[Errno 2] No such file or directory: 'RAxML_bipartitions.tempOut'

[kjl...@gmail.com]

Hi Will,
I'm a new user and i've had some luck generating a useful tree for a small species set with reasonably aligned sequences...really great for a phylogeny-building novice! Now i'm trying to use RAxML on a bunch of Genbank sequences of dubious quality. After aligning and trimming, deleting a few problematic species, I can get it to run for one gene but consistently get an error with two or more genes. Not sure if the problem is somewhere in my sequences or with some other aspect of the run, but the error does not occur with my small species set (34 sp) and 4 genes, using RAxML and integratedBootstrap. However, when loading the larger species set (approx 130 sp), it crashes after starting the integratedBootstrap run. I've done a fresh install and get the same problem repeatedly. The error output is pasted below. Perhaps it's a mistake on my part re: the sequences, but I don't know what the problem is. Any help you can provide would be appreciated!

Thanks,
Kevin


Traceback (most recent call last):
File "/Applications/Phylogenetic/phyloGeneratorMac_1-2/phyloGenerator.app/Contents/Resources/__boot__.py", line 340, in <module>
_run()
File "/Applications/Phylogenetic/phyloGeneratorMac_1-2/phyloGenerator.app/Contents/Resources/__boot__.py", line 311, in _run
exec(compile(source, path, 'exec'), globals(), globals())
File "/Applications/Phylogenetic/phyloGeneratorMac_1-2/phyloGenerator.app/Contents/Resources/phyloGenerator.py", line 4033, in <module>
main()
File "/Applications/Phylogenetic/phyloGeneratorMac_1-2/phyloGenerator.app/Contents/Resources/phyloGenerator.py", line 3996, in main
currentState.phylogen()
File "/Applications/Phylogenetic/phyloGeneratorMac_1-2/phyloGenerator.app/Contents/Resources/phyloGenerator.py", line 3353, in phylogen
raxmlSetup('')
File "/Applications/Phylogenetic/phyloGeneratorMac_1-2/phyloGenerator.app/Contents/Resources/phyloGenerator.py", line 3215, in raxmlSetup
self.phylogeny = RAxML(align, method=self.phylogenyMethods+'localVersion', constraint=self.constraint, timeout=999999, partitions=partitions)
File "/Applications/Phylogenetic/phyloGeneratorMac_1-2/phyloGenerator.app/Contents/Resources/phyloGenerator.py", line 971, in RAxML
tree = Phylo.read('RAxML_bipartitions.' + outputFile, "newick")
File "Bio/Phylo/_io.pyc", line 53, in read
File "Bio/Phylo/_io.pyc", line 40, in parse
File "contextlib.pyc", line 17, in __enter__
File "Bio/File.pyc", line 77, in as_handle
IOError: [Errno 2] No such file or directory: 'RAxML_bipartitions.tempOut'

[Will]

Hello,

Thanks for using the program. I'm actually on holiday right now, but if you send me some more detailed output and input (e.g., the text of the program up until that point, and the files you gave the run) then I can have a look. Also, have a quick look inside the 'phyloGenerator' folder for a files containing 'temp' and delete them, then try the run again. Please send those files to me privately - we don't want to clog up the inboxes of everyone on the list!

It sounds like this is a 'problem' with RAxML that phyloGenerator isn't able to detect and fix. If you can send me those files, I should be able to figure it out. Likely your alignment is a bit weird - that normally causes problems like this (if you have the alignment(s) you're using, please send them too!).

Thanks again,

Will

---

Need a phylogeny? Try phyloGenerator

Measuring phylogenetic structure? Try install.packages('pez')

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Will Pearse
Post-doc, ecology / evolutionary biology
Davies and Peres-Neto labs
Skype: will.pearse
Cell: (+1) 514-973-1987

[Will Pearse]

Hello,

After talking with Kevin, the problem was with a file that he created himself and loaded into phyloGenerator. If you're creating your own FASTA file to load in, RAxML doesn't seem to support comments so I'd advise against putting them in.

Thanks again,

Will