The parameter for the location of the local soft link for the H_and_O_and_specific_genes.fasta file has been changed so the BWA actions now point to original file location, not the local link.
The value of the parameter "database" is set at line 1263 and now includes the full path to the install directory of SeqSero2.
This parameter is passed to map_and_sort() at line 1291 and again to extract_mapped_reads_and_do_assembly_and_blast() at line 1292, resulting in errors when BWA is executed.
The correct value for these parameters should be path to the link created at line 1279, which is not currently saved to a variable.
The parameter for the location of the local soft link for the H_and_O_and_specific_genes.fasta file has been changed so the BWA actions now point to original file location, not the local link.
The value of the parameter "database" is set at line 1263 and now includes the full path to the install directory of SeqSero2.
This parameter is passed to map_and_sort() at line 1291 and again to extract_mapped_reads_and_do_assembly_and_blast() at line 1292, resulting in errors when BWA is executed.
The correct value for these parameters should be path to the link created at line 1279, which is not currently saved to a variable.