Issue with step 8

[jpaganini]

Hello guys, how r u? I'm having a problem with step08. I get the following error message:

======  starting step08: run fasttree and raxml for tree construction
 fasttree time-cost:  1.45 minutes (87.06 seconds)
RAxML tree optimization within the timelimit of 30 minutes
RAxML branch length optimization and rooting
Traceback (most recent call last):
  File "./panX.py", line 303, in <module>
    myPangenome.build_core_tree()
  File "/home/julian/pan-genome-analysis/scripts/pangenome_computation.py", line 200, in build_core_tree
    aln_to_Newick(self.path, self.folders_dict, self.raxml_max_time, self.raxml_path, self.threads)
  File "/home/julian/pan-genome-analysis/scripts/sf_core_tree_build.py", line 75, in aln_to_Newick
    shutil.copy('RAxML_result.branches', out_fname)
  File "/home/julian/miniconda2/envs/panX/lib/python2.7/shutil.py", line 119, in copy
    copyfile(src, dst)
  File "/home/julian/miniconda2/envs/panX/lib/python2.7/shutil.py", line 82, in copyfile
    with open(src, 'rb') as fsrc:
IOError: [Errno 2] No such file or directory: 'RAxML_result.branches'

I checked the raxml log and I found this:

Option -T does not have any effect with the sequential or parallel MPI version. It is used to specify the number of threads for the Pthreads-based parallelization

RAxML can't, parse the alignment file as phylip file it will now try to parse it as FASTA file

ERROR: Sequence AF-673 consists entirely of undetermined values which will be treated as missing data ERROR: Sequence CMC-MDR-Ab59 consists entirely of undetermined values which will be treated as missing data ERROR: Sequence HRAB-85 consists entirely of undetermined values which will be treated as missing data ERROR: Sequence KAB07 consists entirely of undetermined values which will be treated as missing data ERROR: Found 4 sequences that consist entirely of undetermined values, exiting...

So, I figured there might be a problem with the fasta files that gets generated in the previous steps. Any ideas on how to fix this?

[rneher]

This probably means that your core genome is empty. Are your genomes incomplete? or very diverse?

[jpaganini]

Hi Richard. Thx for your prompt response. The genomes are complete. In regards to diversity, they are not clonal strains. But all geomes belong to the same bacterial species.

[avilella]

I have faced the same issue at step 8. In my case, I am analysing phage genomes, each of which is small in size. Some of them are close to each other, but others are further apart. I had success until step 7 running it with -cb 0.3. Is there anything I can do to make it complete the next steps? I can't generate a complete set of files for pan-genome-visualization if I am stuck at step 7.

Any recommendations would be very welcome. Both panX and pan-genome-visualization are great tools that are making my analysis a lot easier and very detailed.

[rneher]

Sorry I dropped the ball here. I was traveling when this one came in and it fell through the cracks. So you say step 7 (greating a SNP alignment from the core genome) completed with -cg 0.3 but step 8 (core genome tree) failed? Could you give some more info on what was written to the log (the panX log and/or the RAXML/fasttree logs). Did step 7 produce a file "geneCluster/SNP_whole_matrix.aln"?