-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_12/scaffold_12_5226263-5545252

-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.51820_t
Valid prediction for GeneMark_model.51832_t
Valid prediction for CodingQuarry_transcript_10191-T1
Valid prediction for GeneMark_model.51822_t
Valid prediction for GeneMark_model.51790_t
Valid prediction for GeneMark_model.51827_t
Valid prediction for CodingQuarry_transcript_10198-T1
Valid prediction for HiQ_model.g19957.t1
Couldn't classify 111588, 111708
Couldn't classify 114629, 114694
Sorry, prediction pasa_asmbl_8609.p1 fails validation.
(GAC)	 TG	111588-111708	GT	AGG
(ATT)	 AG	112161-112338	GT	CAG
(TCT)	 AG	113315-113459	GT	AGG
(ATC)	 AG	114629-114694	CC	ACC
-recovered pasa_asmbl_8609.p1, internal, 112161, 112338
-recovered pasa_asmbl_8609.p1, internal, 113315, 113459
Valid prediction for GeneMark_model.51828_t
Valid prediction for GlimmerHMM_glimmerT_29983-T1
Valid prediction for Augustus_model.g19941.t1
Valid prediction for snap_scaffold_12-snap.1089-T1
Valid prediction for GlimmerHMM_glimmerT_29968-T1
Couldn't classify 121842, 121888
Couldn't classify 126709, 126738
Sorry, prediction pasa_asmbl_8612.p1 fails validation.
(TCC)	 TC	121842-121888	GT	AAG
(CAT)	 AG	122718-122804	GT	GGG
(GGC)	 AG	123071-123173	GT	AGG
(GGT)	 AG	123762-123838	GT	AGG
(GCA)	 AG	124665-124716	GT	GGG
(GAG)	 AG	124890-125016	GT	AGG
(ACC)	 AG	126013-126223	GT	AGG
(GCC)	 AG	126417-126555	GT	AGG
(CCG)	 AG	126709-126738	CC	CCC
-recovered pasa_asmbl_8612.p1, internal, 122718, 122804
-recovered pasa_asmbl_8612.p1, internal, 123071, 123173
-recovered pasa_asmbl_8612.p1, internal, 123762, 123838
-recovered pasa_asmbl_8612.p1, internal, 124665, 124716
-recovered pasa_asmbl_8612.p1, internal, 124890, 125016
-recovered pasa_asmbl_8612.p1, internal, 126013, 126223
-recovered pasa_asmbl_8612.p1, internal, 126417, 126555
Valid prediction for GeneMark_model.51813_t
Valid prediction for Augustus_model.g19942.t1
Valid prediction for GlimmerHMM_glimmerT_29962-T1
Valid prediction for CodingQuarry_transcript_10200-T1
Valid prediction for GlimmerHMM_glimmerT_29960-T1
Valid prediction for GlimmerHMM_glimmerT_29961-T1
Valid prediction for pasa_asmbl_8617.p1
Valid prediction for snap_scaffold_12-snap.1083-T1
Valid prediction for HiQ_model.g19944.t1
Valid prediction for Augustus_model.g19959.t1
Valid prediction for GeneMark_model.51812_t
Valid prediction for Augustus_model.g19939.t1
Couldn't classify 128509, 128724
Sorry, prediction pasa_asmbl_8613.p1 fails validation.
(GAT)	 CA	128509-128724	GT	AGG
(AAA)	 AG	128909-129088	GT	CCG
(GTG)	 AG	129189-129544	GT	ATG
(GCC)	 AG	129809-129910	GT	AGG
(GAC)	 AG	130875-130998	AC	AGA
-recovered pasa_asmbl_8613.p1, terminal, 130875, 130998
-recovered pasa_asmbl_8613.p1, internal, 128909, 129088
-recovered pasa_asmbl_8613.p1, internal, 129189, 129544
-recovered pasa_asmbl_8613.p1, internal, 129809, 129910
Valid prediction for snap_scaffold_12-snap.1101-T1
Valid prediction for pasa_asmbl_8608.p2
Valid prediction for pasa_asmbl_8616.p1
Valid prediction for CodingQuarry_transcript_10190-T1
Valid prediction for GeneMark_model.51802_t
Valid prediction for CodingQuarry_transcript_10201-T1
Valid prediction for snap_scaffold_12-snap.1105-T1
Valid prediction for GeneMark_model.51804_t
Valid prediction for Augustus_model.g19940.t1
Valid prediction for GeneMark_model.51810_t
Valid prediction for GeneMark_model.51800_t
Valid prediction for snap_scaffold_12-snap.1116-T1
Valid prediction for GlimmerHMM_glimmerT_29965-T1
Valid prediction for GeneMark_model.51811_t
Valid prediction for GeneMark_model.51798_t
Valid prediction for Augustus_model.g19945.t1
Valid prediction for Augustus_model.g19938.t1
Valid prediction for CodingQuarry_transcript_10199-T1
Valid prediction for GlimmerHMM_glimmerT_29977-T1
Valid prediction for Augustus_model.g19955.t1
Valid prediction for snap_scaffold_12-snap.1115-T1
Valid prediction for Augustus_model.g19951.t1
Valid prediction for GlimmerHMM_glimmerT_29978-T1
Valid prediction for GeneMark_model.51816_t
Valid prediction for snap_scaffold_12-snap.1117-T1
Valid prediction for GlimmerHMM_glimmerT_29972-T1
Valid prediction for snap_scaffold_12-snap.1109-T1
Valid prediction for snap_scaffold_12-snap.1094-T1
Valid prediction for GeneMark_model.51836_t
Valid prediction for snap_scaffold_12-snap.1093-T1
Couldn't classify 79737, 79911
Sorry, prediction pasa_asmbl_8604.p1 fails validation.
(TCC)	 AC	79737-79911	GT	AGG
(AGC)	 AG	80143-80384	CA	AAC
-recovered pasa_asmbl_8604.p1, terminal, 80143, 80384
Valid prediction for Augustus_model.g19950.t1
Valid prediction for GeneMark_model.51837_t
Valid prediction for GlimmerHMM_glimmerT_29981-T1
Valid prediction for snap_scaffold_12-snap.1106-T1
Valid prediction for GlimmerHMM_glimmerT_29958-T1
Valid prediction for GeneMark_model.51792_t
Valid prediction for snap_scaffold_12-snap.1075-T1
Valid prediction for HiQ_model.g19958.t1
Valid prediction for GeneMark_model.51796_t
Valid prediction for snap_scaffold_12-snap.1084-T1
Valid prediction for snap_scaffold_12-snap.1097-T1
Valid prediction for GlimmerHMM_glimmerT_29967-T1
Valid prediction for GeneMark_model.51814_t
Couldn't classify 243584, 243778
Sorry, prediction pasa_asmbl_8615.p1 fails validation.
(ACC)	 CG	243584-243778	GT	CGG
(AAT)	 AG	244039-244137	GT	TGG
(GTG)	 AG	244387-244553	GT	TGG
(GAT)	 AG	244659-244828	GT	CTG
(GTG)	 AG	245207-245475	TA	GAT
-recovered pasa_asmbl_8615.p1, terminal, 245207, 245475
-recovered pasa_asmbl_8615.p1, internal, 244039, 244137
-recovered pasa_asmbl_8615.p1, internal, 244387, 244553
-recovered pasa_asmbl_8615.p1, internal, 244659, 244828
Valid prediction for CodingQuarry_transcript_10197-T1
Valid prediction for GlimmerHMM_glimmerT_29973-T1
Valid prediction for GlimmerHMM_glimmerT_29974-T1
Valid prediction for Augustus_model.g19954.t1
Valid prediction for GeneMark_model.51834_t
Valid prediction for GeneMark_model.51806_t
Valid prediction for Augustus_model.g19943.t1
Valid prediction for snap_scaffold_12-snap.1080-T1
Valid prediction for GlimmerHMM_glimmerT_29955-T1
Valid prediction for GeneMark_model.51808_t
Valid prediction for GeneMark_model.51786_t
Valid prediction for Augustus_model.g19946.t1
Valid prediction for GeneMark_model.51829_t
Valid prediction for GeneMark_model.51794_t
Valid prediction for snap_scaffold_12-snap.1077-T1
Valid prediction for snap_scaffold_12-snap.1091-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 snap_scaffold_12-snap.1096-T1
Valid prediction for snap_scaffold_12-snap.1102-T1
Valid prediction for GeneMark_model.51795_t
Valid prediction for GeneMark_model.51787_t
Valid prediction for snap_scaffold_12-snap.1092-T1
Valid prediction for CodingQuarry_transcript_10196-T1
Valid prediction for snap_scaffold_12-snap.1099-T1
Valid prediction for GlimmerHMM_glimmerT_29959-T1
Valid prediction for GeneMark_model.51825_t
Valid prediction for pasa_asmbl_7623.p1
Valid prediction for snap_scaffold_12-snap.1104-T1
Valid prediction for snap_scaffold_12-snap.1108-T1
Valid prediction for snap_scaffold_12-snap.1114-T1
Valid prediction for snap_scaffold_12-snap.1086-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_29963-T1
Valid prediction for GeneMark_model.51791_t
Valid prediction for GlimmerHMM_glimmerT_29956-T1
Valid prediction for CodingQuarry_transcript_10193-T1
Valid prediction for GeneMark_model.51799_t
Valid prediction for GeneMark_model.51789_t
Valid prediction for GeneMark_model.51818_t
Valid prediction for GeneMark_model.51797_t
Valid prediction for CodingQuarry_transcript_10195-T1
Valid prediction for snap_scaffold_12-snap.1081-T1
Valid prediction for GeneMark_model.51817_t
Valid prediction for snap_scaffold_12-snap.1113-T1
Valid prediction for GeneMark_model.51809_t
Valid prediction for GlimmerHMM_glimmerT_29980-T1
Valid prediction for snap_scaffold_12-snap.1100-T1
Valid prediction for snap_scaffold_12-snap.1111-T1
Valid prediction for GeneMark_model.51823_t
Valid prediction for snap_scaffold_12-snap.1107-T1
Valid prediction for snap_scaffold_12-snap.1088-T1
Valid prediction for GeneMark_model.51807_t
Valid prediction for GeneMark_model.51830_t
Valid prediction for Augustus_model.g19956.t1
Valid prediction for snap_scaffold_12-snap.1103-T1
Valid prediction for Augustus_model.g19947.t1
Valid prediction for HiQ_model.g19953.t1
Valid prediction for GeneMark_model.51805_t
Valid prediction for GeneMark_model.51803_t
Valid prediction for snap_scaffold_12-snap.1076-T1
Valid prediction for Augustus_model.g19937.t1
Valid prediction for HiQ_model.g19948.t1
Valid prediction for GeneMark_model.51833_t
Valid prediction for snap_scaffold_12-snap.1112-T1
Valid prediction for snap_scaffold_12-snap.1074-T1
Valid prediction for Augustus_model.g19949.t1
Valid prediction for snap_scaffold_12-snap.1085-T1
Valid prediction for GeneMark_model.51831_t
Valid prediction for GeneMark_model.51784_t
Valid prediction for snap_scaffold_12-snap.1073-T1
Valid prediction for GlimmerHMM_glimmerT_29976-T1
Valid prediction for snap_scaffold_12-snap.1087-T1
Couldn't classify 88749, 88817
Sorry, prediction pasa_asmbl_7626.p1 fails validation.
(AAG)	 GA	88749-88817	GT	CTG
(ACG)	 AG	88908-89006	GT	AGG
(GAA)	 AG	89609-89696	GT	GAG
(GTC)	 AG	90229-90350	GT	ATG
(GTT)	 AG	90697-90817	GT	ACG
(TCA)	 AG	91575-91708	GT	GAG
(GTG)	 AG	91832-91980	GT	GGG
(GTA)	 AG	92130-92278	GT	ACG
(AGG)	 AG	92409-92437	GC	AAG
-recovered pasa_asmbl_7626.p1, terminal, 92409, 92437
-recovered pasa_asmbl_7626.p1, internal, 88908, 89006
-recovered pasa_asmbl_7626.p1, internal, 89609, 89696
-recovered pasa_asmbl_7626.p1, internal, 90229, 90350
-recovered pasa_asmbl_7626.p1, internal, 90697, 90817
-recovered pasa_asmbl_7626.p1, internal, 91575, 91708
-recovered pasa_asmbl_7626.p1, internal, 91832, 91980
-recovered pasa_asmbl_7626.p1, internal, 92130, 92278
-recovered pasa_asmbl_7626.p1, internal, 92409, 92437
Valid prediction for HiQ_model.g19952.t1
Couldn't classify 179089, 179206
Couldn't classify 179950, 179969
Sorry, prediction pasa_asmbl_8311.p1 fails validation.
(GTG)	 AG	179089-179206	GT	TGG
(GTG)	 AG	179622-179819	GT	TGG
(GTC)	 AG	179950-179969	TT	CGT
-recovered pasa_asmbl_8311.p1, internal, 179089, 179206
-recovered pasa_asmbl_8311.p1, internal, 179622, 179819
Valid prediction for GeneMark_model.51785_t
Valid prediction for GlimmerHMM_glimmerT_29970-T1
Valid prediction for GeneMark_model.51801_t
Valid prediction for GlimmerHMM_glimmerT_29957-T1
Valid prediction for snap_scaffold_12-snap.1095-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for GeneMark_model.51835_t
Valid prediction for snap_scaffold_12-snap.1098-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for snap_scaffold_12-snap.1110-T1
Valid prediction for GeneMark_model.51824_t
Valid prediction for GlimmerHMM_glimmerT_29975-T1
Valid prediction for GeneMark_model.51821_t
Valid prediction for CodingQuarry_transcript_10194-T1
Valid prediction for GlimmerHMM_glimmerT_29964-T1
Valid prediction for GlimmerHMM_glimmerT_29969-T1
Valid prediction for snap_scaffold_12-snap.1079-T1
Valid prediction for snap_scaffold_12-snap.1090-T1
Valid prediction for GeneMark_model.51819_t
Valid prediction for GlimmerHMM_glimmerT_29984-T1
Valid prediction for GeneMark_model.51826_t
Valid prediction for GlimmerHMM_glimmerT_29982-T1
Valid prediction for pasa_asmbl_7624.p1
Valid prediction for snap_scaffold_12-snap.1082-T1
Valid prediction for GeneMark_model.51815_t
Valid prediction for GeneMark_model.51793_t
Valid prediction for GlimmerHMM_glimmerT_29966-T1
Valid prediction for GeneMark_model.51788_t
Valid prediction for snap_scaffold_12-snap.1078-T1
Valid prediction for GlimmerHMM_glimmerT_29971-T1
Valid prediction for GlimmerHMM_glimmerT_29979-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 7339, rend_intergenic: 5778  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25712, rend_intergenic: 22290  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28404, rend_intergenic: 26364  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32237, rend_intergenic: 32105  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76543, rend_intergenic: 46242  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80799, rend_intergenic: 78421  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87754, rend_intergenic: 85395  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126941, rend_intergenic: 117568  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130998, rend_intergenic: 127113  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140814, rend_intergenic: 138351  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143154, rend_intergenic: 141267  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 318990
-exon list size: 760


building trellis

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58.9    
59.1    
59.2    
59.3    
59.4    
59.6    
59.7    
59.8    
60.0    
60.1    
60.2    
60.4    
60.5    
60.6    
60.8    
60.9    
61.0    
61.2    
61.3    
61.4    
61.5    
61.7    
61.8    
61.9    
62.1    
62.2    
62.3    
62.5    
62.6    
62.7    
62.9    
63.0    
63.1    
63.3    
63.4    
63.5    
63.6    
63.8    
63.9    
64.0    
64.2    
64.3    
64.4    
64.6    
64.7    
64.8    
65.0    
65.1    
65.2    
65.4    
65.5    
65.6    
65.7    
65.9    
66.0    
66.1    
66.3    
66.4    
66.5    
66.7    
66.8    
66.9    
67.1    
67.2    
67.3    
67.5    
67.6    
67.7    
67.8    
68.0    
68.1    
68.2    
68.4    
68.5    
68.6    
68.8    
68.9    
69.0    
69.2    
69.3    
69.4    
69.6    
69.7    
69.8    
69.9    
70.1    
70.2    
70.3    
70.5    
70.6    
70.7    
70.9    
71.0    
71.1    
71.3    
71.4    
71.5    
71.7    
71.8    
71.9    
72.0    
72.2    
72.3    
72.4    
72.6    
72.7    
72.8    
73.0    
73.1    
73.2    
73.4    
73.5    
73.6    
73.8    
73.9    
74.0    
74.1    
74.3    
74.4    
74.5    
74.7    
74.8    
74.9    
75.1    
75.2    
75.3    
75.5    
75.6    
75.7    
75.9    
76.0    
76.1    
76.2    
76.4    
76.5    
76.6    
76.8    
76.9    
77.0    
77.2    
77.3    
77.4    
77.6    
77.7    
77.8    
78.0    
78.1    
78.2    
78.3    
78.5    
78.6    
78.7    
78.9    
79.0    
79.1    
79.3    
79.4    
79.5    
79.7    
79.8    
79.9    
80.1    
80.2    
80.3    
80.4    
80.6    
80.7    
80.8    
81.0    
81.1    
81.2    
81.4    
81.5    
81.6    
81.8    
81.9    
82.0    
82.2    
82.3    
82.4    
82.5    
82.7    
82.8    
82.9    
83.1    
83.2    
83.3    
83.5    
83.6    
83.7    
83.9    
84.0    
84.1    
84.3    
84.4    
84.5    
84.6    
84.8    
84.9    
85.0    
85.2    
85.3    
85.4    
85.6    
85.7    
85.8    
86.0    
86.1    
86.2    
86.4    
86.5    
86.6    
86.7    
86.9    
87.0    
87.1    
87.3    
87.4    
87.5    
87.7    
87.8    
87.9    
88.1    
88.2    
88.3    
88.5    
88.6    
88.7    
88.8    
89.0    
89.1    
89.2    
89.4    
89.5    
89.6    
89.8    
89.9    
90.0    
90.2    
90.3    
90.4    
90.6    
90.7    
90.8    
90.9    
91.1    
91.2    
91.3    
91.5    
91.6    
91.7    
91.9    
92.0    
92.1    
92.3    
92.4    
92.5    
92.7    
92.8    
92.9    
93.0    
93.2    
93.3    
93.4    
93.6    
93.7    
93.8    
94.0    
94.1    
94.2    
94.4    
94.5    
94.6    
94.8    
94.9    
95.0    
95.1    
95.3    
95.4    
95.5    
95.7    
95.8    
95.9    
96.1    
96.2    
96.3    
96.5    
96.6    
96.7    
96.9    
97.0    
97.1    
97.2    
97.4    
97.5    
97.6    
97.8    
97.9    
98.0    
98.2    
98.3    
98.4    
98.6    
98.7    
98.8    
99.0    
99.1    
99.2    
99.3    
99.5    
99.6    
99.7    
99.9    
-found 30 predictions from path traversal
Error with prediction: snap lend_intergenic: 7339, rend_intergenic: 5778  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25712, rend_intergenic: 22290  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28404, rend_intergenic: 26364  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32237, rend_intergenic: 32105  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76543, rend_intergenic: 46242  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80799, rend_intergenic: 78421  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87754, rend_intergenic: 85395  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126941, rend_intergenic: 117568  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130998, rend_intergenic: 127113  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140814, rend_intergenic: 138351  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143154, rend_intergenic: 141267  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 23 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 307699 - 318990
-exon list size: 1


building trellis

33.3    
66.7    
-found 1 predictions from path traversal

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