The arguments fnameA and fnameB passed to the functions map_and_sort() [line 1291] and extract_mapped_reads_and_do_assembly_and_blast() [line 1292] include only the file name and not the full (or relative) path, so that the BWA steps fail if the source files are located in any directory other than the current working directory.
In SeqSero2_package.py:
The arguments fnameA and fnameB passed to the functions map_and_sort() [line 1291] and extract_mapped_reads_and_do_assembly_and_blast() [line 1292] include only the file name and not the full (or relative) path, so that the BWA steps fail if the source files are located in any directory other than the current working directory.