how to use "testnew" commend?

[JChan]

I installed IQ-tree on my mac and use "bin/iqtree-omp -s example.phy -nt AUTO" to run the example file, it works. However, when I follow the manual instruction and type "iqtree -s example.phy -m TESTNEW"in my terminal, it says "-bash: iqtree: command not found". Does anyone know what's the problem here? Thanks.

[Stephen Crotty]

Hi,

I don’t think the problem is with the “TESTNEW” option. I notice that when you run the example you use "bin/iqtree-omp” and it works fine. When you try to use the TESTNEW option you only use “iqtree”. I think this is your issue, the error message suggests that iqtree is not a valid command. Try using “bin/iqtree-omp” if that worked for the example.

Hope this helps,

Stephen

On 4 Oct 2017, at 9:09 pm, JChan <idjoan...@gmail.com> wrote:

I installed IQ-tree on my mac and use "bin/iqtree-omp -s example.phy -nt AUTO" to run the example file, it works. However, when I follow the manual instruction and type "iqtree -s example.phy -m TESTNEW"in my terminal, it says "-bash: iqtree: command not found". Does anyone know what's the problem here? Thanks.

--
You received this message because you are subscribed to the Google Groups "IQ-TREE" group.
To unsubscribe from this group and stop receiving emails from it, send an email to iqtree+un...@googlegroups.com.
To post to this group, send email to iqt...@googlegroups.com.
Visit this group at https://groups.google.com/group/iqtree.
For more options, visit https://groups.google.com/d/optout.

[JChan]

Hello Stephen,

I changed it to "bin/iqtree-omp -s example.phy -m TESTNEW", it told me 

"ERROR: Checkpoint (example.phy.ckp.gz) indicates that a previous run successfully finished

Use `-redo` option if you really want to redo the analysis and overwrite all output files."

Is it because I already run the example.phy successfully? Does it mean if I run a file successfully, then I can't use TESTNEW to run this file again?

Thanks,

Joanna

[Stephen Crotty]

Hi Joanna,

This error occurs to make sure that you don’t accidentally overwrite the output from a previous run. If you do not care about the previous run and are happy to overwrite the output files then all you have to do is add “-redo” to your command. However if you want to keep the output for your old run and also do your new run you will need to use the “-pre” option. This gives you the opportunity to give your output files a name that is meaningful to you. So you could add “-pre exampleTESTNEW” and then all the output files would begin with “exampleTESTNEW”.

Cheers,

Stephen