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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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Error: length(lims) == 2 is not TRUE #13

Closed antoine4ucsd closed 7 years ago

antoine4ucsd commented 7 years ago

Hi I am new in phyloscanner and I have been using it for multiple individuals and sliding windows of 200bp from Illumina. I still need a lot of work to optimize the use of it but I was able to generate my first tree with phyloscanner_make_trees.py I ran the following command: ../phyloscanner_make_trees.py InputFileList.csv --x-raxml '/Users/antoinechaillon/anaconda2/pkgs/raxml-8.2.10-0/bin/raxmlHPC-AVX2 -m GTRCAT -p 1 --no-seq-check' --windows 2200,2350,2500,2650,2800,2950,3100,3250,3400,3550 -A ../InfoAndInputs/3refs_HXB2.fasta --pairwise-align-to B.FR.83.HXB2_LAI_IIIB_BRU_K03455

and it created 4 'best tree' output

screen shot 2017-07-30 at 8 53 13 am

I would like now to test the next step and analyze with phyloscanner_analyse_trees.R but when I run the command below: ../phyloscanner_analyse_trees.R RAxMLfiles/RAxML_bestTree. MyOutput s,0 -og B.FR.83.HXB2_LAI_IIIB_BRU_K03455 -m g I have the following: Warning: package ‘ggtree’ was built under R version 3.3.3 | | 0% Error: length(lims) == 2 is not TRUE Execution halted

Any clue about it? thanks and sorry for the 'basic' questions and possible lack of clarity. Let me know if you need more info and/or if you'd like me to share some data.

mdhall272 commented 7 years ago

Hi Antoine,

See issue #12 - I haven't been able to isolate this yet. A workaround is to use the -tn flag to produce Nexus rather than PDF trees.

What version of R, and OS, are you using? This is definitely a ggtree problem, so try to reinstall it to get rid of that "Warning: package ‘ggtree’ was built under R version 3.3.3" message.

Thanks, Matthew

antoine4ucsd commented 7 years ago

I really appreciate the fast response! I am using R v 3.3.2 on Mac OS I'm really excited about your tool, so I really want to get it working!

mdhall272 commented 7 years ago

If you're able to, try upgrading to 3.4.1 and updating all the packages. With everything up-to-date I don't get this problem. I'll see if I can reinstall an old version and track it down next week. In the meantime, -tn sidesteps it entirely.

mdhall272 commented 7 years ago

Closed as duplicate.

antoine4ucsd commented 7 years ago

Sure thanks again! I wish I will nice data to discuss with you soon

On Jul 30, 2017, at 11:17 AM, Matthew Hall <notifications@github.com mailto:notifications@github.com> wrote:

If you're able to, try upgrading to 3.4.1 and updating all the packages. With everything up-to-date I don't get this problem. I'll see if I can reinstall an old version and track it down next week. In the meantime, try -tn.

— You are receiving this because you modified the open/close state. Reply to this email directly, view it on GitHub https://github.com/BDI-pathogens/phyloscanner/issues/13#issuecomment-318888992, or mute the thread https://github.com/notifications/unsubscribe-auth/ARpT59fflX3WV14V_jrY_hJ3mI7WjeWYks5sTEoRgaJpZM4Onjq9.