-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_10/scaffold_10_6696879-6919241

-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 pasa_asmbl_3252.p1
Valid prediction for snap_scaffold_10-snap.1404-T1
Valid prediction for GlimmerHMM_glimmerT_24933-T1
Valid prediction for Augustus_model.g16607.t1
Valid prediction for snap_scaffold_10-snap.1413-T1
Valid prediction for snap_scaffold_10-snap.1403-T1
Valid prediction for snap_scaffold_10-snap.1395-T1
Valid prediction for snap_scaffold_10-snap.1418-T1
Couldn't classify 206081, 206390
Sorry, prediction pasa_asmbl_3251.p1 fails validation.
(GGG)	 CA	206081-206390	GT	AGG
(GTG)	 AG	206505-206602	GT	AGG
(GGA)	 AG	208506-208619	GT	AGG
(ATG)	 AG	208753-208974	GT	AGG
(ATG)	 AG	209094-209191	GT	AGG
(GGC)	 AG	209858-209972	GT	AGG
(ATG)	 AG	210773-210880	GT	AGG
(GCA)	 AG	211317-211427	GT	GGG
(GGT)	 AG	211582-211721	GT	AGG
(GGG)	 AG	211813-211864	TG	AGT
-recovered pasa_asmbl_3251.p1, initial, 208753, 208974
-recovered pasa_asmbl_3251.p1, initial, 209094, 209191
-recovered pasa_asmbl_3251.p1, initial, 210773, 210880
add_exon() Sorry, pasa_asmbl_3251.p1 211582-211721-terminal-2 is invalid.
-recovered pasa_asmbl_3251.p1, terminal, 211582, 211721
-recovered pasa_asmbl_3251.p1, terminal, 211813, 211864
-recovered pasa_asmbl_3251.p1, internal, 206505, 206602
-recovered pasa_asmbl_3251.p1, internal, 208506, 208619
-recovered pasa_asmbl_3251.p1, internal, 208753, 208974
-recovered pasa_asmbl_3251.p1, internal, 209094, 209191
-recovered pasa_asmbl_3251.p1, internal, 209858, 209972
-recovered pasa_asmbl_3251.p1, internal, 210773, 210880
-recovered pasa_asmbl_3251.p1, internal, 211317, 211427
-recovered pasa_asmbl_3251.p1, internal, 211582, 211721
Valid prediction for GlimmerHMM_glimmerT_24925-T1
Valid prediction for snap_scaffold_10-snap.1420-T1
Valid prediction for snap_scaffold_10-snap.1396-T1
Valid prediction for GlimmerHMM_glimmerT_24935-T1
Valid prediction for snap_scaffold_10-snap.1405-T1
Valid prediction for snap_scaffold_10-snap.1399-T1
Valid prediction for snap_scaffold_10-snap.1415-T1
Valid prediction for snap_scaffold_10-snap.1391-T1
Valid prediction for snap_scaffold_10-snap.1426-T1
Valid prediction for Augustus_model.g16599.t1
Valid prediction for snap_scaffold_10-snap.1427-T1
Valid prediction for GlimmerHMM_glimmerT_24927-T1
Valid prediction for snap_scaffold_10-snap.1406-T1
Valid prediction for GlimmerHMM_glimmerT_24922-T1
Valid prediction for Augustus_model.g16606.t1
Valid prediction for GlimmerHMM_glimmerT_24942-T1
Valid prediction for snap_scaffold_10-snap.1412-T1
Valid prediction for CodingQuarry_transcript_5457-T1
Valid prediction for GlimmerHMM_glimmerT_24916-T1
Valid prediction for GlimmerHMM_glimmerT_24915-T1
Valid prediction for HiQ_model.g16608.t1
Valid prediction for Augustus_model.g16600.t1
Valid prediction for Augustus_model.g16597.t1
Valid prediction for snap_scaffold_10-snap.1388-T1
Valid prediction for GlimmerHMM_glimmerT_24940-T1
Valid prediction for snap_scaffold_10-snap.1411-T1
Valid prediction for snap_scaffold_10-snap.1422-T1
Valid prediction for snap_scaffold_10-snap.1390-T1
Valid prediction for snap_scaffold_10-snap.1424-T1
Valid prediction for snap_scaffold_10-snap.1428-T1
Valid prediction for GlimmerHMM_glimmerT_24943-T1
Valid prediction for GlimmerHMM_glimmerT_24937-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 GlimmerHMM_glimmerT_24931-T1
Valid prediction for HiQ_model.g16604.t1
Valid prediction for snap_scaffold_10-snap.1408-T1
Couldn't classify 38863, 38888
Couldn't classify 40932, 41002
Sorry, prediction pasa_asmbl_4516.p1 fails validation.
(TGG)	 TG	38863-38888	GT	GGG
(GAA)	 AG	39520-39558	GT	AGG
(AGA)	 AG	39774-39869	GT	AGG
(GTT)	 AG	40017-40182	GT	AGG
(AAT)	 AG	40458-40632	GT	CCG
(TGT)	 AG	40932-41002	CT	ACC
-recovered pasa_asmbl_4516.p1, internal, 39520, 39558
-recovered pasa_asmbl_4516.p1, internal, 39774, 39869
-recovered pasa_asmbl_4516.p1, internal, 40017, 40182
-recovered pasa_asmbl_4516.p1, internal, 40458, 40632
Valid prediction for Augustus_model.g16593.t1
Valid prediction for CodingQuarry_transcript_5456-T1
Couldn't classify 162653, 163849
Sorry, prediction pasa_asmbl_4499.p1 fails validation.
(GGA)	 GA	162653-163849	CA	GAC
Valid prediction for GlimmerHMM_glimmerT_24920-T1
Valid prediction for GlimmerHMM_glimmerT_24938-T1
Valid prediction for snap_scaffold_10-snap.1417-T1
Valid prediction for snap_scaffold_10-snap.1393-T1
Valid prediction for snap_scaffold_10-snap.1392-T1
Valid prediction for snap_scaffold_10-snap.1407-T1
Couldn't classify 162271, 162423
Sorry, prediction pasa_asmbl_4500.p1 fails validation.
(ATG)	 CA	155633-155636	GT	GAG
(GTG)	 AG	156317-157120	GT	AGG
(ATG)	 AG	158085-158164	GT	ATG
(CTG)	 AG	159134-159278	GT	AGG
(GCA)	 AG	160202-160375	GT	GGG
(GTG)	 AG	160537-160611	GT	ATG
(CTG)	 AG	160774-160898	GT	CAG
(AAT)	 AG	161200-161334	GT	TGG
(GTT)	 AG	161539-161784	GT	AGG
(GCA)	 AG	161884-162162	GT	AGG
(GTG)	 AG	162271-162423	CT	ACC
-recovered pasa_asmbl_4500.p1, initial, 155633, 155636
add_exon() Sorry, pasa_asmbl_4500.p1 158085-158164-initial-1 is invalid.
-recovered pasa_asmbl_4500.p1, initial, 158085, 158164
-recovered pasa_asmbl_4500.p1, internal, 156317, 157120
-recovered pasa_asmbl_4500.p1, internal, 158085, 158164
-recovered pasa_asmbl_4500.p1, internal, 159134, 159278
-recovered pasa_asmbl_4500.p1, internal, 160202, 160375
-recovered pasa_asmbl_4500.p1, internal, 160537, 160611
-recovered pasa_asmbl_4500.p1, internal, 160774, 160898
-recovered pasa_asmbl_4500.p1, internal, 161200, 161334
-recovered pasa_asmbl_4500.p1, internal, 161539, 161784
-recovered pasa_asmbl_4500.p1, internal, 161884, 162162
Valid prediction for CodingQuarry_transcript_5453-T1
Valid prediction for snap_scaffold_10-snap.1397-T1
Valid prediction for snap_scaffold_10-snap.1409-T1
Valid prediction for Augustus_model.g16605.t1
Valid prediction for GlimmerHMM_glimmerT_24930-T1
Valid prediction for snap_scaffold_10-snap.1400-T1
Valid prediction for snap_scaffold_10-snap.1401-T1
Sorry, intron length (5) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_24919-T1
Valid prediction for snap_scaffold_10-snap.1394-T1
Valid prediction for GlimmerHMM_glimmerT_24932-T1
Couldn't classify 213633, 213655
Couldn't classify 216489, 216520
Sorry, prediction pasa_asmbl_4492.p1 fails validation.
(TCG)	 TG	213633-213655	GT	GGG
(TTT)	 AG	215287-215511	GT	GGG
(GCC)	 AG	216204-216358	GT	GGG
(AGC)	 AG	216489-216520	AG	AGA
-recovered pasa_asmbl_4492.p1, internal, 215287, 215511
-recovered pasa_asmbl_4492.p1, internal, 216204, 216358
Valid prediction for Augustus_model.g16598.t1
Valid prediction for GlimmerHMM_glimmerT_24923-T1
Valid prediction for CodingQuarry_transcript_5454-T1
Couldn't classify 41307, 41417
Couldn't classify 41958, 42041
Sorry, prediction pasa_asmbl_4515.p2 fails validation.
(GAT)	 TG	41307-41417	GT	TGG
(GTG)	 AG	41555-41695	GT	AGG
(GCC)	 AG	41958-42041	TA	AGT
-recovered pasa_asmbl_4515.p2, internal, 41555, 41695
Valid prediction for snap_scaffold_10-snap.1421-T1
Valid prediction for Augustus_model.g16594.t1
Valid prediction for snap_scaffold_10-snap.1389-T1
Valid prediction for snap_scaffold_10-snap.1419-T1
Couldn't classify 35992, 35997
Sorry, prediction pasa_asmbl_4517.p1 fails validation.
(TCT)	 CC	35992-35997	GT	GAG
(GTG)	 AG	36142-36228	GT	AGG
(GCA)	 AG	36425-36502	GT	TGG
(GGA)	 AG	36625-36695	GT	TGG
(GTC)	 AG	36825-36937	GT	AGG
(GTA)	 AG	37032-37213	GT	AGG
-recovered pasa_asmbl_4517.p1, terminal, 37032, 37213
-recovered pasa_asmbl_4517.p1, internal, 36142, 36228
-recovered pasa_asmbl_4517.p1, internal, 36425, 36502
-recovered pasa_asmbl_4517.p1, internal, 36625, 36695
-recovered pasa_asmbl_4517.p1, internal, 36825, 36937
-recovered pasa_asmbl_4517.p1, internal, 37032, 37213
Valid prediction for Augustus_model.g16596.t1
Valid prediction for snap_scaffold_10-snap.1425-T1
Valid prediction for pasa_asmbl_4497.p1
Valid prediction for snap_scaffold_10-snap.1402-T1
Valid prediction for snap_scaffold_10-snap.1423-T1
Valid prediction for GlimmerHMM_glimmerT_24929-T1
Valid prediction for GlimmerHMM_glimmerT_24926-T1
Valid prediction for GlimmerHMM_glimmerT_24918-T1
Valid prediction for snap_scaffold_10-snap.1387-T1
Valid prediction for HiQ_model.g16595.t1
Valid prediction for GlimmerHMM_glimmerT_24917-T1
Valid prediction for CodingQuarry_transcript_5452-T1
Valid prediction for GlimmerHMM_glimmerT_24936-T1
Valid prediction for GlimmerHMM_glimmerT_24941-T1
Valid prediction for snap_scaffold_10-snap.1414-T1
Couldn't classify 33757, 33821
Couldn't classify 35871, 35982
Sorry, prediction pasa_asmbl_4518.p1 fails validation.
(CTG)	 TC	33757-33821	GT	CGG
(GCT)	 AG	34008-34077	GT	CTG
(GAA)	 AG	34357-34460	GT	GGG
(GTT)	 AG	34686-34762	GT	TGG
(GGC)	 AG	34849-34879	GT	TGG
(GTT)	 AG	35047-35207	GT	ATG
(TGT)	 AG	35356-35471	GT	TGG
(GAT)	 AG	35592-35713	GT	AAG
(CGG)	 AG	35871-35982	AC	AGA
-recovered pasa_asmbl_4518.p1, internal, 34008, 34077
-recovered pasa_asmbl_4518.p1, internal, 34357, 34460
-recovered pasa_asmbl_4518.p1, internal, 34686, 34762
-recovered pasa_asmbl_4518.p1, internal, 34849, 34879
-recovered pasa_asmbl_4518.p1, internal, 35047, 35207
-recovered pasa_asmbl_4518.p1, internal, 35356, 35471
-recovered pasa_asmbl_4518.p1, internal, 35592, 35713
Valid prediction for GlimmerHMM_glimmerT_24939-T1
Couldn't classify 207430, 207486
Sorry, prediction pasa_asmbl_4494.p1 fails validation.
(ACC)	 AC	207430-207486	GT	GGG
(GAT)	 AG	207626-207724	GT	AGG
(AAT)	 AG	207919-208116	GT	TGG
(AAT)	 AG	208292-208390	GT	AGG
(TCG)	 AG	208639-208737	GT	TTG
(CGT)	 AG	208842-208940	GT	GGG
(GAG)	 AG	209218-209415	GT	AGG
(AAA)	 AG	209549-209647	GT	AGG
(AAC)	 AG	209764-209862	GT	AGG
(AAT)	 AG	209956-210153	GT	AGG
(ACT)	 AG	210280-210378	GT	AGG
(CTG)	 AG	210469-210567	GT	AGG
(AAT)	 AG	210723-210821	GT	TGG
(AAT)	 AG	211039-211137	GT	CGG
(ACG)	 AG	211323-211395	GT	GGG
(CCC)	 AG	211645-211698	GT	AGG
(GTG)	 AG	213055-213181	GT	AGG
(CAG)	 AG	213289-213361	GT	AGG
(ATG)	 AG	213552-213821	AG	GAA
-recovered pasa_asmbl_4494.p1, terminal, 213552, 213821
-recovered pasa_asmbl_4494.p1, internal, 207626, 207724
-recovered pasa_asmbl_4494.p1, internal, 207919, 208116
-recovered pasa_asmbl_4494.p1, internal, 208292, 208390
-recovered pasa_asmbl_4494.p1, internal, 208639, 208737
-recovered pasa_asmbl_4494.p1, internal, 208842, 208940
-recovered pasa_asmbl_4494.p1, internal, 209218, 209415
-recovered pasa_asmbl_4494.p1, internal, 209549, 209647
-recovered pasa_asmbl_4494.p1, internal, 209764, 209862
-recovered pasa_asmbl_4494.p1, internal, 209956, 210153
-recovered pasa_asmbl_4494.p1, internal, 210280, 210378
-recovered pasa_asmbl_4494.p1, internal, 210469, 210567
-recovered pasa_asmbl_4494.p1, internal, 210723, 210821
-recovered pasa_asmbl_4494.p1, internal, 211039, 211137
-recovered pasa_asmbl_4494.p1, internal, 211323, 211395
-recovered pasa_asmbl_4494.p1, internal, 211645, 211698
-recovered pasa_asmbl_4494.p1, internal, 213055, 213181
-recovered pasa_asmbl_4494.p1, internal, 213289, 213361
Valid prediction for Augustus_model.g16601.t1
Couldn't classify 218520, 218552
Sorry, prediction pasa_asmbl_5160.p1 fails validation.
(ATG)	 AA	217627-217689	GT	AGG
(GTG)	 AG	218058-218183	GT	AAG
(ATC)	 AG	218301-218423	GT	AGG
(GAG)	 AG	218520-218552	GT	AGG
-recovered pasa_asmbl_5160.p1, initial, 217627, 217689
-recovered pasa_asmbl_5160.p1, internal, 218058, 218183
-recovered pasa_asmbl_5160.p1, internal, 218301, 218423
-recovered pasa_asmbl_5160.p1, internal, 218520, 218552
Valid prediction for GlimmerHMM_glimmerT_24928-T1
Valid prediction for snap_scaffold_10-snap.1410-T1
Valid prediction for pasa_asmbl_4506.p1
Valid prediction for snap_scaffold_10-snap.1398-T1
Valid prediction for snap_scaffold_10-snap.1416-T1
Valid prediction for GlimmerHMM_glimmerT_24924-T1
Valid prediction for HiQ_model.g16603.t1
Valid prediction for GlimmerHMM_glimmerT_24921-T1
Valid prediction for Augustus_model.g16602.t1
Valid prediction for GlimmerHMM_glimmerT_24934-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 9298, rend_intergenic: 7676  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 12144, rend_intergenic: 10462  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19114, rend_intergenic: 12229  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25853, rend_intergenic: 19188  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33298, rend_intergenic: 26100  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55512, rend_intergenic: 50466  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66323, rend_intergenic: 60278  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76432, rend_intergenic: 71041  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107664, rend_intergenic: 88989  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109178, rend_intergenic: 108807  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124784, rend_intergenic: 115395  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144556, rend_intergenic: 126054  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151904, rend_intergenic: 144584  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164281, rend_intergenic: 152736  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175612, rend_intergenic: 170993  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 182583, rend_intergenic: 179661  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 222363
-exon list size: 450


building trellis

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65.5    
65.7    
65.9    
66.2    
66.4    
66.6    
66.8    
67.0    
67.3    
67.5    
67.7    
67.9    
68.1    
68.4    
68.6    
68.8    
69.0    
69.2    
69.5    
69.7    
69.9    
70.1    
70.4    
70.6    
70.8    
71.0    
71.2    
71.5    
71.7    
71.9    
72.1    
72.3    
72.6    
72.8    
73.0    
73.2    
73.5    
73.7    
73.9    
74.1    
74.3    
74.6    
74.8    
75.0    
75.2    
75.4    
75.7    
75.9    
76.1    
76.3    
76.5    
76.8    
77.0    
77.2    
77.4    
77.7    
77.9    
78.1    
78.3    
78.5    
78.8    
79.0    
79.2    
79.4    
79.6    
79.9    
80.1    
80.3    
80.5    
80.8    
81.0    
81.2    
81.4    
81.6    
81.9    
82.1    
82.3    
82.5    
82.7    
83.0    
83.2    
83.4    
83.6    
83.8    
84.1    
84.3    
84.5    
84.7    
85.0    
85.2    
85.4    
85.6    
85.8    
86.1    
86.3    
86.5    
86.7    
86.9    
87.2    
87.4    
87.6    
87.8    
88.1    
88.3    
88.5    
88.7    
88.9    
89.2    
89.4    
89.6    
89.8    
90.0    
90.3    
90.5    
90.7    
90.9    
91.2    
91.4    
91.6    
91.8    
92.0    
92.3    
92.5    
92.7    
92.9    
93.1    
93.4    
93.6    
93.8    
94.0    
94.2    
94.5    
94.7    
94.9    
95.1    
95.4    
95.6    
95.8    
96.0    
96.2    
96.5    
96.7    
96.9    
97.1    
97.3    
97.6    
97.8    
98.0    
98.2    
98.5    
98.7    
98.9    
99.1    
99.3    
99.6    
99.8    
-found 30 predictions from path traversal
Error with prediction: snap lend_intergenic: 9298, rend_intergenic: 7676  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 12144, rend_intergenic: 10462  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19114, rend_intergenic: 12229  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25853, rend_intergenic: 19188  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33298, rend_intergenic: 26100  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55512, rend_intergenic: 50466  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66323, rend_intergenic: 60278  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76432, rend_intergenic: 71041  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107664, rend_intergenic: 88989  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109178, rend_intergenic: 108807  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124784, rend_intergenic: 115395  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144556, rend_intergenic: 126054  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151904, rend_intergenic: 144584  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164281, rend_intergenic: 152736  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175612, rend_intergenic: 170993  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 182583, rend_intergenic: 179661  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 19 predictions persist after filtering for low support