BiG-SCAPE Output: Missing BGCs in record_annotations.tsv

[sjtu-piaopiao]

Hi,
I recently ran BiG-SCAPE on a dataset of 36,505 gbk files (antiSMASH-annotated BGCs), but the output file record_annotations.tsv contains only 33,850 BGCs. I would like to know the filtering steps and filtering criteria, are BGCs excluded based on length thresholds (0-500,000 bp)? Or some other parameter? How do I know the details of the process and which BGCs have been removed? Any guidance would be greatly appreciated.

[nlouwen]

Hi!
In principle, record_annotations.tsv only contains BGCs that occur in the network(s). If you ran without --include-singletons, any singletons will therefore not show up here.
If any GBKs were filtered out due to length, the log will show along the lines of x GBKs remain after length constraint .... Other filtering that can happen is not default, but can be supplied by e.g. --include-classes, --exclude-categories or --include-gbk, see the documentation for more info on those. Let me know if you have any more questions!

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