I'm attempting to infer lateral gene transfers from gene and inferred species trees using Prunier2.1.
So far I've been unable to get the software to run to completion (by which I mean it matches the expected outputs given in their example files).
The program seems to invoke without any issues, with the following command:
./prunier input.tree.file=inferred_species_10names.tree aln.file=awked/phylips/awked_PVC1_homologs.phy genetree.file=./awked/gene_trees/awked_PVC1_RAxML_bipartitions.T501 sequence.type=protein raxml.nb_proc=4 raxml.path=./raxml &> outputs/PVC1/PVC1_prunier_output
However around about the point where the program makes a system call to RAxML, I get the following errors appearing:
...
System call to RAxML succeeded. tmp_tree_ML_Branch_estimate_66356.raxml_inputtree
terminate called after throwing an instance of 'bpp::IOException'
what(): Newick::read: failed to read from stream
This is the RAxML Master Pthread........
Some time later I will also recieve:
Aborted (core dumped)
And RAxML seems to go on to execute nonetheless. Consequently I'm not sure whether the error pertains to RAxML or to Pruniers binary.
My input files seem fine to my eye, nothing obviously wrong with them (Newick gene and species trees, and Phylip alignments from CLUSTAL). I won't post them for now for the sake of keeping this question a manageable size, but I can provide them if needed.
Any help appreciated.
