Feature request: timestamp major stages
I suspect that my run of BUSCO 4.0.4 is stuck at Augustus (no log output at all for over 1 hour when I check the current time and the last time log file is modified), but without timestamps it is hard to be sure.
For a test run with Malaria reference, using -c 32
, this is what I get after 6 hours:
INFO: ***** Start a BUSCO v4.0.4 analysis, current time: 02/26/2020 17:17:06 *****
INFO: Configuring BUSCO with /home/shuang/miniconda3/envs/busco4/config/config.ini
INFO: Mode is genome
INFO: Input file is /home/shuang/pfalciparum3D7/PlasmoDB-46_Pfalciparum3D7_Genome.fasta
INFO: Downloading information on latest versions of BUSCO data...
INFO: Running BUSCO using lineage dataset plasmodium_odb10 (eukaryota, 2019-11-21)
INFO: Creating BLAST database with input file
INFO: Running 1 job(s) on makeblastdb
INFO: [makeblastdb] 1 of 1 task(s) completed
INFO: Running a BLAST search for BUSCOs against created database
INFO: Running 1 job(s) on tblastn
INFO: [tblastn] 1 of 1 task(s) completed
INFO: Running Augustus gene predictor on BLAST search results.
INFO: Running Augustus prediction using toxoplasma as species:
INFO: Running 4016 job(s) on augustus
INFO: [augustus] 402 of 4016 task(s) completed
INFO: [augustus] 804 of 4016 task(s) completed
INFO: [augustus] 1205 of 4016 task(s) completed
INFO: [augustus] 1607 of 4016 task(s) completed
INFO: [augustus] 2009 of 4016 task(s) completed
INFO: [augustus] 2410 of 4016 task(s) completed
INFO: [augustus] 2812 of 4016 task(s) completed