4694 39 10171 0.5 1 6936 3235 40 11802 0.5 1 6610 5192 41 10036 0.5 1 4373 5663 42 10201 0.5 1 3897 6304 43 7546 0.5 1 3982 3564 44 7277 0.5 1 3278 3999 45 6507 0.5 1 3634 2873 46 5774 0.5 1 3093 2681 47 5356 0.5 1 1998 3358 48 4427 0.5 1 1669 2758 49 4043 0.5 1 1934 2109 50 5248 0.5 1 1453 3795 51 7087 0.5 1 1453 5634 52 6646 0.5 1 1797 4849 53 4822 0.5 1 1667 3155 54 5450 0.5 1 473 4977 55 5173 0.5 1 783 4390 56 6833 0.5 1 755 6078 57 10395 0.5 1 884 9511 58 11086 0.5 1 751 10335 59 7377 0.5 1 898 6479 60 12412 0.5 1 523 11889 61 16010 0.5 1 614 15396 62 40681 0.5 1 636 40045 63 71709 0.5 1 1313 70396 64 22353 0.5 1 1201 21152 65 27766 0.5 1 296 27470 66 60315 0.5 1 483 59832 67 205212 0.5 1 736 204476 68 445189 0.5 1 1601 443588 69 1354272 0.5 1 2421 1351851 70 645444 0.5 1 4623 640821 71 244073 0.5 1 1185 242888 72 91085 0.5 1 384 90701 73 26529 0.5 1 148 26381 74 13928 0.5 1 82 13846 75 8001 0.5 1 49 7952 76 6494 0.5 1 53 6441 77 8716 0.5 1 54 8662 78 8523 0.5 1 58 8465 79 8002 0.5 1 52 7950 80 6802 0.5 1 17 6785 81 6065 0.5 1 10 6055 82 5812 0.5 1 13 5799 83 5192 0.5 1 17 5175 84 4934 0.5 1 16 4918 85 4964 0.5 1 16 4948 86 5251 0.5 1 23 5228 87 5652 0.5 1 26 5626 88 5278 0.5 1 23 5255 89 5331 0.5 1 34 5297 90 5719 0.5 1 8 5711 91 6034 0.5 1 9 6025 92 6322 0.5 1 18 6304 93 6631 0.5 1 8 6623 94 7224 0.5 1 12 7212 95 7883 0.5 1 10 7873 96 9041 0.5 1 4 9037 97 9978 0.5 1 1 9977 98 11212 0.5 1 6 11206 99 12879 0.5 1 5 12874 100 25791 0.5 1 9 25782 101 108043 0.5 1 10 108033 RUN STATISTICS FOR INPUT FILE: 2112_lane1_ATCACG.fastq.gz ============================================= 33409414 sequences processed in total Sequences removed because they became shorter than the length cutoff of 20 bp: 3771783 (11.3%) >>> Now running FastQC on the data <<< Started analysis of 2112_lane1_ATCACG_trimmed.fq.gz Approx 5% complete for 2112_lane1_ATCACG_trimmed.fq.gz Approx 10% complete for 2112_lane1_ATCACG_trimmed.fq.gz Approx 15% complete for 2112_lane1_ATCACG_trimmed.fq.gz Approx 20% complete for 2112_lane1_ATCACG_trimmed.fq.gz Approx 25% complete for 2112_lane1_ATCACG_trimmed.fq.gz Approx 30% complete for 2112_lane1_ATCACG_trimmed.fq.gz Approx 35% complete for 2112_lane1_ATCACG_trimmed.fq.gz Approx 40% complete for 2112_lane1_ATCACG_trimmed.fq.gz Approx 45% complete for 2112_lane1_ATCACG_trimmed.fq.gz Approx 50% complete for 2112_lane1_ATCACG_trimmed.fq.gz Approx 55% complete for 2112_lane1_ATCACG_trimmed.fq.gz Approx 60% complete for 2112_lane1_ATCACG_trimmed.fq.gz Approx 65% complete for 2112_lane1_ATCACG_trimmed.fq.gz Approx 70% complete for 2112_lane1_ATCACG_trimmed.fq.gz Approx 75% complete for 2112_lane1_ATCACG_trimmed.fq.gz Approx 80% complete for 2112_lane1_ATCACG_trimmed.fq.gz Approx 85% complete for 2112_lane1_ATCACG_trimmed.fq.gz Approx 90% complete for 2112_lane1_ATCACG_trimmed.fq.gz Approx 95% complete for 2112_lane1_ATCACG_trimmed.fq.gz Writing report to '/home/sam/analyses/20180911_virginica_oil_trimgalore_01/2112_lane1_CAGATC.fastq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: 2112_lane1_CAGATC.fastq.gz Trimming mode: single-end Trim Galore version: 0.4.4_dev Cutadapt version: 1.9.1 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; auto-detected) Maximum trimming error rate: 0.1 (default) Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length before a sequence gets removed: 20 bp Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /home/sam/analyses/20180911_virginica_oil_trimgalore_01/20180911_virginica_oil_trimmed_fastqc --threads 16' Output file(s) will be GZIP compressed Writing final adapter and quality trimmed output to 2112_lane1_CAGATC_trimmed.fq.gz >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file 2112_lane1_CAGATC.fastq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed This is cutadapt 1.9.1 with Python 2.7.12 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC 2112_lane1_CAGATC.fastq.gz Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 908.94 s (23 us/read; 2.63 M reads/minute). === Summary === Total reads processed: 39,780,221 Reads with adapters: 23,668,832 (59.5%) Reads written (passing filters): 39,780,221 (100.0%) Total basepairs processed: 4,017,802,321 bp Quality-trimmed: 316,184,920 bp (7.9%) Total written (filtered): 3,168,106,786 bp (78.9%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 23668832 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 33.0% C: 15.7% G: 6.0% T: 18.1% none/other: 27.2% Overview of removed sequences length count expect max.err error counts 1 11462116 9945055.2 0 11462116 2 913629 2486263.8 0 913629 3 452027 621566.0 0 452027 4 350618 155391.5 0 350618 5 306933 38847.9 0 306933 6 287673 9712.0 0 287673 7 281622 2428.0 0 281622 8 223594 607.0 0 223594 9 240116 151.7 0 238205 1911 10 227281 37.9 1 224750 2531 11 163868 9.5 1 161288 2580 12 192839 2.4 1 190444 2395 13 162948 0.6 1 160373 2575 14 155026 0.6 1 152612 2414 15 156135 0.6 1 153474 2661 16 136091 0.6 1 133382 2709 17 150211 0.6 1 146876 3335 18 140793 0.6 1 138808 1985 19 77443 0.6 1 75897 1546 20 101254 0.6 1 99368 1886 21 93085 0.6 1 91238 1847 22 92927 0.6 1 91104 1823 23 72275 0.6 1 70493 1782 24 72096 0.6 1 70374 1722 25 70407 0.6 1 68697 1710 26 59212 0.6 1 56603 2609 27 60402 0.6 1 56761 3641 28 69540 0.6 1 64651 4889 29 44622 0.6 1 41133 3489 30 56254 0.6 1 53841 2413 31 26735 0.6 1 24281 2454 32 44698 0.6 1 38863 5835 33 37973 0.6 1 24758 13215 34 33790 0.6 1 29226 4564 35 32081 0.6 1 27180 4901 36 29448 0.6 1 22077 7371 37 24821 0.6 1 20313 4508 38 22225 0.6 1 17979 4246 39 18973 0.6 1 16137 2836 40 18644 0.6 1 12986 5658 41 17506 0.6 1 12014 5492 42 18109 0.6 1 11098 7011 43 14861 0.6 1 10066 4795 44 15499 0.6 1 8463 7036 45 14330 0.6 1 9724 4606 46 11858 0.6 1 7524 4334 47 10333 0.6 1 4854 5479 48 9714 0.6 1 3768 5946 49 9608 0.6 1 4719 4889 50 9483 0.6 1 3478 6005 51 14031 0.6 1 3385 10646 52 13293 0.6 1 4130 9163 53 8936 0.6 1 3526 5410 54 9880 0.6 1 942 8938 55 9118 0.6 1 1651 7467 56 13037 0.6 1 1504 11533 57 18891 0.6 1 1702 17189 58 20513 0.6 1 1377 19136 59 11927 0.6 1 1601 10326 60 19127 0.6 1 774 18353 61 23847 0.6 1 954 22893 62 75729 0.6 1 1023 74706 63 106543 0.6 1 2066 104477 64 28953 0.6 1 1537 27416 65 37265 0.6 1 412 36853 66 83783 0.6 1 586 83197 67 294910 0.6 1 1013 293897 68 680760 0.6 1 2305 678455 69 2319080 0.6 1 3770 2315310 70 1329812 0.6 1 8452 1321360 71 474084 0.6 1 2222 471862 72 166586 0.6 1 691 165895 73 46783 0.6 1 227 46556 74 24031 0.6 1 123 23908 75 13845 0.6 1 81 13764 76 11129 0.6 1 88 11041 77 15028 0.6 1 90 14938 78 14602 0.6 1 103 14499 79 13582 0.6 1 91 13491 80 11830 0.6 1 47 11783 81 10270 0.6 1 32 10238 82 9814 0.6 1 16 9798 83 9005 0.6 1 15 8990 84 8662 0.6 1 18 8644 85 8888 0.6 1 26 8862 86 9233 0.6 1 24 9209 87 9845 0.6 1 42 9803 88 9350 0.6 1 37 9313 89 9508 0.6 1 55 9453 90 10077 0.6 1 20 10057 91 10706 0.6 1 17 10689 92 11285 0.6 1 25 11260 93 11770 0.6 1 9 11761 94 12970 0.6 1 17 12953 95 13873 0.6 1 6 13867 96 16173 0.6 1 6 16167 97 17692 0.6 1 7 17685 98 19791 0.6 1 6 19785 99 22589 0.6 1 7 22582 100 45074 0.6 1 7 45067 101 187596 0.6 1 13 187583 RUN STATISTICS FOR INPUT FILE: 2112_lane1_CAGATC.fastq.gz ============================================= 39780221 sequences processed in total Sequences removed because they became shorter than the length cutoff of 20 bp: 6470690 (16.3%) >>> Now running FastQC on the data <<< Started analysis of 2112_lane1_CAGATC_trimmed.fq.gz Approx 5% complete for 2112_lane1_CAGATC_trimmed.fq.gz Approx 10% complete for 2112_lane1_CAGATC_trimmed.fq.gz Approx 15% complete for 2112_lane1_CAGATC_trimmed.fq.gz Approx 20% complete for 2112_lane1_CAGATC_trimmed.fq.gz Approx 25% complete for 2112_lane1_CAGATC_trimmed.fq.gz Approx 30% complete for 2112_lane1_CAGATC_trimmed.fq.gz Approx 35% complete for 2112_lane1_CAGATC_trimmed.fq.gz Approx 40% complete for 2112_lane1_CAGATC_trimmed.fq.gz Approx 45% complete for 2112_lane1_CAGATC_trimmed.fq.gz Approx 50% complete for 2112_lane1_CAGATC_trimmed.fq.gz Approx 55% complete for 2112_lane1_CAGATC_trimmed.fq.gz Approx 60% complete for 2112_lane1_CAGATC_trimmed.fq.gz Approx 65% complete for 2112_lane1_CAGATC_trimmed.fq.gz Approx 70% complete for 2112_lane1_CAGATC_trimmed.fq.gz Approx 75% complete for 2112_lane1_CAGATC_trimmed.fq.gz Approx 80% complete for 2112_lane1_CAGATC_trimmed.fq.gz Approx 85% complete for 2112_lane1_CAGATC_trimmed.fq.gz Approx 90% complete for 2112_lane1_CAGATC_trimmed.fq.gz Approx 95% complete for 2112_lane1_CAGATC_trimmed.fq.gz Writing report to '/home/sam/analyses/20180911_virginica_oil_trimgalore_01/2112_lane1_GCCAAT.fastq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: 2112_lane1_GCCAAT.fastq.gz Trimming mode: single-end Trim Galore version: 0.4.4_dev Cutadapt version: 1.9.1 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; auto-detected) Maximum trimming error rate: 0.1 (default) Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length before a sequence gets removed: 20 bp Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /home/sam/analyses/20180911_virginica_oil_trimgalore_01/20180911_virginica_oil_trimmed_fastqc --threads 16' Output file(s) will be GZIP compressed Writing final adapter and quality trimmed output to 2112_lane1_GCCAAT_trimmed.fq.gz >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file 2112_lane1_GCCAAT.fastq.gz <<< 10000000 sequences processed 20000000 sequences processed This is cutadapt 1.9.1 with Python 2.7.12 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC 2112_lane1_GCCAAT.fastq.gz Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 546.65 s (22 us/read; 2.72 M reads/minute). === Summary === Total reads processed: 24,792,684 Reads with adapters: 13,652,723 (55.1%) Reads written (passing filters): 24,792,684 (100.0%) Total basepairs processed: 2,504,061,084 bp Quality-trimmed: 162,739,913 bp (6.5%) Total written (filtered): 2,103,508,344 bp (84.0%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 13652723 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 37.8% C: 17.3% G: 6.2% T: 17.8% none/other: 21.1% Overview of removed sequences length count expect max.err error counts 1 8285474 6198171.0 0 8285474 2 559416 1549542.8 0 559416 3 216338 387385.7 0 216338 4 143815 96846.4 0 143815 5 117955 24211.6 0 117955 6 111642 6052.9 0 111642 7 108539 1513.2 0 108539 8 86050 378.3 0 86050 9 91517 94.6 0 90714 803 10 88443 23.6 1 87249 1194 11 62625 5.9 1 61504 1121 12 74455 1.5 1 73328 1127 13 63753 0.4 1 62538 1215 14 59311 0.4 1 58269 1042 15 59539 0.4 1 58231 1308 16 55250 0.4 1 54149 1101 17 58732 0.4 1 57225 1507 18 58521 0.4 1 57593 928 19 27839 0.4 1 27131 708 20 40399 0.4 1 39530 869 21 37610 0.4 1 36794 816 22 34021 0.4 1 33233 788 23 30471 0.4 1 29631 840 24 29774 0.4 1 28829 945 25 28103 0.4 1 27162 941 26 24228 0.4 1 22988 1240 27 23744 0.4 1 22120 1624 28 25066 0.4 1 22672 2394 29 19955 0.4 1 18259 1696 30 20569 0.4 1 19245 1324 31 12893 0.4 1 11639 1254 32 17686 0.4 1 14475 3211 33 16816 0.4 1 10050 6766 34 13947 0.4 1 12215 1732 35 10733 0.4 1 8237 2496 36 10850 0.4 1 8775 2075 37 10956 0.4 1 8744 2212 38 8624 0.4 1 6206 2418 39 7255 0.4 1 5843 1412 40 7962 0.4 1 5111 2851 41 8308 0.4 1 4244 4064 42 8798 0.4 1 4247 4551 43 6029 0.4 1 3510 2519 44 6198 0.4 1 3128 3070 45 5386 0.4 1 3247 2139 46 4678 0.4 1 2600 2078 47 3677 0.4 1 1794 1883 48 3427 0.4 1 1496 1931 49 3113 0.4 1 1630 1483 50 3613 0.4 1 1203 2410 51 5273 0.4 1 1201 4072 52 4675 0.4 1 1313 3362 53 3187 0.4 1 1168 2019 54 3635 0.4 1 364 3271 55 3449 0.4 1 596 2853 56 5070 0.4 1 589 4481 57 7323 0.4 1 647 6676 58 8103 0.4 1 525 7578 59 4762 0.4 1 627 4135 60 7877 0.4 1 311 7566 61 10083 0.4 1 362 9721 62 26621 0.4 1 392 26229 63 44918 0.4 1 850 44068 64 14573 0.4 1 727 13846 65 18391 0.4 1 213 18178 66 41246 0.4 1 289 40957 67 143024 0.4 1 520 142504 68 320571 0.4 1 1156 319415 69 1097289 0.4 1 1900 1095389 70 537660 0.4 1 4063 533597 71 189910 0.4 1 942 188968 72 67056 0.4 1 296 66760 73 18900 0.4 1 81 18819 74 10062 0.4 1 58 10004 75 5888 0.4 1 47 5841 76 4721 0.4 1 38 4683 77 5866 0.4 1 38 5828 78 5884 0.4 1 60 5824 79 5522 0.4 1 47 5475 80 4957 0.4 1 19 4938 81 4479 0.4 1 12 4467 82 4324 0.4 1 9 4315 83 4003 0.4 1 12 3991 84 3995 0.4 1 13 3982 85 3853 0.4 1 12 3841 86 4026 0.4 1 16 4010 87 4437 0.4 1 22 4415 88 4100 0.4 1 15 4085 89 4291 0.4 1 20 4271 90 4505 0.4 1 5 4500 91 4791 0.4 1 9 4782 92 5060 0.4 1 16 5044 93 5354 0.4 1 4 5350 94 5880 0.4 1 6 5874 95 6341 0.4 1 5 6336 96 7141 0.4 1 4 7137 97 8080 0.4 1 1 8079 98 8935 0.4 1 1 8934 99 10431 0.4 1 2 10429 100 20510 0.4 1 3 20507 101 87588 0.4 1 7 87581 RUN STATISTICS FOR INPUT FILE: 2112_lane1_GCCAAT.fastq.gz ============================================= 24792684 sequences processed in total Sequences removed because they became shorter than the length cutoff of 20 bp: 2906782 (11.7%) >>> Now running FastQC on the data <<< Started analysis of 2112_lane1_GCCAAT_trimmed.fq.gz Approx 5% complete for 2112_lane1_GCCAAT_trimmed.fq.gz Approx 10% complete for 2112_lane1_GCCAAT_trimmed.fq.gz Approx 15% complete for 2112_lane1_GCCAAT_trimmed.fq.gz Approx 20% complete for 2112_lane1_GCCAAT_trimmed.fq.gz Approx 25% complete for 2112_lane1_GCCAAT_trimmed.fq.gz Approx 30% complete for 2112_lane1_GCCAAT_trimmed.fq.gz Approx 35% complete for 2112_lane1_GCCAAT_trimmed.fq.gz Approx 40% complete for 2112_lane1_GCCAAT_trimmed.fq.gz Approx 45% complete for 2112_lane1_GCCAAT_trimmed.fq.gz Approx 50% complete for 2112_lane1_GCCAAT_trimmed.fq.gz Approx 55% complete for 2112_lane1_GCCAAT_trimmed.fq.gz Approx 60% complete for 2112_lane1_GCCAAT_trimmed.fq.gz Approx 65% complete for 2112_lane1_GCCAAT_trimmed.fq.gz Approx 70% complete for 2112_lane1_GCCAAT_trimmed.fq.gz Approx 75% complete for 2112_lane1_GCCAAT_trimmed.fq.gz Approx 80% complete for 2112_lane1_GCCAAT_trimmed.fq.gz Approx 85% complete for 2112_lane1_GCCAAT_trimmed.fq.gz Approx 90% complete for 2112_lane1_GCCAAT_trimmed.fq.gz Approx 95% complete for 2112_lane1_GCCAAT_trimmed.fq.gz Writing report to '/home/sam/analyses/20180911_virginica_oil_trimgalore_01/2112_lane1_TGACCA.fastq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: 2112_lane1_TGACCA.fastq.gz Trimming mode: single-end Trim Galore version: 0.4.4_dev Cutadapt version: 1.9.1 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; auto-detected) Maximum trimming error rate: 0.1 (default) Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length before a sequence gets removed: 20 bp Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /home/sam/analyses/20180911_virginica_oil_trimgalore_01/20180911_virginica_oil_trimmed_fastqc --threads 16' Output file(s) will be GZIP compressed Writing final adapter and quality trimmed output to 2112_lane1_TGACCA_trimmed.fq.gz >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file 2112_lane1_TGACCA.fastq.gz <<< This is cutadapt 1.9.1 with Python 2.7.12 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC 2112_lane1_TGACCA.fastq.gz Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 222.28 s (24 us/read; 2.48 M reads/minute). === Summary === Total reads processed: 9,188,940 Reads with adapters: 7,714,396 (84.0%) Reads written (passing filters): 9,188,940 (100.0%) Total basepairs processed: 928,082,940 bp Quality-trimmed: 208,253,890 bp (22.4%) Total written (filtered): 346,199,587 bp (37.3%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 7714396 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 20.0% C: 5.5% G: 4.6% T: 5.6% none/other: 64.4% Overview of removed sequences length count expect max.err error counts 1 1492673 2297235.0 0 1492673 2 128598 574308.8 0 128598 3 46570 143577.2 0 46570 4 41159 35894.3 0 41159 5 37536 8973.6 0 37536 6 41569 2243.4 0 41569 7 48187 560.8 0 48187 8 28646 140.2 0 28646 9 34011 35.1 0 33552 459 10 40836 8.8 1 40446 390 11 21070 2.2 1 20614 456 12 39375 0.5 1 38852 523 13 28223 0.1 1 27712 511 14 30477 0.1 1 30009 468 15 31572 0.1 1 30949 623 16 34270 0.1 1 33591 679 17 32392 0.1 1 31586 806 18 37144 0.1 1 36578 566 19 16557 0.1 1 16121 436 20 27628 0.1 1 27119 509 21 27318 0.1 1 26715 603 22 29792 0.1 1 29190 602 23 20283 0.1 1 19662 621 24 23742 0.1 1 23010 732 25 27134 0.1 1 26401 733 26 21110 0.1 1 19750 1360 27 24652 0.1 1 22661 1991 28 29900 0.1 1 27077 2823 29 20898 0.1 1 18877 2021 30 26378 0.1 1 24966 1412 31 11675 0.1 1 10195 1480 32 24841 0.1 1 20740 4101 33 19835 0.1 1 13337 6498 34 22072 0.1 1 17701 4371 35 17506 0.1 1 15765 1741 36 19797 0.1 1 15998 3799 37 16923 0.1 1 12762 4161 38 14306 0.1 1 12662 1644 39 26208 0.1 1 13199 13009 40 19199 0.1 1 10916 8283 41 20520 0.1 1 10636 9884 42 18073 0.1 1 9522 8551 43 14909 0.1 1 9560 5349 44 16890 0.1 1 8049 8841 45 15620 0.1 1 10542 5078 46 12395 0.1 1 8215 4180 47 10591 0.1 1 5173 5418 48 9609 0.1 1 4173 5436 49 9523 0.1 1 5244 4279 50 9295 0.1 1 3891 5404 51 13901 0.1 1 3851 10050 52 13243 0.1 1 5125 8118 53 8982 0.1 1 4127 4855 54 9199 0.1 1 1093 8106 55 8068 0.1 1 1833 6235 56 12312 0.1 1 1891 10421 57 16344 0.1 1 2128 14216 58 16997 0.1 1 1515 15482 59 9772 0.1 1 1717 8055 60 15043 0.1 1 825 14218 61 18869 0.1 1 914 17955 62 60104 0.1 1 885 59219 63 81495 0.1 1 1695 79800 64 21625 0.1 1 1087 20538 65 27271 0.1 1 267 27004 66 62437 0.1 1 500 61937 67 216127 0.1 1 644 215483 68 512969 0.1 1 1417 511552 69 1759541 0.1 1 2378 1757163 70 1031227 0.1 1 5431 1025796 71 385531 0.1 1 1504 384027 72 136018 0.1 1 455 135563 73 37324 0.1 1 158 37166 74 18788 0.1 1 90 18698 75 10612 0.1 1 56 10556 76 8749 0.1 1 51 8698 77 11805 0.1 1 34 11771 78 11502 0.1 1 51 11451 79 10571 0.1 1 56 10515 80 9179 0.1 1 14 9165 81 7981 0.1 1 17 7964 82 7509 0.1 1 12 7497 83 6703 0.1 1 18 6685 84 6606 0.1 1 19 6587 85 6518 0.1 1 27 6491 86 6887 0.1 1 43 6844 87 7238 0.1 1 38 7200 88 6963 0.1 1 48 6915 89 7086 0.1 1 61 7025 90 7376 0.1 1 7 7369 91 7796 0.1 1 10 7786 92 8320 0.1 1 10 8310 93 8758 0.1 1 3 8755 94 9533 0.1 1 11 9522 95 10141 0.1 1 3 10138 96 11512 0.1 1 3 11509 97 13094 0.1 1 5 13089 98 14343 0.1 1 3 14340 99 16413 0.1 1 1 16412 100 32725 0.1 1 10 32715 101 135802 0.1 1 12 135790 RUN STATISTICS FOR INPUT FILE: 2112_lane1_TGACCA.fastq.gz ============================================= 9188940 sequences processed in total Sequences removed because they became shorter than the length cutoff of 20 bp: 4981933 (54.2%) >>> Now running FastQC on the data <<< Started analysis of 2112_lane1_TGACCA_trimmed.fq.gz Approx 5% complete for 2112_lane1_TGACCA_trimmed.fq.gz Approx 10% complete for 2112_lane1_TGACCA_trimmed.fq.gz Approx 15% complete for 2112_lane1_TGACCA_trimmed.fq.gz Approx 20% complete for 2112_lane1_TGACCA_trimmed.fq.gz Approx 25% complete for 2112_lane1_TGACCA_trimmed.fq.gz Approx 30% complete for 2112_lane1_TGACCA_trimmed.fq.gz Approx 35% complete for 2112_lane1_TGACCA_trimmed.fq.gz Approx 40% complete for 2112_lane1_TGACCA_trimmed.fq.gz Approx 45% complete for 2112_lane1_TGACCA_trimmed.fq.gz Approx 50% complete for 2112_lane1_TGACCA_trimmed.fq.gz Approx 55% complete for 2112_lane1_TGACCA_trimmed.fq.gz Approx 60% complete for 2112_lane1_TGACCA_trimmed.fq.gz Approx 65% complete for 2112_lane1_TGACCA_trimmed.fq.gz Approx 70% complete for 2112_lane1_TGACCA_trimmed.fq.gz Approx 75% complete for 2112_lane1_TGACCA_trimmed.fq.gz Approx 80% complete for 2112_lane1_TGACCA_trimmed.fq.gz Approx 85% complete for 2112_lane1_TGACCA_trimmed.fq.gz Approx 90% complete for 2112_lane1_TGACCA_trimmed.fq.gz Approx 95% complete for 2112_lane1_TGACCA_trimmed.fq.gz Writing report to '/home/sam/analyses/20180911_virginica_oil_trimgalore_01/2112_lane1_TTAGGC.fastq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: 2112_lane1_TTAGGC.fastq.gz Trimming mode: single-end Trim Galore version: 0.4.4_dev Cutadapt version: 1.9.1 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; auto-detected) Maximum trimming error rate: 0.1 (default) Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length before a sequence gets removed: 20 bp Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /home/sam/analyses/20180911_virginica_oil_trimgalore_01/20180911_virginica_oil_trimmed_fastqc --threads 16' Output file(s) will be GZIP compressed Writing final adapter and quality trimmed output to 2112_lane1_TTAGGC_trimmed.fq.gz >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file 2112_lane1_TTAGGC.fastq.gz <<< 10000000 sequences processed 20000000 sequences processed This is cutadapt 1.9.1 with Python 2.7.12 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC 2112_lane1_TTAGGC.fastq.gz Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 569.15 s (22 us/read; 2.71 M reads/minute). === Summary === Total reads processed: 25,752,634 Reads with adapters: 15,393,563 (59.8%) Reads written (passing filters): 25,752,634 (100.0%) Total basepairs processed: 2,601,016,034 bp Quality-trimmed: 168,252,428 bp (6.5%) Total written (filtered): 2,140,459,636 bp (82.3%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 15393563 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 35.3% C: 17.2% G: 7.1% T: 19.5% none/other: 20.9% Overview of removed sequences length count expect max.err error counts 1 7645997 6438158.5 0 7645997 2 534336 1609539.6 0 534336 3 291105 402384.9 0 291105 4 245902 100596.2 0 245902 5 222809 25149.1 0 222809 6 221201 6287.3 0 221201 7 227983 1571.8 0 227983 8 176189 393.0 0 176189 9 191707 98.2 0 190234 1473 10 196407 24.6 1 194560 1847 11 135415 6.1 1 133356 2059 12 172560 1.5 1 170422 2138 13 142990 0.4 1 140803 2187 14 139835 0.4 1 137590 2245 15 140839 0.4 1 138493 2346 16 128017 0.4 1 125580 2437 17 141709 0.4 1 138594 3115 18 145963 0.4 1 144065 1898 19 61855 0.4 1 60451 1404 20 97268 0.4 1 95653 1615 21 90319 0.4 1 88627 1692 22 85905 0.4 1 84316 1589 23 72813 0.4 1 71243 1570 24 73060 0.4 1 71571 1489 25 65690 0.4 1 64250 1440 26 57685 0.4 1 55768 1917 27 54892 0.4 1 52716 2176 28 60126 0.4 1 57259 2867 29 41472 0.4 1 39372 2100 30 49205 0.4 1 47594 1611 31 23857 0.4 1 22268 1589 32 37275 0.4 1 33618 3657 33 26224 0.4 1 21303 4921 34 29760 0.4 1 25969 3791 35 22547 0.4 1 20747 1800 36 23176 0.4 1 19483 3693 37 18674 0.4 1 15930 2744 38 16053 0.4 1 13708 2345 39 13968 0.4 1 12793 1175 40 11681 0.4 1 9163 2518 41 10475 0.4 1 8039 2436 42 10739 0.4 1 7353 3386 43 8516 0.4 1 6429 2087 44 7285 0.4 1 5372 1913 45 6868 0.4 1 5558 1310 46 6169 0.4 1 4828 1341 47 4628 0.4 1 3103 1525 48 4038 0.4 1 2397 1641 49 4377 0.4 1 2706 1671 50 4702 0.4 1 2022 2680 51 5287 0.4 1 1938 3349 52 5055 0.4 1 1990 3065 53 3894 0.4 1 1797 2097 54 3728 0.4 1 633 3095 55 3840 0.4 1 948 2892 56 4945 0.4 1 854 4091 57 7122 0.4 1 904 6218 58 7223 0.4 1 746 6477 59 5119 0.4 1 898 4221 60 7815 0.4 1 497 7318 61 10538 0.4 1 562 9976 62 26673 0.4 1 635 26038 63 53981 0.4 1 963 53018 64 17769 0.4 1 917 16852 65 22283 0.4 1 264 22019 66 49178 0.4 1 385 48793 67 173176 0.4 1 558 172618 68 380184 0.4 1 1354 378830 69 1270634 0.4 1 1947 1268687 70 552446 0.4 1 4168 548278 71 201233 0.4 1 913 200320 72 72352 0.4 1 272 72080 73 21277 0.4 1 91 21186 74 11114 0.4 1 52 11062 75 6478 0.4 1 37 6441 76 5114 0.4 1 24 5090 77 6703 0.4 1 33 6670 78 6637 0.4 1 40 6597 79 6056 0.4 1 46 6010 80 5622 0.4 1 26 5596 81 5152 0.4 1 13 5139 82 4865 0.4 1 8 4857 83 4602 0.4 1 14 4588 84 4362 0.4 1 19 4343 85 4613 0.4 1 17 4596 86 4742 0.4 1 29 4713 87 5120 0.4 1 19 5101 88 4899 0.4 1 32 4867 89 4742 0.4 1 24 4718 90 5284 0.4 1 5 5279 91 5575 0.4 1 11 5564 92 5872 0.4 1 12 5860 93 6133 0.4 1 4 6129 94 6580 0.4 1 8 6572 95 7236 0.4 1 6 7230 96 8258 0.4 1 3 8255 97 9049 0.4 1 5 9044 98 10113 0.4 1 1 10112 99 11510 0.4 1 0 11510 100 22958 0.4 1 2 22956 101 96156 0.4 1 5 96151 RUN STATISTICS FOR INPUT FILE: 2112_lane1_TTAGGC.fastq.gz ============================================= 25752634 sequences processed in total Sequences removed because they became shorter than the length cutoff of 20 bp: 3234303 (12.6%) >>> Now running FastQC on the data <<< Started analysis of 2112_lane1_TTAGGC_trimmed.fq.gz Approx 5% complete for 2112_lane1_TTAGGC_trimmed.fq.gz Approx 10% complete for 2112_lane1_TTAGGC_trimmed.fq.gz Approx 15% complete for 2112_lane1_TTAGGC_trimmed.fq.gz Approx 20% complete for 2112_lane1_TTAGGC_trimmed.fq.gz Approx 25% complete for 2112_lane1_TTAGGC_trimmed.fq.gz Approx 30% complete for 2112_lane1_TTAGGC_trimmed.fq.gz Approx 35% complete for 2112_lane1_TTAGGC_trimmed.fq.gz Approx 40% complete for 2112_lane1_TTAGGC_trimmed.fq.gz Approx 45% complete for 2112_lane1_TTAGGC_trimmed.fq.gz Approx 50% complete for 2112_lane1_TTAGGC_trimmed.fq.gz Approx 55% complete for 2112_lane1_TTAGGC_trimmed.fq.gz Approx 60% complete for 2112_lane1_TTAGGC_trimmed.fq.gz Approx 65% complete for 2112_lane1_TTAGGC_trimmed.fq.gz Approx 70% complete for 2112_lane1_TTAGGC_trimmed.fq.gz Approx 75% complete for 2112_lane1_TTAGGC_trimmed.fq.gz Approx 80% complete for 2112_lane1_TTAGGC_trimmed.fq.gz Approx 85% complete for 2112_lane1_TTAGGC_trimmed.fq.gz Approx 90% complete for 2112_lane1_TTAGGC_trimmed.fq.gz Approx 95% complete for 2112_lane1_TTAGGC_trimmed.fq.gz