I am using Mauve to align two the whole genome sequences, one of the sequence is in the form of contigs. Another one is in the form of a complete genome.
I could align the two sequences using the following command
progressiveMauve ref.fa contigs.fa --output alignment.xmfa
And to extract the SNPs, I tried the solution from https://bioinformatics.stackexchange.com/questions/3658/can-i-export-the-snps-between-whole-genome-alignments-using-the-command-line/3664#3664
But while exporting the classpath path it shows an error
export CLASSPATH="$(find "$MAUVE_DIR" -name \*.jar -print0 | tr '\0' :)$CLASSPATH" find: ‘‹/home/me/Downloads/mauve_snapshot_2015-02-13/›’: No such file or directory
I have downloaded the mauve file and extracted it in the following location
I am using a linux machine. How can I solve this issue?