Method Of Getting Progress Of A Blast Run

Question

[Cacau]

Are there any parameters in blastall that'll make the program inform the user of the current progress of the blast run?

[Damian Kao]

I reworded the question. I think it's valid question. I don't think there are built-in methods for blast to tell the user how far the blast process has gone. Not all blast programs stream their results into the output file also, so it's not very effective to check the output file for indication of progress. I would be interested if others have some way of telling blast progress.

[Michael]

Thank you for this effort. I hope this is the intended question of the op, but at least we have a valid question now.

[Daniel]

I agree that this is valid (although I see Damian's rewrite helped).

If you're new to command line blast, and you just see a blank space it can be disconcerting whether anything is happening. Whilst to my knowledge there is no built-in option, the questioner could clearly benefit from people explaining how to know whether their job is running and it's progress through other means.

I vote to reopen the question.

[Michael]

What? This is unfortunately unintelligible, at least to me, please improve the question.

Answer 1

[Neilfws]

First, blastall has been superseded by BLAST+ so consider using that instead.

Second, complete parameters for blastall are easy to find: see here, here or from the command line:

blastall - | less

There is no command-line parameter to report progress.

[Cacau]

Thanks a lot!!!!