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  • help with GNU parallel

    Hi,

    I want to run Deconseq on a huge file using GNU parallel. Deconseq input is like this:
    Code:
    deconseq -i [% identity] -c [% coverage] -out_dir [output dir] -id [optional file id] -f [iput fasta/fastq file] -dbs [database to screen against]
    I tried configuring command like that;
    Code:
    cat /home/yaximik/input.fq | parallel --block 100M -k --pipe --recstart @M01227 --recend '\n' deconseq -i 94 -c 70 -out_dir /home/yaximik/outdir -id TESThg19 -f {} -dbs hg19
    However, deconseq exits with an error as {} is not substituted with iput.fq for -f, and {} does not work with -dbs. Is anything wrong here or can I do this differently?

  • #2
    try using the --dry-run flag to see what command parallel is attempting to run. I assume you've got some escape characters getting muddled up. Most of my my parallel commands end up chock full of backslashes

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    • #3
      Originally posted by yaximik View Post
      Hi,

      I tried configuring command like that;
      Code:
      cat /home/yaximik/input.fq | parallel --block 100M -k --pipe --recstart @M01227 --recend '\n' deconseq -i 94 -c 70 -out_dir /home/yaximik/outdir -id TESThg19 -f {} -dbs hg19
      It is extremely rarely that --pipe and {} make sense together. You need to remember that GNU Parallel passes the input on stdin and not as a file when you use --pipe.

      So if deconseq can read from stdin you can use that. Often programs will accept '-' as file for stdin: deconseq ... -f -

      If you run GNU Linux you probably can do: deconseq ... -f /dev/stdin

      If that does not work, you first need to save stdin to a file: cat > {#}; deconseq ... -f {#}

      With the git version of GNU Parallel you can get rid of the ugly --recstart @M01227 and instead use -L4 (each record is 4 lines long).

      If #ilovefs remember to cite: parallel --bibtex
      Last edited by tange; 02-14-2013, 04:36 PM.

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