Error of running phybreak1.generate_maf.py

[TarsLi]

Hi, I tried to find the core gene sweep by the test data using PopCOGenT, but I got an error when running phybreak1.generate_maf.py: sh: 1: source: not found 12 genomes Starting Nucmer: Tue Feb 2 21:05:42 CST 2021 sh: 1: cannot create ./align/sulpho.M1627_contigs.queries.fsa: Directory nonexistent .sh: 1: cannot create ./align/sulpho.M1627_contigs.filt.delta: Directory nonexistent Nucmer search failed. Can't find delta file ./align/sulpho.M1627_contigs.filt.delta at /home/lenovo/software/mugsy_x86-64-v1r2.2/mugsy line 812.

I have unloaded the result files of bash PopCOGenT.sh, log file of running phybreak1.generate_maf.py and phybreak_parameters.txt, could you please give me any suggestions? Thanks. strain_names.txt phybreak_parameters.txt sulfolobus_0.000355362.txt.cluster.tab.txt sulfolobus.length_bias.txt

Best Hao

[Diamonds95]

I got the similar results, and when I changed the "strains_names.txt" with the strains only present in cluster 0.0, it works. Maybe you can have a try!