-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_24/scaffold_24_7665158-7837853

-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 snap_scaffold_24-snap.1594-T1
Couldn't classify 3394, 4680
Sorry, prediction pasa_asmbl_32388.p1 fails validation.
(GTT)	 CC	3394-4680	CA	AAC
Valid prediction for GlimmerHMM_glimmerT_52881-T1
Valid prediction for snap_scaffold_24-snap.1587-T1
Valid prediction for snap_scaffold_24-snap.1599-T1
Valid prediction for snap_scaffold_24-snap.1614-T1
Valid prediction for snap_scaffold_24-snap.1580-T1
Valid prediction for snap_scaffold_24-snap.1610-T1
Valid prediction for snap_scaffold_24-snap.1609-T1
Valid prediction for Augustus_model.g35215.t1
Couldn't classify 33446, 34114
Sorry, prediction pasa_asmbl_32389.p1 fails validation.
(GTT)	 AG	33446-34114	GT	AGG
(GCC)	 AG	34905-35019	GT	GGG
(GTC)	 AG	35169-35254	GT	AGG
(GTT)	 AG	35375-35458	TC	GAT
-recovered pasa_asmbl_32389.p1, terminal, 35375, 35458
-recovered pasa_asmbl_32389.p1, internal, 33446, 34114
-recovered pasa_asmbl_32389.p1, internal, 34905, 35019
-recovered pasa_asmbl_32389.p1, internal, 35169, 35254
Valid prediction for snap_scaffold_24-snap.1592-T1
Sorry, intron length (3) is less than minimum required (10)
Couldn't classify 40515, 40648
Couldn't classify 41251, 41411
Sorry, prediction pasa_asmbl_32390.p1 fails validation.
(GCC)	 GT	40515-40648	GT	AGG
(GAT)	 AG	40744-40934	GT	GGG
(GGG)	 AG	41251-41411	GA	AGG
-recovered pasa_asmbl_32390.p1, internal, 40744, 40934
Valid prediction for HiQ_model.g35218.t1
Valid prediction for GlimmerHMM_glimmerT_52880-T1
Valid prediction for snap_scaffold_24-snap.1601-T1
Valid prediction for HiQ_model.g35213.t1
Valid prediction for snap_scaffold_24-snap.1597-T1
Valid prediction for snap_scaffold_24-snap.1607-T1
Valid prediction for Augustus_model.g35230.t1
Valid prediction for snap_scaffold_24-snap.1581-T1
Valid prediction for snap_scaffold_24-snap.1578-T1
Valid prediction for pasa_asmbl_32392.p1
Valid prediction for snap_scaffold_24-snap.1606-T1
Valid prediction for GlimmerHMM_glimmerT_52888-T1
Valid prediction for Augustus_model.g35225.t1
Couldn't classify 104655, 104752
Couldn't classify 106311, 106353
Sorry, prediction pasa_asmbl_32643.p1 fails validation.
(GGT)	 AA	104655-104752	GT	GGG
(GGG)	 AG	104985-105058	GT	AGG
(GAT)	 AG	105398-105508	GT	AGG
(GGG)	 AG	106086-106200	GT	AGG
(GGC)	 AG	106311-106353	GA	AGG
-recovered pasa_asmbl_32643.p1, internal, 104985, 105058
-recovered pasa_asmbl_32643.p1, internal, 105398, 105508
-recovered pasa_asmbl_32643.p1, internal, 106086, 106200
Couldn't classify 43640, 44194
Sorry, prediction pasa_asmbl_32391.p1 fails validation.
(GCC)	 GC	43640-44194	CA	GAC
Valid prediction for snap_scaffold_24-snap.1588-T1
Valid prediction for GlimmerHMM_glimmerT_52873-T1
Valid prediction for CodingQuarry_transcript_37369-T1
Valid prediction for GlimmerHMM_glimmerT_52883-T1
Valid prediction for Augustus_model.g35226.t1
Valid prediction for GlimmerHMM_glimmerT_52866-T1
Valid prediction for CodingQuarry_transcript_37366-T1
Valid prediction for GlimmerHMM_glimmerT_52878-T1
Valid prediction for Augustus_model.g35219.t1
Valid prediction for GlimmerHMM_glimmerT_52869-T1
Valid prediction for GlimmerHMM_glimmerT_52882-T1
Valid prediction for snap_scaffold_24-snap.1595-T1
Valid prediction for GlimmerHMM_glimmerT_52865-T1
Valid prediction for snap_scaffold_24-snap.1613-T1
Valid prediction for snap_scaffold_24-snap.1602-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for Augustus_model.g35224.t1
Valid prediction for GlimmerHMM_glimmerT_52886-T1
Valid prediction for Augustus_model.g35231.t1
Valid prediction for Augustus_model.g35223.t1
Valid prediction for GlimmerHMM_glimmerT_52870-T1
Couldn't classify 106692, 106854
Couldn't classify 107756, 107822
Sorry, prediction pasa_asmbl_32395.p1 fails validation.
(GAA)	 GT	106692-106854	GT	GAG
(ACC)	 AG	106972-107117	GT	GGG
(GGC)	 AG	107417-107580	GT	AAG
(AAT)	 AG	107756-107822	GA	AGG
-recovered pasa_asmbl_32395.p1, internal, 106972, 107117
-recovered pasa_asmbl_32395.p1, internal, 107417, 107580
Valid prediction for GlimmerHMM_glimmerT_52871-T1
Valid prediction for GlimmerHMM_glimmerT_52874-T1
Valid prediction for CodingQuarry_transcript_37368-T1
Valid prediction for snap_scaffold_24-snap.1584-T1
Valid prediction for snap_scaffold_24-snap.1583-T1
Valid prediction for Augustus_model.g35210.t1
Valid prediction for snap_scaffold_24-snap.1591-T1
Valid prediction for Augustus_model.g35216.t1
Couldn't classify 107919, 107946
Couldn't classify 109403, 109642
Couldn't classify 109936, 110017
Couldn't classify 110240, 110332
Sorry, prediction pasa_asmbl_32396.p1 fails validation.
(GGG)	 GC	107919-107946	GT	TGG
(ATG)	 AG	108103-108201	GT	AGG
(ATC)	 AG	108564-108634	GT	ATG
(CTT)	 AG	108837-108951	GT	AGG
(CAA)	 AG	109137-109245	GT	ATG
(ATA)	 AG	109403-109642	AT	TCA
(GTA)	 AC	109936-110017	GT	AGG
(GAG)	 AG	110240-110332	CA	ACC
add_exon() Sorry, pasa_asmbl_32396.p1 108103-108201-initial-1 is invalid.
-recovered pasa_asmbl_32396.p1, initial, 108103, 108201
-recovered pasa_asmbl_32396.p1, internal, 108103, 108201
-recovered pasa_asmbl_32396.p1, internal, 108564, 108634
-recovered pasa_asmbl_32396.p1, internal, 108837, 108951
-recovered pasa_asmbl_32396.p1, internal, 109137, 109245
Valid prediction for Augustus_model.g35214.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: -)Couldn't classify 156120, 156179
Couldn't classify 161795, 161845
Sorry, prediction pasa_asmbl_33050.p1 fails validation.
(GGA)	 TG	156120-156179	GT	GGG
(GAC)	 AG	158300-158382	GT	AAG
(CTA)	 AG	159448-159553	GT	AGG
(AAC)	 AG	161795-161845	GA	GCG
-recovered pasa_asmbl_33050.p1, internal, 158300, 158382
-recovered pasa_asmbl_33050.p1, internal, 159448, 159553
Valid prediction for GlimmerHMM_glimmerT_52891-T1
Valid prediction for GlimmerHMM_glimmerT_52887-T1
Valid prediction for snap_scaffold_24-snap.1590-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for CodingQuarry_transcript_37365-T1
Valid prediction for GlimmerHMM_glimmerT_52876-T1
Valid prediction for GlimmerHMM_glimmerT_52884-T1
Couldn't classify 39326, 39406
Sorry, prediction pasa_asmbl_33064.p1 fails validation.
(ATG)	 AG	36598-36766	GT	CAG
(AGA)	 AG	37832-38035	GT	TGG
(CAC)	 AG	38705-38781	GT	GGG
(CTG)	 AG	39326-39406	TG	AGT
-recovered pasa_asmbl_33064.p1, initial, 36598, 36766
-recovered pasa_asmbl_33064.p1, internal, 36598, 36766
-recovered pasa_asmbl_33064.p1, internal, 37832, 38035
-recovered pasa_asmbl_33064.p1, internal, 38705, 38781
Valid prediction for snap_scaffold_24-snap.1576-T1
Couldn't classify 102778, 102819
Sorry, prediction pasa_asmbl_33057.p1 fails validation.
(ATG)	 AG	99561-99620	GT	AGG
(ATC)	 AG	99975-100080	GT	CCG
(AGC)	 AG	100358-100562	GT	CGG
(GGA)	 AG	100937-101060	GT	GGG
(CTG)	 AG	101168-101292	GT	AAG
(AGA)	 AG	101418-101464	GT	CAG
(AGA)	 AG	101569-101672	GT	AGG
(GAG)	 AG	101835-101957	GT	AGG
(GAC)	 AG	102222-102314	GT	TGG
(ATG)	 AG	102465-102635	GT	AGG
(AAA)	 AG	102778-102819	GG	TGG
-recovered pasa_asmbl_33057.p1, initial, 99561, 99620
-recovered pasa_asmbl_33057.p1, initial, 102465, 102635
-recovered pasa_asmbl_33057.p1, internal, 99561, 99620
-recovered pasa_asmbl_33057.p1, internal, 99975, 100080
-recovered pasa_asmbl_33057.p1, internal, 100358, 100562
-recovered pasa_asmbl_33057.p1, internal, 100937, 101060
-recovered pasa_asmbl_33057.p1, internal, 101168, 101292
-recovered pasa_asmbl_33057.p1, internal, 101418, 101464
-recovered pasa_asmbl_33057.p1, internal, 101569, 101672
-recovered pasa_asmbl_33057.p1, internal, 101835, 101957
-recovered pasa_asmbl_33057.p1, internal, 102222, 102314
-recovered pasa_asmbl_33057.p1, internal, 102465, 102635
Valid prediction for Augustus_model.g35227.t1
Valid prediction for GlimmerHMM_glimmerT_52875-T1
Valid prediction for snap_scaffold_24-snap.1608-T1
Valid prediction for snap_scaffold_24-snap.1577-T1
Valid prediction for snap_scaffold_24-snap.1605-T1
Valid prediction for CodingQuarry_transcript_37367-T1
Valid prediction for snap_scaffold_24-snap.1600-T1
Sorry, intron length (7) is less than minimum required (10)
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_24-snap.1582-T1
Valid prediction for Augustus_model.g35211.t1
Couldn't classify 108999, 109068
Sorry, prediction pasa_asmbl_33054.p1 fails validation.
(CCC)	 AC	108999-109068	GT	ACG
(CGT)	 AG	109155-109229	GT	AGG
(GCT)	 AG	109319-109397	GT	AGG
(GGC)	 AG	109523-109621	GT	TGG
(GGG)	 AG	109849-109904	GT	CGG
(ACC)	 AG	110200-110294	AC	GAA
-recovered pasa_asmbl_33054.p1, terminal, 110200, 110294
-recovered pasa_asmbl_33054.p1, internal, 109155, 109229
-recovered pasa_asmbl_33054.p1, internal, 109319, 109397
-recovered pasa_asmbl_33054.p1, internal, 109523, 109621
-recovered pasa_asmbl_33054.p1, internal, 109849, 109904
Valid prediction for Augustus_model.g35232.t1
Valid prediction for Augustus_model.g35228.t1
Valid prediction for GlimmerHMM_glimmerT_52868-T1
Valid prediction for snap_scaffold_24-snap.1603-T1
Valid prediction for snap_scaffold_24-snap.1604-T1
Valid prediction for snap_scaffold_24-snap.1596-T1
Valid prediction for pasa_asmbl_33051.p1
Valid prediction for Augustus_model.g35221.t1
Valid prediction for snap_scaffold_24-snap.1589-T1
Valid prediction for snap_scaffold_24-snap.1593-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for Augustus_model.g35212.t1
Valid prediction for snap_scaffold_24-snap.1615-T1
Valid prediction for snap_scaffold_24-snap.1616-T1
Valid prediction for GlimmerHMM_glimmerT_52872-T1
Valid prediction for snap_scaffold_24-snap.1586-T1
Valid prediction for snap_scaffold_24-snap.1575-T1
Couldn't classify 147779, 147833
Couldn't classify 148564, 148705
Sorry, prediction pasa_asmbl_33251.p1 fails validation.
(TTC)	 AG	147779-147833	GT	AGG
(TGA)	 AG	148069-148174	GT	TCG
(GTC)	 AG	148564-148705	AT	TCA
-recovered pasa_asmbl_33251.p1, internal, 147779, 147833
-recovered pasa_asmbl_33251.p1, internal, 148069, 148174
Valid prediction for GlimmerHMM_glimmerT_52889-T1
Valid prediction for GlimmerHMM_glimmerT_52877-T1
Valid prediction for GlimmerHMM_glimmerT_52885-T1
Valid prediction for Augustus_model.g35229.t1
Valid prediction for pasa_asmbl_33060.p1
Valid prediction for snap_scaffold_24-snap.1585-T1
Valid prediction for GlimmerHMM_glimmerT_52879-T1
Valid prediction for snap_scaffold_24-snap.1612-T1
Valid prediction for GlimmerHMM_glimmerT_52890-T1
Couldn't classify 103383, 103525
Sorry, prediction pasa_asmbl_33056.p1 fails validation.
(GGG)	 AG	103383-103525	GT	AGG
(AAT)	 AG	103761-103805	GT	CGG
(GCA)	 AG	104789-104877	GT	AGG
(ACG)	 AG	105009-105144	GT	AGG
(TCA)	 AG	105430-105624	GT	AGG
(GTA)	 AG	105934-106018	GC	AAG
-recovered pasa_asmbl_33056.p1, terminal, 105934, 106018
-recovered pasa_asmbl_33056.p1, internal, 103383, 103525
-recovered pasa_asmbl_33056.p1, internal, 103761, 103805
-recovered pasa_asmbl_33056.p1, internal, 104789, 104877
-recovered pasa_asmbl_33056.p1, internal, 105009, 105144
-recovered pasa_asmbl_33056.p1, internal, 105430, 105624
-recovered pasa_asmbl_33056.p1, internal, 105934, 106018
Couldn't classify 108796, 108884
Sorry, prediction pasa_asmbl_33293.p2 fails validation.
(ATG)	 CC	108005-108032	GT	GAG
(AGT)	 AG	108305-108423	GT	CTG
(GAG)	 AG	108517-108637	GT	AGG
(GCT)	 AG	108796-108884	GT	AGG
-recovered pasa_asmbl_33293.p2, initial, 108005, 108032
-recovered pasa_asmbl_33293.p2, internal, 108305, 108423
-recovered pasa_asmbl_33293.p2, internal, 108517, 108637
-recovered pasa_asmbl_33293.p2, internal, 108796, 108884
Valid prediction for HiQ_model.g35222.t1
Valid prediction for CodingQuarry_transcript_37370-T1
Couldn't classify 47656, 48106
Sorry, prediction pasa_asmbl_33062.p1 fails validation.
(CAC)	 CC	47656-48106	GT	TGG
(GAG)	 AG	48481-48601	GT	AGG
(AGC)	 AG	48895-48975	GT	CTG
(GTA)	 AG	49312-49398	GT	GTG
(GTA)	 AG	49549-49744	GT	TGG
(GGT)	 AG	50081-50251	GT	TGG
(GAC)	 AG	50521-50621	GT	AGG
(GAG)	 AG	50779-50926	GT	AGG
(GTG)	 AG	51169-51333	GT	GGG
(TTA)	 AG	52764-52856	GT	AGG
(CAG)	 AG	52949-53179	GT	AGG
(GTG)	 AG	53301-53425	GT	AGG
(AGA)	 AG	53792-53858	GA	GAG
-recovered pasa_asmbl_33062.p1, terminal, 53792, 53858
-recovered pasa_asmbl_33062.p1, internal, 48481, 48601
-recovered pasa_asmbl_33062.p1, internal, 48895, 48975
-recovered pasa_asmbl_33062.p1, internal, 49312, 49398
-recovered pasa_asmbl_33062.p1, internal, 49549, 49744
-recovered pasa_asmbl_33062.p1, internal, 50081, 50251
-recovered pasa_asmbl_33062.p1, internal, 50521, 50621
-recovered pasa_asmbl_33062.p1, internal, 50779, 50926
-recovered pasa_asmbl_33062.p1, internal, 51169, 51333
-recovered pasa_asmbl_33062.p1, internal, 52764, 52856
-recovered pasa_asmbl_33062.p1, internal, 52949, 53179
-recovered pasa_asmbl_33062.p1, internal, 53301, 53425
Valid prediction for snap_scaffold_24-snap.1598-T1
Valid prediction for Augustus_model.g35233.t1
Valid prediction for snap_scaffold_24-snap.1579-T1
Couldn't classify 142255, 142300
Couldn't classify 147481, 147531
Sorry, prediction pasa_asmbl_33236.p1 fails validation.
(CGA)	 AC	142255-142300	GT	TGG
(GTT)	 AG	144134-144336	GT	AGG
(GTG)	 AG	144777-144854	GT	AGG
(AGA)	 AG	147481-147531	AC	GTA
-recovered pasa_asmbl_33236.p1, internal, 144134, 144336
-recovered pasa_asmbl_33236.p1, internal, 144777, 144854
Valid prediction for Augustus_model.g35220.t1
Valid prediction for GlimmerHMM_glimmerT_52867-T1
Valid prediction for snap_scaffold_24-snap.1611-T1
Valid prediction for HiQ_model.g35217.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 24969, rend_intergenic: 12995  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44465, rend_intergenic: 38707  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73308, rend_intergenic: 70084  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95692, rend_intergenic: 95113  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110362, rend_intergenic: 101585  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137042, rend_intergenic: 119268  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139276, rend_intergenic: 137982  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163959, rend_intergenic: 154053  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 172696
-exon list size: 494


building trellis

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56.7    
56.9    
57.1    
57.3    
57.5    
57.7    
57.9    
58.1    
58.3    
58.5    
58.7    
58.9    
59.1    
59.3    
59.5    
59.7    
59.9    
60.1    
60.3    
60.5    
60.7    
60.9    
61.1    
61.3    
61.5    
61.7    
61.9    
62.1    
62.3    
62.5    
62.7    
62.9    
63.1    
63.3    
63.5    
63.7    
63.9    
64.1    
64.3    
64.5    
64.7    
64.9    
65.1    
65.3    
65.5    
65.7    
65.9    
66.1    
66.3    
66.5    
66.7    
66.9    
67.1    
67.3    
67.5    
67.7    
67.9    
68.1    
68.3    
68.5    
68.8    
69.0    
69.2    
69.4    
69.6    
69.8    
70.0    
70.2    
70.4    
70.6    
70.8    
71.0    
71.2    
71.4    
71.6    
71.8    
72.0    
72.2    
72.4    
72.6    
72.8    
73.0    
73.2    
73.4    
73.6    
73.8    
74.0    
74.2    
74.4    
74.6    
74.8    
75.0    
75.2    
75.4    
75.6    
75.8    
76.0    
76.2    
76.4    
76.6    
76.8    
77.0    
77.2    
77.4    
77.6    
77.8    
78.0    
78.2    
78.4    
78.6    
78.8    
79.0    
79.2    
79.4    
79.6    
79.8    
80.0    
80.2    
80.4    
80.6    
80.8    
81.0    
81.2    
81.5    
81.7    
81.9    
82.1    
82.3    
82.5    
82.7    
82.9    
83.1    
83.3    
83.5    
83.7    
83.9    
84.1    
84.3    
84.5    
84.7    
84.9    
85.1    
85.3    
85.5    
85.7    
85.9    
86.1    
86.3    
86.5    
86.7    
86.9    
87.1    
87.3    
87.5    
87.7    
87.9    
88.1    
88.3    
88.5    
88.7    
88.9    
89.1    
89.3    
89.5    
89.7    
89.9    
90.1    
90.3    
90.5    
90.7    
90.9    
91.1    
91.3    
91.5    
91.7    
91.9    
92.1    
92.3    
92.5    
92.7    
92.9    
93.1    
93.3    
93.5    
93.8    
94.0    
94.2    
94.4    
94.6    
94.8    
95.0    
95.2    
95.4    
95.6    
95.8    
96.0    
96.2    
96.4    
96.6    
96.8    
97.0    
97.2    
97.4    
97.6    
97.8    
98.0    
98.2    
98.4    
98.6    
98.8    
99.0    
99.2    
99.4    
99.6    
99.8    
-found 31 predictions from path traversal
Error with prediction: snap lend_intergenic: 24969, rend_intergenic: 12995  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44465, rend_intergenic: 38707  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73308, rend_intergenic: 70084  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95692, rend_intergenic: 95113  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110362, rend_intergenic: 101585  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137042, rend_intergenic: 119268  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139276, rend_intergenic: 137982  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163959, rend_intergenic: 154053  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 28 predictions persist after filtering for low support