OSError: [Errno 21] Is a directory: 'standard-RAxML'

[rossmounce]

Yes, my alignment was terrible... matk interspersed with rbcl willy-nilly but even with garbage in / garbage out it should still run through the pipeline, right? Any idea what might be happening here? Have I not installed RAxML correctly perhaps?

DNA ALIGNMENT

Choose one alignment method ('muscle', 'mafft', 'clustalo', 'prank'), or... 'everything' - all four and compare their outputs 'quick' - do only the first three Return will use MAFFT; prank is very slow!

DNA Alignment (default - mafft): Starting alignment... ...aligning gene no. 1 ......with MAFFT

Alignment complete!

ALIGNMENT CHECKING

Gene: rbcL ID Alignment Length Med. Gaps SD Gaps Min-Max Gaps Med. Gap Frac. M-M Gap Frac. Warn? 0 mafft 1764 800.0 266.41 249.0 - 1232.0 0.45 0.141-0.698 !!!!

'output' - write out alignments. I recommend you look at your alignment before continuing
'DNA' - return to DNA editing stage
'align' - return to alignment stage, discarding current alignments.
'trimal' - automatically trim your sequences using trimAl
'raxml=X' - run X RAxML runs for each alignment, and calculate the R-F distances between the trees and alignments (slow)
'metal' - calculate SSP distances between alignments using metal
'clustal-x2' - open the Clustal-X2 website to download this alignment viewer

TIPS: *_If the column 'Warn?' has '!!!' in it, BEWARE! Your alignment likely has problems._ Bad sequences cause bad alignments. Be careful in the DNA check stage, and return there now if necessary 'output' your alignments, and open them in something like Clustal-X2. You will immediately see sequences that should be RELOADed or TRIMMed When downloading Clustal, make sure you get the graphical Clustal-X2, not the command line version

Hit enter to continue and choose one final alignment per gene

Alignment Checking:output ...output written! Alignment Checking:

CONSTRAINT TREE I recommend you use a constraint tree with this program 'newick' - supply your own constraint tree 'phylomatic' - use Phylomatic to generate a tree 'taxonomy' - download the NCBI taxonomy for your species (does not generate a constraint tree) Warning: Phylomatic can trim the end off species names, causing conflicts with phyloGenerator that are hard to detect. Rooted phylogenies are not valid constraints. Otherwise, press enter to continue without a constraint tree.

TIPS: If you choose 'taxonomy', it will be written out to your working directory now. Use that to make a constraint tree! If you have access to a reference phylogeny, try using Phylomatic A constraint tree makes your phylogeny much more likely to be right. Use one!

Constraint Method: taxonomy

Creating a 'taxonomy' for your species from GenBank ...lineages found! Constraint Method: ...Continuing without constraint tree

PHYLOGENY BUILDING You can either build a maximum likelihood tree ('raxml') or a Bayesian tree ('beast') If unsure, hit enter to use RAxML - using BEAST safely will require some knowledge of phylogenetics

Phylogeny Building (default raxml):
...using RAxML... RAXML: 'integratedBootstrap=X' - conduct X number of bootstraps and a thorough ML search in one run (!) 'restart=X' - conduct X number of full ML searches (!) 'partitions' - concatenate all genes into a single partition (not the default) Specify multiple options with hyphens (e.g., 'restart=5-partitions'), but do not mix options marked with '(!)' Hit enter to conduct one search

TIPS: The integrated boostrap method is fast, and gives confidence intervals on your tree, and a value of 1000 is probably more than adequate for most trees Phylogeny Building (RAxML - default 1 search): integratedBootstrap=1000 Traceback (most recent call last): File "./phyloGenerator.py", line 3790, in main() File "./phyloGenerator.py", line 3756, in main currentState.phylogen() File "./phyloGenerator.py", line 3122, in phylogen raxmlSetup('') File "./phyloGenerator.py", line 2984, in raxmlSetup self.phylogeny = RAxML(align, method=self.phylogenyMethods+'localVersion', constraint=self.constraint, timeout=999999, partitions=partitions) File "./phyloGenerator.py", line 904, in RAxML os.remove(each) OSError: [Errno 21] Is a directory: 'standard-RAxML'

[willpearse]

Hello,

Thanks for this Ross. While I'm here, thanks for the pull request - I've made a slight alteration (to a slight alteration!) and included it in the main branch.

It does look to me like you've not installed RAxML correctly (you're using Linux, right?); I'd be grateful for the following:

• What the 'setupLinux.py' script shows you when you run it - this will help me determine whether you've setup pG correctly
• The sequences you're putting through phyloGenerator (type 'output' at the DNA download stage) - this will help me determine what's going wrong with your run if you have setup pG correctly

If you could email them to wdpearse asdfg`12345asdfg @ asdf2134 umn.edu I'd be really grateful (go ahead and remove the nonsense I've put in there).

Thanks again for getting in touch, and I'm sorry you've had issues,

Will

[willpearse]

Hello,

After email contact with Ross, it seems this error is caused by keeping source code from RAxML inside the requires folder, which causes problems for pG's ability to detect output from RAxML. I'm putting a warning message about this in the setupLinux.py script.

Thanks very much for bringing this to my attention Ross, and sorry for the bother,

Will