Is there anyone who can help me with running Spandx 3.2? I downloaded the file from, and every time I try to run the program it shows this:

Organism = haploid
Output directory and directory containing sequence files = /home/user/spandx/SPANDx_v3.2 /SPANDx
SNP matrix will be created? = no
Genomes will be annotated? = no
Strain(s) to be processed = all
Sequence technology used = Illumina
Pairing of reads = PE
Variant genome specified for SnpEff = no
Window size for BedTools = 1000
Indels will be merged and corrected = no
------------------------------------- line 237: cd: too many arguments

Couldn't locate reference file. Please make sure that reference file is in the analysis directory,
you have specified the reference name correctly, and that the .fasta extension is not included.

I know I'm doing something wrong. Please help me out.

PS: I don't have enough RAM to run SPANDX4.0

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