time wget -q -O - ftp://ftp.ncbi.nlm.nih.gov/refseq/release/invertebrate/*.genomic.fna.gz | gi2taxid.sh -Xmx1g in=stdin.fna.gz out=refseq.invertebrate.fna pigz=2 unpigz=t zl=2 tree=null table=null accession=null server ow maxbadheaders=5000 badheaders=badHeaders_invertebrate.txt 
time wget -q -O - ftp://ftp.ncbi.nlm.nih.gov/refseq/release/plant/*.genomic.fna.gz | gi2taxid.sh -Xmx1g in=stdin.fna.gz out=refseq.plant.fna pigz=2 unpigz=t zl=2 tree=null table=null accession=null server ow maxbadheaders=5000 badheaders=badHeaders_plant.txt 
time wget -q -O - ftp://ftp.ncbi.nlm.nih.gov/refseq/release/plasmid/*.genomic.fna.gz | gi2taxid.sh -Xmx1g in=stdin.fna.gz out=refseq.plasmid.fna pigz=2 unpigz=t zl=2 tree=null table=null accession=null server ow maxbadheaders=5000 badheaders=badHeaders_plasmid.txt

time wget -q -O - ftp://ftp.ncbi.nlm.nih.gov/refseq/release/plastid/*.genomic.fna.gz | gi2taxid.sh -Xmx1g in=stdin.fna.gz out=refseq.plastid.fna pigz=2 unpigz=t zl=2 tree=null table=null accession=null server ow maxbadheaders=5000 badheaders=badHeaders_plastid.txt 
time wget -q -O - ftp://ftp.ncbi.nlm.nih.gov/refseq/release/protozoa/*.genomic.fna.gz | gi2taxid.sh -Xmx1g in=stdin.fna.gz out=refseq.protozoa.fna pigz=2 unpigz=t zl=2 tree=null table=null accession=null server ow maxbadheaders=5000 badheaders=badHeaders_protozoa.txt 
time wget -q -O - ftp://ftp.ncbi.nlm.nih.gov/refseq/release/mitochondrion/*.genomic.fna.gz | gi2taxid.sh -Xmx1g in=stdin.fna.gz out=refseq.mitochondrion.fna pigz=2 unpigz=t zl=2 tree=null table=null accession=null server ow maxbadheaders=5000 badheaders=badHeaders_mitochondrion.txt

time wget -q -O - ftp://ftp.ncbi.nlm.nih.gov/refseq/release/vertebrate_mammalian/*.genomic.fna.gz | gi2taxid.sh -Xmx1g in=stdin.fna.gz out=refseq.vertebrate_mammalian.fna pigz=2 unpigz=t zl=2 tree=null table=null accession=null server ow maxbadheaders=5000 badheaders=badHeaders_vertebrate_mammalian.txt 
time wget -q -O - ftp://ftp.ncbi.nlm.nih.gov/refseq/release/vertebrate_other/*.genomic.fna.gz | gi2taxid.sh -Xmx1g in=stdin.fna.gz out=refseq.vertebrate_other.fna pigz=2 unpigz=t zl=2 tree=null table=null accession=null server ow maxbadheaders=5000 badheaders=badHeaders_vertebrate_other.txt 
time wget -q -O - ftp://ftp.ncbi.nlm.nih.gov/refseq/release/archaea/*.genomic.fna.gz | gi2taxid.sh -Xmx1g in=stdin.fna.gz out=refseq.archaea.fna pigz=2 unpigz=t zl=2 tree=null table=null accession=null server ow maxbadheaders=5000 badheaders=badHeaders_archaea.txt 

time wget -q -O - ftp://ftp.ncbi.nlm.nih.gov/refseq/release/bacteria/*.genomic.fna.gz | gi2taxid.sh -Xmx1g in=stdin.fna.gz out=refseq.bacteria.fna pigz=2 unpigz=t zl=2 tree=null table=null accession=null server ow maxbadheaders=5000 badheaders=badHeaders_bacteria.txt 
time wget -q -O - ftp://ftp.ncbi.nlm.nih.gov/refseq/release/fungi/*.genomic.fna.gz | gi2taxid.sh -Xmx1g in=stdin.fna.gz out=refseq.fungi.fna pigz=2 unpigz=t zl=2 tree=null table=null accession=null server ow maxbadheaders=5000 badheaders=badHeaders_fungi.txt 
time wget -q -O - ftp://ftp.ncbi.nlm.nih.gov/refseq/release/viral/*.genomic.fna.gz | gi2taxid.sh -Xmx1g in=stdin.fna.gz out=refseq.viral.fna pigz=2 unpigz=t zl=2 tree=null table=null accession=null server ow maxbadheaders=5000 badheaders=badHeaders_viral.txt 

time wget -q -O - ftp://ftp.ncbi.nih.gov/blast/db/FASTA/nt.gz | gi2taxid.sh -Xmx1g in=stdin.fna.gz out=nt.fna pigz=2 unpigz=t zl=2 tree=null table=null accession=null server ow maxbadheaders=5000 badheaders=badHeaders_nt.txt 
time wget -q -O - ftp://ftp.ncbi.nih.gov/blast/db/FASTA/nr.gz | gi2taxid.sh -Xmx1g in=stdin.faa.gz out=nr.faa pigz=2 unpigz=t zl=2 tree=null table=null accession=null server ow maxbadheaders=30000 badheaders=badHeaders_nr.txt

touch done
