Thank you for the excellent tool. bedtools maskfasta does not run properly if there are any mismatches between the fasta file and the bed file. In my case, earlgrey did not mask my mitochondrial chromosome, so there was no line with MT in the bed file. As a result, the entire "species.softmasked.fasta" was unmasked. In my case, removing the MT assembly and masking worked fine. Perhaps it is worth adding a step to earlgrey that filters out contigs that are not present in the final "species.filtered.bed" file, masks the assembly, and then re-appends the unmasked filtered repeats.
Update this wasn't an issue with earl grey, please ignore.
Hey!
Thank you for the excellent tool. bedtools maskfasta does not run properly if there are any mismatches between the fasta file and the bed file. In my case, earlgrey did not mask my mitochondrial chromosome, so there was no line with MT in the bed file. As a result, the entire "species.softmasked.fasta" was unmasked. In my case, removing the MT assembly and masking worked fine. Perhaps it is worth adding a step to earlgrey that filters out contigs that are not present in the final "species.filtered.bed" file, masks the assembly, and then re-appends the unmasked filtered repeats.
Best, Dustin