neherlab/pan-genome-analysis

[Errno 2] No such file or directory: -> tmp_core_diversity.txt

Calvin2077 opened this issue · 2 comments

Calvin2077 commented

Hello everyone,

I am trying to run pan-genome analysis on 32 AOA species using the full genebanks I obtained from the NCBI and this code

./panX.py -fn data/genebanks -sl pratice -t 6

However I ran into this error on Step 6

IOError: [Errno 2] No such file or directory: ./pan-genome-analysis/data/input_GenBank/protein_faa/diamond_matches/tmp_core/tmp_core_diversity.txt'

Does anyone any ideas how to over come this please and thank you. I should note that the TestSet worked without any problems.

Thank you very much

paocorbin commented

I have the same problem.
Did you manage to solve it?
Thank you.

fbaumdicker commented

A common problem that can cause an empty core genome is a too diverse set of strains/species. Try the option to use a relaxed soft core to get some genes into the core genome.