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License: GNU General Public License v3.0
PHYLOgenomic analysis pipeline for HERBarium specimens
License: GNU General Public License v3.0
I run
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
It returns:
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
I run
$HOSTNAME:/home/ktest/pipeline_env/workflow/PhyloHerb$ python phyloherb.py -m ortho -i example/results/2_assemblies/chl/ -o 3a_orthologs -l 120
__ __ ___ __ __
|__) |__| \ / | / \ |__| |__ |__) |__)
| | | | |___ \__/ | | |___ | \ |__)
############################################################
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
############################################################
#ERROR:Input files not found!
When I debug, it turn out that if
PH_path=os.path.dirname(__file__)
--> PH_path=os.path.dirname(os.path.abspath(__file__))
It not error anymore
Please check this anomaly error ?
Hi, can this pipeline be used on transcriptome dataset?
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