I want to run blast that can run in linux as well as windows. However in windows it runs through commandline (cmd=msdos). I can define number of processors in parameters but still on windows it seems to bit slow. Is there any limit on MSDOS regarding maximum RAM or max processors used.
I want to run standalone blast with my downloaded copy of NCBInr database. I have 6 cores=12 logical processors and 50GB RAM (extendable to 256GB) in windows while I have 10 core=10 processors and 200 GB RAM in linux.
I have already running it in windows with a query size of 40000 sequences. It is running since a month and we still have only 15000 sequences in output file. We have defined blast with max hit of 1 and in tab format, so as to minimize the time. We still have no clue, how much time it might take.
Is there anyway to speed up the process or any form of blast where we can know the progress of the task. We dont have financial support and thus cloud blast is not an option for us.