help with GNU parallel

[yaximik]

Hi,

I want to run Deconseq on a huge file using GNU parallel. Deconseq input is like this:

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;

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?

[mdobeson]

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

[tange]

Hi,

I tried configuring command like that;

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