samplefile: /opt/trax/testadapt2.txt adapter: TCGTATGCCGTCTTCT output files: SRR207111_trimmed.fastq.gz,SRR207116_trimmed.fastq.gz /opt/trax/trimadapters.py --runname adapt2 --runfile /opt/trax/testadapt2.txt --firadapter TCGTATGCCGTCTTCT --singleend ************************ SRR207111 cutadapt -m 15 --adapter=TCGTATGCCGTCTTCT SRR207111.fastq.gz | gzip -c >SRR207111_trimmed.fastq.gz This is cutadapt 1.18 with Python 2.7.15 Command line parameters: -m 15 --adapter=TCGTATGCCGTCTTCT SRR207111.fastq.gz Processing reads on 1 core in single-end mode ... Finished in 682.66 s (99 us/read; 0.61 M reads/minute). === Summary === Total reads processed: 6,898,244 Reads with adapters: 6,579,337 (95.4%) Reads that were too short: 155,992 (2.3%) Reads written (passing filters): 6,742,252 (97.7%) Total basepairs processed: 241,438,540 bp Total written (filtered): 149,626,056 bp (62.0%) === Adapter 1 === Sequence: TCGTATGCCGTCTTCT; Type: regular 3'; Length: 16; Trimmed: 6579337 times. No. of allowed errors: 0-9 bp: 0; 10-16 bp: 1 Bases preceding removed adapters: A: 24.5% C: 11.5% G: 10.3% T: 52.0% none/other: 1.6% Overview of removed sequences length count expect max.err error counts 3 1672 107785.1 0 1672 4 2655 26946.3 0 2655 5 3249 6736.6 0 3249 6 8371 1684.1 0 8371 7 26575 421.0 0 26575 8 49219 105.3 0 49219 9 69697 26.3 0 69666 31 10 137891 6.6 1 124876 13015 11 765544 1.6 1 702522 63022 12 1039758 0.4 1 929957 109801 13 2292388 0.1 1 2046577 245811 14 489061 0.0 1 447178 41883 15 351317 0.0 1 315213 36104 16 275294 0.0 1 245873 29421 17 281652 0.0 1 257287 24365 18 380297 0.0 1 351051 29246 19 143270 0.0 1 133072 10198 20 105435 0.0 1 97736 7699 21 36206 0.0 1 33251 2955 22 6522 0.0 1 6056 466 23 1806 0.0 1 1692 114 24 537 0.0 1 505 32 25 295 0.0 1 279 16 26 99 0.0 1 94 5 27 75 0.0 1 71 4 28 214 0.0 1 209 5 29 248 0.0 1 237 11 30 495 0.0 1 481 14 31 525 0.0 1 515 10 32 171 0.0 1 167 4 33 1332 0.0 1 1300 32 34 1084 0.0 1 1058 26 35 106383 0.0 1 102518 3865 SRR207116 cutadapt -m 15 --adapter=TCGTATGCCGTCTTCT SRR207116.fastq.gz | gzip -c >SRR207116_trimmed.fastq.gz This is cutadapt 1.18 with Python 2.7.15 Command line parameters: -m 15 --adapter=TCGTATGCCGTCTTCT SRR207116.fastq.gz Processing reads on 1 core in single-end mode ... Finished in 1774.76 s (94 us/read; 0.64 M reads/minute). === Summary === Total reads processed: 18,944,579 Reads with adapters: 17,763,400 (93.8%) Reads that were too short: 241,906 (1.3%) Reads written (passing filters): 18,702,673 (98.7%) Total basepairs processed: 663,060,265 bp Total written (filtered): 488,513,173 bp (73.7%) === Adapter 1 === Sequence: TCGTATGCCGTCTTCT; Type: regular 3'; Length: 16; Trimmed: 17763400 times. No. of allowed errors: 0-9 bp: 0; 10-16 bp: 1 Bases preceding removed adapters: A: 0.4% C: 98.5% G: 0.2% T: 0.8% none/other: 0.1% WARNING: The adapter is preceded by "C" extremely often. The provided adapter sequence could be incomplete at its 3' end. Overview of removed sequences length count expect max.err error counts 3 272653 296009.0 0 272653 4 424730 74002.3 0 424730 5 421836 18500.6 0 421836 6 278795 4625.1 0 278795 7 378793 1156.3 0 378793 8 974388 289.1 0 974388 9 5051152 72.3 0 5045319 5833 10 6260947 18.1 1 6027920 233027 11 1850753 4.5 1 1758811 91942 12 786142 1.1 1 730168 55974 13 426915 0.3 1 384323 42592 14 229499 0.1 1 205091 24408 15 69679 0.0 1 57526 12153 16 28320 0.0 1 24341 3979 17 22134 0.0 1 19637 2497 18 22297 0.0 1 19826 2471 19 14957 0.0 1 13005 1952 20 7504 0.0 1 6610 894 21 6134 0.0 1 5325 809 22 3984 0.0 1 3231 753 23 3260 0.0 1 2885 375 24 6362 0.0 1 5516 846 25 13402 0.0 1 12305 1097 26 6714 0.0 1 6064 650 27 8463 0.0 1 7716 747 28 5050 0.0 1 4688 362 29 2707 0.0 1 2514 193 30 431 0.0 1 396 35 31 916 0.0 1 831 85 32 167517 0.0 1 155306 12211 33 2677 0.0 1 2377 300 34 2501 0.0 1 2284 217 35 11788 0.0 1 11392 396 WARNING: One or more of your adapter sequences may be incomplete. Please see the detailed output above.