Output Files Inquiry

[Evan Cribbie]

Dear Benoit,

I had a quick question with regards to the output. GeneRax was called as follow:

../../../TOOLS/GeneRax/build/bin/generax -f ../DATA/generax_made_muscle_family_file.txt -s ../DATA/species_tree.tree -p ../EXP/GENERAX/MUSCLE_PARALLEL/1 --per-family-rates --seed 321 --rec-model UndatedDL --strategy SPR

After GeneRax ran successfully with seemingly no errors, I checked the reconciliation folder and noticed that there were only files for 1653 different families whereas there are 5028 families GeneRax was run on and in the results folder there are files for all 5028 families.

The wiki I thought seemed to imply that there should be reconciliation files for all families. Is it the case that only families with gene duplications get reconciliation output? I was just hoping you might be able to clear this up for me.

Best,

Evan

[Benoit Morel]

Dear Evan,

Yes, there should be one output per family... Can you send me the log file?

Best,

Benoit

--
You received this message because you are subscribed to the Google Groups "GeneRax" group.
To unsubscribe from this group and stop receiving emails from it, send an email to generaxusers...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/generaxusers/882179a8-20be-4921-8571-c5ff23f55becn%40googlegroups.com.
For more options, visit https://groups.google.com/d/optout.

[Benoit Morel]

In fact, can you also send me the logs.txt files that are under the following folders (I am not sure about the exact names):

- raxml_light_0

- gene_optimization_1, gene_optimization_2, etc.

The only reason (assuming there is no bug :D) that I can see is that something went wrong for some of those families. For instance, if one family has strictly less than 4 sequences, it will be discarded from the analysis. But I think this should appear in the main logs file (generax.log)

[Evan Cribbie]

Dear Benoit,

As always thanks for the quick reply! I have attached a link to the log file below. There is an error about one invalid family, I am already aware of that and it is not an issue.

https://drive.google.com/file/d/1tyzSMXhaQdj9fPW7PMvMnQJBjN0h1s8Z/view?usp=sharing

Thanks again for the help.

Best,

Evan

[Evan Cribbie]

Dear Benoit,

I just noticed you sent a revised email in between my last. Please find below a folder with the requested files as well as a couple of other sample files since I already had them downloaded anyways.

https://drive.google.com/drive/folders/1tyOAOMsZoEpbEHVW5--YkxUuhHZmWBgq?usp=sharing

Best,

Evan

[Benoit Morel]

Thank you Evan. I still don't understand what could cause the issue. Do you think you could send me the whole output folder? And/or the input MSAs?

Also, can you give me the GeneRax version? You can get it by executing generax without any argument.

Best,

Benoit

[Evan Cribbie]

Dear Benoit,

Sorry for the late reply, I retried running my Generax script yesterday and for some reason, all of the files are now there. Not sure what had happened as I didn't change any of the script or inputs, but everything is now there.

As always thanks for all the help.

Best,

Evan

[Benoit Morel]

Dear Evan,

Nice! Let me know if you encounter the problem again.

Benoit

To view this discussion on the web visit https://groups.google.com/d/msgid/generaxusers/f19a2e06-8b2e-4e99-9aeb-8d229b9378dan%40googlegroups.com.