lmcai / phyloherb Goto Github PK

python /home/ktest/pipeline_env/workflow/PhyloHerb/phyloherb.py -m conc -i Decapoda_mt/Alignment/ -suffix .aln -o phylogeny_cat_decapoda -g gene_order.txt

PhyloHerb v1.1.2
A bioinformatic pipeline for herbariomics based biodiversity research

Concatenate 11 alignments based on the custom gene set

Traceback (most recent call last):
  File "/home/ktest/pipeline_env/workflow/PhyloHerb/phyloherb.py", line 774, in <module>
    concatenation(args.i,files,args.o)
  File "/home/ktest/pipeline_env/workflow/PhyloHerb/phyloherb.py", line 261, in concatenation
    d=AlignIO.convert(output+'.conc.nex', 'nexus', output+'.conc.fas', 'fasta', molecule_type='DNA')
  File "/home/ktest/pipeline_env/software/environment/Trung_conda/PhyloHerb-env/lib/python3.6/site-packages/Bio/AlignIO/__init__.py", line 474, in convert
    return write(alignments, out_file, out_format)
  File "/home/ktest/pipeline_env/software/environment/Trung_conda/PhyloHerb-env/lib/python3.6/site-packages/Bio/AlignIO/__init__.py", line 220, in write
    for alignment in alignments:
  File "/home/ktest/pipeline_env/software/environment/Trung_conda/PhyloHerb-env/lib/python3.6/site-packages/Bio/AlignIO/__init__.py", line 473, in <genexpr>
    alignments = (over_ride(_) for _ in alignments)
  File "/home/ktest/pipeline_env/software/environment/Trung_conda/PhyloHerb-env/lib/python3.6/site-packages/Bio/AlignIO/__init__.py", line 337, in parse
    yield from i
  File "/home/ktest/pipeline_env/software/environment/Trung_conda/PhyloHerb-env/lib/python3.6/site-packages/Bio/AlignIO/NexusIO.py", line 38, in NexusIterator
    n = Nexus.Nexus(handle)
  File "/home/ktest/pipeline_env/software/environment/Trung_conda/PhyloHerb-env/lib/python3.6/site-packages/Bio/Nexus/Nexus.py", line 668, in __init__
    self.read(input)
  File "/home/ktest/pipeline_env/software/environment/Trung_conda/PhyloHerb-env/lib/python3.6/site-packages/Bio/Nexus/Nexus.py", line 718, in read
    self._parse_nexus_block(title, contents)
  File "/home/ktest/pipeline_env/software/environment/Trung_conda/PhyloHerb-env/lib/python3.6/site-packages/Bio/Nexus/Nexus.py", line 759, in _parse_nexus_block
    getattr(self, "_" + line.command)(line.options)
  File "/home/ktest/pipeline_env/software/environment/Trung_conda/PhyloHerb-env/lib/python3.6/site-packages/Bio/Nexus/Nexus.py", line 1276, in _charpartition
    sub, set_type=CHARSET, separator=":"
  File "/home/ktest/pipeline_env/software/environment/Trung_conda/PhyloHerb-env/lib/python3.6/site-packages/Bio/Nexus/Nexus.py", line 1295, in _get_indices
    name = self._name_n_vector(opts, separator=separator)
  File "/home/ktest/pipeline_env/software/environment/Trung_conda/PhyloHerb-env/lib/python3.6/site-packages/Bio/Nexus/Nexus.py", line 1320, in _name_n_vector
    raise NexusError("Formatting error in line: %s " % rest)
Bio.Nexus.Nexus.NexusError: Formatting error in line:  phylogeny_cat_decapoda_tem/CDS-cox2.nex: 1-752

$HOSTNAME:/home/ktest/pipeline_env/workflow/PhyloHerb$ python phyloherb.py -m ortho -i example/results/2_assemblies/chl/ -o 3a_orthologs -l 120
 __                 __        ___  __   __  
|__) |__| \ / |    /  \ |__| |__  |__) |__) 
|    |  |  |  |___ \__/ |  | |___ |  \ |__) 


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PhyloHerb v1.1.2
A bioinformatic pipeline for herbariomics based biodiversity research

Using all 5 species found in example/results/2_assemblies/chl/: sp2, sp3, sp4, sp1, sp5
Using length cutoff 120 bp for BLAST result filtering
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#ERROR:Input files not found!