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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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I run into this error RAxML_bestTree.RECON (No such file or directory) #5

Open akang1414 opened 5 years ago

akang1414 commented 5 years ago

Hi, I am running into following error while running treesub on a server. [1/6] Copying file from '/home/my/data.fasta' to '/home/my/alignment'. Successfully copied file.

[2/6] Converting FASTA file 'alignment' to PHYLIP file 'alignment.phylip'. Alignment has 336 sequences, each with 1751 sites. Successfully converted FASTA file.

[3/6] Running RAxML application. Output from RAxML: couldn't execute "/home/my/standard-RAxML-master/WindowsExecutables_v8.2.10/raxmlHPC.exe": permission denied while executing "spawn -noecho /home/my/standard-RAxML-master/WindowsExecutables_v8.2.10/raxmlHPC.exe -p -m GTRGAMMA -T 2 -# 10 -s alignment.raxml.phylip -n RECON" ("eval" body line 1) invoked from within "eval [list spawn -noecho] $argv" invoked from within "if {[string compare [lindex $argv 0] "-p"] == 0} {

pipeline

set stty_init "-echo"
eval [list spawn -noecho] [lrange $argv 1 end]
clo..."
(file "/usr/bin/unbuffer" line 13)

Successfully ran RAxML.

[4/6] Rooting tree by outgroup sequence. ERROR: java.io.FileNotFoundException: /home/my/RAxML_bestTree.RECON (No such file or directory) /home/my/RAxML_bestTree.RECON (No such file or directory)

tamuri commented 5 years ago

It looks like you're running the program on a Linux machine but pointing to the Windows RAxML executable? That won't work. You need to provide the path to the Linux RAxML executable.