Roary Does not terminated successfully

[Kanwal03]

Hi,
I am using Roary in my own developed pipeline where I need Core/pan sequences to analyze further. I developed Pipeline in my Ubuntu genome. It was installed and run easily there. Due to lack of computational resources I wanted to installed my Pipeline in our university Supercomputer that is centos and I do not have root permissions. SO I installed each and every thing manually from source it was very hectic for me. Now I successfully installed it. But at the end it didn't terminated successfully. and stuck at the end when I use to end it using Ctrl+c it gives following lines.
Core gene file missing: pan_genome_sequences/hspX_1.fa.aln
Core gene file missing: pan_genome_sequences/nirD.fa.aln
Core gene file missing: pan_genome_sequences/cobU.fa.aln
Core gene file missing: pan_genome_sequences/group_3155.fa.aln
Core gene file missing: pan_genome_sequences/eccA1_1.fa.aln
Core gene file missing: pan_genome_sequences/eccB1_1.fa.aln
Core gene file missing: pan_genome_sequences/eccD1_1.fa.aln
Core gene file missing: pan_genome_sequences/group_3765.fa.aln

I don't know what does it mean. I want to terminate it implicitly so that pipeline may work without any interruption. Could you please help me.

[tseemann]

@Kanwal03 what are the full command(s) you used to run roary ?