-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_19/scaffold_19_1587228-1744542

-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: +)Couldn't classify 102609, 103397
Sorry, prediction pasa_asmbl_21254.p1 fails validation.
(ACA)	 AC	102609-103397	AG	AGA
Couldn't classify 24602, 24653
Sorry, prediction pasa_asmbl_21248.p1 fails validation.
(TCA)	 CT	24602-24653	GT	AGG
(ACA)	 AG	25301-25615	GT	AGG
(GAT)	 AG	25952-26210	GT	AGG
(GTT)	 AG	26567-26730	GT	GGG
(TGG)	 AG	26965-27188	AG	AAA
-recovered pasa_asmbl_21248.p1, terminal, 26965, 27188
-recovered pasa_asmbl_21248.p1, internal, 25301, 25615
-recovered pasa_asmbl_21248.p1, internal, 25952, 26210
-recovered pasa_asmbl_21248.p1, internal, 26567, 26730
Valid prediction for snap_scaffold_19-snap.352-T1
Valid prediction for GlimmerHMM_glimmerT_43644-T1
Valid prediction for GlimmerHMM_glimmerT_43649-T1
Valid prediction for snap_scaffold_19-snap.357-T1
Valid prediction for snap_scaffold_19-snap.354-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_19-snap.362-T1
Valid prediction for snap_scaffold_19-snap.351-T1
Valid prediction for HiQ_model.g28979.t1
Valid prediction for Augustus_model.g28980.t1
Valid prediction for snap_scaffold_19-snap.359-T1
Valid prediction for snap_scaffold_19-snap.374-T1
Valid prediction for GlimmerHMM_glimmerT_43648-T1
Valid prediction for snap_scaffold_19-snap.365-T1
Valid prediction for Augustus_model.g28988.t1
Valid prediction for snap_scaffold_19-snap.382-T1
Valid prediction for snap_scaffold_19-snap.370-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_19-snap.381-T1
Valid prediction for GlimmerHMM_glimmerT_43641-T1
Valid prediction for snap_scaffold_19-snap.356-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_43640-T1
Valid prediction for snap_scaffold_19-snap.371-T1
Valid prediction for GlimmerHMM_glimmerT_43635-T1
Valid prediction for snap_scaffold_19-snap.372-T1
Valid prediction for GlimmerHMM_glimmerT_43633-T1
Valid prediction for snap_scaffold_19-snap.350-T1
Valid prediction for snap_scaffold_19-snap.349-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for HiQ_model.g28984.t1
Valid prediction for snap_scaffold_19-snap.366-T1
Valid prediction for CodingQuarry_transcript_25596-T1
Valid prediction for GlimmerHMM_glimmerT_43645-T1
Valid prediction for snap_scaffold_19-snap.376-T1
Valid prediction for snap_scaffold_19-snap.363-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_19-snap.367-T1
Couldn't classify 60876, 61010
Sorry, prediction pasa_asmbl_21252.p1 fails validation.
(GGG)	 GT	60876-61010	GT	GGG
(AGA)	 AG	61408-61518	GT	AGG
(GCT)	 AG	61606-61756	GT	GGG
(GTA)	 AG	62126-62214	TC	AAT
-recovered pasa_asmbl_21252.p1, terminal, 62126, 62214
-recovered pasa_asmbl_21252.p1, internal, 61408, 61518
-recovered pasa_asmbl_21252.p1, internal, 61606, 61756
Valid prediction for GlimmerHMM_glimmerT_43634-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.g28986.t1
Valid prediction for GlimmerHMM_glimmerT_43643-T1
Valid prediction for Augustus_model.g28990.t1
Valid prediction for GlimmerHMM_glimmerT_43651-T1
Valid prediction for snap_scaffold_19-snap.378-T1
Valid prediction for snap_scaffold_19-snap.355-T1
Valid prediction for CodingQuarry_transcript_25598-T1
Valid prediction for snap_scaffold_19-snap.360-T1
Valid prediction for snap_scaffold_19-snap.368-T1
Valid prediction for CodingQuarry_transcript_25600-T1
Couldn't classify 90727, 90910
Sorry, prediction pasa_asmbl_22685.p2 fails validation.
(TCG)	 TT	90727-90910	GT	AGG
(TGG)	 AG	91232-91377	GT	ATG
(GTG)	 AG	91850-91879	AC	GAA
-recovered pasa_asmbl_22685.p2, terminal, 91850, 91879
-recovered pasa_asmbl_22685.p2, internal, 91232, 91377
Valid prediction for Augustus_model.g28985.t1
Valid prediction for GlimmerHMM_glimmerT_43642-T1
Valid prediction for Augustus_model.g28982.t1
Couldn't classify 66761, 66795
Couldn't classify 69544, 69671
Sorry, prediction pasa_asmbl_22043.p2 fails validation.
(CAG)	 AA	66761-66795	GT	AGG
(CCA)	 AG	66910-66923	GT	CGG
(ATG)	 AG	67047-67118	GT	GGG
(GTG)	 AG	68061-68183	GT	AGG
(ACC)	 AG	68780-68873	GT	AAG
(GAA)	 AG	69045-69202	GT	CAG
(AGC)	 AG	69544-69671	TA	GGT
add_exon() Sorry, pasa_asmbl_22043.p2 67047-67118-initial-1 is invalid.
-recovered pasa_asmbl_22043.p2, initial, 67047, 67118
add_exon() Sorry, pasa_asmbl_22043.p2 68061-68183-terminal-1 is invalid.
-recovered pasa_asmbl_22043.p2, terminal, 68061, 68183
-recovered pasa_asmbl_22043.p2, internal, 66910, 66923
-recovered pasa_asmbl_22043.p2, internal, 67047, 67118
-recovered pasa_asmbl_22043.p2, internal, 68061, 68183
-recovered pasa_asmbl_22043.p2, internal, 68780, 68873
-recovered pasa_asmbl_22043.p2, internal, 69045, 69202
Valid prediction for snap_scaffold_19-snap.379-T1
Valid prediction for snap_scaffold_19-snap.373-T1
Valid prediction for snap_scaffold_19-snap.361-T1
Valid prediction for GlimmerHMM_glimmerT_43636-T1
Valid prediction for snap_scaffold_19-snap.377-T1
Valid prediction for GlimmerHMM_glimmerT_43652-T1
Valid prediction for snap_scaffold_19-snap.380-T1
Valid prediction for GlimmerHMM_glimmerT_43632-T1
Valid prediction for GlimmerHMM_glimmerT_43646-T1
Valid prediction for Augustus_model.g28983.t1
Valid prediction for snap_scaffold_19-snap.375-T1
Valid prediction for snap_scaffold_19-snap.353-T1
Valid prediction for GlimmerHMM_glimmerT_43639-T1
Valid prediction for GlimmerHMM_glimmerT_43638-T1
Valid prediction for CodingQuarry_transcript_25597-T1
Couldn't classify 83534, 83567
Sorry, prediction pasa_asmbl_22041.p2 fails validation.
(ATG)	 AA	78299-78415	GT	AGG
(TCT)	 AG	80741-80908	GT	AGG
(ACG)	 AG	81160-81336	GT	AGG
(GCC)	 AG	82305-82405	GT	GGG
(GAG)	 AG	83534-83567	CG	TCC
-recovered pasa_asmbl_22041.p2, initial, 78299, 78415
-recovered pasa_asmbl_22041.p2, internal, 80741, 80908
-recovered pasa_asmbl_22041.p2, internal, 81160, 81336
-recovered pasa_asmbl_22041.p2, internal, 82305, 82405
Valid prediction for GlimmerHMM_glimmerT_43647-T1
Valid prediction for snap_scaffold_19-snap.364-T1
Valid prediction for snap_scaffold_19-snap.369-T1
Couldn't classify 48171, 48277
Couldn't classify 48823, 48929
Couldn't classify 49893, 50016
Couldn't classify 50997, 51171
Sorry, prediction CodingQuarry_transcript_25599-T1 fails validation.
(ATG)	 AG	42100-42272	GT	AGG
(GAG)	 AG	42765-42828	GT	AGG
(AAG)	 AG	43649-43759	GT	AGG
(AAA)	 AG	45892-45952	GT	TCG
(ACT)	 AG	46785-46909	GT	AGG
(GTC)	 AG	47720-47787	GT	GAG
(CGT)	 AG	48171-48277	GG	GAG
(TCA)	 GA	48823-48929	GT	AGG
(GAC)	 AG	49893-50016	AT	GAA
(CCC)	 AC	50997-51171	GT	AGG
(TGT)	 AG	51403-51511	GT	AGG
(GCG)	 AG	51618-51701	AG	GAA
-recovered CodingQuarry_transcript_25599-T1, initial, 42100, 42272
add_exon() Sorry, CodingQuarry_transcript_25599-T1 48171-48277-terminal-2 is invalid.
-recovered CodingQuarry_transcript_25599-T1, terminal, 48171, 48277
-recovered CodingQuarry_transcript_25599-T1, terminal, 51618, 51701
-recovered CodingQuarry_transcript_25599-T1, internal, 42100, 42272
-recovered CodingQuarry_transcript_25599-T1, internal, 42765, 42828
-recovered CodingQuarry_transcript_25599-T1, internal, 43649, 43759
-recovered CodingQuarry_transcript_25599-T1, internal, 45892, 45952
-recovered CodingQuarry_transcript_25599-T1, internal, 46785, 46909
-recovered CodingQuarry_transcript_25599-T1, internal, 47720, 47787
-recovered CodingQuarry_transcript_25599-T1, internal, 51403, 51511
Couldn't classify 3591, 3609
Couldn't classify 8655, 9091
Sorry, prediction pasa_asmbl_22047.p1 fails validation.
(CAG)	 TG	3591-3609	GT	AGG
(TTG)	 AG	6011-6204	GT	AGG
(AGC)	 AG	7434-7559	GT	TAG
(ACG)	 AG	7677-7854	GT	AGG
(ATT)	 AG	8313-8498	GT	GTG
(ATC)	 AG	8655-9091	CC	TCC
-recovered pasa_asmbl_22047.p1, internal, 6011, 6204
-recovered pasa_asmbl_22047.p1, internal, 7434, 7559
-recovered pasa_asmbl_22047.p1, internal, 7677, 7854
-recovered pasa_asmbl_22047.p1, internal, 8313, 8498
Valid prediction for Augustus_model.g28987.t1
Valid prediction for Augustus_model.g28978.t1
Valid prediction for Augustus_model.g28981.t1
Valid prediction for GlimmerHMM_glimmerT_43650-T1
Valid prediction for GlimmerHMM_glimmerT_43637-T1
Valid prediction for snap_scaffold_19-snap.348-T1
Valid prediction for snap_scaffold_19-snap.358-T1
Valid prediction for Augustus_model.g28989.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 22278, rend_intergenic: 2348  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37504, rend_intergenic: 35673  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49647, rend_intergenic: 40124  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52854, rend_intergenic: 50561  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54887, rend_intergenic: 53813  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61697, rend_intergenic: 60073  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66623, rend_intergenic: 65909  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77003, rend_intergenic: 66901  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90572, rend_intergenic: 84910  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104087, rend_intergenic: 101119  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105588, rend_intergenic: 104417  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109379, rend_intergenic: 105615  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112080, rend_intergenic: 109504  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136391, rend_intergenic: 112087  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153728, rend_intergenic: 138549  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 157315
-exon list size: 353


building trellis

0.3    
0.6    
0.8    
1.1    
1.4    
1.7    
2.0    
2.3    
2.5    
2.8    
3.1    
3.4    
3.7    
3.9    
4.2    
4.5    
4.8    
5.1    
5.4    
5.6    
5.9    
6.2    
6.5    
6.8    
7.0    
7.3    
7.6    
7.9    
8.2    
8.5    
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9.0    
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10.1    
10.4    
10.7    
11.0    
11.3    
11.5    
11.8    
12.1    
12.4    
12.7    
13.0    
13.2    
13.5    
13.8    
14.1    
14.4    
14.6    
14.9    
15.2    
15.5    
15.8    
16.1    
16.3    
16.6    
16.9    
17.2    
17.5    
17.7    
18.0    
18.3    
18.6    
18.9    
19.2    
19.4    
19.7    
20.0    
20.3    
20.6    
20.8    
21.1    
21.4    
21.7    
22.0    
22.3    
22.5    
22.8    
23.1    
23.4    
23.7    
23.9    
24.2    
24.5    
24.8    
25.1    
25.4    
25.6    
25.9    
26.2    
26.5    
26.8    
27.0    
27.3    
27.6    
27.9    
28.2    
28.5    
28.7    
29.0    
29.3    
29.6    
29.9    
30.1    
30.4    
30.7    
31.0    
31.3    
31.5    
31.8    
32.1    
32.4    
32.7    
33.0    
33.2    
33.5    
33.8    
34.1    
34.4    
34.6    
34.9    
35.2    
35.5    
35.8    
36.1    
36.3    
36.6    
36.9    
37.2    
37.5    
37.7    
38.0    
38.3    
38.6    
38.9    
39.2    
39.4    
39.7    
40.0    
40.3    
40.6    
40.8    
41.1    
41.4    
41.7    
42.0    
42.3    
42.5    
42.8    
43.1    
43.4    
43.7    
43.9    
44.2    
44.5    
44.8    
45.1    
45.4    
45.6    
45.9    
46.2    
46.5    
46.8    
47.0    
47.3    
47.6    
47.9    
48.2    
48.5    
48.7    
49.0    
49.3    
49.6    
49.9    
50.1    
50.4    
50.7    
51.0    
51.3    
51.5    
51.8    
52.1    
52.4    
52.7    
53.0    
53.2    
53.5    
53.8    
54.1    
54.4    
54.6    
54.9    
55.2    
55.5    
55.8    
56.1    
56.3    
56.6    
56.9    
57.2    
57.5    
57.7    
58.0    
58.3    
58.6    
58.9    
59.2    
59.4    
59.7    
60.0    
60.3    
60.6    
60.8    
61.1    
61.4    
61.7    
62.0    
62.3    
62.5    
62.8    
63.1    
63.4    
63.7    
63.9    
64.2    
64.5    
64.8    
65.1    
65.4    
65.6    
65.9    
66.2    
66.5    
66.8    
67.0    
67.3    
67.6    
67.9    
68.2    
68.5    
68.7    
69.0    
69.3    
69.6    
69.9    
70.1    
70.4    
70.7    
71.0    
71.3    
71.5    
71.8    
72.1    
72.4    
72.7    
73.0    
73.2    
73.5    
73.8    
74.1    
74.4    
74.6    
74.9    
75.2    
75.5    
75.8    
76.1    
76.3    
76.6    
76.9    
77.2    
77.5    
77.7    
78.0    
78.3    
78.6    
78.9    
79.2    
79.4    
79.7    
80.0    
80.3    
80.6    
80.8    
81.1    
81.4    
81.7    
82.0    
82.3    
82.5    
82.8    
83.1    
83.4    
83.7    
83.9    
84.2    
84.5    
84.8    
85.1    
85.4    
85.6    
85.9    
86.2    
86.5    
86.8    
87.0    
87.3    
87.6    
87.9    
88.2    
88.5    
88.7    
89.0    
89.3    
89.6    
89.9    
90.1    
90.4    
90.7    
91.0    
91.3    
91.5    
91.8    
92.1    
92.4    
92.7    
93.0    
93.2    
93.5    
93.8    
94.1    
94.4    
94.6    
94.9    
95.2    
95.5    
95.8    
96.1    
96.3    
96.6    
96.9    
97.2    
97.5    
97.7    
98.0    
98.3    
98.6    
98.9    
99.2    
99.4    
99.7    
-found 17 predictions from path traversal
Error with prediction: snap lend_intergenic: 22278, rend_intergenic: 2348  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37504, rend_intergenic: 35673  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49647, rend_intergenic: 40124  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52854, rend_intergenic: 50561  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54887, rend_intergenic: 53813  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61697, rend_intergenic: 60073  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66623, rend_intergenic: 65909  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77003, rend_intergenic: 66901  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90572, rend_intergenic: 84910  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104087, rend_intergenic: 101119  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105588, rend_intergenic: 104417  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109379, rend_intergenic: 105615  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112080, rend_intergenic: 109504  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136391, rend_intergenic: 112087  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153728, rend_intergenic: 138549  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 14 predictions persist after filtering for low support