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cutadapt: error: unrecognized arguments: -f #6

Description

@SadotR

Hello,
I have a problem with one of the arguments when starting the step of removing the adapters with cutadapt. the -f argument is not recognized.

Problem message:

SUMMARISING RUN PARAMETERS

Input filename: /home/sadotr/RRBS/RefFreeDMA/RefFreeDMA_test/fastq/BSF_0116_C55NLACXX_3__Hum_2_L.fastq
Quality Phred score cutoff: 20
Quality encoding type selected: ASCII+33
Adapter sequence: 'AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC'
Maximum trimming error rate: 0.1 (default)
Minimum required adapter overlap (stringency): 1 bp
Minimum required sequence length before a sequence gets removed: 16 bp

This is cutadapt 3.5 with Python 3.10.12
Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC /home/sadotr/RRBS/RefFreeDMA/RefFreeDMA_test/fastq/BSF_0116_C55NLACXX_3__Hum_2_L.fastq
Run "cutadapt --help" to see command-line options.
See https://cutadapt.readthedocs.io/ for full documentation.

cutadapt: error: unrecognized arguments: -f /home/sadotr/RRBS/RefFreeDMA/RefFreeDMA_test/fastq/BSF_0116_C55NLACXX_3__Hum_2_L.fastq

RUN STATISTICS FOR INPUT FILE: /home/sadotr/RRBS/RefFreeDMA/RefFreeDMA_test/fastq/BSF_0116_C55NLACXX_3__Hum_2_L.fastq

0 sequences processed in total

prepareReads_BSF_0116_C55NLACXX_3__Hum_2_L.log

I hope you can help me.
greetings

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