Commit 2cb54e51 authored by Mosè's avatar Mosè Committed by Mosè

BUSCO v3.1.0 update

create folder for pplacer mmap-file, and delete it after pplacer run
parent fbf31b31
......@@ -285,8 +285,14 @@ done
# run hmmalign
hmmalign -o $WD/$folder/place_input.sto --mapali $WD/$clade/supermatrix.aln.faa $WD/$clade/refseqs.hmm $WD/$folder/marker_genes.fasta
# create a temp forlder for storing pplacer --mmap-file (Note: it can take up to ~18Gb! for placing a bacterial species)
mkdir $WD/$folder/mmap-file_tmp
# run pplacer
pplacer --out-dir $WD/$folder/ -t $WD/$clade/tree.nwk -s $WD/$clade/tree_metadata.txt $WD/$folder/place_input.sto
pplacer --out-dir $WD/$folder/ --mmap-file $WD/$folder/mmap-file_tmp --keep-at-most 3 --groups 20 -t $WD/$clade/tree.nwk -s $WD/$clade/tree_metadata.txt $WD/$folder/place_input.sto
# rm --mmap-file
rm -r $WD/$folder/mmap-file_tmp
# run guppy
guppy fat --out-dir $WD/$folder/ $WD/$folder/place_input.jplace
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