[2025-08-31 08:07:52] Starting ortholog annotation pipeline...
[2025-08-31 08:07:52] Creating output directory...
[2025-08-31 08:07:52] SUCCESS: Output directory created: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/M-multi-species/output/11.3-ortholog-annotation
[2025-08-31 08:07:52] Checking dependencies...
[2025-08-31 08:07:52] WARNING: InterProScan is not installed. Some annotation steps may be skipped.
[2025-08-31 08:07:52] Checking R packages...
[2025-08-31 08:07:52] Checking Python packages...
[2025-08-31 08:08:16] Starting ortholog annotation pipeline...
[2025-08-31 08:08:16] Creating output directory...
[2025-08-31 08:08:16] SUCCESS: Output directory created: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/M-multi-species/output/11.3-ortholog-annotation
[2025-08-31 08:08:16] Checking dependencies...
[2025-08-31 08:08:16] WARNING: InterProScan is not installed. Some annotation steps may be skipped.
[2025-08-31 08:08:16] Checking R packages...
[2025-08-31 08:08:16] Checking Python packages...
[2025-08-31 08:08:17] SUCCESS: Dependency check completed
[2025-08-31 08:08:17] Checking input files...
[2025-08-31 08:08:17] Found protein file: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/M-multi-species/../D-Apul/data/Apulchra-genome.pep.faa
[2025-08-31 08:08:17] Found protein file: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/M-multi-species/../E-Peve/data/Porites_evermanni_v1.annot.pep.fa
[2025-08-31 08:08:17] Found protein file: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/M-multi-species/../F-Ptua/data/Pocillopora_meandrina_HIv1.genes.pep.faa
[2025-08-31 08:08:17] SUCCESS: Input file check completed
[2025-08-31 08:08:17] Running R annotation script...
[2025-08-31 08:08:18] ERROR: R annotation script failed