samplefile: /opt/trax/testadapt1.txt adapter: TCGTATGCCGTCTTCT output files: SRR029131_trimmed.fastq.gz,SRR029124_trimmed.fastq.gz /opt/trax/trimadapters.py --runname adapt1 --runfile /opt/trax/testadapt1.txt --firadapter TCGTATGCCGTCTTCT --singleend ************************ SRR029131 cutadapt -m 15 --adapter=TCGTATGCCGTCTTCT SRR029131.fastq.gz | gzip -c >SRR029131_trimmed.fastq.gz This is cutadapt 1.18 with Python 2.7.15 Command line parameters: -m 15 --adapter=TCGTATGCCGTCTTCT SRR029131.fastq.gz Processing reads on 1 core in single-end mode ... Finished in 380.75 s (92 us/read; 0.65 M reads/minute). === Summary === Total reads processed: 4,152,385 Reads with adapters: 3,614,301 (87.0%) Reads that were too short: 192,648 (4.6%) Reads written (passing filters): 3,959,737 (95.4%) Total basepairs processed: 149,485,860 bp Total written (filtered): 94,926,707 bp (63.5%) === Adapter 1 === Sequence: TCGTATGCCGTCTTCT; Type: regular 3'; Length: 16; Trimmed: 3614301 times. No. of allowed errors: 0-9 bp: 0; 10-16 bp: 1 Bases preceding removed adapters: A: 46.2% C: 19.0% G: 14.9% T: 19.9% none/other: 0.1% Overview of removed sequences length count expect max.err error counts 3 36397 64881.0 0 36397 4 48218 16220.3 0 48218 5 56529 4055.1 0 56529 6 55745 1013.8 0 55745 7 29373 253.4 0 29373 8 52760 63.4 0 52760 9 27260 15.8 0 27151 109 10 108830 4.0 1 88315 20515 11 54627 1.0 1 44246 10381 12 148340 0.2 1 125451 22889 13 624536 0.1 1 540745 83791 14 1044432 0.0 1 904226 140206 15 308206 0.0 1 261417 46789 16 119724 0.0 1 102190 17534 17 79142 0.0 1 66162 12980 18 389763 0.0 1 336529 53234 19 101898 0.0 1 86315 15583 20 67894 0.0 1 57177 10717 21 67979 0.0 1 56608 11371 22 62948 0.0 1 52164 10784 23 57478 0.0 1 50006 7472 24 23451 0.0 1 19701 3750 25 16830 0.0 1 13523 3307 26 11136 0.0 1 9331 1805 27 6659 0.0 1 5819 840 28 2723 0.0 1 2383 340 29 1460 0.0 1 1261 199 30 1093 0.0 1 973 120 31 3805 0.0 1 3323 482 32 415 0.0 1 358 57 33 1166 0.0 1 1045 121 34 121 0.0 1 104 17 35 54 0.0 1 49 5 36 3309 0.0 1 3071 238 SRR029124 cutadapt -m 15 --adapter=TCGTATGCCGTCTTCT SRR029124.fastq.gz | gzip -c >SRR029124_trimmed.fastq.gz This is cutadapt 1.18 with Python 2.7.15 Command line parameters: -m 15 --adapter=TCGTATGCCGTCTTCT SRR029124.fastq.gz Processing reads on 1 core in single-end mode ... Finished in 394.69 s (84 us/read; 0.72 M reads/minute). === Summary === Total reads processed: 4,712,823 Reads with adapters: 3,071,351 (65.2%) Reads that were too short: 18,472 (0.4%) Reads written (passing filters): 4,694,351 (99.6%) Total basepairs processed: 169,661,628 bp Total written (filtered): 126,165,169 bp (74.4%) === Adapter 1 === Sequence: TCGTATGCCGTCTTCT; Type: regular 3'; Length: 16; Trimmed: 3071351 times. No. of allowed errors: 0-9 bp: 0; 10-16 bp: 1 Bases preceding removed adapters: A: 41.3% C: 15.4% G: 12.8% T: 30.4% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 3 43643 73637.9 0 43643 4 49042 18409.5 0 49042 5 56772 4602.4 0 56772 6 73319 1150.6 0 73319 7 44787 287.6 0 44787 8 66251 71.9 0 66251 9 42137 18.0 0 40143 1994 10 163322 4.5 1 109171 54151 11 65076 1.1 1 46443 18633 12 142218 0.3 1 66964 75254 13 427615 0.1 1 286631 140984 14 649708 0.0 1 439507 210201 15 167949 0.0 1 52184 115765 16 102793 0.0 1 57651 45142 17 106485 0.0 1 68545 37940 18 504603 0.0 1 325251 179352 19 188768 0.0 1 130672 58096 20 122558 0.0 1 85049 37509 21 35833 0.0 1 23750 12083 22 10630 0.0 1 7440 3190 23 4430 0.0 1 3003 1427 24 1786 0.0 1 1181 605 25 533 0.0 1 409 124 26 107 0.0 1 84 23 27 50 0.0 1 39 11 28 25 0.0 1 17 8 29 13 0.0 1 11 2 30 19 0.0 1 16 3 31 22 0.0 1 16 6 32 16 0.0 1 13 3 33 6 0.0 1 5 1 34 6 0.0 1 5 1 35 1 0.0 1 1 36 828 0.0 1 765 63