-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_12/scaffold_12_11232889-11405673

-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 GlimmerHMM_glimmerT_30704-T1
Valid prediction for snap_scaffold_12-snap.2124-T1
Valid prediction for GeneMark_model.53020_t
Valid prediction for GlimmerHMM_glimmerT_30707-T1
Valid prediction for Augustus_model.g20477.t1
Valid prediction for GeneMark_model.53004_t
Valid prediction for GeneMark_model.53018_t
Valid prediction for snap_scaffold_12-snap.2129-T1
Valid prediction for GeneMark_model.53007_t
Valid prediction for CodingQuarry_transcript_10358-T1
Valid prediction for HiQ_model.g20475.t1
Valid prediction for GeneMark_model.53001_t
Couldn't classify 87484, 87492
Couldn't classify 89891, 89963
Sorry, prediction pasa_asmbl_8924.p1 fails validation.
(CCA)	 AC	87484-87492	GT	AGG
(ATA)	 AG	87770-87851	GT	TGG
(TAG)	 AG	88068-88196	GT	AGG
(GAT)	 AG	88329-88387	GT	AAG
(GAG)	 AG	88539-88723	GT	GGG
(CAA)	 AG	88971-89033	GT	GAG
(CTG)	 AG	89236-89290	GT	AGG
(AAC)	 AG	89384-89463	GT	GGG
(GGA)	 AG	89891-89963	CA	AGC
-recovered pasa_asmbl_8924.p1, terminal, 88971, 89033
-recovered pasa_asmbl_8924.p1, internal, 87770, 87851
-recovered pasa_asmbl_8924.p1, internal, 88068, 88196
-recovered pasa_asmbl_8924.p1, internal, 88329, 88387
-recovered pasa_asmbl_8924.p1, internal, 88539, 88723
-recovered pasa_asmbl_8924.p1, internal, 88971, 89033
-recovered pasa_asmbl_8924.p1, internal, 89236, 89290
-recovered pasa_asmbl_8924.p1, internal, 89384, 89463
Valid prediction for GeneMark_model.53003_t
Valid prediction for GlimmerHMM_glimmerT_30702-T1
Valid prediction for GeneMark_model.53005_t
Valid prediction for GlimmerHMM_glimmerT_30709-T1
Valid prediction for GeneMark_model.52995_t
Valid prediction for snap_scaffold_12-snap.2137-T1
Valid prediction for GeneMark_model.52992_t
Valid prediction for Augustus_model.g20471.t1
Valid prediction for snap_scaffold_12-snap.2142-T1
Valid prediction for CodingQuarry_transcript_10359-T1
Valid prediction for snap_scaffold_12-snap.2126-T1
Valid prediction for GlimmerHMM_glimmerT_30718-T1
Couldn't classify 90979, 91080
Sorry, prediction pasa_asmbl_8925.p1 fails validation.
(TTG)	 GT	90979-91080	GT	TGG
(GCA)	 AG	91219-91283	GT	AGG
(GTA)	 AG	91377-91495	GT	TGG
(GAG)	 AG	91585-91742	GT	AGG
(AAG)	 AG	91843-91914	GT	AAG
-recovered pasa_asmbl_8925.p1, terminal, 91843, 91914
-recovered pasa_asmbl_8925.p1, internal, 91219, 91283
-recovered pasa_asmbl_8925.p1, internal, 91377, 91495
-recovered pasa_asmbl_8925.p1, internal, 91585, 91742
-recovered pasa_asmbl_8925.p1, internal, 91843, 91914
Valid prediction for snap_scaffold_12-snap.2138-T1
Valid prediction for snap_scaffold_12-snap.2130-T1
Valid prediction for GlimmerHMM_glimmerT_30703-T1
Valid prediction for snap_scaffold_12-snap.2123-T1
Valid prediction for snap_scaffold_12-snap.2140-T1
Valid prediction for GlimmerHMM_glimmerT_30716-T1
Valid prediction for snap_scaffold_12-snap.2132-T1
Valid prediction for Augustus_model.g20472.t1
Valid prediction for GeneMark_model.53022_t
Valid prediction for GeneMark_model.53006_t
Valid prediction for GeneMark_model.53012_t
Valid prediction for GeneMark_model.53008_t
Valid prediction for GeneMark_model.53000_t
Valid prediction for snap_scaffold_12-snap.2120-T1
Valid prediction for GlimmerHMM_glimmerT_30710-T1
Valid prediction for snap_scaffold_12-snap.2143-T1
Valid prediction for GeneMark_model.52997_t
Valid prediction for GlimmerHMM_glimmerT_30698-T1
Valid prediction for Augustus_model.g20474.t1
Valid prediction for GeneMark_model.52998_t
Valid prediction for GlimmerHMM_glimmerT_30699-T1
Valid prediction for GeneMark_model.53015_t
Valid prediction for snap_scaffold_12-snap.2134-T1
Valid prediction for snap_scaffold_12-snap.2127-T1
Valid prediction for GeneMark_model.53010_t
Couldn't classify 97714, 97858
Sorry, prediction pasa_asmbl_8929.p1 fails validation.
(AGA)	 CC	97714-97858	GT	AGG
(GTA)	 AG	97939-98273	GT	AGG
(GTG)	 AG	98457-99650	AC	AAA
-recovered pasa_asmbl_8929.p1, terminal, 98457, 99650
-recovered pasa_asmbl_8929.p1, internal, 97939, 98273
Valid prediction for snap_scaffold_12-snap.2117-T1
Valid prediction for GlimmerHMM_glimmerT_30712-T1
Valid prediction for Augustus_model.g20470.t1
Valid prediction for Augustus_model.g20481.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 GeneMark_model.53002_t
Valid prediction for GlimmerHMM_glimmerT_30715-T1
Valid prediction for GeneMark_model.53009_t
Valid prediction for GeneMark_model.53013_t
Valid prediction for snap_scaffold_12-snap.2125-T1
Valid prediction for Augustus_model.g20483.t1
Valid prediction for snap_scaffold_12-snap.2131-T1
Couldn't classify 88939, 88959
Sorry, prediction pasa_asmbl_7925.p1 fails validation.
(CTG)	 GT	88939-88959	GT	TGG
(GTC)	 AG	89596-89701	GT	GGG
(GTA)	 AG	89792-89859	GT	AGG
(GCC)	 AG	89955-90077	GT	AGG
(GGC)	 AG	90366-90386	AC	AAA
-recovered pasa_asmbl_7925.p1, terminal, 90366, 90386
-recovered pasa_asmbl_7925.p1, internal, 89596, 89701
-recovered pasa_asmbl_7925.p1, internal, 89792, 89859
-recovered pasa_asmbl_7925.p1, internal, 89955, 90077
Valid prediction for HiQ_model.g20479.t1
Valid prediction for pasa_asmbl_7938.p1
Valid prediction for GlimmerHMM_glimmerT_30697-T1
Valid prediction for snap_scaffold_12-snap.2133-T1
Valid prediction for Augustus_model.g20480.t1
Valid prediction for snap_scaffold_12-snap.2121-T1
Couldn't classify 9472, 9628
Couldn't classify 16703, 16809
Sorry, prediction pasa_asmbl_7948.p2 fails validation.
(GAT)	 CA	9472-9628	GT	CAG
(ACC)	 AG	10868-11074	GT	TGG
(GCT)	 AG	12506-12739	GT	AGG
(ACG)	 AG	13953-14165	GT	ATG
(TTG)	 AG	16703-16809	GT	AGG
-recovered pasa_asmbl_7948.p2, internal, 10868, 11074
-recovered pasa_asmbl_7948.p2, internal, 12506, 12739
-recovered pasa_asmbl_7948.p2, internal, 13953, 14165
-recovered pasa_asmbl_7948.p2, internal, 16703, 16809
Valid prediction for GlimmerHMM_glimmerT_30713-T1
Valid prediction for GlimmerHMM_glimmerT_30708-T1
Valid prediction for snap_scaffold_12-snap.2119-T1
Valid prediction for GlimmerHMM_glimmerT_30711-T1
Valid prediction for snap_scaffold_12-snap.2136-T1
Valid prediction for GeneMark_model.52993_t
Valid prediction for snap_scaffold_12-snap.2118-T1
Valid prediction for CodingQuarry_transcript_10362-T1
Couldn't classify 24275, 24331
Sorry, prediction pasa_asmbl_7941.p3 fails validation.
(CTG)	 AG	24275-24331	GT	GTG
(GAT)	 AG	25464-25569	GT	TGG
(GGA)	 AG	26381-26466	GT	AGG
(ATC)	 AG	28152-28283	AG	AGA
-recovered pasa_asmbl_7941.p3, terminal, 28152, 28283
-recovered pasa_asmbl_7941.p3, internal, 24275, 24331
-recovered pasa_asmbl_7941.p3, internal, 25464, 25569
-recovered pasa_asmbl_7941.p3, internal, 26381, 26466
Valid prediction for Augustus_model.g20478.t1
Valid prediction for GeneMark_model.52999_t
Valid prediction for GeneMark_model.53023_t
Couldn't classify 57054, 57131
Sorry, prediction pasa_asmbl_7934.p1 fails validation.
(ATG)	 GG	54368-54469	GT	AGG
(GAT)	 AG	55462-55566	GT	AGG
(ATC)	 AG	55666-55857	GT	AGG
(GTG)	 AG	56169-56328	GT	AGG
(AAT)	 AG	56564-56739	GT	AGG
(GAT)	 AG	57054-57131	CT	AGC
-recovered pasa_asmbl_7934.p1, initial, 54368, 54469
add_exon() Sorry, pasa_asmbl_7934.p1 56169-56328-terminal-3 is invalid.
-recovered pasa_asmbl_7934.p1, terminal, 56169, 56328
-recovered pasa_asmbl_7934.p1, internal, 55462, 55566
-recovered pasa_asmbl_7934.p1, internal, 55666, 55857
-recovered pasa_asmbl_7934.p1, internal, 56169, 56328
-recovered pasa_asmbl_7934.p1, internal, 56564, 56739
Valid prediction for GeneMark_model.53016_t
Valid prediction for GlimmerHMM_glimmerT_30705-T1
Valid prediction for GlimmerHMM_glimmerT_30717-T1
Valid prediction for GeneMark_model.53014_t
Couldn't classify 22086, 22276
Sorry, prediction pasa_asmbl_7945.p2 fails validation.
(ATG)	 AC	20135-20243	GT	AGG
(GAG)	 AG	22086-22276	GT	AGG
-recovered pasa_asmbl_7945.p2, initial, 20135, 20243
-recovered pasa_asmbl_7945.p2, internal, 22086, 22276
Valid prediction for HiQ_model.g20473.t1
Valid prediction for GlimmerHMM_glimmerT_30701-T1
Valid prediction for GeneMark_model.52996_t
Valid prediction for GeneMark_model.53011_t
Valid prediction for snap_scaffold_12-snap.2128-T1
Couldn't classify 44932, 45003
Sorry, prediction pasa_asmbl_7940.p1 fails validation.
(ATG)	 AC	37394-37572	GT	AAG
(GCA)	 AG	38095-38250	GT	AGG
(ATT)	 AG	40156-40303	GT	CTG
(GCC)	 AG	41416-41649	GT	AGG
(TTG)	 AG	41949-42122	GT	TGG
(ATG)	 AG	42650-42797	GT	CAG
(AGG)	 AG	44024-44172	GT	AGG
(GCC)	 AG	44266-44373	GT	AGG
(AGG)	 AG	44485-44844	GT	GGG
(GGT)	 AG	44932-45003	GT	AGG
-recovered pasa_asmbl_7940.p1, initial, 37394, 37572
-recovered pasa_asmbl_7940.p1, initial, 42650, 42797
-recovered pasa_asmbl_7940.p1, internal, 38095, 38250
-recovered pasa_asmbl_7940.p1, internal, 40156, 40303
-recovered pasa_asmbl_7940.p1, internal, 41416, 41649
-recovered pasa_asmbl_7940.p1, internal, 41949, 42122
-recovered pasa_asmbl_7940.p1, internal, 42650, 42797
-recovered pasa_asmbl_7940.p1, internal, 44024, 44172
-recovered pasa_asmbl_7940.p1, internal, 44266, 44373
-recovered pasa_asmbl_7940.p1, internal, 44485, 44844
-recovered pasa_asmbl_7940.p1, internal, 44932, 45003
Couldn't classify 58197, 58296
Couldn't classify 62036, 62101
Sorry, prediction pasa_asmbl_7933.p1 fails validation.
(GTC)	 AG	58197-58296	GT	TGG
(GTT)	 AG	58417-58553	GT	AGG
(ATG)	 AG	58919-59050	GT	AGG
(CGC)	 AG	59511-59637	GT	CAG
(CGG)	 AG	60044-60273	GC	AGG
(GAC)	 AG	60404-60463	GC	AGG
(ATG)	 AG	60571-60741	GT	AGG
(GAG)	 AG	60921-61065	GT	AGG
(GAG)	 AG	61789-61907	GT	AGG
(GTG)	 AG	62036-62101	GT	TGG
-recovered pasa_asmbl_7933.p1, initial, 58919, 59050
-recovered pasa_asmbl_7933.p1, initial, 60571, 60741
-recovered pasa_asmbl_7933.p1, internal, 58197, 58296
-recovered pasa_asmbl_7933.p1, internal, 58417, 58553
-recovered pasa_asmbl_7933.p1, internal, 58919, 59050
-recovered pasa_asmbl_7933.p1, internal, 59511, 59637
-recovered pasa_asmbl_7933.p1, internal, 60044, 60273
-recovered pasa_asmbl_7933.p1, internal, 60404, 60463
-recovered pasa_asmbl_7933.p1, internal, 60571, 60741
-recovered pasa_asmbl_7933.p1, internal, 60921, 61065
-recovered pasa_asmbl_7933.p1, internal, 61789, 61907
-recovered pasa_asmbl_7933.p1, internal, 62036, 62101
Valid prediction for GeneMark_model.53021_t
Valid prediction for Augustus_model.g20482.t1
Valid prediction for snap_scaffold_12-snap.2122-T1
Valid prediction for GeneMark_model.53019_t
Valid prediction for GlimmerHMM_glimmerT_30706-T1
Valid prediction for snap_scaffold_12-snap.2135-T1
Valid prediction for GlimmerHMM_glimmerT_30714-T1
Valid prediction for snap_scaffold_12-snap.2139-T1
Valid prediction for Augustus_model.g20476.t1
Couldn't classify 62625, 62716
Sorry, prediction pasa_asmbl_7932.p1 fails validation.
(TGC)	 AT	62625-62716	GT	AGG
(CGA)	 AG	62832-63059	GC	AGG
(GGT)	 AG	63176-63320	GT	ATG
(GTG)	 AG	63424-63544	GT	TGG
(CTT)	 AG	64850-64960	GT	AGG
(ATA)	 AG	65092-65205	GT	GGG
(GGG)	 AG	65308-65444	GT	AGG
(GAG)	 AG	66135-66314	GT	AGG
(AAC)	 AG	66680-66751	GT	ACG
(GAG)	 AG	66863-67023	GT	AGG
(TTC)	 AG	67149-67310	GT	AGG
(TAT)	 AG	67632-67743	GT	AGG
(ATT)	 AG	67980-68069	GT	TGG
(GTG)	 AG	68268-68377	GT	AAG
(TGA)	 AG	68585-68720	GT	GGG
(AAG)	 AG	68994-69143	GT	AGG
(GGG)	 AG	69246-69614	GT	AGG
(GAC)	 AG	69796-69943	GT	AGG
(GTG)	 AG	70098-70309	GT	TGG
(AAC)	 AG	70513-70587	GC	AGG
(AAC)	 AG	70748-70971	GT	AGG
(GTT)	 AG	71176-71347	GT	GAG
(GCC)	 AG	71684-71944	GT	TGG
(TTC)	 AG	72108-72189	GT	AAG
(ATA)	 AG	72351-72388	TT	GAT
-recovered pasa_asmbl_7932.p1, terminal, 72351, 72388
-recovered pasa_asmbl_7932.p1, internal, 62832, 63059
-recovered pasa_asmbl_7932.p1, internal, 63176, 63320
-recovered pasa_asmbl_7932.p1, internal, 63424, 63544
-recovered pasa_asmbl_7932.p1, internal, 64850, 64960
-recovered pasa_asmbl_7932.p1, internal, 65092, 65205
-recovered pasa_asmbl_7932.p1, internal, 65308, 65444
-recovered pasa_asmbl_7932.p1, internal, 66135, 66314
-recovered pasa_asmbl_7932.p1, internal, 66680, 66751
-recovered pasa_asmbl_7932.p1, internal, 66863, 67023
-recovered pasa_asmbl_7932.p1, internal, 67149, 67310
-recovered pasa_asmbl_7932.p1, internal, 67632, 67743
-recovered pasa_asmbl_7932.p1, internal, 67980, 68069
-recovered pasa_asmbl_7932.p1, internal, 68268, 68377
-recovered pasa_asmbl_7932.p1, internal, 68585, 68720
-recovered pasa_asmbl_7932.p1, internal, 68994, 69143
-recovered pasa_asmbl_7932.p1, internal, 69246, 69614
-recovered pasa_asmbl_7932.p1, internal, 69796, 69943
-recovered pasa_asmbl_7932.p1, internal, 70098, 70309
-recovered pasa_asmbl_7932.p1, internal, 70513, 70587
-recovered pasa_asmbl_7932.p1, internal, 70748, 70971
-recovered pasa_asmbl_7932.p1, internal, 71176, 71347
-recovered pasa_asmbl_7932.p1, internal, 71684, 71944
-recovered pasa_asmbl_7932.p1, internal, 72108, 72189
Valid prediction for GeneMark_model.52994_t
Valid prediction for GlimmerHMM_glimmerT_30700-T1
Valid prediction for GeneMark_model.53017_t
Couldn't classify 77565, 78215
Sorry, prediction pasa_asmbl_7927.p1 fails validation.
(GTA)	 TC	77565-78215	AG	GAA

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 64530, rend_intergenic: 60663  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112215, rend_intergenic: 101269  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135392, rend_intergenic: 123723  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155659, rend_intergenic: 144503  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163290, rend_intergenic: 155800  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 172785
-exon list size: 464


building trellis

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67.8    
68.0    
68.2    
68.5    
68.7    
68.9    
69.1    
69.3    
69.5    
69.7    
70.0    
70.2    
70.4    
70.6    
70.8    
71.0    
71.2    
71.5    
71.7    
71.9    
72.1    
72.3    
72.5    
72.7    
73.0    
73.2    
73.4    
73.6    
73.8    
74.0    
74.2    
74.5    
74.7    
74.9    
75.1    
75.3    
75.5    
75.8    
76.0    
76.2    
76.4    
76.6    
76.8    
77.0    
77.3    
77.5    
77.7    
77.9    
78.1    
78.3    
78.5    
78.8    
79.0    
79.2    
79.4    
79.6    
79.8    
80.0    
80.3    
80.5    
80.7    
80.9    
81.1    
81.3    
81.5    
81.8    
82.0    
82.2    
82.4    
82.6    
82.8    
83.0    
83.3    
83.5    
83.7    
83.9    
84.1    
84.3    
84.5    
84.8    
85.0    
85.2    
85.4    
85.6    
85.8    
86.1    
86.3    
86.5    
86.7    
86.9    
87.1    
87.3    
87.6    
87.8    
88.0    
88.2    
88.4    
88.6    
88.8    
89.1    
89.3    
89.5    
89.7    
89.9    
90.1    
90.3    
90.6    
90.8    
91.0    
91.2    
91.4    
91.6    
91.8    
92.1    
92.3    
92.5    
92.7    
92.9    
93.1    
93.3    
93.6    
93.8    
94.0    
94.2    
94.4    
94.6    
94.8    
95.1    
95.3    
95.5    
95.7    
95.9    
96.1    
96.4    
96.6    
96.8    
97.0    
97.2    
97.4    
97.6    
97.9    
98.1    
98.3    
98.5    
98.7    
98.9    
99.1    
99.4    
99.6    
99.8    
-found 19 predictions from path traversal
Error with prediction: snap lend_intergenic: 64530, rend_intergenic: 60663  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112215, rend_intergenic: 101269  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135392, rend_intergenic: 123723  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155659, rend_intergenic: 144503  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163290, rend_intergenic: 155800  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 13 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 21707
-exon list size: 10


building trellis

8.3    
16.7    
25.0    
33.3    
41.7    
50.0    
58.3    
66.7    
75.0    
83.3    
91.7    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 21576
-exon list size: 9


building trellis

9.1    
18.2    
27.3    
36.4    
45.5    
54.5    
63.6    
72.7    
81.8    
90.9    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 20083
-exon list size: 7


building trellis

11.1    
22.2    
33.3    
44.4    
55.6    
66.7    
77.8    
88.9    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 20043
-exon list size: 6


building trellis

12.5    
25.0    
37.5    
50.0    
62.5    
75.0    
87.5    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 19959
-exon list size: 5


building trellis

14.3    
28.6    
42.9    
57.1    
71.4    
85.7    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 12031
-exon list size: 1


building trellis

33.3    
66.7    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support