Question: raxmlGUI spend time
gravatar for mauricio.morales
4 days ago by
mauricio.morales0 wrote:

Hello I'm doing my thesis in genome sequence analysis and I'm relatively new in bioinformatics. Anyone know how long an "ML + rapid bootstrap" scan with 100 replicates takes?

I have 723 protein sequences in the analysis, but the analysis never end! I understand that the time depends on the operating system. Has anyone experience with the delay it can take on Windows 10, interl core i7 8th Gen?

Any comments regarding how long the scan takes, regardless of the operating system, helps. Thank you!

sequence alignment genome • 58 views
ADD COMMENTlink modified 3 days ago • written 4 days ago by mauricio.morales0

I understand. I will review the parameters and follow your recommendations. Thank for the help!!!

ADD REPLYlink written 3 days ago by mauricio.morales0
gravatar for Mensur Dlakic
4 days ago by
Mensur Dlakic6.4k
Mensur Dlakic6.4k wrote:

It is difficult to predict the exact run time for RAxML, as it depends on many factors that you didn't disclose here. For example, 723 protein sequences is a not a huge alignment, but we don't know the alignment width. If you have 5000 aligned columns in your dataset, that will take longer than an alignment that is 150 columns wide. Next, how many threads are you using? The speed-up is not exactly linear, but more threads means less running time. I have no experience with how Windows handles RAxML, but anything running under a GUI could be less than optimal, especially if you are using computer for other purposes in parallel.

To give you a point of reference: under Linux, an alignment of ~2000 sequences that is ~3500 residues wide takes less than a day on 30 CPUs. To get an idea how far along the run is, count the number of lines in a file that begins with RAxML_bootstrap. as the run will be done when you have 100 lines (100 trees) in that file. On Linux, that would be as simple as:

wc -l RAxML_bootstrap.*
ADD COMMENTlink written 4 days ago by Mensur Dlakic6.4k
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