busco 3 vs 4 results, what accounts for the differences?
A pointer to the relevant section of a paper or web page would suffice.
I ran a test set of mRNAs previously analyzed with busco 3 in busco 4.
Method for busco 3 (on avery large machine)
run_BUSCO.py -i 266_trinity_SRR532046.Trinity.fasta -o busco_266_trinity_SRR5320 46 -l /home/mathog/src/busco-10-13-2017/data_sets/metazoa_odb9/ -m transcriptome -c 48
which ran in 4m25s and had results:
Busco 4.0.2 on a smaller machine
busco --offline -l metazoa -i 266_trinity_SRR532046.Trinity.fasta -c 6 -m geno -f --out foobar 2>&1 | tee foobar2.log
ran in almost exactly an HOUR. Results are:
The speed difference is mostly because 3 used all threads for blast but 4 used only 1, and elsewhere because 48 is 8X more than 6. But the busco results are also not the same. There are two variables: busco 3 vs. 4, and metazoa dataset 9 vs 10.