Hi,
I want to run Deconseq on a huge file using GNU parallel. Deconseq input is like this:
I tried configuring command like that;
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?
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]
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
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