Commit 07e58c4c authored by npappas's avatar npappas

centrifuge build job

parent f68cd9c0
#!/bin/bash
#$ -q all.q
#$ -N cntf_index
#$ -l h_vmem=100G
#$ -cwd
#$ -j Y
#$ -V
#$ -pe BWA 16
echo Start time : `date`
PROJECT_DIR=/exports/sascstudent/project-RefseqRelease
FILTERED_DIR=$PROJECT_DIR/analysis/complete90/library_filtered
source activate /exports/sasc/nikos/src/biowdl/pipeline-template/conda_envs/centrifuge
centrifuge-build \
--bmax 1000000000 --dcv 2048 \
-p 16 --conversion-table $PROJECT_DIR/data/taxonomy/seqid2taxid.map \
--taxonomy-tree $PROJECT_DIR/data/taxonomy/nodes.dmp \
--name-table $PROJECT_DIR/data/taxonomy/nodes.dmp \
$FILTERED_DIR/archaea/archaea.fna,\
$FILTERED_DIR/bacteria/bacteria.fna,\
$FILTERED_DIR/viral/viral.fna,\
$FILTERED_DIR/plant/plant.fna,\
$FILTERED_DIR/protozoa/protozoa.fna,\
$FILTERED_DIR/fungi/fungi.fna,\
$FILTERED_DIR/invertebrate/invertebrate.fna,\
$FILTERED_DIR/vertebrate_mammalian/vertebrate_mammalian.fna,\
$FILTERED_DIR/vertebrate_other/vertebrate_other.fna,\
$PROJECT_DIR/analysis/complete90/centrifuge_index/refseq_v90 > centrifuge_build.log
echo End time : `date`
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