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  • Trouble With Trim_Galore processing paired reads

    Hello Everyone,

    I am new to this, and have been havigjn soem trouble with trim galore. I think I've reached that point where I cannot see what is causing my error and I thought I would ask you for your colelctive input:

    Here is my trim_galore command:
    ./trim_galore -a AGATCGGAAGAGC -t --paired /media/daveboBaggins/R2_001.fastq /media/daveboBaggins/R1_001.fastq

    I get as an output:
    SUMMARISING RUN PARAMETERS
    ==========================
    Input filename: /media/daveboBaggins/R2_001.fastq
    Quality Phred score cutoff: 20
    Quality encoding type selected: ASCII+33
    Adapter sequence: 'AGATCGGAAGAGC'
    Maximum trimming error rate: 0.1 (default)
    Minimum required adapter overlap (stringency): 1 bp
    Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
    All sequences will be trimmed by 1 bp on their 3' end to avoid problems with invalid paired-end alignments with Bowtie 1

    Writing final adapter and quality trimmed output to
    R2_001_trimmed.fq


    >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file


    I get the following error message:
    open3: exec of /home/daveboBaggins/cutadapt-1.2.1/cutadapt -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /media/daveboBaggins/7_R2_001.fastq failed at /home/daveboBaggins/trim_galore_zip/trim_galore line 453

    I have gone back to line 453 which is as follows:
    open3 (\*WRITER, \*TRIM, \*ERROR, "$path_to_cutadapt -f fastq -e $error_rate -q $cutoff -O $stringency -a $adapter $filename") or die "Failed to launch Cutadapt: $!";

    I have made sure I added the path to cutadapt in the perl code. But still cannot see what I am doing wrong? I have gone back and the pathway to cutadapt is in the $PATH variable. Any suggestions will be much appreciated

    -Dave-Bo Baggins

  • #2
    While we wait for trimgalore folks to chime in (tomorrow) here is something to test:

    Have you checked to make sure that cutadapt has execute permissions?

    Comment


    • #3
      Originally posted by GenoMax View Post
      While we wait for trimgalore folks to chime in (tomorrow) here is something to test:

      Have you checked to make sure that cutadapt has execute permissions?
      That's exactly what I would have asked. When you enter the same path to Cutadapt that you also find within Trim Galore into a command line, e.g.

      /home/user/cutadapt/bin/cutadapt

      do you see the Cutadapt help? If not, you need to get Cutadapt to run before launching Trim Galore.

      Comment


      • #4
        Originally posted by GenoMax View Post
        While we wait for trimgalore folks to chime in (tomorrow) here is something to test:

        Have you checked to make sure that cutadapt has execute permissions?
        Thanks for your reply I appreciate it. I will be in front of my work computer in an hour and change and will check that out

        Dave

        Comment


        • #5
          Thanks a lot, Ill will be looking into this and will get back to you all asap!

          Comment

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