Biopython Parser Warning

[kbojanic]

Hi,
I would kindly ask for some assistance. I tried panX with 22 genomes of a marine bacteria downloaded from Patric server (files downloaded as gto and converted to gbk files) but the script did not complete the task. From the outputs the most frequent error included:

home/kruno/miniconda2/envs/panX/lib/python2.7/site-packages/Bio/GenBank/Scanner.py:1310: BiopythonParserWarning: Truncated LOCUS line found - is this correct?
:'LOCUS BAUG01000064 15005 bp dna linear UNK \n'
"correct?\n:%r" % line, BiopythonParserWarning)

that was repeated multiple times but the analysis continued and then the script halted with the last error message, the traceback call, being the following:

Traceback (most recent call last):
File "./panX.py", line 287, in
myPangenome.process_clusters()
File "/home/kruno/pan-genome-analysis/scripts/pangenome_computation.py", line 180, in process_clusters
myClusterCollector.estimate_raw_core_diversity()
File "/home/kruno/pan-genome-analysis/scripts/cluster_collective_processing.py", line 17, in estimate_raw_core_diversity
self.folders_dict, self.strain_list, self.threads, self.core_genome_threshold, self.factor_core_diversity, self.species)
File "/home/kruno/pan-genome-analysis/scripts/sf_core_diversity.py", line 102, in estimate_core_gene_diversity
calculated_core_diversity=tmp_average_core_diversity(tmp_core_seq_path)
File "home/kruno/pan-genome-analysis/scripts/sf_core_diversity.py", line 42, in tmp_average_core_diversity
with open(file_path+'tmp_core_diversity.txt', 'r') as tmp_core_diversity_file:
IOError: [Errno 2] No such file or directory: '/home/kruno/pan-genome-analysis/data/Tenacibaculum_maritimum/protein_faa/diamond_matches/tmp_core/tmp_core_diversity.txt'

The problem in troubleshooting this for me is that in the log folder there are no raxml nor fasttree logs and do not know how to proceed, I mean I neither understand what went wrong nor what to do to fix it. I am using Ubuntu 18.04 LTS and panX was installed following instructions and panX environment created successfully.

If more information is needed please let me know what to add.

Thank you in advance.
Kruno