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tothuhien / lsd-0.3beta

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input tree - size limit? #9

Closed antoine4ucsd closed 5 years ago

antoine4ucsd commented 5 years ago

Hi I am trying to run LSD on a very large tree (35k) but I get an error message when loading the tree. I don't have such error with smaller trees. is it a size limit or something else? my tree is unrooted. Would you have time to take a quick look?

lsd
Enter your Input Tree File name> 
All_sequences.newick.txt
Errors in the input trees

I also tried with the following but get the same error :

lsd -i ./All_sequences.newick.txt -d ./All_sequences.dates4lsd.txt -o ./LSD.output -r a

a All_sequences.dates4lsd.txt

All_sequences.newick.txt

tothuhien commented 5 years ago

Hi @antoine4ucsd , I've tried to run your data on the current version but didn't get that error. It's indeed a very large tree and takes long time to run. But so far, the tree was read and the rooting function is running. Have you recently downloaded the current one on GitHub? Otherwise what's the configuration of computer that you're using? Cheers, Hien

antoine4ucsd commented 5 years ago

Thank you Hien Maybe This is related to the version of LSD I am using... I will try to update it! I will keep you posted (Currently working on a Mac.) Best, a

On Feb 28, 2019, at 4:32 AM, Thu-Hien To notifications@github.com wrote:

Hi @antoine4ucsd , I've tried to run your data on the current version but didn't get that error. It's indeed a very large tree and takes long time to run. But so far, the tree was read and the rooting function is running. Have you recently downloaded the current one on GitHub? Otherwise what's the configuration of computer that you're using? Cheers, Hien

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or mute the thread.

antoine4ucsd commented 5 years ago

do you have a pre-compiled version of LSD running on mac? I tried running make from within src but I am always having problem with c++/gcc 

$ make
g++ -std=c++11 -o confidence_interval.o -c confidence_interval.cpp 
In file included from ~/anaconda2/gcc/include/c++/random:38:0,
                 from confidence_interval.h:1,
                 from confidence_interval.cpp:17:
~/anaconda2/gcc/include/c++/cmath:41:28: fatal error: bits/c++config.h: No such file or directory
 #include <bits/c++config.h>
                            ^
compilation terminated.
make: *** [confidence_interval.o] Error 1
tothuhien commented 5 years ago

Hi you can try the one in the directory bin: bin/lsd_mac, it was compiled on my Mac High Sierra.

antoine4ucsd commented 5 years ago

it seems to work! thank you ++ a

On Feb 28, 2019, at 7:13 AM, Thu-Hien To <notifications@github.com mailto:notifications@github.com> wrote:

Hi you can try the one in the directory bin: bin/lsd_mac, it was compiled on my Mac High Sierra.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/tothuhien/lsd-0.3beta/issues/9#issuecomment-468309747, or mute the thread https://github.com/notifications/unsubscribe-auth/ARpT58EUb66HTRgTHxjXJJP1_NEhBBLnks5vR_ItgaJpZM4bVDJH.