Error

[glaudelrio]

I got it running with genind2bcg, but once I try to run:

bcg.genes I got an error although I have the files in the indicated directory.

Any ideas on what is wrong?
Thank you very much!

[btmartin721]

Hi. it's hard to tell here, but for some reason it isn't finding the input files. Are you sure that you provided the correct path to the input directory?

Are you using Windows? If so, you might need the drive name, such as "C:", placed before "/Users". But it depends on your operating system and computer setup.

Could you try running this R command?

getwd()

just before combine_bgc_output() and show me what it prints out? And also could you try running:

dir()

in R and show me what it prints out? That will show the directories that are present in your current working directory.

[glaudelrio]

Hi! Thank you so much! I am working in the results directory just in case.

as you can see in the image, my files are in the results directory.
Thank you!

[btmartin721]

Ah ok I think I see the issue. It is not finding your LnL files because in your results directory they are labeled

ln1 and not lnl

So in other words, with a one and not an L.

This is actually a bug in ClineHelpR that I've been meaning to fix. In the meantime, could you try renaming eatt_stat_ln1_[replicate] to eatt_stat_lnl_[replicate]?

Let me know if this fixes the issue.

-Bradley

[btmartin721]

I fixed the file naming issue in the run_bgc.sh script. Now it correctly names the lnl file as lnl instead of ln1 when running estpost. But in your case you can just rename the lnl file instead of rerunning the whole script.

[glaudelrio]

Sounds good! Does it mean that I need to start a new container for the new function to run?
Thank you!

[glaudelrio]

Changing the ln1 to lnl alone did not fix the problem. Thank you so much for the help and sorry for the inconvenience.

[btmartin721]

Regarding the container, I will have to rebuild it in order to get run_bgc.sh to run, but I didn't change any of the R files so you shouldn't need a new container to get combine_bgc_output() to run.

Regarding the LnL file, I just realized that I made it to where it has to be capital L's like this:

prefix_LnL_[replicateNumber]

Could you try changing the L's to capital and let me know if it works?

Sorry for the confusion. I will change it to where it is not case sensitive anymore when I get home tonight.

-Bradley

[glaudelrio]

Hi Bradley, thank you so much! Changing it to capital letters solved the issue! Now the issue is in the run per se... my plot traces look like this:

any idea on what could be causing this?
Thank you so much!

[btmartin721]

Hi. I apologize for my delayed reply. Glad you were able to get it to load.

I am not 100% sure why the likelihoods are all 0. Do they appear to be equal to or close to 0 in the LnL file generated by BGC? Just trying to determine if this is a BGC or ClineHelpR issue.

Thanks,

-Bradley