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2026-10-10 09:06:04,900 - INFO - Populating features table and first-order relations: 261187 features
2026-10-10 09:06:04,901 - INFO - Updating relations
2026-10-10 09:06:07,531 - INFO - Creating relations(parent) index
2026-10-10 09:06:07,613 - INFO - Creating relations(child) index
2026-10-10 09:06:07,705 - INFO - Creating features(featuretype) index
2026-10-10 09:06:07,785 - INFO - Creating features (seqid, start, end) index
2026-10-10 09:06:07,868 - INFO - Creating features (seqid, start, end, strand) index
2026-10-10 09:06:07,965 - INFO - Running ANALYZE features
extracting features
[M::mm_idx_gen::9.013*1.46] collected minimizers
[M::mm_idx_gen::9.891*2.35] sorted minimizers
[M::main::11.360*2.18] loaded/built the index for 10 target sequence(s)
[M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 10
[M::mm_idx_stat::11.733*2.14] distinct minimizers: 42348626 (58.78% are singletons); average occurrences: 3.512; average spacing: 5.309; total length: 789630056
@HD	VN:1.6	SO:unsorted	GO:query
@SQ	SN:Chromosome_1A	LN:100680956
@SQ	SN:Chromosome_2A	LN:98156180
@SQ	SN:Chromosome_3A	LN:93095432
@SQ	SN:Chromosome_4A	LN:93973257
@SQ	SN:Chromosome_5A	LN:90413844
@SQ	SN:Chromosome_6A	LN:76092957
@SQ	SN:Chromosome_7A	LN:74165749
@SQ	SN:Chromosome_8A	LN:54853936
@SQ	SN:Chromosome_9A	LN:66796497
@SQ	SN:Chromosome_10A	LN:41401248
@PG	ID:minimap2	PN:minimap2	VN:2.31-r1302	CL:minimap2 -d data/13-wgbs-genome-hapa/Och_HapA_assembly.fa.mmi -a --end-bonus 5 --eqx -N 50 -p 0.5 -t 16 data/13-wgbs-genome-hapa/Och_HapA_assembly.fa
[M::main] Version: 2.31-r1302
[M::main] CMD: minimap2 -d data/13-wgbs-genome-hapa/Och_HapA_assembly.fa.mmi -a --end-bonus 5 --eqx -N 50 -p 0.5 -t 16 data/13-wgbs-genome-hapa/Och_HapA_assembly.fa
[M::main] Real time: 11.757 sec; CPU: 25.105 sec; Peak RSS: 3.437 GB
[M::main::2.140*0.98] loaded/built the index for 10 target sequence(s)
[M::mm_mapopt_update::2.693*0.98] mid_occ = 584
[M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 10
[M::mm_idx_stat::3.043*0.99] distinct minimizers: 42348626 (58.78% are singletons); average occurrences: 3.512; average spacing: 5.309; total length: 789630056
[M::worker_pipeline::67.108*14.53] mapped 21444 sequences
[M::main] Version: 2.31-r1302
[M::main] CMD: minimap2 -o output/13-wgbs-hapa/13.11-liftoff/intermediate/reference_all_to_target_all.sam -a --end-bonus 5 --eqx -N 50 -p 0.5 -t 16 data/13-wgbs-genome-hapa/Och_HapA_assembly.fa.mmi output/13-wgbs-hapa/13.11-liftoff/intermediate/reference_all_genes.fa
[M::main] Real time: 67.120 sec; CPU: 975.413 sec; Peak RSS: 6.648 GB
aligning features
lifting features
reference_genes	21444
lifted_genes	17889
unmapped_features	3555
shared_chrom_genes_same_coords	7158 of 7427
genes_Chromosome_1A	3213
genes_Chromosome_2A	2523
genes_Chromosome_3A	2512
genes_Chromosome_4A	2200
genes_Chromosome_5A	2374
genes_Chromosome_6A	1755
genes_Chromosome_7A	941
genes_Chromosome_8A	500
genes_Chromosome_9A	922
genes_Chromosome_10A	949
[Sat Oct 10 09:08:23 PDT 2026] done: data/13-wgbs-genome-hapa/GN.gene.hapa.gff3