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To speed up the demultiplexing (which would have taken several days on each input file), I split the concatenated raw files into files with 16 million lines each.
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mkdir -p /gscratch/buerkle/data/alfalfa/rawreads cd /gscratch/buerkle/data/alfalfa/rawreads cat /project/evolgen/data/local/alfalfa/alf1GBS_NS1_mar21/Pool*_S* | split -l 16000000 -d --suffix-length=3 --additional-suffix=.fastq - alf1_ mkdir rawreads mv alf1_* rawreads/ /project/evolgen/assem/alf1GBS_NS1_mar21/demultiplex/run_parsebarcodes_onSplitInput.pl |
In /project/evolgen/assem/alf1GBS_NS1_mar21/demulitplex I launched
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