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  • Seqclean indexing problem

    I downloaded Seqcleanx86_64. I want to remove contaminants from a powdery mildew DNA sequence data using databases I created using makeblast. I use Mac operating system. I tried running the following command line:

    $ Vperl ~/bin/seqclean-x86_64/seqclean LA_Run18_R1.fa -s /Volumes/Data_2/Sandile/raw_data/cont_db/bgh -o LA_Run18_R1clean1 -N -A

    The terminal output recorded the following error:

    Process terminated with an error!
    seqclean (LA_Run18_R1.fa) encountered an error.
    Working directory was /Volumes/Data_2/Sandile/raw_data
    seqclean (LA_Run18_R1.fa) encountered an error.
    Working directory was /Vperl ~/bin/seqclean-x86_64/seqclean LA_Run18_R1.fa -s /Volumes/Data_2/Sandile/raw_data/cont_db/bgh -o LA_Run18_R1clean1 -N -A
    * Using screening files:

    /Volumes/Data_2/Sandile/raw_data/cont_db/bgh
    seqclean running options:
    seqclean LA_Run18_R1.fa -s /Volumes/Data_2/Sandile/raw_data/cont_db/bgh -o LA_Run18_R1clean1 -N -A
    Standard log file: seqcl_LA_Run18_R1.fa.log
    Error log file: err_seqcl_LA_Run18_R1.fa.log
    Using 1 CPUs for cleaning
    -= Rebuilding LA_Run18_R1.fa cdb index =-
    Error at cdbfasta LA_Run18_R1.fa -o LA_Run18_R1.fa.cidx

    Process terminated with an error!
    seqclean (LA_Run18_R1.fa) encountered an error.
    Working directory was /Volumes/Data_2/Sandile/raw_data
    seqclean (LA_Run18_R1.fa) encountered an error.
    Working directory was /Vperl ~/bin/seqclean-x86_64/seqclean LA_Run18_R1.fa -s /Volumes/Data_2/Sandile/raw_data/cont_db/bgh -o LA_Run18_R1clean1 -N -A

    I am beginner level at bioinformatics, hence may not have phrased my question properly. Please advise on the probable cause of this error and ways to overcome it.

  • #2
    I've had the same problem. It's unclear to me if SeqClean can actually run on a Mac - does anybody know this? Since the download appears to be already compiled - I'm assuming it is compiled for Linux and not Mac - hence I've run into the same problems and can't seem to get it to work on my Mac.

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