search

jujubix / simulfold

simultaneously inferring RNA structures including pseudoknots, alignments, and trees using a Bayesian MCMC framework
http://www.e-rna.org/simulfold/
Other
0 stars 1 forks source link

Seems to fail on example input. #3

Open drwatsoncode opened 6 years ago

drwatsoncode commented 6 years ago

I downloaded the git repository and compiled it with javac -O *.java (I'm using Oracle Java 1.8.0_144)

I then ran the following command: java SimulFold tRNA_low.in tRNA_low.dnd -S (where the files are directly from the manuscript data in simulfold.tar.bz2 from your website)

When I run the command, the output is as shown below. (I get the same output for any other input I've tried).

temperature: 1.0
Structure Sampling on temperature[0]: ACCEPTED
Structure Sampling on temperature[0]: ACCEPTED
Structure Sampling on temperature[0]: REJECTED
Structure Sampling on temperature[0]: REJECTED
Structure Sampling on temperature[0]: REJECTED
Structure Sampling on temperature[0]: REJECTED
Structure Sampling on temperature[0]: REJECTED
Structure Sampling on temperature[0]: REJECTED
Structure Sampling on temperature[0]: ACCEPTED
Structure Sampling on temperature[0]: REJECTED
Structure Sampling on temperature[0]: ACCEPTED
Structure Sampling on temperature[0]: REJECTED
Structure Sampling on temperature[0]: REJECTED
Structure Sampling on temperature[0]: REJECTED
Structure Sampling on temperature[0]: REJECTED
Structure Sampling on temperature[0]: REJECTED
Structure Sampling on temperature[0]: REJECTED
Structure Sampling on temperature[0]: REJECTED
Structure Sampling on temperature[0]: REJECTED
Structure Sampling on temperature[0]: REJECTED
Structure Sampling on temperature[0]: REJECTED
Structure Sampling on temperature[0]: REJECTED
Structure Sampling on temperature[0]: REJECTED
Structure Sampling on temperature[0]: ACCEPTED
Structure Sampling on temperature[0]: REJECTED
Structure Sampling on temperature[0]: REJECTED
... (continues like this until I kill it)

Am I running the command incorrectly? Is there an argument I should be passing to set the temperature? Is my java version (Java 8) not supported? I got the same results on Windows (Win10) and Linux (Ubuntu 16.04).

drwatsoncode commented 6 years ago

I switched to using the following command: java SimulFold tRNA_low.in tRNA_low.dnd -O simulfold -B 800 -N 400 -I 20 This allowed the program to complete and produce a file "output.txt". However the "Structure Sampling on temperature[0]: REJECTED" output still appeared. Is this normal output, or is that a sign of some problem? Note that no other files were produced (I was expecting perhaps simulfold.fasta, simulfold.db etc) In particular, I do not see any output that contains a base-pairing probability matrix that I think I would need in order to use bp2bistruc.

jujubix commented 6 years ago

The REJECTED print outs are normal. It's an MCMC process and it's simply reporting whether it's accepting or rejected proposed moves, or in this case, sampled structures.

Unfortunately I'm no longer working on this code base and actually never wrote it in the first place. If you want up to date help, I would recommend contacting the original author Dr. Meyer here: https://www.mdc-berlin.de/meyer