makefile exits with error 2 --> no reports

Good afternoon, I do get roary results but I do not get any reports. I am at loss on what is happening here... any idea or help would be greatly appreciated.

The only error I am seeing in my log is:

roary -v -f roary -p 4 -t 11 A_363.gff B_Aus2.gff G_Aus1.gff D_Aus11.gff C_Aus8.gff E_Aus13.gff Use of uninitialized value in require at /usr/local/nullarbor/miniconda3/lib/perl5/5.22.0/x86_64-linux-thread-multi/Encode.pm line 59. 2018/08/14 02:00:30 Error: Cant access file A_363.gff

and then at the end:

make: *** [roary/accessory_binary_genes.fa.newick] Error 2 make: *** Deleting file roary/accessory_binary_genes.fa.newick' make: Leaving directory /home/mkleinecke2/TEST/nullarbor/OUTTEST'

I have checked and there only is a contig.gff file in the A_363 folder and that one looks okay to me. But maybe that is not the correct one? From googling trough issues I have seen that the "Use of uninitialized value in require" is a known perl issue and should not effect the results?

The exact command I ran was:

qsub -v command="nice make -j 1 -l 4 -C OUTTEST" /usr/local/nullarbor/Header.pbs

Thank you and kind regards, Mariana