5.7.0 huge single-thread delay after miniprot and before HMMER
Tested the just released 5.7.0 BUSCO Docker image on a dataset I just ran 5.6.1 on earlier today. It works, but there is a huge 30 minute delay after miniprot completes and before HMMER starts (see the log excerpt below, I marked the time jump with **) where top just shows a single thread working. There was no such delay between metaeuk completion and HMMER start on 5.6.1. It might be some post-processing or data collection from miniprot going on, but in that case an INFO msg should probably printed as right now you have no idea what is happening during this long period.
I run busco with -c 24 in genome mode. Total run-time for both 5.6.1 and 5.7.0 is around 30-40 minutes on my dataset so weirdly it's around the same. The same delay in log output is not in 5.6.1 though, there metaeuk stands for the long time instead. The HMMER step is just like 2 minutes in both cases.
2024-03-15 22:55:46 INFO: ***** Start a BUSCO v5.7.0 analysis, current time: 03/15/2024 22:55:46 *****
2024-03-15 22:55:46 INFO: Configuring BUSCO with local environment
2024-03-15 22:55:46 INFO: Running genome mode
2024-03-15 22:55:46 INFO: Downloading information on latest versions of BUSCO data...
2024-03-15 22:55:49 INFO: Input file is /busco_wd/scaffolds.fasta
2024-03-15 22:55:53 INFO: Running BUSCO using lineage dataset lepidoptera_odb10 (eukaryota, 2024-01-08)
2024-03-15 22:55:53 INFO: Running 1 job(s) on bbtools, starting at 03/15/2024 22:55:53
2024-03-15 22:55:56 INFO: [bbtools] 1 of 1 task(s) completed
2024-03-15 22:55:56 INFO: Running 1 job(s) on miniprot_index, starting at 03/15/2024 22:55:56
2024-03-15 22:56:02 INFO: [miniprot_index] 1 of 1 task(s) completed
2024-03-15 22:56:02 INFO: Running 1 job(s) on miniprot_align, starting at 03/15/2024 22:56:02
2024-03-15 **22:56:27** INFO: [miniprot_align] 1 of 1 task(s) completed
2024-03-15 **23:24:42** INFO: ***** Run HMMER on gene sequences *****
2024-03-15 23:24:52 INFO: Running 5241 job(s) on hmmsearch, starting at 03/15/2024 23:24:52
2024-03-15 23:25:11 INFO: [hmmsearch] 525 of 5241 task(s) completed
2024-03-15 23:25:17 INFO: [hmmsearch] 1049 of 5241 task(s) completed
2024-03-15 23:25:23 INFO: [hmmsearch] 1573 of 5241 task(s) completed
2024-03-15 23:25:30 INFO: [hmmsearch] 2097 of 5241 task(s) completed
2024-03-15 23:25:36 INFO: [hmmsearch] 2621 of 5241 task(s) completed
2024-03-15 23:25:42 INFO: [hmmsearch] 3145 of 5241 task(s) completed
2024-03-15 23:25:48 INFO: [hmmsearch] 3669 of 5241 task(s) completed
2024-03-15 23:25:54 INFO: [hmmsearch] 4193 of 5241 task(s) completed
2024-03-15 23:26:00 INFO: [hmmsearch] 4717 of 5241 task(s) completed
2024-03-15 23:26:06 INFO: [hmmsearch] 5241 of 5241 task(s) completed
2024-03-15 23:26:07 INFO: 4960 exons in total
2024-03-15 23:26:07 WARNING: 16 of 737 Complete matches (2.2%) contain internal stop codons in Miniprot gene predictions