Issue running analyse trees

[KELEONUCSF]

Hi All,

I'm having a problem running the analyse_trees part of phyloscanner. The make_trees script worked fine, but now I keep receiving this message:

Error: length(lims) == 2 is not TRUE Execution halted

when I try to execute the phyloscanner_analyse_trees.r script. Any help would be greatly appreciated!

[mdhall272]

Hi,

Could you let me know which command line options you used to run it, and also re-run it with --verbose and attach the screen output?

Thanks, Matthew

[KELEONUCSF]

Hi Matthew,

I really appreciate the fast response! I'm really excited about your tool, so I really want to get it working!

My command line:

/Users/kristofferleon/Documents/Apps_Files/phyloscanner-master/phyloscanner_analyse_trees.R /Users/kristofferleon/Documents/UCSF/Wilson_Lab/Catalonia/SAM_files/RAxMLfiles/RAxML_bestTree. Catalonia_CSF_Phyloscanner s,0 --outgroupName Enterovirus.CATALONIA_14L_S14_Assembly_Contig_Assembly_consensus_sequence_extraction --multifurcationThreshold g

Reading tree file /Users/kristofferleon/Documents/UCSF/Wilson_Lab/Catalonia/SAM_files/RAxMLfiles/RAxML_bestTree.InWindow_1_to_112.tree

Reading tree file /Users/kristofferleon/Documents/UCSF/Wilson_Lab/Catalonia/SAM_files/RAxMLfiles/RAxML_bestTree.InWindow_1008_to_1116.tree

Reading tree file /Users/kristofferleon/Documents/UCSF/Wilson_Lab/Catalonia/SAM_files/RAxMLfiles/RAxML_bestTree.InWindow_1116_to_1231.tree

Reading tree file /Users/kristofferleon/Documents/UCSF/Wilson_Lab/Catalonia/SAM_files/RAxMLfiles/RAxML_bestTree.InWindow_112_to_228.tree

Reading tree file /Users/kristofferleon/Documents/UCSF/Wilson_Lab/Catalonia/SAM_files/RAxMLfiles/RAxML_bestTree.InWindow_1231_to_1352.tree

Reading tree file /Users/kristofferleon/Documents/UCSF/Wilson_Lab/Catalonia/SAM_files/RAxMLfiles/RAxML_bestTree.InWindow_1352_to_1472.tree

Reading tree file /Users/kristofferleon/Documents/UCSF/Wilson_Lab/Catalonia/SAM_files/RAxMLfiles/RAxML_bestTree.InWindow_1472_to_1588.tree

Reading tree file /Users/kristofferleon/Documents/UCSF/Wilson_Lab/Catalonia/SAM_files/RAxMLfiles/RAxML_bestTree.InWindow_1588_to_1714.tree

Reading tree file /Users/kristofferleon/Documents/UCSF/Wilson_Lab/Catalonia/SAM_files/RAxMLfiles/RAxML_bestTree.InWindow_1714_to_1853.tree

Reading tree file /Users/kristofferleon/Documents/UCSF/Wilson_Lab/Catalonia/SAM_files/RAxMLfiles/RAxML_bestTree.InWindow_1853_to_1960.tree

Reading tree file /Users/kristofferleon/Documents/UCSF/Wilson_Lab/Catalonia/SAM_files/RAxMLfiles/RAxML_bestTree.InWindow_1960_to_2069.tree

Reading tree file /Users/kristofferleon/Documents/UCSF/Wilson_Lab/Catalonia/SAM_files/RAxMLfiles/RAxML_bestTree.InWindow_2069_to_2172.tree

Reading tree file /Users/kristofferleon/Documents/UCSF/Wilson_Lab/Catalonia/SAM_files/RAxMLfiles/RAxML_bestTree.InWindow_2172_to_2274.tree

Reading tree file /Users/kristofferleon/Documents/UCSF/Wilson_Lab/Catalonia/SAM_files/RAxMLfiles/RAxML_bestTree.InWindow_2274_to_2377.tree

Reading tree file /Users/kristofferleon/Documents/UCSF/Wilson_Lab/Catalonia/SAM_files/RAxMLfiles/RAxML_bestTree.InWindow_228_to_332.tree

Reading tree file /Users/kristofferleon/Documents/UCSF/Wilson_Lab/Catalonia/SAM_files/RAxMLfiles/RAxML_bestTree.InWindow_2377_to_2483.tree

Reading tree file /Users/kristofferleon/Documents/UCSF/Wilson_Lab/Catalonia/SAM_files/RAxMLfiles/RAxML_bestTree.InWindow_2483_to_2591.tree

Reading tree file /Users/kristofferleon/Documents/UCSF/Wilson_Lab/Catalonia/SAM_files/RAxMLfiles/RAxML_bestTree.InWindow_2591_to_2709.tree

Reading tree file /Users/kristofferleon/Documents/UCSF/Wilson_Lab/Catalonia/SAM_files/RAxMLfiles/RAxML_bestTree.InWindow_2709_to_2818.tree

Reading tree file /Users/kristofferleon/Documents/UCSF/Wilson_Lab/Catalonia/SAM_files/RAxMLfiles/RAxML_bestTree.InWindow_2818_to_2946.tree

Reading tree file /Users/kristofferleon/Documents/UCSF/Wilson_Lab/Catalonia/SAM_files/RAxMLfiles/RAxML_bestTree.InWindow_2946_to_3066.tree

Reading tree file /Users/kristofferleon/Documents/UCSF/Wilson_Lab/Catalonia/SAM_files/RAxMLfiles/RAxML_bestTree.InWindow_3066_to_3181.tree

Reading tree file /Users/kristofferleon/Documents/UCSF/Wilson_Lab/Catalonia/SAM_files/RAxMLfiles/RAxML_bestTree.InWindow_3181_to_3329.tree

Reading tree file /Users/kristofferleon/Documents/UCSF/Wilson_Lab/Catalonia/SAM_files/RAxMLfiles/RAxML_bestTree.InWindow_332_to_455.tree

Reading tree file /Users/kristofferleon/Documents/UCSF/Wilson_Lab/Catalonia/SAM_files/RAxMLfiles/RAxML_bestTree.InWindow_3329_to_3461.tree

Reading tree file /Users/kristofferleon/Documents/UCSF/Wilson_Lab/Catalonia/SAM_files/RAxMLfiles/RAxML_bestTree.InWindow_3461_to_3566.tree

Reading tree file /Users/kristofferleon/Documents/UCSF/Wilson_Lab/Catalonia/SAM_files/RAxMLfiles/RAxML_bestTree.InWindow_3566_to_3675.tree

Reading tree file /Users/kristofferleon/Documents/UCSF/Wilson_Lab/Catalonia/SAM_files/RAxMLfiles/RAxML_bestTree.InWindow_3675_to_3788.tree

Reading tree file /Users/kristofferleon/Documents/UCSF/Wilson_Lab/Catalonia/SAM_files/RAxMLfiles/RAxML_bestTree.InWindow_3788_to_3898.tree

Reading tree file /Users/kristofferleon/Documents/UCSF/Wilson_Lab/Catalonia/SAM_files/RAxMLfiles/RAxML_bestTree.InWindow_3898_to_4024.tree

Reading tree file /Users/kristofferleon/Documents/UCSF/Wilson_Lab/Catalonia/SAM_files/RAxMLfiles/RAxML_bestTree.InWindow_4024_to_4137.tree

Reading tree file /Users/kristofferleon/Documents/UCSF/Wilson_Lab/Catalonia/SAM_files/RAxMLfiles/RAxML_bestTree.InWindow_4137_to_4262.tree

Reading tree file /Users/kristofferleon/Documents/UCSF/Wilson_Lab/Catalonia/SAM_files/RAxMLfiles/RAxML_bestTree.InWindow_4262_to_4379.tree

Reading tree file /Users/kristofferleon/Documents/UCSF/Wilson_Lab/Catalonia/SAM_files/RAxMLfiles/RAxML_bestTree.InWindow_4379_to_4483.tree

Reading tree file /Users/kristofferleon/Documents/UCSF/Wilson_Lab/Catalonia/SAM_files/RAxMLfiles/RAxML_bestTree.InWindow_4483_to_4596.tree

Reading tree file /Users/kristofferleon/Documents/UCSF/Wilson_Lab/Catalonia/SAM_files/RAxMLfiles/RAxML_bestTree.InWindow_455_to_564.tree

Reading tree file /Users/kristofferleon/Documents/UCSF/Wilson_Lab/Catalonia/SAM_files/RAxMLfiles/RAxML_bestTree.InWindow_4596_to_4706.tree

Reading tree file /Users/kristofferleon/Documents/UCSF/Wilson_Lab/Catalonia/SAM_files/RAxMLfiles/RAxML_bestTree.InWindow_4706_to_4821.tree

Reading tree file /Users/kristofferleon/Documents/UCSF/Wilson_Lab/Catalonia/SAM_files/RAxMLfiles/RAxML_bestTree.InWindow_4821_to_4932.tree

Reading tree file /Users/kristofferleon/Documents/UCSF/Wilson_Lab/Catalonia/SAM_files/RAxMLfiles/RAxML_bestTree.InWindow_4932_to_5041.tree

Reading tree file /Users/kristofferleon/Documents/UCSF/Wilson_Lab/Catalonia/SAM_files/RAxMLfiles/RAxML_bestTree.InWindow_5041_to_5147.tree

Reading tree file /Users/kristofferleon/Documents/UCSF/Wilson_Lab/Catalonia/SAM_files/RAxMLfiles/RAxML_bestTree.InWindow_5147_to_5260.tree

Reading tree file /Users/kristofferleon/Documents/UCSF/Wilson_Lab/Catalonia/SAM_files/RAxMLfiles/RAxML_bestTree.InWindow_5260_to_5367.tree

Reading tree file /Users/kristofferleon/Documents/UCSF/Wilson_Lab/Catalonia/SAM_files/RAxMLfiles/RAxML_bestTree.InWindow_5367_to_5472.tree

Reading tree file /Users/kristofferleon/Documents/UCSF/Wilson_Lab/Catalonia/SAM_files/RAxMLfiles/RAxML_bestTree.InWindow_5472_to_5580.tree

Reading tree file /Users/kristofferleon/Documents/UCSF/Wilson_Lab/Catalonia/SAM_files/RAxMLfiles/RAxML_bestTree.InWindow_5580_to_5696.tree

Reading tree file /Users/kristofferleon/Documents/UCSF/Wilson_Lab/Catalonia/SAM_files/RAxMLfiles/RAxML_bestTree.InWindow_564_to_676.tree

Reading tree file /Users/kristofferleon/Documents/UCSF/Wilson_Lab/Catalonia/SAM_files/RAxMLfiles/RAxML_bestTree.InWindow_5696_to_5801.tree

Reading tree file /Users/kristofferleon/Documents/UCSF/Wilson_Lab/Catalonia/SAM_files/RAxMLfiles/RAxML_bestTree.InWindow_5801_to_5911.tree

Reading tree file /Users/kristofferleon/Documents/UCSF/Wilson_Lab/Catalonia/SAM_files/RAxMLfiles/RAxML_bestTree.InWindow_5911_to_6014.tree

Reading tree file /Users/kristofferleon/Documents/UCSF/Wilson_Lab/Catalonia/SAM_files/RAxMLfiles/RAxML_bestTree.InWindow_6014_to_6131.tree

Reading tree file /Users/kristofferleon/Documents/UCSF/Wilson_Lab/Catalonia/SAM_files/RAxMLfiles/RAxML_bestTree.InWindow_6131_to_6251.tree

Reading tree file /Users/kristofferleon/Documents/UCSF/Wilson_Lab/Catalonia/SAM_files/RAxMLfiles/RAxML_bestTree.InWindow_6251_to_6382.tree

Reading tree file /Users/kristofferleon/Documents/UCSF/Wilson_Lab/Catalonia/SAM_files/RAxMLfiles/RAxML_bestTree.InWindow_6382_to_6494.tree

Reading tree file /Users/kristofferleon/Documents/UCSF/Wilson_Lab/Catalonia/SAM_files/RAxMLfiles/RAxML_bestTree.InWindow_6494_to_6600.tree

Reading tree file /Users/kristofferleon/Documents/UCSF/Wilson_Lab/Catalonia/SAM_files/RAxMLfiles/RAxML_bestTree.InWindow_6600_to_6704.tree

Reading tree file /Users/kristofferleon/Documents/UCSF/Wilson_Lab/Catalonia/SAM_files/RAxMLfiles/RAxML_bestTree.InWindow_6704_to_6819.tree

Reading tree file /Users/kristofferleon/Documents/UCSF/Wilson_Lab/Catalonia/SAM_files/RAxMLfiles/RAxML_bestTree.InWindow_676_to_776.tree

Reading tree file /Users/kristofferleon/Documents/UCSF/Wilson_Lab/Catalonia/SAM_files/RAxMLfiles/RAxML_bestTree.InWindow_6819_to_6925.tree

Reading tree file /Users/kristofferleon/Documents/UCSF/Wilson_Lab/Catalonia/SAM_files/RAxMLfiles/RAxML_bestTree.InWindow_6925_to_7030.tree

Reading tree file /Users/kristofferleon/Documents/UCSF/Wilson_Lab/Catalonia/SAM_files/RAxMLfiles/RAxML_bestTree.InWindow_7030_to_7133.tree

Reading tree file /Users/kristofferleon/Documents/UCSF/Wilson_Lab/Catalonia/SAM_files/RAxMLfiles/RAxML_bestTree.InWindow_7133_to_7262.tree

Reading tree file /Users/kristofferleon/Documents/UCSF/Wilson_Lab/Catalonia/SAM_files/RAxMLfiles/RAxML_bestTree.InWindow_7262_to_7388.tree

Reading tree file /Users/kristofferleon/Documents/UCSF/Wilson_Lab/Catalonia/SAM_files/RAxMLfiles/RAxML_bestTree.InWindow_7388_to_7496.tree

Reading tree file /Users/kristofferleon/Documents/UCSF/Wilson_Lab/Catalonia/SAM_files/RAxMLfiles/RAxML_bestTree.InWindow_7496_to_7606.tree

Reading tree file /Users/kristofferleon/Documents/UCSF/Wilson_Lab/Catalonia/SAM_files/RAxMLfiles/RAxML_bestTree.InWindow_7606_to_7712.tree

Reading tree file /Users/kristofferleon/Documents/UCSF/Wilson_Lab/Catalonia/SAM_files/RAxMLfiles/RAxML_bestTree.InWindow_7712_to_7824.tree

Reading tree file /Users/kristofferleon/Documents/UCSF/Wilson_Lab/Catalonia/SAM_files/RAxMLfiles/RAxML_bestTree.InWindow_776_to_899.tree

Reading tree file /Users/kristofferleon/Documents/UCSF/Wilson_Lab/Catalonia/SAM_files/RAxMLfiles/RAxML_bestTree.InWindow_7824_to_7954.tree

Reading tree file /Users/kristofferleon/Documents/UCSF/Wilson_Lab/Catalonia/SAM_files/RAxMLfiles/RAxML_bestTree.InWindow_7954_to_8083.tree

Reading tree file /Users/kristofferleon/Documents/UCSF/Wilson_Lab/Catalonia/SAM_files/RAxMLfiles/RAxML_bestTree.InWindow_8083_to_8189.tree

Reading tree file /Users/kristofferleon/Documents/UCSF/Wilson_Lab/Catalonia/SAM_files/RAxMLfiles/RAxML_bestTree.InWindow_899_to_1008.tree

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Gathering host IDs...

Reconstructing internal node hosts on tree suffix InWindow_1_to_112

Getting tip read counts...

Identifying tips with host...

Finding list of hosts...

Finding tips for each host...

Finding MRCAs for each host...

Reconstructing internal node hosts with the Sankoff algorithm...

Calculating node costs...

Building full cost matrix...

|==================================================| 100%

Reconstructing...

Identifying split hosts...

Drawing PDF tree...

Error: length(lims) == 2 is not TRUE

Execution halted

Thanks,

Kristoffer

---

From: Matthew Hall notifications@github.com Sent: Thursday, July 27, 2017 11:20:21 AM To: BDI-pathogens/phyloscanner Cc: Leon, Kristoffer; Author Subject: Re: [BDI-pathogens/phyloscanner] Issue running analyse trees (#12)

Hi,

Could you let me know which command line options you used to run it, and also re-run it with --verbose and attach the screen output?

Thanks, Matthew

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/BDI-pathogens/phyloscanner/issues/12#issuecomment-318444913, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AdF8AKHDDnbERQoHJtLXvRVUkAxxvDjyks5sSNTlgaJpZM4Olmi1.

[mdhall272]

Hi Kristoffer,

No worries, we need to know about bugs!

I haven't worked out exactly what's wrong yet - as a workaround, try running with -tn to get Nexus rather than PDF trees, since it's the latter that is causing this.

What version of R are you using?

Thanks, Matthew

[KELEONUCSF]

Hi Matthew,

I'm currently using R version 3.4.0 (2017-04-21) -- "You Stupid Darkness".

Using -tn worked! Thanks a ton for your help!

Kristoffer

---

From: Matthew Hall notifications@github.com Sent: Thursday, July 27, 2017 2:02:42 PM To: BDI-pathogens/phyloscanner Cc: Leon, Kristoffer; Author Subject: Re: [BDI-pathogens/phyloscanner] Issue running analyse trees (#12)

Hi Kristoffer,

No worries, we need to know about bugs!

I haven't worked out exactly what's wrong yet - as a workaround, try running with -tn to get Nexus rather than PDF trees, since it's the latter that is causing this.

What version of R are you using?

Thanks, Matthew

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/BDI-pathogens/phyloscanner/issues/12#issuecomment-318485703, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AdF8AKURHvA_2uMmqhqXdHM55He6EZNgks5sSPrygaJpZM4Olmi1.

[mdhall272]

It would be good to know what went wrong - is the data sensitive, or could you send me a tree? (Just one tree should do, I think.)

[KELEONUCSF]

ProcessedTree_Catalonia_CSF_Phyloscanner_InWindow_1_to_112.txt

[KELEONUCSF]

The tree should be posted above!

[KELEONUCSF]

RAxML_bestTree.InWindow_1_to_112.txt

Realised that you might have the meant the tree used for input instead of the output. This should be the corresponding tree.

[mdhall272]

Strange. I can't replicate this at all on that tree, in 3.4.1 or 3.3.3. Is it possible you aren't using an up-to-date ggplot2 or ggtree?

[KELEONUCSF]

I'm currently using ggtree version 1.8.1.

I've also noticed an issue trying to import the .tree output files into Geneious saying there is a problem with duplicate tips. Is there a way around this?

---

From: Matthew Hall notifications@github.com Sent: Friday, July 28, 2017 2:18:17 AM To: BDI-pathogens/phyloscanner Cc: Leon, Kristoffer; Author Subject: Re: [BDI-pathogens/phyloscanner] Issue running analyse trees (#12)

Strange. I can't replicate this at all on that tree, in 3.4.1 or 3.3.3. Is it possible you aren't using an up-to-date ggtree?

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/BDI-pathogens/phyloscanner/issues/12#issuecomment-318603970, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AdF8APOlAldYhdvlBc5LXQZbKFDyrE9nks5sSadZgaJpZM4Olmi1.

[mdhall272]

I'm not sure why this would happen if the BAMs have different names - @ChrisHIV ?

Stranger and stranger on the original issue - which OS are you on?

[ChrisHIV]

Hi Kristoffer, the format of the input tree is Newick, and that of the output tree is Nexus. I see a similar sounding Geneious error if I incorrectly tell it the output tree is Newick, but it imports fine as Nexus. Over to @twoseventwo for the length(lims) issue...

[tgolubch]

Does the tree file open in Figtree instead of Geneious?

[mdhall272]

I'm still not able to replicate the length(lims) issue. Since it doesn't happen to me when everything is up-to-date, using trees which experienced it on other systems, I'm assuming it's due to some combination of older package and R versions. For anyone experiencing it: if you can, please update everything and try again.

The -tn solution will work but may not be ideal for everyone.

[KELEONUCSF]

Hey all,

Thanks for the help! I'm currently on OSX 10.12.5. I have everything updated as well, and I can't seem to figure out the issue, but I'll keep tweaking things to see if I can get it to work! I agree it's most likely a combination of either older packages or R versions that are interrupting normal functioning.

Thanks for the help! the -tn solution works just fine for me!

[mdhall272]

I have finally identified and fixed this. It was caused by use of ggplot2 2.2.1.9000 (the current GitHub development version) rather than 2.2.1 (the CRAN version). Either should work now.