2026-06-17 17:10:11,928 - INFO - Populating features
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Populating features table and first-order relations: 1064000 features
Populating features table and first-order relations: 1065000 features
Populating features table and first-order relations: 1066000 features
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Populating features table and first-order relations: 1165000 features
Populating features table and first-order relations: 1166000 features
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Populating features table and first-order relations: 1168000 features
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Populating features table and first-order relations: 1173000 features
Populating features table and first-order relations: 1174000 features
Populating features table and first-order relations: 1175000 features
Populating features table and first-order relations: 1176000 features
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Populating features table and first-order relations: 1178000 features
Populating features table and first-order relations: 1179000 features
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Populating features table and first-order relations: 1182000 features
Populating features table and first-order relations: 1183000 features
Populating features table and first-order relations: 1184000 features
Populating features table and first-order relations: 1185000 features
Populating features table and first-order relations: 1186000 features
Populating features table and first-order relations: 1187000 features
Populating features table and first-order relations: 1188000 features
Populating features table and first-order relations: 1189000 features
Populating features table and first-order relations: 1190000 features
Populating features table and first-order relations: 1191000 features
Populating features table and first-order relations: 1192000 features
Populating features table and first-order relations: 1193000 features
Populating features table and first-order relations: 1194000 features
Populating features table and first-order relations: 1195000 features
Populating features table and first-order relations: 1196000 features
Populating features table and first-order relations: 1197000 features
Populating features table and first-order relations: 1198000 features
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Populating features table and first-order relations: 1202000 features
Populating features table and first-order relations: 1203000 features
Populating features table and first-order relations: 1204000 features
Populating features table and first-order relations: 1205000 features
Populating features table and first-order relations: 1206000 features
Populating features table and first-order relations: 1207000 features
Populating features table and first-order relations: 1208000 features
Populating features table and first-order relations: 1209000 features
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Populating features table and first-order relations: 1338000 features
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Populating features table and first-order relations: 1348000 features
Populating features table and first-order relations: 1349000 features
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Populating features table and first-order relations: 1356000 features
Populating features table and first-order relations: 1357000 features
Populating features table and first-order relations: 1358000 features
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Populating features table and first-order relations: 1368000 features
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Populating features table and first-order relations: 1375000 features
Populating features table and first-order relations: 1376000 features
Populating features table and first-order relations: 1377000 features
Populating features table and first-order relations: 1378000 features
Populating features table and first-order relations: 1379000 features
Populating features table and first-order relations: 1380000 features
Populating features table and first-order relations: 1381000 features
Populating features table and first-order relations: 1382000 features
Populating features table and first-order relations: 1383000 features
Populating features table and first-order relations: 1384000 features
Populating features table and first-order relations: 1385000 features
Populating features table and first-order relations: 1386000 features
Populating features table and first-order relations: 1387000 features
Populating features table and first-order relations: 1388000 features
Populating features table and first-order relations: 1389000 features
Populating features table and first-order relations: 1390000 features
Populating features table and first-order relations: 1391000 features
Populating features table and first-order relations: 1392000 features
Populating features table and first-order relations: 1393000 features
Populating features table and first-order relations: 1394000 features
Populating features table and first-order relations: 1395000 features
Populating features table and first-order relations: 1396000 features
Populating features table and first-order relations: 1397000 features
Populating features table and first-order relations: 1398000 features
Populating features table and first-order relations: 1399000 features
Populating features table and first-order relations: 1400000 features
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Populating features table and first-order relations: 1402000 features
Populating features table and first-order relations: 1403000 features
Populating features table and first-order relations: 1404000 features
Populating features table and first-order relations: 1405000 features
Populating features table and first-order relations: 1406000 features
Populating features table and first-order relations: 1407000 features
Populating features table and first-order relations: 1408000 features
Populating features table and first-order relations: 1409000 features
Populating features table and first-order relations: 1410000 features
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Populating features table and first-order relations: 1417000 features
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Populating features table and first-order relations: 1419000 features
Populating features table and first-order relations: 1420000 features
Populating features table and first-order relations: 1421000 features
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Populating features table and first-order relations: 1426000 features
Populating features table and first-order relations: 1427000 features
Populating features table and first-order relations: 1428000 features
Populating features table and first-order relations: 1429000 features
Populating features table and first-order relations: 1430000 features
Populating features table and first-order relations: 1431000 features
Populating features table and first-order relations: 1432000 features
Populating features table and first-order relations: 1433000 features
Populating features table and first-order relations: 1434000 features
2026-06-17 17:11:32,718 - INFO - Populating features table and first-order relations: 1434194 features
2026-06-17 17:11:32,719 - INFO - Updating relations
2026-06-17 17:11:42,790 - INFO - Creating relations(parent) index
2026-06-17 17:11:43,703 - INFO - Creating relations(child) index
2026-06-17 17:11:44,842 - INFO - Creating features(featuretype) index
2026-06-17 17:11:45,494 - INFO - Creating features (seqid, start, end) index
2026-06-17 17:11:46,339 - INFO - Creating features (seqid, start, end, strand) index
2026-06-17 17:11:47,248 - INFO - Running ANALYZE features
extracting features
[M::mm_idx_gen::63.822*1.63] collected minimizers
[M::mm_idx_gen::73.029*6.26] sorted minimizers
[M::main::73.029*6.26] loaded/built the index for 24184 target sequence(s)
[M::mm_mapopt_update::74.533*6.16] mid_occ = 2839
[M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 24184
[M::mm_idx_stat::75.366*6.10] distinct minimizers: 83551710 (34.57% are singletons); average occurrences: 9.021; average spacing: 5.318; total length: 4008351139
[M::worker_pipeline::804.302*35.64] mapped 21745 sequences
[M::worker_pipeline::1753.515*37.37] mapped 24614 sequences
[M::worker_pipeline::1756.465*37.31] mapped 21745 sequences
[M::worker_pipeline::1757.720*37.28] mapped 24614 sequences
[M::main] Version: 2.31-r1302
[M::main] CMD: /opt/anaconda/anaconda3/envs/liftoff_env/bin/minimap2 -o siscowet_intermediate/reference_all_to_target_all.sam -a --end-bonus 5 --eqx -N 50 -p 0.5 --split-prefix siscowet_intermediate/reference_all_to_target_all_split -t 40 /home/shared/16TB_HDD_01/sr320/github/project-lake-trout/data/genome/pb-hifiasm-siscowet-assembly.fa siscowet_intermediate/reference_all_genes.fa
[M::main] Real time: 1757.799 sec; CPU: 65535.772 sec; Peak RSS: 45.996 GB
aligning features
lifting features
mapping gene copies
[M::mm_idx_gen::62.735*1.60] collected minimizers
[M::mm_idx_gen::65.271*2.98] sorted minimizers
[M::main::65.271*2.98] loaded/built the index for 24184 target sequence(s)
[M::mm_mapopt_update::66.695*2.94] mid_occ = 2839
[M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 24184
[M::mm_idx_stat::67.524*2.91] distinct minimizers: 83551710 (34.57% are singletons); average occurrences: 9.021; average spacing: 5.318; total length: 4008351139
[M::worker_pipeline::799.146*35.59] mapped 21745 sequences
[M::worker_pipeline::1748.738*37.44] mapped 24614 sequences
[M::worker_pipeline::1751.701*37.38] mapped 21745 sequences
[M::worker_pipeline::1752.909*37.36] mapped 24614 sequences
[M::main] Version: 2.31-r1302
[M::main] CMD: /opt/anaconda/anaconda3/envs/liftoff_env/bin/minimap2 -o siscowet_intermediate/reference_all_to_target_all.sam -a --end-bonus 5 --eqx -N 50 -p 0.5 --split-prefix siscowet_intermediate/reference_all_to_target_all_split -t 40 /home/shared/16TB_HDD_01/sr320/github/project-lake-trout/data/genome/pb-hifiasm-siscowet-assembly.fa siscowet_intermediate/reference_all_genes.fa
[M::main] Real time: 1752.992 sec; CPU: 65484.325 sec; Peak RSS: 47.214 GB
aligning features
lifting features
polishing annotations