ERROR: Could not find .aligned.fa/.vcf in 'file' make: *** [Makefile:108: core.aln] Error 2

Hi, I keep getting the above error: ERROR: Could not find .aligned.fa/.vcf in PC0086b-S0390 make: *** [Makefile:108: core.aln] Error 2 make: *** Waiting for unfinished jobs.... make: Leaving directory '/home/.....

My make preview file was ok. I'm using the same ref.fasta file I've been using for ages. The file named above 'PC00....' changes when I retry to make again.

I've also tried the following: rm -fv */resistome.tab rm -fv */virulome.tab rm -f *.gff rm -fr roary find . -type f -size 0 -delete -print make

I've attached the makefile and log file. Thank you. nullarborlog.txt Makefile.txt

Tried to use another input file, all else the same, and got the following makefile and log file for make preview. nullarborlog2.txt

Makefile2.txt