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bbuchfink / diamond

Accelerated BLAST compatible local sequence aligner.
GNU General Public License v3.0
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Status/progress bar? #221

Open cjfields opened 6 years ago

cjfields commented 6 years ago

More a feature request, if it's possible. We're testing a few optimizations for running DIAMOND on our local HPC, and one item that would really help is generating an optional status/progress. I noticed that in the normal standard output there are a few 'Sequences = ' blocks, but it's not clear how this correlates to the number of input sequences. block size, database, etc.

bbuchfink commented 6 years ago

That would certainly be a useful feature and I'll put it on my todo list. It is however not that simple to estimate the total progress.

If you use the --log option there is a heartbeat message every second during the alignment computation that gives the number of processed queries.

The number of reference blocks is the total reference letters / blocks size (2 GB by default). The number of query blocks is calculated the same way. So for each query and reference block there will be n shapes (2 is default mode, 16 in sensitive mode) x c index chunks (what you set as -c, 4 by default).