Sometimes some version has formatting errors that make it impossible to read the contig files. For example, some old svn files have a premature EOF, likely because Artemis was closed before finishing saving them. You can simply exclude those files from the analysis. For that, add them to the file valid_ids_data/revisions2skip.tsv.
Some of the files are missing a space between the number and BP in the first line:
# first line is this
ID chromosome_1 standard; DNA; FUN; 5579133BP.
# should be this
ID chromosome_1 standard; DNA; FUN; 5579133 BP.
To support this, we override the function EmblScanner._feed_seq_length from BioPython in pombe_svn_full_diff.py.
Some of the old files from svn need fixing. This can be done by running the script:
python fix_known_errors_svn_files.py
Some of the pre-svn files are directly fixed in get_ftp_site_files.py