No phylogenies after step 2

[Jesse Gibson]

Hi,

I'm trying to run on the example dataset using the command

python ~/Broccoli/broccoli.py -dir ~/Broccoli/example_dataset/ -ext '.fasta'

with diamond version 4.0.515 and fasttree version 2.1.11 but am getting completely empty results. It seems like step 1 is able to read the proteome files just fine and perform the kmer clustering, but by the time we reach step three it says that there are 0 nodes/0 edges for the graph clustering analysis. Any idea what could be happening? Here's the complete output

            Broccoli v1.1


 --- STEP 1: kmer clustering

 # parameters
 input dir     : /home/gary/Broccoli/example_dataset
 kmer size     : 100
 kmer nb aa    : 15

 # check input files
 6 input files
 879 sequences

 # kmer clustering
 6 proteomes on 1 threads
 -> 868 proteins saved for the next step


 --- STEP 2: phylomes

 # parameters
 e_value     : 0.001
 nb_hits     : 6
 gaps        : 0.7
 phylogenies : neighbor joining
 threads     : 1

 # check input files
 6 input fasta files
 868 sequences

 # build phylomes ... be patient
 done


 --- STEP 3: network analysis

 ## parameters
 species overlap  : 0.5
 min edge weight  : 0.1
 min nb hits      : 2
 chimeric edges   : 0.5
 chimeric species : 3
 threads          : 1

 ## get ortho and para
 extract ortho from similarity
 extract ortho from trees
 remove ortho found only once
 extract para from trees

 ## network analysis
 build network:
      _ 0 nodes
      _ 0 edges
 load similarity search outputs
 compute lcc for each node
 apply LPA and corrections:
      _ 0 connected components
      _ 0 communities
      _ 0 chimeric proteins
      _ 0 spurious hits removed


 --- STEP 4: orthologous pairs

 ## parameters
 ratio ortho  : 0.5
 not same sp  : False
 threads      : 1

 ## load data
 load NO tree results
 load tree results
 load OGs

 ## analyse 0 orthologous groups 1 by 1
 done

Thanks!
Jesse

[Romain Derelle]

Hi Jesse,

my apologies for this late reply.

It might be due to the new version of Diamond you are using. What the files in dir_step2 and dir_step3 look like? Are they empty?

Thanks
Romain