02c_annotation with run_dbcan - esogin/seagrassOmics GitHub Wiki
02c_annotation with run_dbcan
Created: July 16 2019
Updated: July 16 2019
Re-run dbcan on all bins so we have comparable results for all bins detected (even low quality ones). Filter out the low quality bins afterwards.
1. Call prodigal on all bins
bins=$(echo ls *fa)
for i in $bins;
do
# run prodigial
prodigal -i bins/$i -o genes/${i%%.fa}_genes.fa -a proteins/${i%%.fa}_proteins.faa;
done
Copy proteins over to run_dbcan directory
2. Implement run_dbcan on all protein calls.
bins=$(echo *.faa)
for i in $bins; do
python run_dbcan.py $i protein --out_dir ${i%%.faa}_output --dia_cpu 24 --hmm_cpu 24 --hotpep_cpu 24;
done