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tamuri / treesub

A small program that glues together other programs allowing a user to input a codon alignment in FASTA format and produce an annotated phylogenetic tree showing which substitutions occurred on a given branch. Originally written for colleagues at the MRC NIMR.
Apache License 2.0
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ERROR: java.io.FileNotFoundException: C:\Users\...\RAxML_bestTree.RECON (The system cannot find the file specified) #13

Open Jwongwh opened 2 years ago

Jwongwh commented 2 years ago

Hello,

I'm new to phylogenetic analysis and so would be grateful for advice. I attempted to implement treesub on Windows - however when I run it, I'm getting the following error:

[4/6] Rooting tree by outgroup sequence. ERROR: java.io.FileNotFoundException: C:\Users\j\Documents\treesub_01\RAxML_bestTree.RECON (The system cannot find the file specified) C:\Users\j\Documents\treesub_01\RAxML_bestTree.RECON (The system cannot find the file specified)

Unless I'm mistaken, I believe this is because my RAxML isn't running properly. At part [3/6], I receive the following message:

[3/6] Running RAxML application. Output from RAxML: (You're running on Windows. No real-time output available!) Model GTRGAMMA -T 2 -# 10 -p 12345 does not exist

For BINARY data use: BINCAT[X] or BINGAMMA[X] or BINCATI[X] or BINGAMMAI[X] or ASC_BINGAMMA[X] or ASC_BINCAT[X] For DNA data use: GTRCAT[X] or GTRGAMMA[X] or GTRCATI[X] or GTRGAMMAI[X] or ASC_GTRGAMMA[X] or ASC_GTRCAT[X] For Multi-state data: MULTICAT[X] or MULTIGAMMA[X] or MULTICATI[X] or MULTIGAMMAI[X] or ASC_MULTIGAMMA[X] or ASC_MULTICAT[X] For AA data use: PROTCATmatrixName[F|X] or PROTGAMMAmatrixName[F|X] or PROTCATImatrixName[F|X] or PROTGAMMAImatrixName[F|X] or ASC_PROTGAMMAmatrixName[X] or ASC_PROTCATmatrixName[X] The AA substitution matrix can be one of the following:

DAYHOFF, DCMUT, JTT, MTREV, WAG, RTREV, CPREV, VT, BLOSUM62, MTMAM, LG, MTART, MTZOA, PMB, HIVB, HIVW, JTTDCMUT, FLU, STMTREV, DUMMY, DUMMY2, AUTO, LG4M, LG4X, PROT_FILE, GTR_UNLINKED, GTR

With the optional "F" appendix you can specify if you want to use empirical base frequencies. With the optional "X" appendix you can specify that you want to do a ML estimate of base frequencies. Please note that for mixed models you can in addition specify the per-gene model in the mixed model file (see manual for details).

Successfully ran RAxML.

Is it something to do with the default model specified? I've tried changing the arguments, etc. to no avail - I still get "model does not exist". The version of RAxML I've installed is v8.2.X, with options to use Windows executables either v8.2.4 or v8.2.10 (no difference in error messages).

Thanks in advance!

drpies286 commented 2 years ago

I get the same and other similar errors when using windows. I've tried numerous combinations of Raxml with treesub and its never worked. Had more success with macOS, although that was fussy too.

Guojiahuii commented 1 year ago

I get the same errors when using windows. Did you solve these problem?

Jwongwh commented 1 year ago

Unfortunately no! I only know it isn't a model selection issue, as far as I can tell it's RAxML itself. I tried different versions with no success. Running it through WSL might be a solution since you're on Windows, but I ended up using a colleague's Linux setup to run. As the first reply said, Linux/macOS seems to give less problems.

Guojiahuii commented 1 year ago

thanks, I am using my colleague's Linux to try to run it. i hope i can success. If there are any questions I wish I could ask you！