"Running Host Db building function " takes very long time

[Yufei Yue]

Hi Simon,

Thanks for providing this wonderful tool!

I met a problem was that, I added my 100 MAGs (270Mb) to the standard database,everything looked ok, but at the step of Running Host Db building function, it has running for 99h, I don’t know whether it’s normal.

Processing GCA_002721915.1_ASM272191v1_genomic (approx. 94/100)
Processing GCA_013043285.1_ASM1304328v1_genomic (approx. 95/100)
Processing GCA_013003155.1_ASM1300315v1_genomic (approx. 96/100)
Processing GCA_003228345.1_ASM322834v1_genomic (approx. 97/100)
Processing GCA_003229615.1_ASM322961v1_genomic (approx. 98/100)
Processing GCA_011776105.1_ASM1177610v1_genomic (approx. 99/100)
Processing GCA_007132245.1_ASM713224v1_genomic (approx. 100/100)
Finished all right
[6] Add new genomes to VHM database...
Loading custom packages...
Load existing database
Running Host Db building function

[Simon Roux]

I agree, 99 hours seems suspiciously long, especially if all other steps went ok. How many threads do you give to the command ? If it only has 1 or 2 threads, then you may want to give more (these last steps can really benefit from multithreading). Otherwise, I would try with only a fraction of your MAGs first (e.g. 10) to make sure the program finishes as expected, and then increase the number to see if maybe there is 1 specific MAG that causes some issues.