-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_26/scaffold_26_9011384-9302858

-reading genomic sequence.

** Processing features (+)

-finding all potential splice sites, looking for GT/GC donors and AG acceptors.
-finding all potential starts and stops. (strand: +)
-loading gene prediction evidence. (strand: +)Valid prediction for GeneMark_model.100506_t
Valid prediction for GlimmerHMM_glimmerT_57683-T1
Valid prediction for Augustus_model.g38432.t1
Valid prediction for snap_scaffold_26-snap.2073-T1
Valid prediction for GlimmerHMM_glimmerT_57676-T1
Valid prediction for snap_scaffold_26-snap.2081-T1
Valid prediction for GlimmerHMM_glimmerT_57663-T1
Valid prediction for GlimmerHMM_glimmerT_57678-T1
Valid prediction for GlimmerHMM_glimmerT_57664-T1
Valid prediction for GlimmerHMM_glimmerT_57689-T1
Valid prediction for snap_scaffold_26-snap.2074-T1
Valid prediction for GlimmerHMM_glimmerT_57681-T1
Valid prediction for HiQ_model.g38420.t1
Valid prediction for GeneMark_model.100512_t
Valid prediction for Augustus_model.g38418.t1
Couldn't classify 14822, 14851
Sorry, prediction pasa_asmbl_35719.p1 fails validation.
(GGA)	 GA	14822-14851	GT	TGG
(GAG)	 AG	15283-16220	GT	GAG
(GGA)	 AG	16334-16458	GT	AGG
(GTA)	 AG	16649-16834	GT	CGG
(CTG)	 AG	17126-17204	GT	ATG
(GTT)	 AG	17296-17420	GT	TGG
(CCA)	 AG	17533-17740	GT	TGG
(GAT)	 AG	17994-18083	GT	AGG
(GCT)	 AG	18254-18319	GT	GGG
(AAA)	 AG	18420-18505	GT	TGG
(ATA)	 AG	18605-18777	GG	AGG
-recovered pasa_asmbl_35719.p1, terminal, 18605, 18777
-recovered pasa_asmbl_35719.p1, internal, 15283, 16220
-recovered pasa_asmbl_35719.p1, internal, 16334, 16458
-recovered pasa_asmbl_35719.p1, internal, 16649, 16834
-recovered pasa_asmbl_35719.p1, internal, 17126, 17204
-recovered pasa_asmbl_35719.p1, internal, 17296, 17420
-recovered pasa_asmbl_35719.p1, internal, 17533, 17740
-recovered pasa_asmbl_35719.p1, internal, 17994, 18083
-recovered pasa_asmbl_35719.p1, internal, 18254, 18319
-recovered pasa_asmbl_35719.p1, internal, 18420, 18505
Valid prediction for snap_scaffold_26-snap.2084-T1
Couldn't classify 98836, 98911
Sorry, prediction pasa_asmbl_35852.p1 fails validation.
(ATG)	 GC	95851-95857	GT	TGG
(CTA)	 AG	96293-96387	GT	TGG
(GGG)	 AG	97246-97294	GT	CGG
(GTA)	 AG	97414-97486	GT	GGG
(GGG)	 AG	98836-98911	GT	CGG
-recovered pasa_asmbl_35852.p1, initial, 95851, 95857
-recovered pasa_asmbl_35852.p1, internal, 96293, 96387
-recovered pasa_asmbl_35852.p1, internal, 97246, 97294
-recovered pasa_asmbl_35852.p1, internal, 97414, 97486
-recovered pasa_asmbl_35852.p1, internal, 98836, 98911
Valid prediction for GeneMark_model.100510_t
Valid prediction for Augustus_model.g38434.t1
Valid prediction for CodingQuarry_transcript_40332-T1
Valid prediction for GeneMark_model.100493_t
Valid prediction for snap_scaffold_26-snap.2079-T1
Valid prediction for GlimmerHMM_glimmerT_57667-T1
Valid prediction for Augustus_model.g38417.t1
Valid prediction for GeneMark_model.100491_t
Valid prediction for snap_scaffold_26-snap.2070-T1
Valid prediction for snap_scaffold_26-snap.2107-T1
Valid prediction for GlimmerHMM_glimmerT_57670-T1
Valid prediction for GeneMark_model.100507_t
Valid prediction for snap_scaffold_26-snap.2101-T1
Valid prediction for GeneMark_model.100487_t
Valid prediction for GeneMark_model.100508_t
Valid prediction for GlimmerHMM_glimmerT_57690-T1
Valid prediction for snap_scaffold_26-snap.2083-T1
Valid prediction for Augustus_model.g38427.t1
Valid prediction for GeneMark_model.100475_t
Couldn't classify 143840, 144023
Sorry, prediction pasa_asmbl_35734.p1 fails validation.
(ATG)	 CC	137436-137474	GT	AGG
(ACA)	 AG	137670-137761	GT	TGG
(GTT)	 AG	138080-138191	GT	AGG
(TCT)	 AG	138782-138923	GT	AGG
(GGC)	 AG	139029-139179	GT	GGG
(TTT)	 AG	139298-139436	GT	AGG
(GTC)	 AG	139836-139979	GT	AGG
(AAA)	 AG	140176-140419	GT	TGG
(AGA)	 AG	140583-140699	GT	AGG
(ACC)	 AG	140886-141052	GT	AGG
(CTG)	 AG	141282-141510	GT	AGG
(GTG)	 AG	141866-142034	GT	AAG
(GAA)	 AG	142138-142225	GT	TGG
(TAC)	 AG	142709-142841	GT	GAG
(GAT)	 AG	143252-143440	GT	GGG
(AGT)	 AG	143636-143738	GT	CCG
(GTC)	 AG	143840-144023	GG	ATG
-recovered pasa_asmbl_35734.p1, initial, 137436, 137474
-recovered pasa_asmbl_35734.p1, internal, 137670, 137761
-recovered pasa_asmbl_35734.p1, internal, 138080, 138191
-recovered pasa_asmbl_35734.p1, internal, 138782, 138923
-recovered pasa_asmbl_35734.p1, internal, 139029, 139179
-recovered pasa_asmbl_35734.p1, internal, 139298, 139436
-recovered pasa_asmbl_35734.p1, internal, 139836, 139979
-recovered pasa_asmbl_35734.p1, internal, 140176, 140419
-recovered pasa_asmbl_35734.p1, internal, 140583, 140699
-recovered pasa_asmbl_35734.p1, internal, 140886, 141052
-recovered pasa_asmbl_35734.p1, internal, 141282, 141510
-recovered pasa_asmbl_35734.p1, internal, 141866, 142034
-recovered pasa_asmbl_35734.p1, internal, 142138, 142225
-recovered pasa_asmbl_35734.p1, internal, 142709, 142841
-recovered pasa_asmbl_35734.p1, internal, 143252, 143440
-recovered pasa_asmbl_35734.p1, internal, 143636, 143738
Valid prediction for GlimmerHMM_glimmerT_57675-T1
Valid prediction for GeneMark_model.100483_t
Couldn't classify 150042, 150127
Sorry, prediction pasa_asmbl_35736.p1 fails validation.
(CCC)	 AT	150042-150127	GT	CCG
(GTC)	 AG	150229-150413	GT	TGG
(ACC)	 AG	150528-150706	GC	GAG
-recovered pasa_asmbl_35736.p1, terminal, 150528, 150706
-recovered pasa_asmbl_35736.p1, internal, 150229, 150413
-recovered pasa_asmbl_35736.p1, internal, 150528, 150706
Valid prediction for snap_scaffold_26-snap.2090-T1
Valid prediction for HiQ_model.g38428.t1
Valid prediction for pasa_asmbl_35722.p1
Valid prediction for GlimmerHMM_glimmerT_57658-T1
Valid prediction for CodingQuarry_transcript_40331-T1
Valid prediction for GlimmerHMM_glimmerT_57691-T1
Valid prediction for GlimmerHMM_glimmerT_57661-T1
Valid prediction for CodingQuarry_transcript_40333-T1
Valid prediction for pasa_asmbl_35727.p1
Valid prediction for snap_scaffold_26-snap.2085-T1
Valid prediction for snap_scaffold_26-snap.2071-T1
Valid prediction for GeneMark_model.100489_t
Valid prediction for GeneMark_model.100495_t
Valid prediction for GeneMark_model.100480_t
Valid prediction for Augustus_model.g38424.t1
Valid prediction for GeneMark_model.100499_t
Valid prediction for GeneMark_model.100490_t
Valid prediction for snap_scaffold_26-snap.2088-T1
Valid prediction for GlimmerHMM_glimmerT_57672-T1
Valid prediction for GeneMark_model.100504_t
Valid prediction for snap_scaffold_26-snap.2078-T1
Valid prediction for Augustus_model.g38426.t1
Valid prediction for GeneMark_model.100477_t
Valid prediction for GlimmerHMM_glimmerT_57693-T1
Valid prediction for Augustus_model.g38439.t1
Valid prediction for snap_scaffold_26-snap.2087-T1
Couldn't classify 89972, 90032
Sorry, prediction pasa_asmbl_35729.p1 fails validation.
(ATG)	 AC	81239-81346	GT	AGG
(ACC)	 AG	82880-82988	GT	AGG
(GAT)	 AG	83288-83378	GT	GGG
(GGT)	 AG	85674-85809	GT	AGG
(GGG)	 AG	88699-88848	GT	AGG
(GTG)	 AG	88967-89073	GT	AGG
(GAA)	 AG	89972-90032	GT	AGG
-recovered pasa_asmbl_35729.p1, initial, 81239, 81346
-recovered pasa_asmbl_35729.p1, internal, 82880, 82988
-recovered pasa_asmbl_35729.p1, internal, 83288, 83378
-recovered pasa_asmbl_35729.p1, internal, 85674, 85809
-recovered pasa_asmbl_35729.p1, internal, 88699, 88848
-recovered pasa_asmbl_35729.p1, internal, 88967, 89073
-recovered pasa_asmbl_35729.p1, internal, 89972, 90032
Valid prediction for GeneMark_model.100505_t
Valid prediction for GeneMark_model.100497_t
Valid prediction for GeneMark_model.100478_t
Valid prediction for Augustus_model.g38430.t1
Valid prediction for GeneMark_model.100486_t
Valid prediction for GlimmerHMM_glimmerT_57674-T1
Valid prediction for snap_scaffold_26-snap.2102-T1
Valid prediction for snap_scaffold_26-snap.2080-T1
Valid prediction for GlimmerHMM_glimmerT_57671-T1
Valid prediction for GlimmerHMM_glimmerT_57660-T1
Valid prediction for CodingQuarry_transcript_40336-T1
Valid prediction for GeneMark_model.100488_t
Valid prediction for snap_scaffold_26-snap.2082-T1
Valid prediction for GeneMark_model.100492_t
Valid prediction for Augustus_model.g38429.t1
Valid prediction for GlimmerHMM_glimmerT_57673-T1

-loading the search evidence (protein and EST search results, strand: +)
-scoring exons (strand: +)

** Processing features (-)

-finding all potential splice sites, looking for GT/GC donors and AG acceptors.
-finding all potential starts and stops. (strand: -)
-loading gene prediction evidence. (strand: -)Valid prediction for CodingQuarry_transcript_40334-T1
Valid prediction for snap_scaffold_26-snap.2077-T1
Valid prediction for Augustus_model.g38425.t1
Valid prediction for GeneMark_model.100482_t
Valid prediction for snap_scaffold_26-snap.2092-T1
Couldn't classify 51206, 51303
Sorry, prediction pasa_asmbl_35044.p2 fails validation.
(AGT)	 TC	51206-51303	GT	GAG
(CTG)	 AG	53711-53795	GT	TGG
(CTG)	 AG	54820-54984	AG	GAA
-recovered pasa_asmbl_35044.p2, terminal, 54820, 54984
-recovered pasa_asmbl_35044.p2, internal, 53711, 53795
Valid prediction for snap_scaffold_26-snap.2072-T1
Valid prediction for pasa_asmbl_35039.p1
Valid prediction for GeneMark_model.100485_t
Valid prediction for Augustus_model.g38416.t1
Valid prediction for GlimmerHMM_glimmerT_57659-T1
Valid prediction for Augustus_model.g38435.t1
Valid prediction for Augustus_model.g38437.t1
Valid prediction for Augustus_model.g38438.t1
Valid prediction for GeneMark_model.100511_t
Valid prediction for snap_scaffold_26-snap.2094-T1
Valid prediction for GeneMark_model.100509_t
Valid prediction for GeneMark_model.100476_t
Valid prediction for snap_scaffold_26-snap.2076-T1
Valid prediction for snap_scaffold_26-snap.2099-T1
Valid prediction for GeneMark_model.100498_t
Valid prediction for Augustus_model.g38436.t1
Valid prediction for GeneMark_model.100474_t
Valid prediction for Augustus_model.g38421.t1
Valid prediction for GeneMark_model.100479_t
Valid prediction for Augustus_model.g38419.t1
Valid prediction for GlimmerHMM_glimmerT_57668-T1
Valid prediction for GeneMark_model.100500_t
Valid prediction for snap_scaffold_26-snap.2086-T1
Couldn't classify 264565, 264670
Sorry, prediction pasa_asmbl_35029.p1 fails validation.
(CGT)	 AC	264565-264670	GT	CCG
(TAT)	 AG	264852-264941	GT	AGG
(TCC)	 AG	265301-265442	GT	AGG
(AGT)	 AG	265880-265960	GT	AGG
(GTA)	 AG	266318-266576	GG	AAG
-recovered pasa_asmbl_35029.p1, terminal, 266318, 266576
-recovered pasa_asmbl_35029.p1, internal, 264852, 264941
-recovered pasa_asmbl_35029.p1, internal, 265301, 265442
-recovered pasa_asmbl_35029.p1, internal, 265880, 265960
Valid prediction for snap_scaffold_26-snap.2104-T1
Valid prediction for GlimmerHMM_glimmerT_57685-T1
Valid prediction for snap_scaffold_26-snap.2100-T1
Valid prediction for Augustus_model.g38441.t1
Valid prediction for GlimmerHMM_glimmerT_57694-T1
Valid prediction for GlimmerHMM_glimmerT_57666-T1
Valid prediction for GlimmerHMM_glimmerT_57679-T1
Valid prediction for snap_scaffold_26-snap.2091-T1
Valid prediction for Augustus_model.g38444.t1
Valid prediction for GlimmerHMM_glimmerT_57692-T1
Valid prediction for GeneMark_model.100481_t
Valid prediction for GeneMark_model.100502_t
Valid prediction for GlimmerHMM_glimmerT_57669-T1
Valid prediction for GeneMark_model.100494_t
Valid prediction for Augustus_model.g38442.t1
Valid prediction for snap_scaffold_26-snap.2075-T1
Valid prediction for HiQ_model.g38423.t1
Valid prediction for Augustus_model.g38433.t1
Valid prediction for GlimmerHMM_glimmerT_57665-T1
Valid prediction for Augustus_model.g38440.t1
Valid prediction for GlimmerHMM_glimmerT_57680-T1
Valid prediction for GeneMark_model.100503_t
Couldn't classify 241484, 241626
Sorry, prediction pasa_asmbl_35032.p1 fails validation.
(TCA)	 GC	241484-241626	GT	AAG
(CTC)	 AG	241733-241902	GT	TGG
(TGC)	 AG	242347-242525	GT	CAG
(CTG)	 AG	242611-242764	GT	AGG
(AGT)	 AG	242956-243046	GT	AGG
(ACT)	 AG	243182-243251	GT	AGG
(AAA)	 AG	243510-243742	GT	AGG
(TAT)	 AG	243831-244668	AA	AAA
add_exon() Sorry, pasa_asmbl_35032.p1 243510-243742-terminal-2 is invalid.
-recovered pasa_asmbl_35032.p1, terminal, 243510, 243742
-recovered pasa_asmbl_35032.p1, terminal, 243831, 244668
-recovered pasa_asmbl_35032.p1, internal, 241733, 241902
-recovered pasa_asmbl_35032.p1, internal, 242347, 242525
-recovered pasa_asmbl_35032.p1, internal, 242611, 242764
-recovered pasa_asmbl_35032.p1, internal, 242956, 243046
-recovered pasa_asmbl_35032.p1, internal, 243182, 243251
-recovered pasa_asmbl_35032.p1, internal, 243510, 243742
Valid prediction for CodingQuarry_transcript_40335-T1
Valid prediction for Augustus_model.g38443.t1
Valid prediction for snap_scaffold_26-snap.2103-T1
Valid prediction for snap_scaffold_26-snap.2098-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_26-snap.2108-T1
Valid prediction for snap_scaffold_26-snap.2093-T1
Valid prediction for snap_scaffold_26-snap.2106-T1
Valid prediction for GlimmerHMM_glimmerT_57662-T1
Valid prediction for GlimmerHMM_glimmerT_57684-T1
Valid prediction for snap_scaffold_26-snap.2069-T1
Valid prediction for snap_scaffold_26-snap.2067-T1
Valid prediction for pasa_asmbl_35036.p1
Valid prediction for snap_scaffold_26-snap.2095-T1
Valid prediction for GeneMark_model.100501_t
Valid prediction for GlimmerHMM_glimmerT_57677-T1
Valid prediction for snap_scaffold_26-snap.2097-T1
Valid prediction for GlimmerHMM_glimmerT_57687-T1
Valid prediction for Augustus_model.g38431.t1
Valid prediction for snap_scaffold_26-snap.2096-T1
Valid prediction for GeneMark_model.100484_t
Valid prediction for Augustus_model.g38415.t1
Valid prediction for snap_scaffold_26-snap.2105-T1
Valid prediction for snap_scaffold_26-snap.2089-T1
Valid prediction for GlimmerHMM_glimmerT_57688-T1
Valid prediction for GeneMark_model.100496_t
Valid prediction for GlimmerHMM_glimmerT_57686-T1
Valid prediction for snap_scaffold_26-snap.2068-T1
Valid prediction for Augustus_model.g38422.t1
Valid prediction for GlimmerHMM_glimmerT_57682-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 29501, rend_intergenic: 25537  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 251406, rend_intergenic: 249128  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 283163, rend_intergenic: 269478  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 291475
-exon list size: 622


building trellis

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57.5    
57.7    
57.9    
58.0    
58.2    
58.3    
58.5    
58.7    
58.8    
59.0    
59.1    
59.3    
59.5    
59.6    
59.8    
59.9    
60.1    
60.3    
60.4    
60.6    
60.7    
60.9    
61.1    
61.2    
61.4    
61.5    
61.7    
61.9    
62.0    
62.2    
62.3    
62.5    
62.7    
62.8    
63.0    
63.1    
63.3    
63.5    
63.6    
63.8    
63.9    
64.1    
64.3    
64.4    
64.6    
64.7    
64.9    
65.1    
65.2    
65.4    
65.5    
65.7    
65.9    
66.0    
66.2    
66.3    
66.5    
66.7    
66.8    
67.0    
67.1    
67.3    
67.5    
67.6    
67.8    
67.9    
68.1    
68.3    
68.4    
68.6    
68.8    
68.9    
69.1    
69.2    
69.4    
69.6    
69.7    
69.9    
70.0    
70.2    
70.4    
70.5    
70.7    
70.8    
71.0    
71.2    
71.3    
71.5    
71.6    
71.8    
72.0    
72.1    
72.3    
72.4    
72.6    
72.8    
72.9    
73.1    
73.2    
73.4    
73.6    
73.7    
73.9    
74.0    
74.2    
74.4    
74.5    
74.7    
74.8    
75.0    
75.2    
75.3    
75.5    
75.6    
75.8    
76.0    
76.1    
76.3    
76.4    
76.6    
76.8    
76.9    
77.1    
77.2    
77.4    
77.6    
77.7    
77.9    
78.0    
78.2    
78.4    
78.5    
78.7    
78.8    
79.0    
79.2    
79.3    
79.5    
79.6    
79.8    
80.0    
80.1    
80.3    
80.4    
80.6    
80.8    
80.9    
81.1    
81.2    
81.4    
81.6    
81.7    
81.9    
82.1    
82.2    
82.4    
82.5    
82.7    
82.9    
83.0    
83.2    
83.3    
83.5    
83.7    
83.8    
84.0    
84.1    
84.3    
84.5    
84.6    
84.8    
84.9    
85.1    
85.3    
85.4    
85.6    
85.7    
85.9    
86.1    
86.2    
86.4    
86.5    
86.7    
86.9    
87.0    
87.2    
87.3    
87.5    
87.7    
87.8    
88.0    
88.1    
88.3    
88.5    
88.6    
88.8    
88.9    
89.1    
89.3    
89.4    
89.6    
89.7    
89.9    
90.1    
90.2    
90.4    
90.5    
90.7    
90.9    
91.0    
91.2    
91.3    
91.5    
91.7    
91.8    
92.0    
92.1    
92.3    
92.5    
92.6    
92.8    
92.9    
93.1    
93.3    
93.4    
93.6    
93.8    
93.9    
94.1    
94.2    
94.4    
94.6    
94.7    
94.9    
95.0    
95.2    
95.4    
95.5    
95.7    
95.8    
96.0    
96.2    
96.3    
96.5    
96.6    
96.8    
97.0    
97.1    
97.3    
97.4    
97.6    
97.8    
97.9    
98.1    
98.2    
98.4    
98.6    
98.7    
98.9    
99.0    
99.2    
99.4    
99.5    
99.7    
99.8    
-found 35 predictions from path traversal
Error with prediction: snap lend_intergenic: 29501, rend_intergenic: 25537  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 251406, rend_intergenic: 249128  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 283163, rend_intergenic: 269478  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 32 predictions persist after filtering for low support