Closed manuss11 closed 4 years ago
Thanks for your interest in ISEScan.
Two questions before we go to the next step to solve your issue.
Thanks, Xie
I am trying to answer your questions based on a few assumptions:
python3 /home/qiime2/ISEScan-1.7/isescan.py genome1.fa proteome hmm
where genome1.fa is your genome sequence file in fasta format. By default, ISEScan will use two CPU cores but you can change 'nproc = 2' (at the bottom of constants.py) to 'nproc = 1' or 'nproc = 4' or greater numbers in constants.py
file.nproc
(nproc could be 2 or 4 or 6 or 8 or ....) CPU cores.Now, let's run 200 genomes in one line of command and then wait for all computing jobs to complete (probably several days or weeks, depending on how many hours are required for each of your 200 genomes in average). If your computer has 8 CPU cores and You can execute the command below:
nohup cat test.fna.list | xargs -n 1 -P 4 -I{} python3 /home/qiime2/ISEScan-1.7/isescan.py {} proteome hmm > log.txt &
In the command line,
/N/dc2/scratch/zhiqxie/hmp/HMASM/SRS014235.scaffolds.fa /N/dc2/scratch/zhiqxie/hmp/HMASM/SRS049959.scaffolds.fa /N/dc2/scratch/zhiqxie/hmp/HMASM/SRS020233.scaffolds.fa /N/dc2/scratch/zhiqxie/hmp/HMASM/SRS022609.scaffolds.fa /N/dc2/scratch/zhiqxie/hmp/HMASM/SRS024132.scaffolds.fa
log.txt
.top -c -u qiime2
(assuming your user name is qiime2
). It might take several days or weeks for 200 genomes to complete. It depends on how many CPU cores you have on your computer and how fast each CPU core is. Please do not load too many ISEScan jobs because each ISEScan job will consume part of your RAM on your computer. However, you can always test and estimate how many GB RAM and how many hours are required for a genome.
Hope it helps.
Xie
Thanks a lot Xie, that is just what I needed. Each genome is in a multi-fasta file, and I'm using a computer with 8 cores and 32gb RAM. My priority was to run all genomes using just one script. Parallel working was not my goal itself, but it's good to know. Many thanks!
Hi, I'm using ISEScan, but I'm newby in linux and I don't know how to run a set of 200 genomes in fasta format in one single script. I tried:
python3 /home/qiime2/ISEScan-1.7/isescan.py *.fa proteome hmm
But it doesn't seem correct,
Many thanks