weights not properly taken into account on a fresh run #99

[Oct 15 02:56 PM] Calculated ab initio weights from data: ['helixer:4', 'augustus-hiq:4', 'augustus:2', 'glimmerhmm:1', 'miniprot-gene:1', 'snap:1']
[...]
[Oct 15 02:58 PM] Using these filtered loci, the calculated gene model source weights to use as tiebreakers:
{"helixer": 4, "augustus-hiq": 4, "augustus": 2, "snap": 1, "glimmerhmm": 1, "miniprot-gene": 1}

[Oct 15 02:01 PM] Python v3.11.15; funannotate2 v26.6.9; gfftk v26.5.22; buscolite v26.6.21; annorefine v2026.2.22
[Oct 15 02:01 PM] Parsed data from --input-dir /data/train_aspalli
  --fasta /data/GCF_009176365.1_Aspalli1_genomic.cleaned.fna
  --species "Aspergillus"
  --params /data/train_aspalli/train_results/Aspergillus.params.json
  --out /data/annotated
[Oct 15 02:01 PM] Loaded training params for Aspergillus: ['augustus', 'glimmerhmm', 'snap']
[Oct 15 02:01 PM] temporary files located in: /tmp/predict_e379c39e-ee80-4245-9db8-9c1eeef095e2
[Oct 15 02:01 PM] Loading genome assembly, running QC checks, searching for mitochondrial contigs, calculating softmasked regions and assembly gaps
[Oct 15 02:01 PM] Genome stats:
{
  "n_contigs": 331,
  "size": 40168528,
  "softmasked": "7.44%",
  "gaps": "0.07%",
  "n50": 499171,
  "n90": 152365,
  "l50": 24,
  "l90": 77,
  "avg_length": 121355
}
[Oct 15 02:01 PM] Parsed 487237 [out of 575503] proteins to align for evidence, derived from:
/opt/funannotate2_db/uniprot_sprot.fasta
[Oct 15 02:01 PM] Aligning protein evidence to the genome assembly with miniprot
[Oct 15 02:01 PM] miniprot --outn=4 -G 3000 --gff-only -t 2 /data/annotated/predict_misc/genome.fasta /data/annotated/predict_misc/proteins.to.align.fasta
[Oct 15 02:31 PM] [M::mp_ntseq_read@0.060*0.95] read 40168528 bases in 331 contigs
[M::mp_idx_build@0.060*0.95] 314120 blocks
[M::mp_idx_build@0.583*1.77] collected syncmers
[M::mp_idx_build@1.116*1.37] 22094268 kmer-block pairs
[M::mp_idx_print_stat] 2014936 distinct k-mers; mean occ of infrequent k-mers: 10.97; 0 frequent k-mers accounting for 0 occurrences
[M::worker_pipeline::22.698*2.00] mapped 5146 sequences
[M::worker_pipeline::41.026*1.94] mapped 4680 sequences
[M::worker_pipeline::58.764*1.98] mapped 4481 sequences
[M::worker_pipeline::76.592*2.01] mapped 4588 sequences
[M::worker_pipeline::94.499*1.98] mapped 4917 sequences
[M::worker_pipeline::109.676*2.00] mapped 5045 sequences
[M::worker_pipeline::126.614*1.98] mapped 5497 sequences
[M::worker_pipeline::146.140*1.99] mapped 4836 sequences
[M::worker_pipeline::164.467*2.00] mapped 4824 sequences
[M::worker_pipeline::182.388*2.01] mapped 4041 sequences
[M::worker_pipeline::203.319*1.99] mapped 5251 sequences
[M::worker_pipeline::221.334*2.00] mapped 4667 sequences
[M::worker_pipeline::239.967*1.99] mapped 4800 sequences
[M::worker_pipeline::257.115*2.00] mapped 5057 sequences
[M::worker_pipeline::274.450*2.00] mapped 5240 sequences
[M::worker_pipeline::295.663*2.00] mapped 5922 sequences
[M::worker_pipeline::313.563*2.00] mapped 5718 sequences
[M::worker_pipeline::331.622*2.00] mapped 5475 sequences
[M::worker_pipeline::350.927*2.00] mapped 4139 sequences
[M::worker_pipeline::370.854*2.00] mapped 3269 sequences
[M::worker_pipeline::388.863*2.00] mapped 4255 sequences
[M::worker_pipeline::405.786*1.99] mapped 4689 sequences
[M::worker_pipeline::420.769*2.00] mapped 4732 sequences
[M::worker_pipeline::440.517*2.00] mapped 5273 sequences
[M::worker_pipeline::461.245*1.99] mapped 5188 sequences
[M::worker_pipeline::480.870*2.00] mapped 5424 sequences
[M::worker_pipeline::497.313*2.00] mapped 4317 sequences
[M::worker_pipeline::517.453*2.00] mapped 4893 sequences
[M::worker_pipeline::531.494*2.00] mapped 4292 sequences
[M::worker_pipeline::548.621*1.99] mapped 5157 sequences
[M::worker_pipeline::566.459*2.00] mapped 5106 sequences
[M::worker_pipeline::583.366*2.00] mapped 5703 sequences
[M::worker_pipeline::602.598*2.00] mapped 6240 sequences
[M::worker_pipeline::621.994*2.00] mapped 5286 sequences
[M::worker_pipeline::642.252*2.00] mapped 5395 sequences
[M::worker_pipeline::659.409*2.00] mapped 4778 sequences
[M::worker_pipeline::678.466*2.00] mapped 5250 sequences
[M::worker_pipeline::700.993*2.00] mapped 4575 sequences
[M::worker_pipeline::717.998*2.00] mapped 5099 sequences
[M::worker_pipeline::734.968*2.00] mapped 5542 sequences
[M::worker_pipeline::753.684*2.00] mapped 4674 sequences
[M::worker_pipeline::773.543*2.00] mapped 3991 sequences
[M::worker_pipeline::792.774*2.00] mapped 4240 sequences
[M::worker_pipeline::811.128*2.00] mapped 4864 sequences
[M::worker_pipeline::829.017*2.00] mapped 4811 sequences
[M::worker_pipeline::853.006*2.00] mapped 5398 sequences
[M::worker_pipeline::869.940*2.00] mapped 4808 sequences
[M::worker_pipeline::894.047*2.00] mapped 3359 sequences
[M::worker_pipeline::912.724*2.00] mapped 5837 sequences
[M::worker_pipeline::931.382*2.00] mapped 4781 sequences
[M::worker_pipeline::953.912*2.00] mapped 5259 sequences
[M::worker_pipeline::973.486*2.00] mapped 6409 sequences
[M::worker_pipeline::993.485*2.00] mapped 5520 sequences
[M::worker_pipeline::1011.042*2.00] mapped 4501 sequences
[M::worker_pipeline::1028.409*2.00] mapped 5469 sequences
[M::worker_pipeline::1048.672*2.00] mapped 4730 sequences
[M::worker_pipeline::1074.736*2.00] mapped 3716 sequences
[M::worker_pipeline::1091.758*2.00] mapped 2116 sequences
[M::worker_pipeline::1110.071*2.00] mapped 4797 sequences
[M::worker_pipeline::1128.385*2.00] mapped 6928 sequences
[M::worker_pipeline::1142.642*2.00] mapped 4707 sequences
[M::worker_pipeline::1158.675*2.00] mapped 5166 sequences
[M::worker_pipeline::1177.908*2.00] mapped 4822 sequences
[M::worker_pipeline::1199.988*2.00] mapped 5371 sequences
[M::worker_pipeline::1221.616*2.00] mapped 9392 sequences
[M::worker_pipeline::1244.280*2.00] mapped 15134 sequences
[M::worker_pipeline::1261.992*2.00] mapped 6823 sequences
[M::worker_pipeline::1280.900*2.00] mapped 3292 sequences
[M::worker_pipeline::1305.871*2.00] mapped 5437 sequences
[M::worker_pipeline::1327.717*2.00] mapped 12478 sequences
[M::worker_pipeline::1347.367*2.00] mapped 5976 sequences
[M::worker_pipeline::1364.050*2.00] mapped 4409 sequences
[M::worker_pipeline::1385.228*2.00] mapped 4206 sequences
[M::worker_pipeline::1406.754*2.00] mapped 4722 sequences
[M::worker_pipeline::1429.187*2.00] mapped 4730 sequences
[M::worker_pipeline::1447.847*2.00] mapped 4537 sequences
[M::worker_pipeline::1465.354*2.00] mapped 3780 sequences
[M::worker_pipeline::1477.415*2.00] mapped 2901 sequences
[M::worker_pipeline::1494.967*2.00] mapped 3544 sequences
[M::worker_pipeline::1513.329*2.00] mapped 5020 sequences
[M::worker_pipeline::1531.196*2.00] mapped 4896 sequences
[M::worker_pipeline::1553.258*2.00] mapped 4575 sequences
[M::worker_pipeline::1570.188*2.00] mapped 5142 sequences
[M::worker_pipeline::1587.038*2.00] mapped 5668 sequences
[M::worker_pipeline::1607.383*2.00] mapped 6010 sequences
[M::worker_pipeline::1626.549*2.00] mapped 5192 sequences
[M::worker_pipeline::1645.606*2.00] mapped 5477 sequences
[M::worker_pipeline::1666.263*2.00] mapped 4502 sequences
[M::worker_pipeline::1685.370*2.00] mapped 7909 sequences
[M::worker_pipeline::1706.848*2.00] mapped 7841 sequences
[M::worker_pipeline::1728.497*2.00] mapped 7100 sequences
[M::worker_pipeline::1751.673*2.00] mapped 7299 sequences
[M::worker_pipeline::1771.837*2.00] mapped 4184 sequences
[M::main] Version: 0.18-r281
[M::main] CMD: miniprot --outn=4 -G 3000 --gff-only -t 2 /data/annotated/predict_misc/genome.fasta /data/annotated/predict_misc/proteins.to.align.fasta
[M::main] Real time: 1771.847 sec; CPU: 3541.558 sec; Peak RSS: 0.966 GB

[Oct 15 02:35 PM] Generated 101716 alignments: 710 were valid gene models
[Oct 15 02:35 PM] Parsed 14320 external gene models [source=helixer] from /data/helixerlite.gff
[Oct 15 02:35 PM] Parsing alignments and generating hintsfile for Augustus
[Oct 15 02:36 PM] Augustus hints saved to: /data/annotated/predict_misc/augustus.hints.gff
[Oct 15 02:36 PM] Memory monitoring: using 17.6 GB limit (90% of 19.5 GB total)
[Oct 15 02:36 PM] Running ab initio gene predictions using 2 cpus
[Oct 15 02:36 PM] Processing all 331 contigs in parallel
[Oct 15 02:37 PM] Successfully ran tools for contig_1.fasta: snap, glimmerhmm, augustus
[Oct 15 02:37 PM] Successfully ran tools for contig_2.fasta: snap, glimmerhmm, augustus
[Oct 15 02:38 PM] Successfully ran tools for contig_4.fasta: snap, glimmerhmm, augustus
[Oct 15 02:38 PM] Successfully ran tools for contig_3.fasta: snap, glimmerhmm, augustus
[Oct 15 02:39 PM] Successfully ran tools for contig_6.fasta: snap, glimmerhmm, augustus
[Oct 15 02:39 PM] Successfully ran tools for contig_5.fasta: snap, glimmerhmm, augustus
[Oct 15 02:39 PM] Successfully ran tools for contig_8.fasta: snap, glimmerhmm, augustus
[Oct 15 02:40 PM] Successfully ran tools for contig_7.fasta: snap, glimmerhmm, augustus
[Oct 15 02:40 PM] Successfully ran tools for contig_9.fasta: snap, glimmerhmm, augustus
[Oct 15 02:40 PM] Successfully ran tools for contig_10.fasta: snap, glimmerhmm, augustus
[Oct 15 02:41 PM] Successfully ran tools for contig_12.fasta: snap, glimmerhmm, augustus
[Oct 15 02:41 PM] Successfully ran tools for contig_11.fasta: snap, glimmerhmm, augustus
[Oct 15 02:41 PM] Successfully ran tools for contig_14.fasta: snap, glimmerhmm, augustus
[Oct 15 02:41 PM] Successfully ran tools for contig_13.fasta: snap, glimmerhmm, augustus
[Oct 15 02:41 PM] Successfully ran tools for contig_16.fasta: snap, glimmerhmm, augustus
[Oct 15 02:41 PM] Successfully ran tools for contig_15.fasta: snap, glimmerhmm, augustus
[Oct 15 02:42 PM] Successfully ran tools for contig_18.fasta: snap, glimmerhmm, augustus
[Oct 15 02:42 PM] Successfully ran tools for contig_17.fasta: snap, glimmerhmm, augustus
[Oct 15 02:42 PM] Successfully ran tools for contig_20.fasta: snap, glimmerhmm, augustus
[Oct 15 02:42 PM] Successfully ran tools for contig_19.fasta: snap, glimmerhmm, augustus
[Oct 15 02:42 PM] Successfully ran tools for contig_22.fasta: snap, glimmerhmm, augustus
[Oct 15 02:42 PM] Successfully ran tools for contig_21.fasta: snap, glimmerhmm, augustus
[Oct 15 02:43 PM] Successfully ran tools for contig_24.fasta: snap, glimmerhmm, augustus
[Oct 15 02:43 PM] Successfully ran tools for contig_23.fasta: snap, glimmerhmm, augustus
[Oct 15 02:43 PM] Successfully ran tools for contig_25.fasta: snap, glimmerhmm, augustus
[Oct 15 02:43 PM] Successfully ran tools for contig_26.fasta: snap, glimmerhmm, augustus
[Oct 15 02:43 PM] Successfully ran tools for contig_27.fasta: snap, glimmerhmm, augustus
[Oct 15 02:43 PM] Successfully ran tools for contig_28.fasta: snap, glimmerhmm, augustus
[Oct 15 02:44 PM] Successfully ran tools for contig_29.fasta: snap, glimmerhmm, augustus
[Oct 15 02:44 PM] Successfully ran tools for contig_30.fasta: snap, glimmerhmm, augustus
[Oct 15 02:44 PM] Successfully ran tools for contig_31.fasta: snap, glimmerhmm, augustus
[Oct 15 02:44 PM] Successfully ran tools for contig_32.fasta: snap, glimmerhmm, augustus
[Oct 15 02:44 PM] Successfully ran tools for contig_34.fasta: snap, glimmerhmm, augustus
[Oct 15 02:44 PM] Successfully ran tools for contig_33.fasta: snap, glimmerhmm, augustus
[Oct 15 02:45 PM] Successfully ran tools for contig_36.fasta: snap, glimmerhmm, augustus
[Oct 15 02:45 PM] Successfully ran tools for contig_35.fasta: snap, glimmerhmm, augustus
[Oct 15 02:45 PM] Successfully ran tools for contig_37.fasta: snap, glimmerhmm, augustus
[Oct 15 02:45 PM] Successfully ran tools for contig_38.fasta: snap, glimmerhmm, augustus
[Oct 15 02:45 PM] Successfully ran tools for contig_40.fasta: snap, glimmerhmm, augustus
[Oct 15 02:45 PM] Successfully ran tools for contig_39.fasta: snap, glimmerhmm, augustus
[Oct 15 02:45 PM] Successfully ran tools for contig_41.fasta: snap, glimmerhmm, augustus
[Oct 15 02:45 PM] Successfully ran tools for contig_42.fasta: snap, glimmerhmm, augustus
[Oct 15 02:45 PM] Successfully ran tools for contig_43.fasta: snap, glimmerhmm, augustus
[Oct 15 02:45 PM] Successfully ran tools for contig_44.fasta: snap, glimmerhmm, augustus
[Oct 15 02:46 PM] Successfully ran tools for contig_45.fasta: snap, glimmerhmm, augustus
[Oct 15 02:46 PM] Successfully ran tools for contig_46.fasta: snap, glimmerhmm, augustus
[Oct 15 02:46 PM] Successfully ran tools for contig_47.fasta: snap, glimmerhmm, augustus
[Oct 15 02:46 PM] Successfully ran tools for contig_48.fasta: snap, glimmerhmm, augustus
[Oct 15 02:46 PM] Successfully ran tools for contig_49.fasta: snap, glimmerhmm, augustus
[Oct 15 02:46 PM] Successfully ran tools for contig_50.fasta: snap, glimmerhmm, augustus
[Oct 15 02:46 PM] Successfully ran tools for contig_51.fasta: snap, glimmerhmm, augustus
[Oct 15 02:46 PM] Successfully ran tools for contig_52.fasta: snap, glimmerhmm, augustus
[Oct 15 02:46 PM] Successfully ran tools for contig_54.fasta: snap, glimmerhmm, augustus
[Oct 15 02:46 PM] Successfully ran tools for contig_53.fasta: snap, glimmerhmm, augustus
[Oct 15 02:46 PM] Successfully ran tools for contig_55.fasta: snap, glimmerhmm, augustus
[Oct 15 02:47 PM] Successfully ran tools for contig_56.fasta: snap, glimmerhmm, augustus
[Oct 15 02:47 PM] Successfully ran tools for contig_58.fasta: snap, glimmerhmm, augustus
[Oct 15 02:47 PM] Successfully ran tools for contig_57.fasta: snap, glimmerhmm, augustus
[Oct 15 02:47 PM] Successfully ran tools for contig_60.fasta: snap, glimmerhmm, augustus
[Oct 15 02:47 PM] Successfully ran tools for contig_59.fasta: snap, glimmerhmm, augustus
[Oct 15 02:47 PM] Successfully ran tools for contig_61.fasta: snap, glimmerhmm, augustus
[Oct 15 02:47 PM] Successfully ran tools for contig_62.fasta: snap, glimmerhmm, augustus
[Oct 15 02:47 PM] Successfully ran tools for contig_63.fasta: snap, glimmerhmm, augustus
[Oct 15 02:47 PM] Successfully ran tools for contig_64.fasta: snap, glimmerhmm, augustus
[Oct 15 02:47 PM] Successfully ran tools for contig_66.fasta: snap, glimmerhmm, augustus
[Oct 15 02:47 PM] Successfully ran tools for contig_65.fasta: snap, glimmerhmm, augustus
[Oct 15 02:47 PM] Successfully ran tools for contig_68.fasta: snap, glimmerhmm, augustus
[Oct 15 02:47 PM] Successfully ran tools for contig_67.fasta: snap, glimmerhmm, augustus
[Oct 15 02:47 PM] Successfully ran tools for contig_69.fasta: snap, glimmerhmm, augustus
[Oct 15 02:47 PM] Successfully ran tools for contig_70.fasta: snap, glimmerhmm, augustus
[Oct 15 02:48 PM] Successfully ran tools for contig_71.fasta: snap, glimmerhmm, augustus
[Oct 15 02:48 PM] Successfully ran tools for contig_72.fasta: snap, glimmerhmm, augustus
[Oct 15 02:48 PM] Successfully ran tools for contig_73.fasta: snap, glimmerhmm, augustus
[Oct 15 02:48 PM] Successfully ran tools for contig_74.fasta: snap, glimmerhmm, augustus
[Oct 15 02:48 PM] Successfully ran tools for contig_75.fasta: snap, glimmerhmm, augustus
[Oct 15 02:48 PM] Successfully ran tools for contig_76.fasta: snap, glimmerhmm, augustus
[Oct 15 02:48 PM] Successfully ran tools for contig_77.fasta: snap, glimmerhmm, augustus
[Oct 15 02:48 PM] Successfully ran tools for contig_78.fasta: snap, glimmerhmm, augustus
[Oct 15 02:48 PM] Successfully ran tools for contig_80.fasta: snap, glimmerhmm, augustus
[Oct 15 02:48 PM] Successfully ran tools for contig_79.fasta: snap, glimmerhmm, augustus
[Oct 15 02:48 PM] Successfully ran tools for contig_81.fasta: snap, glimmerhmm, augustus
[Oct 15 02:48 PM] Successfully ran tools for contig_82.fasta: snap, glimmerhmm, augustus
[Oct 15 02:48 PM] Successfully ran tools for contig_83.fasta: snap, glimmerhmm, augustus
[Oct 15 02:48 PM] Successfully ran tools for contig_84.fasta: snap, glimmerhmm, augustus
[Oct 15 02:48 PM] Successfully ran tools for contig_85.fasta: snap, glimmerhmm, augustus
[Oct 15 02:48 PM] Successfully ran tools for contig_86.fasta: snap, glimmerhmm, augustus
[Oct 15 02:48 PM] Successfully ran tools for contig_87.fasta: snap, glimmerhmm, augustus
[Oct 15 02:48 PM] Successfully ran tools for contig_88.fasta: snap, glimmerhmm, augustus
[Oct 15 02:48 PM] Successfully ran tools for contig_89.fasta: snap, glimmerhmm, augustus
[Oct 15 02:48 PM] Successfully ran tools for contig_90.fasta: snap, glimmerhmm, augustus
[Oct 15 02:48 PM] Successfully ran tools for contig_91.fasta: snap, glimmerhmm, augustus
[Oct 15 02:48 PM] Successfully ran tools for contig_92.fasta: snap, glimmerhmm, augustus
[Oct 15 02:48 PM] Successfully ran tools for contig_94.fasta: snap, glimmerhmm, augustus
[Oct 15 02:48 PM] Successfully ran tools for contig_93.fasta: snap, glimmerhmm, augustus
[Oct 15 02:48 PM] Successfully ran tools for contig_96.fasta: snap, glimmerhmm, augustus
[Oct 15 02:48 PM] Successfully ran tools for contig_95.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_97.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_98.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_99.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_100.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_101.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_102.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_103.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_104.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_106.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_105.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_107.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_108.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_109.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_110.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_111.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_112.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_114.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_113.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_115.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_116.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_117.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_118.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_120.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_119.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_122.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_121.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_123.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_124.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_125.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_126.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_127.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_128.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_129.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_130.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_131.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_132.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_134.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_133.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_135.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_136.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_137.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_139.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_138.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_140.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_141.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_142.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_143.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_144.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_145.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_146.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_147.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_148.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_149.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_150.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_151.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_152.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_153.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_154.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_155.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_156.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_157.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_158.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_159.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_160.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_161.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_162.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_163.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_164.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_165.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_166.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_167.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_168.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_169.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_170.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_171.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_172.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_173.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_174.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_175.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_176.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_177.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_178.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_179.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_180.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_181.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_182.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_183.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_184.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_185.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_186.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_187.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_188.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_189.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_190.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_191.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_192.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_193.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_194.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_195.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_196.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_197.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_198.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_199.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_200.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_201.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_202.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_203.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_204.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_206.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_205.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_208.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_207.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_210.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_209.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_212.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_211.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_213.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_214.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_215.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_216.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_218.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_217.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_219.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_220.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_221.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_222.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_224.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_223.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_226.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_225.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_227.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_228.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_229.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_230.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_232.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_231.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_233.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_234.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_235.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_236.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_238.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_237.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_240.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_239.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_241.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_242.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_243.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_244.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_245.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_246.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_247.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_248.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_250.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_249.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_251.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_252.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_253.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_254.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_255.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_256.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_257.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_258.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_259.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_260.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_261.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_262.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_264.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_263.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_265.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_266.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_268.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_267.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_269.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_270.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_272.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_271.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_274.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_273.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_276.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_275.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_277.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_278.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_280.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_279.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_282.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_281.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_283.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_284.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_286.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_285.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_288.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_287.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_289.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_290.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_291.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_292.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_294.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_293.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_295.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_296.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_297.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_298.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_299.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_300.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_302.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_301.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_303.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_304.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_305.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_306.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_307.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_308.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_309.fasta: snap, glimmerhmm, augustus
[Oct 15 02:49 PM] Successfully ran tools for contig_310.fasta: snap, glimmerhmm, augustus
[Oct 15 02:50 PM] Successfully ran tools for contig_311.fasta: snap, glimmerhmm, augustus
[Oct 15 02:50 PM] Successfully ran tools for contig_312.fasta: snap, glimmerhmm, augustus
[Oct 15 02:50 PM] Successfully ran tools for contig_314.fasta: snap, glimmerhmm, augustus
[Oct 15 02:50 PM] Successfully ran tools for contig_313.fasta: snap, glimmerhmm, augustus
[Oct 15 02:50 PM] Successfully ran tools for contig_315.fasta: snap, glimmerhmm, augustus
[Oct 15 02:50 PM] Successfully ran tools for contig_316.fasta: snap, glimmerhmm, augustus
[Oct 15 02:50 PM] Successfully ran tools for contig_317.fasta: snap, glimmerhmm, augustus
[Oct 15 02:50 PM] Successfully ran tools for contig_318.fasta: snap, glimmerhmm, augustus
[Oct 15 02:50 PM] Successfully ran tools for contig_319.fasta: snap, glimmerhmm, augustus
[Oct 15 02:50 PM] Successfully ran tools for contig_320.fasta: snap, glimmerhmm, augustus
[Oct 15 02:50 PM] Successfully ran tools for contig_321.fasta: snap, glimmerhmm, augustus
[Oct 15 02:50 PM] Successfully ran tools for contig_322.fasta: snap, glimmerhmm, augustus
[Oct 15 02:50 PM] Successfully ran tools for contig_323.fasta: snap, glimmerhmm, augustus
[Oct 15 02:50 PM] Successfully ran tools for contig_324.fasta: snap, glimmerhmm, augustus
[Oct 15 02:50 PM] Successfully ran tools for contig_325.fasta: snap, glimmerhmm, augustus
[Oct 15 02:50 PM] Successfully ran tools for contig_326.fasta: snap, glimmerhmm, augustus
[Oct 15 02:50 PM] Successfully ran tools for contig_327.fasta: snap, glimmerhmm, augustus
[Oct 15 02:50 PM] Successfully ran tools for contig_328.fasta: snap, glimmerhmm, augustus
[Oct 15 02:50 PM] Successfully ran tools for contig_329.fasta: snap, glimmerhmm, augustus
[Oct 15 02:50 PM] Successfully ran tools for contig_330.fasta: snap, glimmerhmm, augustus
[Oct 15 02:50 PM] Successfully ran tools for contig_331.fasta: snap, glimmerhmm, augustus
[Oct 15 02:50 PM] Augustus predictions filtered: 9234 kept, 0 filtered (protein length 30-30000 aa)
[Oct 15 02:50 PM] Augustus-hiq predictions filtered: 861 kept, 0 filtered (protein length 30-30000 aa)
[Oct 15 02:50 PM] glimmerhmm predictions filtered: 8873 kept, 0 filtered (protein length 30-30000 aa)
[Oct 15 02:50 PM] snap predictions filtered: 13221 kept, 0 filtered (protein length 30-30000 aa)
[Oct 15 02:50 PM] Ab initio predictions finished:
{
  "helixer": 14320,
  "augustus": 9234,
  "augustus-hiq": 861,
  "glimmerhmm": 8873,
  "snap": 13221
}
[Oct 15 02:50 PM] Memory monitoring data written to: /data/annotated/logfiles/predict-abinitio-memory-monitoring.jsonl
[Oct 15 02:50 PM] Downloading fungi_odb12.2 model from https://busco-data.ezlab.org/v6/data/lineages/fungi_odb12.2.2026-05-13.tar.gz
[Oct 15 02:51 PM] tar -zxf fungi_odb12.2.2026-05-13.tar.gz
[Oct 15 02:51 PM] Measuring assembly completeness with buscolite [lineage=fungi_odb12.2] for all ab initio predictions
[Oct 15 02:56 PM] ab initio models scoring by algorithm:
{
  "augustus": {
    "busco": 0.9656526005888125,
    "train": {
      "tool": "augustus",
      "model": "e865bd2d-8805-42eb-a690-763bdc4c3899",
      "n_test_genes": 200,
      "ref_genes_found": 199,
      "ref_genes_missed": 1,
      "extra_query_genes": 92,
      "average_aed": 0.0428491985257352,
      "nucleotide_sensitivity": 0.9490846676107876,
      "nucleotide_precision": 0.9778462432093619,
      "exon_sensitivity": 0.7948717948717948,
      "exon_precision": 0.8240720390720392,
      "gene_sensitivity": 0.9919354838709677,
      "gene_precision": 0.5720930232558139
    }
  },
  "glimmerhmm": {
    "busco": 0.8969578017664377,
    "train": {
      "tool": "glimmerhmm",
      "model": "train",
      "n_test_genes": 200,
      "ref_genes_found": 193,
      "ref_genes_missed": 7,
      "extra_query_genes": 61,
      "average_aed": 0.08284273425401169,
      "nucleotide_sensitivity": 0.9129714753921636,
      "nucleotide_precision": 0.9431045069056567,
      "exon_sensitivity": 0.6424731182795699,
      "exon_precision": 0.6950076804915513,
      "gene_sensitivity": 0.9078947368421053,
      "gene_precision": 0.5307692307692308
    }
  },
  "helixer": {
    "busco": 0.9990186457311089
  },
  "miniprot-gene": {
    "busco": 0.15309126594700687
  },
  "snap": {
    "busco": 0.9558390578999019,
    "train": {
      "tool": "snap",
      "model": "snap-trained.hmm",
      "n_test_genes": 200,
      "ref_genes_found": 199,
      "ref_genes_missed": 1,
      "extra_query_genes": 171,
      "average_aed": 0.06991765493959197,
      "nucleotide_sensitivity": 0.9245395674848199,
      "nucleotide_precision": 0.9546734215990075,
      "exon_sensitivity": 0.6843434343434344,
      "exon_precision": 0.7187008978675644,
      "gene_sensitivity": 0.989010989010989,
      "gene_precision": 0.3448275862068966
    }
  }
}
[Oct 15 02:56 PM] Calculated ab initio weights from data: ['helixer:4', 'augustus-hiq:4', 'augustus:2', 'glimmerhmm:1', 'miniprot-gene:1', 'snap:1']
[Oct 15 02:56 PM] GFFtk consensus will generate the best gene model at each locus
[Oct 15 02:56 PM] Parsing GFF3 files and clustering data into strand specific loci
[Oct 15 02:58 PM] Merging gene predictions from 6 source files
{'predictions': {'miniprot-gene', 'glimmerhmm', 'helixer', 'augustus-hiq', 'augustus', 'snap'}, 'evidence': {'miniprot'}}
[Oct 15 02:58 PM] Parsed 47219 gene models into 12593 loci. Dropped 141 genes models that were pseudo [labled as such or internal stop codons]
{'augustus': 141}
[Oct 15 02:58 PM] Using these filtered loci, the calculated gene model source weights to use as tiebreakers:
{"helixer": 4, "augustus-hiq": 4, "augustus": 2, "snap": 1, "glimmerhmm": 1, "miniprot-gene": 1}
[Oct 15 02:58 PM] Processing 12593 loci using 2 processes
[Oct 15 02:59 PM] Setting minimum gene model score to 7
[Oct 15 02:59 PM] Loaded repeats representing 7.44% of the genome and filtering out loci that are > 90% overlap with repeats
[Oct 15 02:59 PM] 0 gene models were dropped due to repeat overlap
[Oct 15 02:59 PM] 13430 consensus gene models derived from these sources:
[["helixer", 11903], ["augustus", 572], ["augustus-hiq", 456], ["glimmerhmm", 254], ["snap", 245]]
[Oct 15 02:59 PM] UTR extension not enabled, using CDS-only gene models
[Oct 15 02:59 PM] GFFtk consensus is finished: /data/annotated/predict_misc/consensus.predictions.gff3
[Oct 15 02:59 PM] Predicting tRNA genes
[Oct 15 02:59 PM] tRNAscan-SE -o /tmp/trnascan-1268ac90-821d-4033-8a2c-c5f51c0d351f/tRNAscan.out --thread 2 /data/annotated/predict_misc/genome.fasta
[Oct 15 03:00 PM] Status: Phase I: Searching for tRNAs with HMM-enabled Infernal
Status: Phase II: Infernal verification of candidate tRNAs detected with first-pass scan

[Oct 15 03:00 PM] 
tRNAscan-SE v.2.0.12 (Nov 2022) - scan sequences for transfer RNAs
Copyright (C) 2022 Patricia Chan and Todd Lowe
                   University of California Santa Cruz
Freely distributed under the GNU General Public License (GPLv3)

------------------------------------------------------------
Sequence file(s) to search:        /data/annotated/predict_misc/genome.fasta
Search Mode:                       Eukaryotic
Results written to:                /tmp/trnascan-1268ac90-821d-4033-8a2c-c5f51c0d351f/tRNAscan.out
Output format:                     Tabular
Searching with:                    Infernal First Pass->Infernal
Isotype-specific model scan:       Yes
Covariance model:                  /app/.pixi/envs/default/lib/tRNAscan-SE/models/TRNAinf-euk.cm
                                   /app/.pixi/envs/default/lib/tRNAscan-SE/models/TRNAinf-euk-SeC.cm
Infernal first pass cutoff score:  10

Temporary directory:               /tmp
------------------------------------------------------------


[Oct 15 03:00 PM] Merging all gene models, sorting, and renaming using locus_tag=FUN2_
[Oct 15 03:01 PM] Converting to GenBank format
[Oct 15 03:02 PM] Annotation statistics:
{
  "genes": 13669,
  "common_name": 0,
  "mRNA": 13430,
  "tRNA": 239,
  "ncRNA": 0,
  "rRNA": 0,
  "repeat_region": 0,
  "misc_feature": 0,
  "avg_gene_length": 1529.9,
  "transcript-level": {
    "CDS_transcripts": 13430,
    "CDS_five_utr": 0,
    "CDS_three_utr": 0,
    "CDS_no_utr": 13430,
    "CDS_five_three_utr": 0,
    "CDS_complete": 13393,
    "CDS_no-start": 12,
    "CDS_no-stop": 25,
    "CDS_no-start_no-stop": 0,
    "total_exons": 42850,
    "total_cds_exons": 42850,
    "average_number_transcripts_per_gene": 1.0,
    "multiple_exon_transcript": 10784,
    "single_exon_transcript": 2646,
    "average_number_cds_exons": 3.19,
    "avg_exon_length": 426.67,
    "median_number_exons": 3.0,
    "max_number_exons": 27,
    "avg_protein_length": 453.84,
    "avg_transcript_length": 1361.34,
    "functional": {
      "go_terms": 0,
      "interproscan": 0,
      "eggnog": 0,
      "pfam": 0,
      "cazyme": 0,
      "merops": 0,
      "busco": 0,
      "secretion": 0
    }
  }
}
[Oct 15 03:02 PM] Measuring assembly completeness with buscolite [lineage=fungi_odb12.2]
[Oct 15 03:03 PM] Assembly completeness:
 complete=1001 [98.23%]
 single-copy=980 [96.17%]
 fragmented=4 [0.39%]
 duplicated=21 [2.06%]
 missing=14 [1.37%]
 total=1019 [100.00%]
[Oct 15 03:03 PM] funannotate2.predict module finished: peak memory usage=1.09 GiB