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FelixKrueger / TrimGalore

A wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS data
GNU General Public License v3.0
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Adapter sequence must contain DNA characters only (A,C,T,G or N)! #111

Closed titand98 closed 3 years ago

titand98 commented 3 years ago

base) erpl@erpl-HP-Z840-Workstation:~/sayak/pilot study/downloaded_Raw_files$ trim_galore --fastqc -a -dont_gzip o ../trimmed_files(trial)/ SRR1777087.1 _Multicore support not enabled. Proceeding with single-core trimming. Path to Cutadapt set as: 'cutadapt' (default) Cutadapt seems to be working fine (tested command 'cutadapt --version') Cutadapt version: 3.1 single-core operation. No quality encoding type selected. Assuming that the data provided uses Sanger encoded Phred scores (default)

Adapter sequence must contain DNA characters only (A,C,T,G or N)!

I have tried commenting out line 2 two lines in perl file still getting that error else{ # default

unless ($adapter =~ /^[ACTGNXactgnx]+$/){

            #die "Adapter sequence must contain DNA characters only (A,C,T,G or N)!\n";
        }    
        $adapter = uc$adapter;
    }

plz help!!!!!!!!!!!!!!!!!!

FelixKrueger commented 3 years ago

You command line uses -a -dont_gzip. Specifying -a overrides the adapter auto-detection, and instead tries to use -dont_gzip as the adapter sequence (which isn't allowed). I would also try to use weird symbols in the directory file, e.g. ()!/# etc, as they will most likely cause trouble. The following command should work just fine:

trim_galore --fastqc -o ../trimmed_files/ SRR1777087.1.fastq.gz
titand98 commented 3 years ago

thanks sir.issue resolved