-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_5/scaffold_5_13151044-13374798

-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.22225_t
Valid prediction for snap_scaffold_5-snap.2453-T1
Valid prediction for snap_scaffold_5-snap.2471-T1
Couldn't classify 100729, 100977
Sorry, prediction pasa_asmbl_44547.p1 fails validation.
(ATG)	 CC	100053-100212	GT	ACG
(CAA)	 AG	100336-100598	GT	AAG
(CTG)	 AG	100729-100977	TG	ACT
-recovered pasa_asmbl_44547.p1, initial, 100053, 100212
-recovered pasa_asmbl_44547.p1, internal, 100336, 100598
Valid prediction for GeneMark_model.22222_t
Valid prediction for snap_scaffold_5-snap.2464-T1
Valid prediction for GeneMark_model.22213_t
Valid prediction for Augustus_model.g8820.t1
Valid prediction for snap_scaffold_5-snap.2472-T1
Valid prediction for GlimmerHMM_glimmerT_13181-T1
Valid prediction for GeneMark_model.22210_t
Valid prediction for GeneMark_model.22233_t
Valid prediction for GeneMark_model.22208_t
Valid prediction for snap_scaffold_5-snap.2458-T1
Valid prediction for Augustus_model.g8808.t1
Valid prediction for GlimmerHMM_glimmerT_13191-T1
Valid prediction for GlimmerHMM_glimmerT_13200-T1
Valid prediction for snap_scaffold_5-snap.2456-T1
Valid prediction for snap_scaffold_5-snap.2473-T1
Valid prediction for GeneMark_model.22209_t
Valid prediction for Augustus_model.g8797.t1
Valid prediction for GeneMark_model.22199_t
Valid prediction for snap_scaffold_5-snap.2450-T1
Valid prediction for CodingQuarry_transcript_52193-T1
Valid prediction for GeneMark_model.22204_t
Valid prediction for GeneMark_model.22220_t
Valid prediction for GeneMark_model.22218_t
Valid prediction for GlimmerHMM_glimmerT_13187-T1
Valid prediction for GlimmerHMM_glimmerT_13197-T1
Valid prediction for snap_scaffold_5-snap.2455-T1
Valid prediction for snap_scaffold_5-snap.2468-T1
Valid prediction for GlimmerHMM_glimmerT_13198-T1
Valid prediction for GeneMark_model.22230_t
Valid prediction for snap_scaffold_5-snap.2462-T1
Valid prediction for CodingQuarry_transcript_52196-T1
Valid prediction for CodingQuarry_transcript_52194-T1
Valid prediction for Augustus_model.g8804.t1
Valid prediction for snap_scaffold_5-snap.2446-T1
Valid prediction for pasa_asmbl_44550.p1
Valid prediction for CodingQuarry_transcript_52201-T1
Valid prediction for snap_scaffold_5-snap.2451-T1
Valid prediction for Augustus_model.g8814.t1
Valid prediction for pasa_asmbl_44539.p1
Valid prediction for HiQ_model.g8815.t1
Valid prediction for GeneMark_model.22227_t
Valid prediction for GlimmerHMM_glimmerT_13199-T1
Valid prediction for snap_scaffold_5-snap.2467-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_13196-T1
Valid prediction for HiQ_model.g8812.t1
Valid prediction for Augustus_model.g8802.t1
Valid prediction for GlimmerHMM_glimmerT_13195-T1
Valid prediction for Augustus_model.g8799.t1
Couldn't classify 101586, 102059
Sorry, prediction pasa_asmbl_44548.p1 fails validation.
(TCA)	 TG	101586-102059	TA	AGT
Valid prediction for snap_scaffold_5-snap.2461-T1
Valid prediction for GlimmerHMM_glimmerT_13186-T1
Valid prediction for GeneMark_model.22228_t
Valid prediction for GeneMark_model.22215_t
Valid prediction for snap_scaffold_5-snap.2469-T1
Valid prediction for snap_scaffold_5-snap.2452-T1
Valid prediction for CodingQuarry_transcript_52197-T1
Valid prediction for CodingQuarry_transcript_52199-T1
Valid prediction for snap_scaffold_5-snap.2470-T1
Valid prediction for GlimmerHMM_glimmerT_13185-T1
Valid prediction for HiQ_model.g8806.t1
Valid prediction for snap_scaffold_5-snap.2440-T1
Valid prediction for snap_scaffold_5-snap.2475-T1
Valid prediction for CodingQuarry_transcript_52198-T1
Valid prediction for CodingQuarry_transcript_52190-T1
Valid prediction for GlimmerHMM_glimmerT_13183-T1
Valid prediction for GeneMark_model.22234_t
Valid prediction for GlimmerHMM_glimmerT_13175-T1
Valid prediction for GeneMark_model.22229_t
Valid prediction for HiQ_model.g8807.t1
Valid prediction for GlimmerHMM_glimmerT_13204-T1
Valid prediction for GeneMark_model.22206_t
Valid prediction for snap_scaffold_5-snap.2443-T1
Couldn't classify 139957, 140058
Sorry, prediction pasa_asmbl_45064.p1 fails validation.
(GGG)	 CA	139957-140058	GT	TGG
(GCC)	 AG	140595-140718	GT	AGG
(AGT)	 AG	141216-141277	GT	AGG
(GAT)	 AG	141393-141438	GT	AGG
(GCC)	 AG	141540-141665	GT	AGG
(GAT)	 AG	141830-141874	GT	AGG
(ATT)	 AG	142132-142175	GT	TGG
(GTG)	 AG	142415-142471	GT	AGG
(ATG)	 AG	143224-143276	GT	GGG
(GCT)	 AG	143404-143612	GT	CGG
(ACG)	 AG	143857-144048	GT	AGG
(ATC)	 AG	144148-144193	GT	AGG
(GTC)	 AG	144340-144453	GT	TGG
(TGT)	 AG	145729-145784	GT	CGG
(ACT)	 AG	146230-146387	GT	GGG
(GAT)	 AG	146495-146632	GT	AGG
(GCC)	 AG	148864-148931	GT	GGG
(GGA)	 AG	150442-150592	GT	AGG
(AGC)	 AG	150777-150869	GT	GTG
(CTA)	 AG	152218-152297	GT	AGG
(CAA)	 AG	152454-152534	GT	GGG
(AGT)	 AG	152725-152830	GT	AGG
(CTG)	 AG	153241-153399	GT	AGG
(CTC)	 AG	154311-154418	GT	TGG
(TCC)	 AG	156686-156799	GT	AGG
(AAA)	 AG	157741-157842	GT	AGG
(GTG)	 AG	158012-158134	GT	AGG
(CTC)	 AG	158257-158340	AA	AAA
-recovered pasa_asmbl_45064.p1, initial, 143224, 143276
-recovered pasa_asmbl_45064.p1, terminal, 158257, 158340
-recovered pasa_asmbl_45064.p1, internal, 140595, 140718
-recovered pasa_asmbl_45064.p1, internal, 141216, 141277
-recovered pasa_asmbl_45064.p1, internal, 141393, 141438
-recovered pasa_asmbl_45064.p1, internal, 141540, 141665
-recovered pasa_asmbl_45064.p1, internal, 141830, 141874
-recovered pasa_asmbl_45064.p1, internal, 142132, 142175
-recovered pasa_asmbl_45064.p1, internal, 142415, 142471
-recovered pasa_asmbl_45064.p1, internal, 143224, 143276
-recovered pasa_asmbl_45064.p1, internal, 143404, 143612
-recovered pasa_asmbl_45064.p1, internal, 143857, 144048
-recovered pasa_asmbl_45064.p1, internal, 144148, 144193
-recovered pasa_asmbl_45064.p1, internal, 144340, 144453
-recovered pasa_asmbl_45064.p1, internal, 145729, 145784
-recovered pasa_asmbl_45064.p1, internal, 146230, 146387
-recovered pasa_asmbl_45064.p1, internal, 146495, 146632
-recovered pasa_asmbl_45064.p1, internal, 148864, 148931
-recovered pasa_asmbl_45064.p1, internal, 150442, 150592
-recovered pasa_asmbl_45064.p1, internal, 150777, 150869
-recovered pasa_asmbl_45064.p1, internal, 152218, 152297
-recovered pasa_asmbl_45064.p1, internal, 152454, 152534
-recovered pasa_asmbl_45064.p1, internal, 152725, 152830
-recovered pasa_asmbl_45064.p1, internal, 153241, 153399
-recovered pasa_asmbl_45064.p1, internal, 154311, 154418
-recovered pasa_asmbl_45064.p1, internal, 156686, 156799
-recovered pasa_asmbl_45064.p1, internal, 157741, 157842
-recovered pasa_asmbl_45064.p1, internal, 158012, 158134
Valid prediction for GlimmerHMM_glimmerT_13177-T1
Valid prediction for snap_scaffold_5-snap.2448-T1
Valid prediction for Augustus_model.g8817.t1
Valid prediction for Augustus_model.g8816.t1
Valid prediction for pasa_asmbl_44542.p1

-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_13203-T1
Valid prediction for snap_scaffold_5-snap.2447-T1
Valid prediction for GeneMark_model.22224_t
Valid prediction for CodingQuarry_transcript_52195-T1
Valid prediction for snap_scaffold_5-snap.2449-T1
Valid prediction for GeneMark_model.22235_t
Valid prediction for GeneMark_model.22223_t
Valid prediction for GeneMark_model.22219_t
Valid prediction for Augustus_model.g8819.t1
Valid prediction for GeneMark_model.22231_t
Valid prediction for CodingQuarry_transcript_52200-T1
Valid prediction for HiQ_model.g8796.t1
Valid prediction for GlimmerHMM_glimmerT_13184-T1
Couldn't classify 142108, 142252
Sorry, prediction pasa_asmbl_45913.p1 fails validation.
(CAT)	 AC	142108-142252	GT	AGG
(GTT)	 AG	142930-143048	GT	AGG
(ATA)	 AG	143147-143395	GT	CTG
(CCC)	 AG	143530-143658	CA	AAC
-recovered pasa_asmbl_45913.p1, terminal, 143530, 143658
-recovered pasa_asmbl_45913.p1, internal, 142930, 143048
-recovered pasa_asmbl_45913.p1, internal, 143147, 143395
Valid prediction for snap_scaffold_5-snap.2439-T1
Valid prediction for GlimmerHMM_glimmerT_13176-T1
Valid prediction for GeneMark_model.22198_t
Valid prediction for GeneMark_model.22214_t
Valid prediction for snap_scaffold_5-snap.2457-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GeneMark_model.22201_t
Valid prediction for Augustus_model.g8801.t1
Valid prediction for HiQ_model.g8803.t1
Valid prediction for GeneMark_model.22232_t
Valid prediction for CodingQuarry_transcript_52189-T1
Valid prediction for CodingQuarry_transcript_52192-T1
Valid prediction for GeneMark_model.22217_t
Valid prediction for GlimmerHMM_glimmerT_13194-T1
Valid prediction for snap_scaffold_5-snap.2474-T1
Valid prediction for GeneMark_model.22226_t
Valid prediction for GlimmerHMM_glimmerT_13201-T1
Valid prediction for pasa_asmbl_45906.p1
Valid prediction for GlimmerHMM_glimmerT_13182-T1
Valid prediction for GlimmerHMM_glimmerT_13178-T1
Valid prediction for GlimmerHMM_glimmerT_13193-T1
Valid prediction for GlimmerHMM_glimmerT_13179-T1
Valid prediction for snap_scaffold_5-snap.2444-T1
Valid prediction for snap_scaffold_5-snap.2459-T1
Valid prediction for Augustus_model.g8798.t1
Valid prediction for CodingQuarry_transcript_52191-T1
Valid prediction for Augustus_model.g8818.t1
Valid prediction for Augustus_model.g8809.t1
Couldn't classify 54490, 54599
Couldn't classify 57718, 57796
Couldn't classify 58101, 58251
Sorry, prediction pasa_asmbl_45919.p1 fails validation.
(CAG)	 TC	54490-54599	GT	AGG
(ACA)	 AG	54706-54827	GT	CGG
(TGA)	 AG	54981-55158	GT	TGG
(CCC)	 AG	55405-55489	GT	CGG
(GTG)	 AG	55657-55717	GT	GTG
(TAT)	 AG	56019-56095	GT	AGG
(GGG)	 AG	56200-56346	GT	AGG
(GAT)	 AG	56537-56643	GT	AAG
(GTA)	 AG	57389-57477	GT	AGG
(ATC)	 AG	57718-57796	AT	CAA
(CTA)	 AC	58101-58251	GT	AGG
(AGG)	 AG	58370-58452	GT	GTG
(GCT)	 AG	58548-58578	GT	AGG
(GCC)	 AG	58673-58751	GT	AGG
(TGT)	 AG	58842-58979	GT	AGG
(AGC)	 AG	59121-59218	GT	TGG
(ACG)	 AG	59508-59633	GT	AGG
(GTA)	 AG	60237-60418	GT	GTG
(TTT)	 AG	60718-60808	GT	AGG
(AGA)	 AG	60897-60947	GT	TGG
(GAT)	 AG	61129-61216	GT	AGG
(ACA)	 AG	61326-61390	GT	TGG
(CGC)	 AG	61531-61585	GT	TGG
(TGC)	 AG	61828-61899	GT	ATG
(ATT)	 AG	61990-62108	GG	AAG
add_exon() Sorry, pasa_asmbl_45919.p1 57389-57477-terminal-2 is invalid.
-recovered pasa_asmbl_45919.p1, terminal, 57389, 57477
-recovered pasa_asmbl_45919.p1, terminal, 61990, 62108
-recovered pasa_asmbl_45919.p1, internal, 54706, 54827
-recovered pasa_asmbl_45919.p1, internal, 54981, 55158
-recovered pasa_asmbl_45919.p1, internal, 55405, 55489
-recovered pasa_asmbl_45919.p1, internal, 55657, 55717
-recovered pasa_asmbl_45919.p1, internal, 56019, 56095
-recovered pasa_asmbl_45919.p1, internal, 56200, 56346
-recovered pasa_asmbl_45919.p1, internal, 56537, 56643
-recovered pasa_asmbl_45919.p1, internal, 57389, 57477
-recovered pasa_asmbl_45919.p1, internal, 58370, 58452
-recovered pasa_asmbl_45919.p1, internal, 58548, 58578
-recovered pasa_asmbl_45919.p1, internal, 58673, 58751
-recovered pasa_asmbl_45919.p1, internal, 58842, 58979
-recovered pasa_asmbl_45919.p1, internal, 59121, 59218
-recovered pasa_asmbl_45919.p1, internal, 59508, 59633
-recovered pasa_asmbl_45919.p1, internal, 60237, 60418
-recovered pasa_asmbl_45919.p1, internal, 60718, 60808
-recovered pasa_asmbl_45919.p1, internal, 60897, 60947
-recovered pasa_asmbl_45919.p1, internal, 61129, 61216
-recovered pasa_asmbl_45919.p1, internal, 61326, 61390
-recovered pasa_asmbl_45919.p1, internal, 61531, 61585
-recovered pasa_asmbl_45919.p1, internal, 61828, 61899
Valid prediction for GlimmerHMM_glimmerT_13202-T1
Valid prediction for GeneMark_model.22216_t
Valid prediction for GlimmerHMM_glimmerT_13189-T1
Valid prediction for GeneMark_model.22211_t
Valid prediction for GeneMark_model.22203_t
Valid prediction for GeneMark_model.22221_t
Valid prediction for GlimmerHMM_glimmerT_13190-T1
Valid prediction for GeneMark_model.22207_t
Valid prediction for GeneMark_model.22202_t
Valid prediction for pasa_asmbl_45911.p1
Valid prediction for GlimmerHMM_glimmerT_13188-T1
Valid prediction for Augustus_model.g8811.t1
Valid prediction for snap_scaffold_5-snap.2465-T1
Valid prediction for snap_scaffold_5-snap.2463-T1
Valid prediction for pasa_asmbl_45910.p1
Valid prediction for snap_scaffold_5-snap.2460-T1
Valid prediction for snap_scaffold_5-snap.2466-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for snap_scaffold_5-snap.2441-T1
Valid prediction for GlimmerHMM_glimmerT_13192-T1
Valid prediction for HiQ_model.g8813.t1
Valid prediction for snap_scaffold_5-snap.2442-T1
Valid prediction for GlimmerHMM_glimmerT_13180-T1
Valid prediction for GeneMark_model.22200_t
Valid prediction for GeneMark_model.22205_t
Valid prediction for Augustus_model.g8810.t1
Valid prediction for GeneMark_model.22197_t
Valid prediction for Augustus_model.g8805.t1
Valid prediction for HiQ_model.g8800.t1
Valid prediction for GeneMark_model.22212_t
Valid prediction for snap_scaffold_5-snap.2454-T1
Valid prediction for GlimmerHMM_glimmerT_13174-T1
Valid prediction for GeneMark_model.22196_t
Valid prediction for snap_scaffold_5-snap.2445-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 128333, rend_intergenic: 126919  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131030, rend_intergenic: 130097  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135537, rend_intergenic: 131240  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148935, rend_intergenic: 144307  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152120, rend_intergenic: 149168  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158340, rend_intergenic: 153286  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175094, rend_intergenic: 163700  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 223755
-exon list size: 686


building trellis

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49.6    
49.7    
49.9    
50.0    
50.1    
50.3    
50.4    
50.6    
50.7    
50.9    
51.0    
51.2    
51.3    
51.5    
51.6    
51.7    
51.9    
52.0    
52.2    
52.3    
52.5    
52.6    
52.8    
52.9    
53.1    
53.2    
53.3    
53.5    
53.6    
53.8    
53.9    
54.1    
54.2    
54.4    
54.5    
54.7    
54.8    
54.9    
55.1    
55.2    
55.4    
55.5    
55.7    
55.8    
56.0    
56.1    
56.2    
56.4    
56.5    
56.7    
56.8    
57.0    
57.1    
57.3    
57.4    
57.6    
57.7    
57.8    
58.0    
58.1    
58.3    
58.4    
58.6    
58.7    
58.9    
59.0    
59.2    
59.3    
59.4    
59.6    
59.7    
59.9    
60.0    
60.2    
60.3    
60.5    
60.6    
60.8    
60.9    
61.0    
61.2    
61.3    
61.5    
61.6    
61.8    
61.9    
62.1    
62.2    
62.4    
62.5    
62.6    
62.8    
62.9    
63.1    
63.2    
63.4    
63.5    
63.7    
63.8    
64.0    
64.1    
64.2    
64.4    
64.5    
64.7    
64.8    
65.0    
65.1    
65.3    
65.4    
65.6    
65.7    
65.8    
66.0    
66.1    
66.3    
66.4    
66.6    
66.7    
66.9    
67.0    
67.2    
67.3    
67.4    
67.6    
67.7    
67.9    
68.0    
68.2    
68.3    
68.5    
68.6    
68.8    
68.9    
69.0    
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    
71.4    
71.5    
71.7    
71.8    
71.9    
72.1    
72.2    
72.4    
72.5    
72.7    
72.8    
73.0    
73.1    
73.3    
73.4    
73.5    
73.7    
73.8    
74.0    
74.1    
74.3    
74.4    
74.6    
74.7    
74.9    
75.0    
75.1    
75.3    
75.4    
75.6    
75.7    
75.9    
76.0    
76.2    
76.3    
76.5    
76.6    
76.7    
76.9    
77.0    
77.2    
77.3    
77.5    
77.6    
77.8    
77.9    
78.1    
78.2    
78.3    
78.5    
78.6    
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    
81.0    
81.1    
81.2    
81.4    
81.5    
81.7    
81.8    
82.0    
82.1    
82.3    
82.4    
82.6    
82.7    
82.8    
83.0    
83.1    
83.3    
83.4    
83.6    
83.7    
83.9    
84.0    
84.2    
84.3    
84.4    
84.6    
84.7    
84.9    
85.0    
85.2    
85.3    
85.5    
85.6    
85.8    
85.9    
86.0    
86.2    
86.3    
86.5    
86.6    
86.8    
86.9    
87.1    
87.2    
87.4    
87.5    
87.6    
87.8    
87.9    
88.1    
88.2    
88.4    
88.5    
88.7    
88.8    
89.0    
89.1    
89.2    
89.4    
89.5    
89.7    
89.8    
90.0    
90.1    
90.3    
90.4    
90.6    
90.7    
90.8    
91.0    
91.1    
91.3    
91.4    
91.6    
91.7    
91.9    
92.0    
92.2    
92.3    
92.4    
92.6    
92.7    
92.9    
93.0    
93.2    
93.3    
93.5    
93.6    
93.8    
93.9    
94.0    
94.2    
94.3    
94.5    
94.6    
94.8    
94.9    
95.1    
95.2    
95.3    
95.5    
95.6    
95.8    
95.9    
96.1    
96.2    
96.4    
96.5    
96.7    
96.8    
96.9    
97.1    
97.2    
97.4    
97.5    
97.7    
97.8    
98.0    
98.1    
98.3    
98.4    
98.5    
98.7    
98.8    
99.0    
99.1    
99.3    
99.4    
99.6    
99.7    
99.9    
-found 32 predictions from path traversal
Error with prediction: snap lend_intergenic: 128333, rend_intergenic: 126919  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131030, rend_intergenic: 130097  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135537, rend_intergenic: 131240  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148935, rend_intergenic: 144307  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152120, rend_intergenic: 149168  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158340, rend_intergenic: 153286  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175094, rend_intergenic: 163700  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