Panakeia.py: FileNotFoundError

[nicola-palmieri]

Hello

I have started testing Panakeia on a set of 59 Ornithobacterium isolates. Here is my protocol:

• Prepare folder with gff files: gff-files-59isolates

• Prepare folder with fasta proteins: fasta-proteins-59isolates

• Rename ORT-UMN_88 to ORT_UMN_88 since dash might create problems in the Panakeia pipeline

• Concatenate all protein sequences cat fasta-proteins-59isolates/*faa > fasta-proteins-59isolates.fasta

cd panakeia-output python ../Panakeia/PangenomeAnalysis/Clustering.py ../fasta-proteins-59isolates.fasta 59 python ../Panakeia/PangenomeAnalysis/Panakeia.py output ../gff-files-59isolates protein_clusters.txt representative_seq.faa

The Panakeia.py scripts reads the strains correctly, but generates an error at the Read GFFs step:

Read GFFs! Traceback (most recent call last): File "/Volumes/Data3/2023/ORT/run1+2/10-panakeia/panakeia-output/../Panakeia/PangenomeAnalysis/Panakeia.py", line 786, in main() File "/Volumes/Data3/2023/ORT/run1+2/10-panakeia/panakeia-output/../Panakeia/PangenomeAnalysis/Panakeia.py", line 772, in main draw_clusters() File "/Volumes/Data3/2023/ORT/run1+2/10-panakeia/panakeia-output/../Panakeia/PangenomeAnalysis/Panakeia.py", line 701, in draw_clusters draw_genomes() File "/Volumes/Data3/2023/ORT/run1+2/10-panakeia/panakeia-output/../Panakeia/PangenomeAnalysis/Panakeia.py", line 758, in draw_genomes nx.writegraphml(straingraph, args.output+"/"+"strain"+s+".graphML") File "/Users/nicola.palmieri/opt/miniconda3/lib/python3.9/site-packages/networkx/utils/decorators.py", line 766, in func return argmap._lazy_compile(__wrapper)(*args, **kwargs) File "<class 'networkx.utils.decorators.argmap'> compilation 5", line 3, in argmap_write_graphml_lxml_1 File "/Users/nicola.palmieri/opt/miniconda3/lib/python3.9/site-packages/networkx/utils/decorators.py", line 189, in _open_file fobj = _dispatch_dict[ext](path, mode=mode) FileNotFoundError: [Errno 2] No such file or directory: 'output/strain_ORT_UMN_88.graphML'

[bharat1912]

Hi Nicola-Palmieri The error is because Panakeia.py does not create the output dir "outfile" to which the analysis files will be written to. You will need to mkdir outfile (or any other dir of your choice) and include the path to the dir in your CLi.

[nicola-palmieri]

Thanks a lot! That solved the problem!