I have a query related to the Standalone BLAST . I am running a BLASTp of thousands of proteins with the NR database. Obviously it will take a lot of time. But many times due to the abrupt ending of process, the process is finished in midway.
Is there some option in BLAST or some other add-on that can start the process from the last point itself instead of initializing from the first protein? I have checked on Google but I've got nothing in this regard.
Hey Gnanavel,
I am also using the same approach. This removing option is the same that I m following till now. But I have to go and remove the names and when the matter is for many files it is problematic. So I was just thinking if there is some direct option which can automatically start the job from the last point becoz the command will be the same in both run.
The "easiest" thing to do would be to write a script that reads a list of files of sequences, then editing the list to delete out the ones that are finished.
The better question is: Why is your process stopping? Is it crashing? Are you not able to keep the computer running long enough for some reason? You might also speed up significantly if you don't actually need to run against all of NR. ie maybe at the end of the day you're really just interested in mammalian hits, or microbial hits? Are you able to use more than one processor? (ie change num_threads setting in standalone blast). Even cheap computers nowadays have more than one core.
Hello Daniel,
Thanks for the reply. U might be well aware of maker pipeline.. if it get stopped due to some reasons, it start again from the last point. I was interested in that kind of option. Although I am using high class servers, so processors or any other machine based things are out of concern.
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