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BDI-pathogens / phyloscanner

Phylogenetics between and within hosts at once, all along the genome.
GNU General Public License v3.0
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Problem with phyloscanner_analyse_trees.R #39

Closed SteveKemp closed 5 years ago

SteveKemp commented 5 years ago

Hi guys,

When running the second part of the analysis i.e. using phyloscanner_analyse_trees.R, following the online practical, when I run:

~/phyloscanner/phyloscanner_analyse_trees.R RAxMLfiles/RAxMLbestTree.InWindow \ RunWithoutBlacklisting s,20 --outgroupName C.BW.00.00BW07621.AF443088 \ --multifurcationThreshold g

I'm getting the following error:

Stevens-MacBook-Pro:MyTestDir steve$ ~/phyloscanner/phyloscanner_analyse_trees.R RAxMLfiles/RAxMLbestTree.InWindow RunWithoutBlacklisting s,20 --outgroupName C.BW.00.00BW07621.AF443088 --multifurcationThreshold g Random number seed is 566921380 Warning in initialise.phyloscanner(tree.file.directory, tree.file.regex, : Attempting to guess a branch length threshold for multifurcations from the tree. Please visually examine the tree or trees for multifurcations before using the results of this analysis. Warning in FUN(X[[i]], ...) : For tree ID 1000_to_1299 no non-blacklisted tips remain; this window will be removed from the analysis. Warning in FUN(X[[i]], ...) : For tree ID 2000_to_2299 no non-blacklisted tips remain; this window will be removed from the analysis. Warning in FUN(X[[i]], ...) : For tree ID 3000_to_3299 no non-blacklisted tips remain; this window will be removed from the analysis. Warning in FUN(X[[i]], ...) : For tree ID 4000_to_4299 no non-blacklisted tips remain; this window will be removed from the analysis. Warning in FUN(X[[i]], ...) : For tree ID 5000_to_5299 no non-blacklisted tips remain; this window will be removed from the analysis. Warning in FUN(X[[i]], ...) : For tree ID 6000_to_6299 no non-blacklisted tips remain; this window will be removed from the analysis. Warning in FUN(X[[i]], ...) : For tree ID 7000_to_7299 no non-blacklisted tips remain; this window will be removed from the analysis. Warning in FUN(X[[i]], ...) : For tree ID 8000_to_8299 no non-blacklisted tips remain; this window will be removed from the analysis. Error in phyloscanner.analyse.trees(tree.directory, tree.file.regex, reconstruction.mode, : All hosts have been blacklisted from all trees; nothing to do. Execution halted

Any ideas on what's happening there? Thanks, Steve

mdhall272 commented 5 years ago

Hi Steve,

Is this on your data, or on the sample data? My guess (if it's not the latter in which case it's clearly a bug and I should look ASAP) is that nothing in the tips actually matches the regex.

Matthew

SteveKemp commented 5 years ago

Hi Matthew,

This is on the included example/sample data, yes. I’ve made trees for my own data separately, but never tried the phyloscanner_analyse_trees.R myself, so I followed the online practical step-by-step to get used to it ☹

Thanks, Steve

From: Matthew Hall notifications@github.com Reply-To: BDI-pathogens/phyloscanner reply@reply.github.com Date: Friday, 8 February 2019 at 15:26 To: BDI-pathogens/phyloscanner phyloscanner@noreply.github.com Cc: Steve steven-kemp@live.co.uk, Author author@noreply.github.com Subject: Re: [BDI-pathogens/phyloscanner] Problem with phyloscanner_analyse_trees.R (#39)

Hi Steve,

Is this on your data, or on the sample data? My guess (if it's not the latter in which case it's clearly a bug and I should look ASAP) is that nothing in the tips actually matches the regex.

Matthew

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mdhall272 commented 5 years ago

Ah, there was a file from the development branch that I really shouldn't have brought over in its entirety. Try pulling now?

SteveKemp commented 5 years ago

Hi Matthew,

Sorry I got distracted, I pulled from git and follow the instructions here: https://github.com/BDI-pathogens/phyloscanner/blob/master/InfoAndInputs/UpdatingPhyloscanner.sh

But when I run the install(“.”, dependencies = T), nothing happens. Is this the error – it’s not set up correctly on my mac?

Thanks, Steve

From: Matthew Hall notifications@github.com Reply-To: BDI-pathogens/phyloscanner reply@reply.github.com Date: Friday, 8 February 2019 at 16:00 To: BDI-pathogens/phyloscanner phyloscanner@noreply.github.com Cc: Steve steven-kemp@live.co.uk, Author author@noreply.github.com Subject: Re: [BDI-pathogens/phyloscanner] Problem with phyloscanner_analyse_trees.R (#39)

Ah, there was a file from the development branch that I really shouldn't have brought over in its entirety. Try pulling now?

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mdhall272 commented 5 years ago

Did literally nothing happen? No error messages or anything?

You could also try install_github("BDI-pathogens/phyloscanner/phyloscannerR")

SteveKemp commented 5 years ago

Yep, literally just hangs, no error.

I tried install_github("BDI-pathogens/phyloscanner/phyloscannerR") and similarly, just hanging. I could let you take a look via Zoom is you have time a little later? I feel like I’m just missing something really simple, but frustrating!

Thanks, Steve

From: Matthew Hall notifications@github.com Reply-To: BDI-pathogens/phyloscanner reply@reply.github.com Date: Thursday, 14 February 2019 at 11:00 To: BDI-pathogens/phyloscanner phyloscanner@noreply.github.com Cc: Steve steven-kemp@live.co.uk, Author author@noreply.github.com Subject: Re: [BDI-pathogens/phyloscanner] Problem with phyloscanner_analyse_trees.R (#39)

Did literally nothing happen? No error messages or anything?

You could also try install_github("BDI-pathogens/phyloscanner/phyloscannerR")

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mdhall272 commented 5 years ago

That's weird and it works fine for me. What version of R are you using? I'm happy to try Zoom if you show me how...

SteveKemp commented 5 years ago

Really strange!

I fixed the other error however, my mac had a corrupted gfortran install (don’t even know how!?), so the binaries weren’t compiling in R. That’s all fixed now however!

However, it doesn’t seem to have changed my issue with tip blacklisting. I’ll give this a go with some of my own data tomorrow and see what happens too! See attached .txt file?

Thanks, Steve

From: Matthew Hall notifications@github.com Reply-To: BDI-pathogens/phyloscanner reply@reply.github.com Date: Thursday, 14 February 2019 at 12:22 To: BDI-pathogens/phyloscanner phyloscanner@noreply.github.com Cc: Steve steven-kemp@live.co.uk, Author author@noreply.github.com Subject: Re: [BDI-pathogens/phyloscanner] Problem with phyloscanner_analyse_trees.R (#39)

That's weird and it works fine for me. What version of R are you using? I'm happy to try Zoom if you show me how...

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/BDI-pathogens/phyloscanner/issues/39#issuecomment-463574015, or mute the threadhttps://github.com/notifications/unsubscribe-auth/As9nKjNAEacjMFmnTcO8v1ehZvBC80pKks5vNTjngaJpZM4avRD0.

Last login: Thu Feb 14 11:12:29 on ttys000 Stevens-MacBook-Pro:~ steve$ diff RunWithoutBlacklisting_hostRelationshipSummary.csv RunWithBlacklisting_hostRelationshipSummary.csv diff: RunWithoutBlacklisting_hostRelationshipSummary.csv: No such file or directory diff: RunWithBlacklisting_hostRelationshipSummary.csv: No such file or directory Stevens-MacBook-Pro:~ steve$ cd MyTestDir/ Stevens-MacBook-Pro:MyTestDir steve$ diff RunWithoutBlacklisting_hostRelationshipSummary.csv RunWithBlacklisting_hostRelationshipSummary.csv diff: RunWithoutBlacklisting_hostRelationshipSummary.csv: No such file or directory diff: RunWithBlacklisting_hostRelationshipSummary.csv: No such file or directory Stevens-MacBook-Pro:MyTestDir steve$ ~/phyloscanner/phyloscanner_analyse_trees.R RAxMLfiles/RAxMLbestTree.InWindow RunWithoutBlacklisting s,20 --outgroupName C.BW.00.00BW07621.AF443088 --multifurcationThreshold g Random number seed is 493425755 Warning in initialise.phyloscanner(tree.file.directory, tree.file.regex, : Attempting to guess a branch length threshold for multifurcations from the tree. Please visually examine the tree or trees for multifurcations before using the results of this analysis. Warning in FUN(X[[i]], ...) : For tree ID 1000_to_1299 no non-blacklisted tips remain; this window will be removed from the analysis. Warning in FUN(X[[i]], ...) : For tree ID 2000_to_2299 no non-blacklisted tips remain; this window will be removed from the analysis. Warning in FUN(X[[i]], ...) : For tree ID 3000_to_3299 no non-blacklisted tips remain; this window will be removed from the analysis. Warning in FUN(X[[i]], ...) : For tree ID 4000_to_4299 no non-blacklisted tips remain; this window will be removed from the analysis. Warning in FUN(X[[i]], ...) : For tree ID 5000_to_5299 no non-blacklisted tips remain; this window will be removed from the analysis. Warning in FUN(X[[i]], ...) : For tree ID 6000_to_6299 no non-blacklisted tips remain; this window will be removed from the analysis. Warning in FUN(X[[i]], ...) : For tree ID 7000_to_7299 no non-blacklisted tips remain; this window will be removed from the analysis. Warning in FUN(X[[i]], ...) : For tree ID 8000_to_8299 no non-blacklisted tips remain; this window will be removed from the analysis. Error in phyloscanner.analyse.trees(tree.directory, tree.file.regex, reconstruction.mode, : All hosts have been blacklisted from all trees; nothing to do. Execution halted Stevens-MacBook-Pro:MyTestDir steve$

mdhall272 commented 5 years ago

That really seems like you aren't using the most up-to-date version. That bug is definitely fixed.

SteveKemp commented 5 years ago

V1.6.9?

From: Matthew Hall notifications@github.com Reply-To: BDI-pathogens/phyloscanner reply@reply.github.com Date: Thursday, 14 February 2019 at 12:29 To: BDI-pathogens/phyloscanner phyloscanner@noreply.github.com Cc: Steve steven-kemp@live.co.uk, Author author@noreply.github.com Subject: Re: [BDI-pathogens/phyloscanner] Problem with phyloscanner_analyse_trees.R (#39)

That really seems like you aren't using the most up-to-date version. That bug is definitely fixed.

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mdhall272 commented 5 years ago

I haven't actually put that fix in a numbered release, but if you download the current version it should be in (see https://github.com/BDI-pathogens/phyloscanner/commit/0527a4d3ff615d3f4d9bf1870911b6dcf26e928b)

SteveKemp commented 5 years ago

It was me being silly - I hadn't installed phyloscannerR after pulling from git (doh!)