Augustus warnings | Jobs being killed when using the <--long> flag/option with a large masked genome

[cement-head]

Using a masked genome and getting a few of these warning messages from Augustus when being used from within BUSCO

WARNING:	The following job was killed as it was taking too long (>1hr) to complete.
/usr/bin/augustus --codingseq=1 --proteinprofile=/home/cbfgws6/Documents/busco_analysis/busco_downloads/lineages/tetrapoda_odb10/prfl/1528at32523.prfl --predictionStart=210701 --predictionEnd=596681 --species=BUSCO_wfgenomebusco-masked-human /home/cbfgws6/Documents/busco_analysis/wfgenomebusco-masked-human/run_tetrapoda_odb10/blast_output/sequences/ctg837.temp

The non-masked genome did not generate these warnings - should I be worried/concerned?

TIA

[cement-head]

Another, related/unrelated query: I believe that lowercase sequence (DNA) is treated as masked due to changes in BLAST+ wherein the lowercase letters are used as soft-masked DNA as opposed to non-masked UPPERCASE letters. This looks as if it was introduced some time ago: https://academic.oup.com/nar/article/34/suppl_2/W6/2505541