Hi. I also had the same problem
cutadapt -u 4 –a GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGGACTACHVGGGTATCTAATCC –g TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGNNNNCCTACGGGNGGCWGCAG –o 21I-C1_S2_L001_R1_001_t.fastq -p 21I-C1_S2_L001_R2_001_t.fastq 21I_C1 21I-C1_S2_L001_R1_001.fastq 21I-C1_S2_L001_R2_001.fastq
I tried to remove the f and r primers with the removal of first 4 bases for each read but this error came out
shaufi@ppplives-Precision-T5610[cutadapt-1.11] cutadapt -u 4 –a GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGGACTACHVGGGTATCTAATCC –g TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGNNNNCCTACGGGNGGCWGCAG –o 21I-C1_S2_L001_R1_001_t.fastq -p 21I-C1_S2_L001_R2_001_t.fastq 21I_C1 21I-C1_S2_L001_R1_001.fastq 21I-C1_S2_L001_R2_001.fastq
/usr/lib/python2.7/dist-packages/pkg_resources.py:1031: UserWarning: /home/shaufi/.python-eggs is writable by group/others and vulnerable to attack when used with get_resource_filename. Consider a more secure location (set with .set_extraction_path or the PYTHON_EGG_CACHE environment variable).
cutadapt version 1.11
Copyright (C) 2010-2016 Marcel Martin email@example.com
cutadapt removes adapter sequences from high-throughput sequencing reads.
cutadapt -a ADAPTER [options] [-o output.fastq] input.fastq
For paired-end reads:
cutadapt -a ADAPT1 -A ADAPT2 [options] -o out1.fastq -p out2.fastq in1.fastq in2.fastq
Replace "ADAPTER" with the actual sequence of your 3' adapter. IUPAC wildcard
characters are supported. The reverse complement is not automatically
searched. All reads from input.fastq will be written to output.fastq with the
adapter sequence removed. Adapter matching is error-tolerant. Multiple adapter
sequences can be given (use further -a options), but only the best-matching
adapter will be removed.
Input may also be in FASTA format. Compressed input and output is supported and
auto-detected from the file name (.gz, .xz, .bz2). Use the file name '-' for
standard input/output. Without the -o option, output is sent to standard output.
Marcel Martin. Cutadapt removes adapter sequences from high-throughput
sequencing reads. EMBnet.Journal, 17(1):10-12, May 2011.
Use "cutadapt --help" to see all command-line options.
See http://cutadapt.readthedocs.org/ for full documentation.
cutadapt: error: Too many parameters.
What do you think could be the problem? Thanks