-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_1/scaffold_1_5452904-5661643

-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 Augustus_model.g526.t1
Valid prediction for snap_scaffold_1-snap.870-T1
Valid prediction for GeneMark_model.899_t
Valid prediction for snap_scaffold_1-snap.901-T1
Valid prediction for GeneMark_model.862_t
Valid prediction for GeneMark_model.878_t
Valid prediction for GeneMark_model.892_t
Valid prediction for Augustus_model.g520.t1
Valid prediction for GeneMark_model.888_t
Valid prediction for GeneMark_model.876_t
Valid prediction for GeneMark_model.900_t
Valid prediction for CodingQuarry_transcript_2611-T1
Couldn't classify 165824, 166154
Sorry, prediction pasa_asmbl_1726.p1 fails validation.
(ACA)	 CT	165824-166154	GT	TGG
(CAG)	 AG	166479-166654	AC	AAA
-recovered pasa_asmbl_1726.p1, terminal, 166479, 166654
Valid prediction for Augustus_model.g524.t1
Valid prediction for snap_scaffold_1-snap.875-T1
Valid prediction for HiQ_model.g541.t1
Valid prediction for GlimmerHMM_glimmerT_689-T1
Valid prediction for snap_scaffold_1-snap.871-T1
Valid prediction for GlimmerHMM_glimmerT_706-T1
Valid prediction for snap_scaffold_1-snap.872-T1
Couldn't classify 88178, 88304
Sorry, prediction pasa_asmbl_1722.p2 fails validation.
(ATC)	 AC	88178-88304	GT	TGG
(GTA)	 AG	88436-88550	GT	AAG
(GAA)	 AG	88664-88800	GT	CGG
(AAT)	 AG	88884-88915	AG	AGA
-recovered pasa_asmbl_1722.p2, terminal, 88884, 88915
-recovered pasa_asmbl_1722.p2, internal, 88436, 88550
-recovered pasa_asmbl_1722.p2, internal, 88664, 88800
Valid prediction for CodingQuarry_transcript_2613-T1
Valid prediction for GlimmerHMM_glimmerT_676-T1
Valid prediction for CodingQuarry_transcript_2612-T1
Valid prediction for CodingQuarry_transcript_2608-T1
Valid prediction for snap_scaffold_1-snap.863-T1
Valid prediction for snap_scaffold_1-snap.894-T1
Valid prediction for GlimmerHMM_glimmerT_677-T1
Valid prediction for GeneMark_model.894_t
Valid prediction for GlimmerHMM_glimmerT_696-T1
Valid prediction for Augustus_model.g540.t1
Valid prediction for snap_scaffold_1-snap.878-T1
Valid prediction for GeneMark_model.874_t
Valid prediction for GlimmerHMM_glimmerT_705-T1
Valid prediction for Augustus_model.g531.t1
Valid prediction for snap_scaffold_1-snap.900-T1
Valid prediction for GlimmerHMM_glimmerT_698-T1
Valid prediction for GeneMark_model.866_t
Valid prediction for GeneMark_model.898_t
Valid prediction for snap_scaffold_1-snap.866-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_709-T1
Couldn't classify 164439, 164574
Sorry, prediction pasa_asmbl_1724.p1 fails validation.
(ATG)	 CC	162799-162865	GT	TGG
(CTG)	 AG	163623-163776	GT	AGG
(ATT)	 AG	164439-164574	CG	GAC
-recovered pasa_asmbl_1724.p1, initial, 162799, 162865
-recovered pasa_asmbl_1724.p1, internal, 163623, 163776
Valid prediction for GeneMark_model.864_t
Valid prediction for GeneMark_model.882_t
Valid prediction for HiQ_model.g535.t1
Valid prediction for GlimmerHMM_glimmerT_681-T1
Valid prediction for GlimmerHMM_glimmerT_685-T1
Valid prediction for HiQ_model.g537.t1
Valid prediction for snap_scaffold_1-snap.898-T1
Valid prediction for snap_scaffold_1-snap.891-T1
Valid prediction for snap_scaffold_1-snap.864-T1
Valid prediction for GeneMark_model.870_t
Valid prediction for GlimmerHMM_glimmerT_700-T1
Valid prediction for GlimmerHMM_glimmerT_686-T1
Valid prediction for pasa_asmbl_1734.p1
Valid prediction for GeneMark_model.859_t
Valid prediction for GlimmerHMM_glimmerT_710-T1
Valid prediction for snap_scaffold_1-snap.888-T1
Valid prediction for snap_scaffold_1-snap.884-T1
Valid prediction for snap_scaffold_1-snap.897-T1
Couldn't classify 175899, 175919
Sorry, prediction pasa_asmbl_1730.p1 fails validation.
(TCC)	 CT	175899-175919	GT	AGG
(CCA)	 AG	176645-176734	GT	AGG
(CTG)	 AG	177250-177308	GT	GGG
(GAA)	 AG	177446-177518	GT	AGG
(GGA)	 AG	177638-177920	GT	CGG
(GAA)	 AG	179356-179491	GT	AGG
(AAG)	 AG	179677-179779	GT	AGG
(GTT)	 AG	179986-180068	GT	GGG
(GTT)	 AG	180297-180528	GA	GAG
-recovered pasa_asmbl_1730.p1, terminal, 180297, 180528
-recovered pasa_asmbl_1730.p1, internal, 176645, 176734
-recovered pasa_asmbl_1730.p1, internal, 177250, 177308
-recovered pasa_asmbl_1730.p1, internal, 177446, 177518
-recovered pasa_asmbl_1730.p1, internal, 177638, 177920
-recovered pasa_asmbl_1730.p1, internal, 179356, 179491
-recovered pasa_asmbl_1730.p1, internal, 179677, 179779
-recovered pasa_asmbl_1730.p1, internal, 179986, 180068
Valid prediction for GeneMark_model.880_t
Valid prediction for GeneMark_model.860_t
Valid prediction for GlimmerHMM_glimmerT_678-T1
Valid prediction for pasa_asmbl_1731.p1
Valid prediction for GeneMark_model.868_t
Couldn't classify 38748, 39509
Sorry, prediction pasa_asmbl_269.p1 fails validation.
(ATG)	 GC	38748-39509	TC	CTT
Valid prediction for snap_scaffold_1-snap.880-T1
Valid prediction for GeneMark_model.884_t
Valid prediction for CodingQuarry_transcript_2609-T1
Valid prediction for snap_scaffold_1-snap.862-T1
Valid prediction for snap_scaffold_1-snap.877-T1
Valid prediction for GeneMark_model.895_t
Valid prediction for snap_scaffold_1-snap.874-T1
Valid prediction for GlimmerHMM_glimmerT_680-T1
Valid prediction for GeneMark_model.886_t
Valid prediction for GlimmerHMM_glimmerT_711-T1
Valid prediction for GlimmerHMM_glimmerT_684-T1
Valid prediction for Augustus_model.g523.t1
Valid prediction for snap_scaffold_1-snap.896-T1
Valid prediction for snap_scaffold_1-snap.865-T1
Valid prediction for GlimmerHMM_glimmerT_692-T1
Valid prediction for snap_scaffold_1-snap.882-T1
Valid prediction for pasa_asmbl_1737.p1
Valid prediction for GlimmerHMM_glimmerT_683-T1
Valid prediction for GeneMark_model.897_t
Valid prediction for GlimmerHMM_glimmerT_703-T1
Valid prediction for snap_scaffold_1-snap.899-T1
Valid prediction for GlimmerHMM_glimmerT_693-T1
Valid prediction for GlimmerHMM_glimmerT_694-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 HiQ_model.g528.t1
Valid prediction for snap_scaffold_1-snap.883-T1
Valid prediction for GeneMark_model.863_t
Valid prediction for GlimmerHMM_glimmerT_690-T1
Valid prediction for Augustus_model.g530.t1
Valid prediction for GeneMark_model.875_t
Valid prediction for pasa_asmbl_281.p1
Valid prediction for HiQ_model.g534.t1
Valid prediction for Augustus_model.g532.t1
Valid prediction for GeneMark_model.893_t
Valid prediction for GeneMark_model.857_t
Valid prediction for GeneMark_model.861_t
Valid prediction for GlimmerHMM_glimmerT_691-T1
Valid prediction for GlimmerHMM_glimmerT_708-T1
Valid prediction for GlimmerHMM_glimmerT_682-T1
Valid prediction for GeneMark_model.872_t
Valid prediction for snap_scaffold_1-snap.885-T1
Valid prediction for snap_scaffold_1-snap.879-T1
Valid prediction for GlimmerHMM_glimmerT_687-T1
Valid prediction for Augustus_model.g521.t1
Valid prediction for Augustus_model.g536.t1
Valid prediction for snap_scaffold_1-snap.869-T1
Couldn't classify 127595, 127690
Sorry, prediction pasa_asmbl_273.p1 fails validation.
(ATG)	 CC	122820-122938	GT	AAG
(ATA)	 AG	123095-123251	GT	TGG
(GAA)	 AG	123941-124060	GT	AGG
(ACG)	 AG	124185-124267	GT	TGG
(GTG)	 AG	124444-124561	GT	AGG
(GAT)	 AG	124813-124960	GT	AGG
(ACA)	 AG	126315-126402	GT	AAG
(ATT)	 AG	127336-127399	GT	AGG
(TAC)	 AG	127595-127690	GT	CTG
-recovered pasa_asmbl_273.p1, initial, 122820, 122938
-recovered pasa_asmbl_273.p1, internal, 123095, 123251
-recovered pasa_asmbl_273.p1, internal, 123941, 124060
-recovered pasa_asmbl_273.p1, internal, 124185, 124267
-recovered pasa_asmbl_273.p1, internal, 124444, 124561
-recovered pasa_asmbl_273.p1, internal, 124813, 124960
-recovered pasa_asmbl_273.p1, internal, 126315, 126402
-recovered pasa_asmbl_273.p1, internal, 127336, 127399
-recovered pasa_asmbl_273.p1, internal, 127595, 127690
Valid prediction for GeneMark_model.869_t
Valid prediction for snap_scaffold_1-snap.867-T1
Valid prediction for CodingQuarry_transcript_2607-T1
Valid prediction for snap_scaffold_1-snap.886-T1
Valid prediction for CodingQuarry_transcript_2610-T1
Valid prediction for snap_scaffold_1-snap.861-T1
Valid prediction for snap_scaffold_1-snap.892-T1
Valid prediction for GeneMark_model.881_t
Couldn't classify 39481, 39552
Sorry, prediction pasa_asmbl_282.p1 fails validation.
(ATT)	 AG	39481-39552	GT	AGG
(ATG)	 AG	39713-39799	GT	AGG
(GTG)	 AG	39998-40253	GT	AGG
(AAC)	 AG	40391-40458	GT	AGG
-recovered pasa_asmbl_282.p1, initial, 39713, 39799
-recovered pasa_asmbl_282.p1, terminal, 40391, 40458
-recovered pasa_asmbl_282.p1, internal, 39481, 39552
-recovered pasa_asmbl_282.p1, internal, 39713, 39799
-recovered pasa_asmbl_282.p1, internal, 39998, 40253
-recovered pasa_asmbl_282.p1, internal, 40391, 40458
Valid prediction for GlimmerHMM_glimmerT_699-T1
Valid prediction for GeneMark_model.889_t
Valid prediction for Augustus_model.g525.t1
Valid prediction for GlimmerHMM_glimmerT_701-T1
Valid prediction for GeneMark_model.885_t
Valid prediction for snap_scaffold_1-snap.895-T1
Valid prediction for GlimmerHMM_glimmerT_695-T1
Valid prediction for CodingQuarry_transcript_2605-T1
Valid prediction for GeneMark_model.871_t
Valid prediction for Augustus_model.g519.t1
Valid prediction for snap_scaffold_1-snap.893-T1
Valid prediction for GeneMark_model.891_t
Couldn't classify 135219, 135344
Couldn't classify 145719, 145774
Sorry, prediction pasa_asmbl_271.p1 fails validation.
(GTC)	 GG	135219-135344	GT	AGG
(GTG)	 AG	137132-137205	GT	AGG
(CAT)	 AG	137586-137780	GT	TGG
(GTT)	 AG	137920-138006	GT	AGG
(CGA)	 AG	138323-138406	GT	AGG
(GCT)	 AG	139403-139547	GT	AGG
(GAG)	 AG	140039-140159	GT	TGG
(CCT)	 AG	140414-140505	GT	AGG
(GGA)	 AG	140749-140826	GT	TGG
(GCT)	 AG	141045-141166	GT	AGG
(GGA)	 AG	142619-142721	GT	AGG
(TAT)	 AG	142847-142930	GT	AGG
(GAG)	 AG	144637-144811	GT	AGG
(GCT)	 AG	145719-145774	AC	ANA
-recovered pasa_asmbl_271.p1, internal, 137132, 137205
-recovered pasa_asmbl_271.p1, internal, 137586, 137780
-recovered pasa_asmbl_271.p1, internal, 137920, 138006
-recovered pasa_asmbl_271.p1, internal, 138323, 138406
-recovered pasa_asmbl_271.p1, internal, 139403, 139547
-recovered pasa_asmbl_271.p1, internal, 140039, 140159
-recovered pasa_asmbl_271.p1, internal, 140414, 140505
-recovered pasa_asmbl_271.p1, internal, 140749, 140826
-recovered pasa_asmbl_271.p1, internal, 141045, 141166
-recovered pasa_asmbl_271.p1, internal, 142619, 142721
-recovered pasa_asmbl_271.p1, internal, 142847, 142930
-recovered pasa_asmbl_271.p1, internal, 144637, 144811
Valid prediction for Augustus_model.g539.t1
Valid prediction for GeneMark_model.877_t
Valid prediction for Augustus_model.g533.t1
Valid prediction for snap_scaffold_1-snap.889-T1
Couldn't classify 38447, 38815
Sorry, prediction pasa_asmbl_283.p1 fails validation.
(CTG)	 GC	38447-38815	CT	TGC
Valid prediction for snap_scaffold_1-snap.873-T1
Valid prediction for CodingQuarry_transcript_2606-T1
Valid prediction for Augustus_model.g538.t1
Valid prediction for GlimmerHMM_glimmerT_697-T1
Valid prediction for GlimmerHMM_glimmerT_704-T1
Valid prediction for snap_scaffold_1-snap.887-T1
Valid prediction for GeneMark_model.890_t
Valid prediction for Augustus_model.g527.t1
Valid prediction for snap_scaffold_1-snap.868-T1
Valid prediction for GeneMark_model.873_t
Valid prediction for GlimmerHMM_glimmerT_702-T1
Valid prediction for GeneMark_model.896_t
Valid prediction for GeneMark_model.879_t
Couldn't classify 36324, 36426
Couldn't classify 37338, 37479
Sorry, prediction pasa_asmbl_284.p1 fails validation.
(GAA)	 AC	36324-36426	GT	TGG
(GTA)	 AG	36638-36708	GT	AGG
(CTA)	 AG	36843-37013	GT	AGG
(GTA)	 AG	37099-37217	GT	AGG
(CCC)	 AG	37338-37479	TC	GAT
-recovered pasa_asmbl_284.p1, internal, 36638, 36708
-recovered pasa_asmbl_284.p1, internal, 36843, 37013
-recovered pasa_asmbl_284.p1, internal, 37099, 37217
Valid prediction for GeneMark_model.865_t
Valid prediction for snap_scaffold_1-snap.876-T1
Valid prediction for GeneMark_model.867_t
Valid prediction for Augustus_model.g522.t1
Valid prediction for pasa_asmbl_277.p1
Valid prediction for GeneMark_model.858_t
Valid prediction for snap_scaffold_1-snap.890-T1
Valid prediction for GlimmerHMM_glimmerT_688-T1
Valid prediction for Augustus_model.g529.t1
Valid prediction for GlimmerHMM_glimmerT_679-T1
Valid prediction for snap_scaffold_1-snap.881-T1
Valid prediction for GeneMark_model.887_t
Valid prediction for GlimmerHMM_glimmerT_707-T1
Valid prediction for GeneMark_model.856_t
Valid prediction for GlimmerHMM_glimmerT_675-T1
Valid prediction for GeneMark_model.883_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 21067, rend_intergenic: 19443  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35101, rend_intergenic: 31648  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73750, rend_intergenic: 59759  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139178, rend_intergenic: 132423  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146829, rend_intergenic: 142465  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 208740
-exon list size: 696


building trellis

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61.0    
61.2    
61.3    
61.5    
61.6    
61.7    
61.9    
62.0    
62.2    
62.3    
62.5    
62.6    
62.8    
62.9    
63.0    
63.2    
63.3    
63.5    
63.6    
63.8    
63.9    
64.0    
64.2    
64.3    
64.5    
64.6    
64.8    
64.9    
65.0    
65.2    
65.3    
65.5    
65.6    
65.8    
65.9    
66.0    
66.2    
66.3    
66.5    
66.6    
66.8    
66.9    
67.0    
67.2    
67.3    
67.5    
67.6    
67.8    
67.9    
68.1    
68.2    
68.3    
68.5    
68.6    
68.8    
68.9    
69.1    
69.2    
69.3    
69.5    
69.6    
69.8    
69.9    
70.1    
70.2    
70.3    
70.5    
70.6    
70.8    
70.9    
71.1    
71.2    
71.3    
71.5    
71.6    
71.8    
71.9    
72.1    
72.2    
72.3    
72.5    
72.6    
72.8    
72.9    
73.1    
73.2    
73.4    
73.5    
73.6    
73.8    
73.9    
74.1    
74.2    
74.4    
74.5    
74.6    
74.8    
74.9    
75.1    
75.2    
75.4    
75.5    
75.6    
75.8    
75.9    
76.1    
76.2    
76.4    
76.5    
76.6    
76.8    
76.9    
77.1    
77.2    
77.4    
77.5    
77.7    
77.8    
77.9    
78.1    
78.2    
78.4    
78.5    
78.7    
78.8    
78.9    
79.1    
79.2    
79.4    
79.5    
79.7    
79.8    
79.9    
80.1    
80.2    
80.4    
80.5    
80.7    
80.8    
80.9    
81.1    
81.2    
81.4    
81.5    
81.7    
81.8    
81.9    
82.1    
82.2    
82.4    
82.5    
82.7    
82.8    
83.0    
83.1    
83.2    
83.4    
83.5    
83.7    
83.8    
84.0    
84.1    
84.2    
84.4    
84.5    
84.7    
84.8    
85.0    
85.1    
85.2    
85.4    
85.5    
85.7    
85.8    
86.0    
86.1    
86.2    
86.4    
86.5    
86.7    
86.8    
87.0    
87.1    
87.2    
87.4    
87.5    
87.7    
87.8    
88.0    
88.1    
88.3    
88.4    
88.5    
88.7    
88.8    
89.0    
89.1    
89.3    
89.4    
89.5    
89.7    
89.8    
90.0    
90.1    
90.3    
90.4    
90.5    
90.7    
90.8    
91.0    
91.1    
91.3    
91.4    
91.5    
91.7    
91.8    
92.0    
92.1    
92.3    
92.4    
92.6    
92.7    
92.8    
93.0    
93.1    
93.3    
93.4    
93.6    
93.7    
93.8    
94.0    
94.1    
94.3    
94.4    
94.6    
94.7    
94.8    
95.0    
95.1    
95.3    
95.4    
95.6    
95.7    
95.8    
96.0    
96.1    
96.3    
96.4    
96.6    
96.7    
96.8    
97.0    
97.1    
97.3    
97.4    
97.6    
97.7    
97.9    
98.0    
98.1    
98.3    
98.4    
98.6    
98.7    
98.9    
99.0    
99.1    
99.3    
99.4    
99.6    
99.7    
99.9    
-found 38 predictions from path traversal
Error with prediction: snap lend_intergenic: 21067, rend_intergenic: 19443  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35101, rend_intergenic: 31648  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73750, rend_intergenic: 59759  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139178, rend_intergenic: 132423  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146829, rend_intergenic: 142465  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 30 predictions persist after filtering for low support