Here is my script for running DIAMOND on a server, please see DIAMOND help for more details:
if [ $# != “2” ]
echo “Usage: run-diamond.sh infile outfile”
echo “time ~/software/diamond blastx -b 20 -t /dev/shm --db /abprojects/daniel/nr/nr-Jan2017/nr --out $2 --outfmt 100 --query $1”
time ~/software/diamond blastx -b 20 -t /dev/shm --db /abprojects/daniel/nr/nr-Jan2017/nr --out $2 --outfmt 100 --query $1
Here is my script for running DAA-MEGANIZER for shoer reads on a server, please see daa-meganizer -h for more details:
if [ $# != 1 ]
echo “Usage: meganize daa-file"
options="-v -fun EGGNOG KEGG INTERPRO2GO SEED --parseTaxonNames false"
~/software/megan6ue/tools/daa-meganizer $input $options $tax $kegg $eggnog $interpro $seed
This may seem crazy simple, but is there a way to simply have the bash script then save/export the meganized summary files (ideally) into a new sub-directory, without having to call JavaApplicationStub?
I would love to iterate through 40 samples with daa-meganizer, then save the megan summary files for export to my computer/hard drive…
Once you have a meganized-DAA file, then you can run the daa-info tool to extract a MEGAN summary file.
Or you can use the compute-comparison tool to compute a comparison file for multiple meganized-DAA files.
Thanks for the reply Daniel. I eventually did it the old fashioned way… clicking through lots of files and exporting megan summaries.
That said, I had written a little bash script to meganize 40+ .daa files on a compute cluster. Had I known about daa-info and compute-comparison, would this work as well? Replacing e.g. daa-meganizer with daa-info.
if ls $INPUT_DIR/.daa &>/dev/null; then
for file in $INPUT_DIR/.daa
megan_app/tools/daa-meganizer -i $file -mdb megan/databases/megan-map-Feb2022-ue.db -t $threads
You always have to first run daa-meganizer because that program computes the classifications of the reads. Only then can you use daa2info to extract summaries or compute-comparison to compute a comparison of samples.