-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_19/scaffold_19_13309524-13485613

-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.80556_t
Valid prediction for Augustus_model.g30905.t1
Valid prediction for snap_scaffold_19-snap.2638-T1
Valid prediction for GeneMark_model.80548_t
Valid prediction for GlimmerHMM_glimmerT_46290-T1
Valid prediction for snap_scaffold_19-snap.2631-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for snap_scaffold_19-snap.2637-T1
Valid prediction for snap_scaffold_19-snap.2663-T1
Valid prediction for GlimmerHMM_glimmerT_46288-T1
Valid prediction for Augustus_model.g30913.t1
Valid prediction for GlimmerHMM_glimmerT_46286-T1
Valid prediction for snap_scaffold_19-snap.2635-T1
Valid prediction for Augustus_model.g30897.t1
Valid prediction for GlimmerHMM_glimmerT_46307-T1
Valid prediction for GeneMark_model.80550_t
Valid prediction for snap_scaffold_19-snap.2651-T1
Valid prediction for GlimmerHMM_glimmerT_46281-T1
Valid prediction for Augustus_model.g30903.t1
Valid prediction for GlimmerHMM_glimmerT_46293-T1
Valid prediction for Augustus_model.g30908.t1
Valid prediction for Augustus_model.g30916.t1
Valid prediction for GlimmerHMM_glimmerT_46299-T1
Valid prediction for GeneMark_model.80561_t
Valid prediction for snap_scaffold_19-snap.2636-T1
Valid prediction for GlimmerHMM_glimmerT_46291-T1
Valid prediction for GeneMark_model.80558_t
Valid prediction for Augustus_model.g30918.t1
Valid prediction for Augustus_model.g30900.t1
Valid prediction for GlimmerHMM_glimmerT_46304-T1
Valid prediction for Augustus_model.g30894.t1
Valid prediction for Augustus_model.g30910.t1
Valid prediction for Augustus_model.g30912.t1
Valid prediction for GlimmerHMM_glimmerT_46292-T1
Valid prediction for GlimmerHMM_glimmerT_46302-T1
Valid prediction for GlimmerHMM_glimmerT_46303-T1
Valid prediction for Augustus_model.g30893.t1
Valid prediction for Augustus_model.g30899.t1
Valid prediction for snap_scaffold_19-snap.2633-T1
Valid prediction for GlimmerHMM_glimmerT_46305-T1
Valid prediction for GlimmerHMM_glimmerT_46277-T1
Valid prediction for snap_scaffold_19-snap.2654-T1
Valid prediction for Augustus_model.g30909.t1
Valid prediction for snap_scaffold_19-snap.2650-T1
Valid prediction for snap_scaffold_19-snap.2648-T1
Valid prediction for snap_scaffold_19-snap.2645-T1
Valid prediction for Augustus_model.g30907.t1
Valid prediction for GeneMark_model.80571_t
Valid prediction for GeneMark_model.80568_t
Valid prediction for GeneMark_model.80575_t
Valid prediction for GlimmerHMM_glimmerT_46310-T1
Valid prediction for GlimmerHMM_glimmerT_46285-T1
Valid prediction for GeneMark_model.80563_t
Couldn't classify 61023, 61027
Sorry, prediction pasa_asmbl_22680.p1 fails validation.
(ATG)	 GG	59609-60156	GT	AGG
(ACG)	 AG	60720-60805	GT	AGG
(GTA)	 AG	61023-61027	AG	TCA
-recovered pasa_asmbl_22680.p1, initial, 59609, 60156
-recovered pasa_asmbl_22680.p1, internal, 60720, 60805
Couldn't classify 61043, 61133
Couldn't classify 63838, 63846
Sorry, prediction pasa_asmbl_22682.p1 fails validation.
(TCC)	 TC	61043-61133	GT	TGG
(GTG)	 AG	62403-62559	GT	AGG
(CTA)	 AG	62759-62841	GT	AGG
(GGA)	 AG	62947-63042	GT	AGG
(CAA)	 AG	63403-63491	GT	AGG
(ACC)	 AG	63666-63752	GT	AGG
(GTA)	 AG	63838-63846	CT	CCC
add_exon() Sorry, pasa_asmbl_22682.p1 62947-63042-terminal-1 is invalid.
-recovered pasa_asmbl_22682.p1, terminal, 62947, 63042
-recovered pasa_asmbl_22682.p1, internal, 62403, 62559
-recovered pasa_asmbl_22682.p1, internal, 62759, 62841
-recovered pasa_asmbl_22682.p1, internal, 62947, 63042
-recovered pasa_asmbl_22682.p1, internal, 63403, 63491
-recovered pasa_asmbl_22682.p1, internal, 63666, 63752
Couldn't classify 43540, 43686
Sorry, prediction pasa_asmbl_22679.p1 fails validation.
(GCG)	 GT	43540-43686	GT	TTG
(AAC)	 AG	45763-45868	GT	TGG
(ACC)	 AG	47296-47369	GC	GAG
-recovered pasa_asmbl_22679.p1, terminal, 47296, 47369
-recovered pasa_asmbl_22679.p1, internal, 45763, 45868
-recovered pasa_asmbl_22679.p1, internal, 47296, 47369
Valid prediction for GeneMark_model.80554_t
Valid prediction for GlimmerHMM_glimmerT_46296-T1
Valid prediction for GlimmerHMM_glimmerT_46300-T1
Valid prediction for GlimmerHMM_glimmerT_46276-T1
Valid prediction for Augustus_model.g30896.t1
Valid prediction for snap_scaffold_19-snap.2626-T1
Valid prediction for GeneMark_model.80573_t
Valid prediction for Augustus_model.g30898.t1
Valid prediction for GeneMark_model.80552_t
Valid prediction for GlimmerHMM_glimmerT_46313-T1
Valid prediction for snap_scaffold_19-snap.2661-T1
Couldn't classify 34915, 35347
Sorry, prediction pasa_asmbl_22677.p1 fails validation.
(GTT)	 CA	34915-35347	GT	AGG
(AGA)	 AG	35545-35588	GT	AGG
(TTT)	 AG	35704-35763	GG	AAG
-recovered pasa_asmbl_22677.p1, terminal, 35704, 35763
-recovered pasa_asmbl_22677.p1, internal, 35545, 35588
Couldn't classify 140613, 141011
Sorry, prediction pasa_asmbl_21899.p1 fails validation.
(CAC)	 GC	140613-141011	TC	AAT
Valid prediction for snap_scaffold_19-snap.2640-T1
Valid prediction for GeneMark_model.80565_t
Valid prediction for Augustus_model.g30891.t1
Valid prediction for GeneMark_model.80570_t
Valid prediction for GlimmerHMM_glimmerT_46314-T1
Valid prediction for snap_scaffold_19-snap.2641-T1
Valid prediction for GeneMark_model.80566_t
Valid prediction for Augustus_model.g30915.t1
Valid prediction for snap_scaffold_19-snap.2639-T1
Valid prediction for snap_scaffold_19-snap.2652-T1
Valid prediction for CodingQuarry_transcript_25846-T1
Valid prediction for GlimmerHMM_glimmerT_46306-T1
Valid prediction for snap_scaffold_19-snap.2649-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_19-snap.2634-T1
Valid prediction for GeneMark_model.80560_t
Valid prediction for GlimmerHMM_glimmerT_46308-T1
Couldn't classify 79920, 79971
Couldn't classify 83443, 83598
Sorry, prediction pasa_asmbl_21873.p1 fails validation.
(TAT)	 CC	79920-79971	GT	CGG
(GTC)	 AG	80810-80902	GT	CGG
(GTT)	 AG	81052-81232	GT	GGG
(GAG)	 AG	81677-81764	GT	AGG
(GAC)	 AG	83443-83598	GC	ATG
-recovered pasa_asmbl_21873.p1, internal, 80810, 80902
-recovered pasa_asmbl_21873.p1, internal, 81052, 81232
-recovered pasa_asmbl_21873.p1, internal, 81677, 81764
-recovered pasa_asmbl_21873.p1, internal, 83443, 83598
Valid prediction for GlimmerHMM_glimmerT_46297-T1
Valid prediction for snap_scaffold_19-snap.2642-T1
Valid prediction for GlimmerHMM_glimmerT_46295-T1
Valid prediction for Augustus_model.g30911.t1
Valid prediction for GlimmerHMM_glimmerT_46284-T1
Valid prediction for snap_scaffold_19-snap.2657-T1
Valid prediction for GeneMark_model.80546_t
Couldn't classify 87281, 87460
Couldn't classify 89338, 89469
Sorry, prediction pasa_asmbl_21872.p1 fails validation.
(GTT)	 TG	87281-87460	GT	AGG
(TCC)	 AG	87641-87751	GT	AGG
(GAG)	 AG	87873-88007	GT	AGG
(GAG)	 AG	89338-89469	TA	GGT
-recovered pasa_asmbl_21872.p1, internal, 87641, 87751
-recovered pasa_asmbl_21872.p1, internal, 87873, 88007
Valid prediction for snap_scaffold_19-snap.2659-T1
Valid prediction for GlimmerHMM_glimmerT_46287-T1
Valid prediction for GlimmerHMM_glimmerT_46309-T1
Valid prediction for snap_scaffold_19-snap.2660-T1
Couldn't classify 104334, 104375
Sorry, prediction pasa_asmbl_21868.p1 fails validation.
(CTG)	 TG	104334-104375	GT	CGG
(GTT)	 AG	104858-105512	GT	AGG
(GTA)	 AG	105711-105937	GA	GAG
-recovered pasa_asmbl_21868.p1, terminal, 105711, 105937
-recovered pasa_asmbl_21868.p1, internal, 104858, 105512
Valid prediction for snap_scaffold_19-snap.2653-T1
Valid prediction for HiQ_model.g30906.t1
Valid prediction for GlimmerHMM_glimmerT_46312-T1
Valid prediction for GlimmerHMM_glimmerT_46294-T1
Valid prediction for snap_scaffold_19-snap.2644-T1
Valid prediction for GeneMark_model.80547_t
Couldn't classify 92000, 92083
Sorry, prediction pasa_asmbl_21871.p1 fails validation.
(ATG)	 CC	90426-90557	GT	AGG
(GGT)	 AG	90649-90761	GT	AGG
(GGA)	 AG	90871-91033	GT	AAG
(CGT)	 AG	91158-91304	GT	TTG
(GTG)	 AG	91423-91572	GT	AGG
(GTT)	 AG	91744-91869	GT	TGG
(ATC)	 AG	92000-92083	CC	AGC
-recovered pasa_asmbl_21871.p1, initial, 90426, 90557
-recovered pasa_asmbl_21871.p1, internal, 90649, 90761
-recovered pasa_asmbl_21871.p1, internal, 90871, 91033
-recovered pasa_asmbl_21871.p1, internal, 91158, 91304
-recovered pasa_asmbl_21871.p1, internal, 91423, 91572
-recovered pasa_asmbl_21871.p1, internal, 91744, 91869
Valid prediction for snap_scaffold_19-snap.2632-T1
Valid prediction for GlimmerHMM_glimmerT_46298-T1
Valid prediction for Augustus_model.g30890.t1
Valid prediction for GeneMark_model.80545_t
Valid prediction for snap_scaffold_19-snap.2643-T1
Valid prediction for GeneMark_model.80572_t
Valid prediction for Augustus_model.g30902.t1
Valid prediction for GlimmerHMM_glimmerT_46301-T1
Valid prediction for snap_scaffold_19-snap.2647-T1
Valid prediction for Augustus_model.g30901.t1
Valid prediction for GeneMark_model.80553_t
Valid prediction for HiQ_model.g30892.t1
Couldn't classify 92357, 92430
Couldn't classify 97524, 97578
Sorry, prediction pasa_asmbl_21870.p1 fails validation.
(GCT)	 AG	92357-92430	GT	CGG
(ATG)	 AG	92546-92678	GT	AGG
(GGC)	 AG	92782-92958	GT	AGG
(GAG)	 AG	95430-95529	GT	AGG
(AGA)	 AG	97229-97355	GT	TGG
(GGT)	 AG	97524-97578	GG	GTG
-recovered pasa_asmbl_21870.p1, initial, 92546, 92678
-recovered pasa_asmbl_21870.p1, internal, 92357, 92430
-recovered pasa_asmbl_21870.p1, internal, 92546, 92678
-recovered pasa_asmbl_21870.p1, internal, 92782, 92958
-recovered pasa_asmbl_21870.p1, internal, 95430, 95529
-recovered pasa_asmbl_21870.p1, internal, 97229, 97355
Valid prediction for GlimmerHMM_glimmerT_46289-T1
Valid prediction for GeneMark_model.80551_t
Valid prediction for Augustus_model.g30895.t1
Valid prediction for GeneMark_model.80557_t
Valid prediction for Augustus_model.g30917.t1
Valid prediction for GlimmerHMM_glimmerT_46278-T1
Valid prediction for snap_scaffold_19-snap.2627-T1
Valid prediction for snap_scaffold_19-snap.2658-T1
Valid prediction for HiQ_model.g30889.t1
Valid prediction for GeneMark_model.80555_t
Valid prediction for snap_scaffold_19-snap.2646-T1
Valid prediction for Augustus_model.g30904.t1
Valid prediction for snap_scaffold_19-snap.2656-T1
Valid prediction for Augustus_model.g30914.t1
Valid prediction for CodingQuarry_transcript_25847-T1
Valid prediction for GeneMark_model.80564_t
Valid prediction for snap_scaffold_19-snap.2628-T1
Valid prediction for GeneMark_model.80562_t
Couldn't classify 166001, 166102
Sorry, prediction pasa_asmbl_21863.p1 fails validation.
(CAT)	 TG	166001-166102	GT	GGG
(ATT)	 AG	167112-167176	GT	AAG
(GGA)	 AG	167393-167543	AG	GAA
add_exon() Sorry, pasa_asmbl_21863.p1 167112-167176-terminal-2 is invalid.
-recovered pasa_asmbl_21863.p1, terminal, 167112, 167176
-recovered pasa_asmbl_21863.p1, terminal, 167393, 167543
-recovered pasa_asmbl_21863.p1, internal, 167112, 167176
Valid prediction for GlimmerHMM_glimmerT_46280-T1
Valid prediction for GlimmerHMM_glimmerT_46283-T1
Valid prediction for snap_scaffold_19-snap.2662-T1
Valid prediction for GeneMark_model.80559_t
Couldn't classify 145214, 145347
Sorry, prediction pasa_asmbl_21865.p1 fails validation.
(ATG)	 AC	143567-143609	GT	AGG
(GGC)	 AG	144391-144475	GT	GAG
(TTT)	 AG	144628-144727	GT	AGG
(GTG)	 AG	144919-145075	GT	AGG
(GTA)	 AG	145214-145347	GT	CTG
-recovered pasa_asmbl_21865.p1, initial, 143567, 143609
-recovered pasa_asmbl_21865.p1, internal, 144391, 144475
-recovered pasa_asmbl_21865.p1, internal, 144628, 144727
-recovered pasa_asmbl_21865.p1, internal, 144919, 145075
-recovered pasa_asmbl_21865.p1, internal, 145214, 145347
Valid prediction for snap_scaffold_19-snap.2629-T1
Valid prediction for GeneMark_model.80549_t
Valid prediction for GlimmerHMM_glimmerT_46279-T1
Valid prediction for snap_scaffold_19-snap.2655-T1
Couldn't classify 149925, 150025
Couldn't classify 162772, 162930
Sorry, prediction pasa_asmbl_21864.p1 fails validation.
(TCG)	 AG	149925-150025	GT	GGG
(ATA)	 AG	150205-150331	GT	AGG
(GTC)	 AG	150521-150713	GT	CTG
(CGG)	 AG	150941-151112	GT	AGG
(AGT)	 AG	151764-151997	GT	TGG
(GGA)	 AG	152642-152726	GT	AGG
(GGT)	 AG	152849-152908	GT	AGG
(GTA)	 AG	154864-154974	GT	AGG
(AAT)	 AG	155260-155396	GT	AAG
(AGA)	 AG	155549-155756	GC	AGG
(CTG)	 AG	155890-156002	GT	AGG
(CCC)	 AG	156234-156348	GT	CAG
(CCT)	 AG	156585-156731	GT	AGG
(GCC)	 AG	156900-157076	GT	AGG
(GAC)	 AG	157194-157412	GT	AGG
(GAC)	 AG	157726-157950	GT	AAG
(GAC)	 AG	158182-158400	GT	AAG
(GAC)	 AG	158684-158908	GT	AGG
(GAC)	 AG	160034-160290	GT	AGG
(GTT)	 AG	160391-160442	GT	AGG
(GTG)	 AG	160614-160823	GT	AGG
(GTT)	 AG	160959-161031	GT	AGG
(TCA)	 AG	161108-161187	GT	TGG
(AGG)	 AG	161326-161427	GT	AGG
(GTG)	 AG	161555-161710	GT	AGG
(GGT)	 AG	161863-162060	GT	AGG
(ATC)	 AG	162239-162412	GT	AGG
(GGT)	 AG	162772-162930	CG	CCC
-recovered pasa_asmbl_21864.p1, internal, 149925, 150025
-recovered pasa_asmbl_21864.p1, internal, 150205, 150331
-recovered pasa_asmbl_21864.p1, internal, 150521, 150713
-recovered pasa_asmbl_21864.p1, internal, 150941, 151112
-recovered pasa_asmbl_21864.p1, internal, 151764, 151997
-recovered pasa_asmbl_21864.p1, internal, 152642, 152726
-recovered pasa_asmbl_21864.p1, internal, 152849, 152908
-recovered pasa_asmbl_21864.p1, internal, 154864, 154974
-recovered pasa_asmbl_21864.p1, internal, 155260, 155396
-recovered pasa_asmbl_21864.p1, internal, 155549, 155756
-recovered pasa_asmbl_21864.p1, internal, 155890, 156002
-recovered pasa_asmbl_21864.p1, internal, 156234, 156348
-recovered pasa_asmbl_21864.p1, internal, 156585, 156731
-recovered pasa_asmbl_21864.p1, internal, 156900, 157076
-recovered pasa_asmbl_21864.p1, internal, 157194, 157412
-recovered pasa_asmbl_21864.p1, internal, 157726, 157950
-recovered pasa_asmbl_21864.p1, internal, 158182, 158400
-recovered pasa_asmbl_21864.p1, internal, 158684, 158908
-recovered pasa_asmbl_21864.p1, internal, 160034, 160290
-recovered pasa_asmbl_21864.p1, internal, 160391, 160442
-recovered pasa_asmbl_21864.p1, internal, 160614, 160823
-recovered pasa_asmbl_21864.p1, internal, 160959, 161031
-recovered pasa_asmbl_21864.p1, internal, 161108, 161187
-recovered pasa_asmbl_21864.p1, internal, 161326, 161427
-recovered pasa_asmbl_21864.p1, internal, 161555, 161710
-recovered pasa_asmbl_21864.p1, internal, 161863, 162060
-recovered pasa_asmbl_21864.p1, internal, 162239, 162412
Valid prediction for GlimmerHMM_glimmerT_46311-T1
Valid prediction for snap_scaffold_19-snap.2630-T1
Valid prediction for GlimmerHMM_glimmerT_46282-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 64798, rend_intergenic: 59917  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146152, rend_intergenic: 142708  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 176090
-exon list size: 540


building trellis

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48.5    
48.7    
48.9    
49.1    
49.3    
49.4    
49.6    
49.8    
50.0    
50.2    
50.4    
50.6    
50.7    
50.9    
51.1    
51.3    
51.5    
51.7    
51.8    
52.0    
52.2    
52.4    
52.6    
52.8    
53.0    
53.1    
53.3    
53.5    
53.7    
53.9    
54.1    
54.2    
54.4    
54.6    
54.8    
55.0    
55.2    
55.4    
55.5    
55.7    
55.9    
56.1    
56.3    
56.5    
56.6    
56.8    
57.0    
57.2    
57.4    
57.6    
57.7    
57.9    
58.1    
58.3    
58.5    
58.7    
58.9    
59.0    
59.2    
59.4    
59.6    
59.8    
60.0    
60.1    
60.3    
60.5    
60.7    
60.9    
61.1    
61.3    
61.4    
61.6    
61.8    
62.0    
62.2    
62.4    
62.5    
62.7    
62.9    
63.1    
63.3    
63.5    
63.7    
63.8    
64.0    
64.2    
64.4    
64.6    
64.8    
64.9    
65.1    
65.3    
65.5    
65.7    
65.9    
66.1    
66.2    
66.4    
66.6    
66.8    
67.0    
67.2    
67.3    
67.5    
67.7    
67.9    
68.1    
68.3    
68.5    
68.6    
68.8    
69.0    
69.2    
69.4    
69.6    
69.7    
69.9    
70.1    
70.3    
70.5    
70.7    
70.8    
71.0    
71.2    
71.4    
71.6    
71.8    
72.0    
72.1    
72.3    
72.5    
72.7    
72.9    
73.1    
73.2    
73.4    
73.6    
73.8    
74.0    
74.2    
74.4    
74.5    
74.7    
74.9    
75.1    
75.3    
75.5    
75.6    
75.8    
76.0    
76.2    
76.4    
76.6    
76.8    
76.9    
77.1    
77.3    
77.5    
77.7    
77.9    
78.0    
78.2    
78.4    
78.6    
78.8    
79.0    
79.2    
79.3    
79.5    
79.7    
79.9    
80.1    
80.3    
80.4    
80.6    
80.8    
81.0    
81.2    
81.4    
81.5    
81.7    
81.9    
82.1    
82.3    
82.5    
82.7    
82.8    
83.0    
83.2    
83.4    
83.6    
83.8    
83.9    
84.1    
84.3    
84.5    
84.7    
84.9    
85.1    
85.2    
85.4    
85.6    
85.8    
86.0    
86.2    
86.3    
86.5    
86.7    
86.9    
87.1    
87.3    
87.5    
87.6    
87.8    
88.0    
88.2    
88.4    
88.6    
88.7    
88.9    
89.1    
89.3    
89.5    
89.7    
89.9    
90.0    
90.2    
90.4    
90.6    
90.8    
91.0    
91.1    
91.3    
91.5    
91.7    
91.9    
92.1    
92.3    
92.4    
92.6    
92.8    
93.0    
93.2    
93.4    
93.5    
93.7    
93.9    
94.1    
94.3    
94.5    
94.6    
94.8    
95.0    
95.2    
95.4    
95.6    
95.8    
95.9    
96.1    
96.3    
96.5    
96.7    
96.9    
97.0    
97.2    
97.4    
97.6    
97.8    
98.0    
98.2    
98.3    
98.5    
98.7    
98.9    
99.1    
99.3    
99.4    
99.6    
99.8    
-found 37 predictions from path traversal
Error with prediction: snap lend_intergenic: 64798, rend_intergenic: 59917  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146152, rend_intergenic: 142708  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 36 predictions persist after filtering for low support