-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_13758396-13975660

-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 snap_scaffold_10-snap.2738-T1
Couldn't classify 146894, 146986
Sorry, prediction pasa_asmbl_3630.p1 fails validation.
(GAC)	 GT	146894-146986	GT	AGG
(ATG)	 AG	147119-147231	GT	CAG
(CCC)	 AG	147497-147602	GT	AGG
(CAA)	 AG	147887-147973	GT	CAG
(GAG)	 AG	148706-148836	GT	AGG
(ACA)	 AG	149249-149343	GT	AGG
(ACC)	 AG	149441-149486	GT	AGG
(CAG)	 AG	149870-149921	GT	CTG
(CTC)	 AG	150093-150165	GT	AGG
(TGT)	 AG	150407-150504	GT	AGG
(GGC)	 AG	150858-150969	GT	AGG
(ATG)	 AG	151078-151229	GT	AGG
(AGC)	 AG	151543-151695	GT	AGG
(CTG)	 AG	153961-154167	GT	ACG
(ATT)	 AG	154452-154541	GT	GGG
(GGC)	 AG	155528-155610	GT	GGG
(CGT)	 AG	156127-156333	GT	AGG
(CTT)	 AG	157511-157574	GT	AGG
(AGA)	 AG	158123-158332	TT	GAT
-recovered pasa_asmbl_3630.p1, initial, 147119, 147231
add_exon() Sorry, pasa_asmbl_3630.p1 151078-151229-initial-1 is invalid.
-recovered pasa_asmbl_3630.p1, initial, 151078, 151229
-recovered pasa_asmbl_3630.p1, terminal, 158123, 158332
-recovered pasa_asmbl_3630.p1, internal, 147119, 147231
-recovered pasa_asmbl_3630.p1, internal, 147497, 147602
-recovered pasa_asmbl_3630.p1, internal, 147887, 147973
-recovered pasa_asmbl_3630.p1, internal, 148706, 148836
-recovered pasa_asmbl_3630.p1, internal, 149249, 149343
-recovered pasa_asmbl_3630.p1, internal, 149441, 149486
-recovered pasa_asmbl_3630.p1, internal, 149870, 149921
-recovered pasa_asmbl_3630.p1, internal, 150093, 150165
-recovered pasa_asmbl_3630.p1, internal, 150407, 150504
-recovered pasa_asmbl_3630.p1, internal, 150858, 150969
-recovered pasa_asmbl_3630.p1, internal, 151078, 151229
-recovered pasa_asmbl_3630.p1, internal, 151543, 151695
-recovered pasa_asmbl_3630.p1, internal, 153961, 154167
-recovered pasa_asmbl_3630.p1, internal, 154452, 154541
-recovered pasa_asmbl_3630.p1, internal, 155528, 155610
-recovered pasa_asmbl_3630.p1, internal, 156127, 156333
-recovered pasa_asmbl_3630.p1, internal, 157511, 157574
Valid prediction for GlimmerHMM_glimmerT_25804-T1
Valid prediction for HiQ_model.g17164.t1
Valid prediction for snap_scaffold_10-snap.2763-T1
Valid prediction for GlimmerHMM_glimmerT_25807-T1
Valid prediction for Augustus_model.g17179.t1
Valid prediction for HiQ_model.g17177.t1
Valid prediction for snap_scaffold_10-snap.2739-T1
Valid prediction for snap_scaffold_10-snap.2746-T1
Valid prediction for snap_scaffold_10-snap.2732-T1
Valid prediction for CodingQuarry_transcript_5644-T1
Valid prediction for snap_scaffold_10-snap.2745-T1
Sorry, intron length (6) is less than minimum required (10)
Valid prediction for snap_scaffold_10-snap.2757-T1
Valid prediction for GlimmerHMM_glimmerT_25809-T1
Valid prediction for Augustus_model.g17167.t1
Valid prediction for snap_scaffold_10-snap.2773-T1
Valid prediction for CodingQuarry_transcript_5649-T1
Valid prediction for snap_scaffold_10-snap.2771-T1
Valid prediction for snap_scaffold_10-snap.2743-T1
Valid prediction for GlimmerHMM_glimmerT_25789-T1
Valid prediction for CodingQuarry_transcript_5647-T1
Valid prediction for GlimmerHMM_glimmerT_25793-T1
Valid prediction for snap_scaffold_10-snap.2755-T1
Valid prediction for snap_scaffold_10-snap.2770-T1
Valid prediction for GlimmerHMM_glimmerT_25792-T1
Valid prediction for GlimmerHMM_glimmerT_25799-T1
Valid prediction for snap_scaffold_10-snap.2766-T1
Valid prediction for GlimmerHMM_glimmerT_25800-T1
Valid prediction for HiQ_model.g17173.t1
Valid prediction for snap_scaffold_10-snap.2749-T1
Valid prediction for CodingQuarry_transcript_5646-T1
Valid prediction for snap_scaffold_10-snap.2747-T1
Valid prediction for pasa_asmbl_3633.p2
Valid prediction for pasa_asmbl_3632.p1
Valid prediction for GlimmerHMM_glimmerT_25794-T1
Valid prediction for snap_scaffold_10-snap.2764-T1
Valid prediction for GlimmerHMM_glimmerT_25785-T1
Valid prediction for pasa_asmbl_3626.p1
Valid prediction for CodingQuarry_transcript_5648-T1
Valid prediction for GlimmerHMM_glimmerT_25783-T1
Valid prediction for HiQ_model.g17172.t1
Valid prediction for snap_scaffold_10-snap.2762-T1
Valid prediction for snap_scaffold_10-snap.2759-T1
Valid prediction for snap_scaffold_10-snap.2751-T1
Couldn't classify 19768, 20208
Sorry, prediction pasa_asmbl_3619.p1 fails validation.
(TCT)	 GG	19768-20208	GT	AGG
(TTG)	 AG	20724-20932	GT	GAG
(TGC)	 AG	23519-23553	GT	AGG
(GCG)	 AG	24869-25018	GT	CGG
(GAG)	 AG	25438-25502	GT	TGG
(CTC)	 AG	25647-25763	GT	AGG
(GAT)	 AG	26102-26181	GT	GGG
(AAC)	 AG	26392-26473	GT	AGG
(ACA)	 AG	26745-26837	GT	AGG
(TAT)	 AG	27821-27967	GT	AGG
(GAG)	 AG	28603-28778	GT	AAG
(GTG)	 AG	29031-29129	GT	AAG
(GAT)	 AG	29571-29659	GT	AGG
(GCC)	 AG	30353-30543	GT	AAG
add_exon() Sorry, pasa_asmbl_3619.p1 29571-29659-terminal-2 is invalid.
-recovered pasa_asmbl_3619.p1, terminal, 29571, 29659
-recovered pasa_asmbl_3619.p1, terminal, 30353, 30543
-recovered pasa_asmbl_3619.p1, internal, 20724, 20932
-recovered pasa_asmbl_3619.p1, internal, 23519, 23553
-recovered pasa_asmbl_3619.p1, internal, 24869, 25018
-recovered pasa_asmbl_3619.p1, internal, 25438, 25502
-recovered pasa_asmbl_3619.p1, internal, 25647, 25763
-recovered pasa_asmbl_3619.p1, internal, 26102, 26181
-recovered pasa_asmbl_3619.p1, internal, 26392, 26473
-recovered pasa_asmbl_3619.p1, internal, 26745, 26837
-recovered pasa_asmbl_3619.p1, internal, 27821, 27967
-recovered pasa_asmbl_3619.p1, internal, 28603, 28778
-recovered pasa_asmbl_3619.p1, internal, 29031, 29129
-recovered pasa_asmbl_3619.p1, internal, 29571, 29659
-recovered pasa_asmbl_3619.p1, internal, 30353, 30543
Valid prediction for pasa_asmbl_3637.p1
Valid prediction for snap_scaffold_10-snap.2753-T1
Valid prediction for HiQ_model.g17170.t1
Valid prediction for snap_scaffold_10-snap.2737-T1
Valid prediction for GlimmerHMM_glimmerT_25781-T1
Valid prediction for GlimmerHMM_glimmerT_25801-T1
Valid prediction for GlimmerHMM_glimmerT_25796-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_10-snap.2733-T1
Valid prediction for snap_scaffold_10-snap.2754-T1
Valid prediction for snap_scaffold_10-snap.2758-T1
Valid prediction for Augustus_model.g17166.t1
Valid prediction for CodingQuarry_transcript_5650-T1
Valid prediction for GlimmerHMM_glimmerT_25802-T1
Valid prediction for GlimmerHMM_glimmerT_25782-T1
Valid prediction for snap_scaffold_10-snap.2748-T1
Valid prediction for GlimmerHMM_glimmerT_25788-T1
Valid prediction for Augustus_model.g17176.t1
Valid prediction for GlimmerHMM_glimmerT_25786-T1
Valid prediction for snap_scaffold_10-snap.2769-T1
Valid prediction for CodingQuarry_transcript_5643-T1
Valid prediction for Augustus_model.g17162.t1
Valid prediction for GlimmerHMM_glimmerT_25798-T1
Valid prediction for Augustus_model.g17171.t1
Valid prediction for snap_scaffold_10-snap.2734-T1
Valid prediction for snap_scaffold_10-snap.2735-T1
Valid prediction for GlimmerHMM_glimmerT_25795-T1
Valid prediction for snap_scaffold_10-snap.2761-T1
Valid prediction for Augustus_model.g17169.t1
Valid prediction for snap_scaffold_10-snap.2774-T1
Valid prediction for GlimmerHMM_glimmerT_25803-T1
Valid prediction for pasa_asmbl_4939.p1
Valid prediction for GlimmerHMM_glimmerT_25791-T1
Valid prediction for GlimmerHMM_glimmerT_25805-T1
Valid prediction for GlimmerHMM_glimmerT_25810-T1
Valid prediction for snap_scaffold_10-snap.2756-T1
Valid prediction for GlimmerHMM_glimmerT_25808-T1
Valid prediction for GlimmerHMM_glimmerT_25806-T1
Couldn't classify 200639, 200919
Sorry, prediction pasa_asmbl_4930.p1 fails validation.
(TGC)	 TC	200639-200919	GT	AGG
(GTG)	 AG	201143-201271	GT	AAG
(TTG)	 AG	201571-201674	GT	CCG
(AGC)	 AG	201891-202005	GT	GAG
(CCC)	 AG	202234-202337	GT	TGG
(TGT)	 AG	203074-203234	TC	GAT
add_exon() Sorry, pasa_asmbl_4930.p1 201143-201271-terminal-1 is invalid.
-recovered pasa_asmbl_4930.p1, terminal, 201143, 201271
-recovered pasa_asmbl_4930.p1, terminal, 203074, 203234
-recovered pasa_asmbl_4930.p1, internal, 201143, 201271
-recovered pasa_asmbl_4930.p1, internal, 201571, 201674
-recovered pasa_asmbl_4930.p1, internal, 201891, 202005
-recovered pasa_asmbl_4930.p1, internal, 202234, 202337
Valid prediction for HiQ_model.g17163.t1
Valid prediction for pasa_asmbl_4937.p1
Valid prediction for Augustus_model.g17168.t1
Valid prediction for Augustus_model.g17174.t1
Valid prediction for CodingQuarry_transcript_5645-T1
Valid prediction for snap_scaffold_10-snap.2767-T1
Valid prediction for snap_scaffold_10-snap.2752-T1
Valid prediction for snap_scaffold_10-snap.2772-T1
Valid prediction for GlimmerHMM_glimmerT_25787-T1
Valid prediction for GlimmerHMM_glimmerT_25790-T1
Valid prediction for Augustus_model.g17165.t1
Valid prediction for GlimmerHMM_glimmerT_25784-T1
Valid prediction for snap_scaffold_10-snap.2736-T1
Valid prediction for CodingQuarry_transcript_5651-T1
Valid prediction for GlimmerHMM_glimmerT_25797-T1
Valid prediction for snap_scaffold_10-snap.2750-T1
Valid prediction for snap_scaffold_10-snap.2776-T1
Valid prediction for snap_scaffold_10-snap.2765-T1
Valid prediction for snap_scaffold_10-snap.2768-T1
Valid prediction for snap_scaffold_10-snap.2744-T1
Valid prediction for Augustus_model.g17175.t1
Valid prediction for snap_scaffold_10-snap.2760-T1
Valid prediction for HiQ_model.g17178.t1
Valid prediction for snap_scaffold_10-snap.2740-T1
Valid prediction for snap_scaffold_10-snap.2742-T1
Valid prediction for pasa_asmbl_4926.p1
Valid prediction for Augustus_model.g17180.t1
Valid prediction for snap_scaffold_10-snap.2741-T1
Sorry, intron length (4) is less than minimum required (10)

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 92383, rend_intergenic: 88998  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95875, rend_intergenic: 94608  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97156, rend_intergenic: 96370  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140148, rend_intergenic: 138833  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156829, rend_intergenic: 147812  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 183260, rend_intergenic: 172298  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 206281, rend_intergenic: 204615  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 217265
-exon list size: 377


building trellis

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1.1    
1.3    
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3.7    
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4.5    
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5.3    
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6.6    
6.9    
7.1    
7.4    
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7.9    
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8.4    
8.7    
9.0    
9.2    
9.5    
9.8    
10.0    
10.3    
10.6    
10.8    
11.1    
11.3    
11.6    
11.9    
12.1    
12.4    
12.7    
12.9    
13.2    
13.5    
13.7    
14.0    
14.2    
14.5    
14.8    
15.0    
15.3    
15.6    
15.8    
16.1    
16.4    
16.6    
16.9    
17.2    
17.4    
17.7    
17.9    
18.2    
18.5    
18.7    
19.0    
19.3    
19.5    
19.8    
20.1    
20.3    
20.6    
20.8    
21.1    
21.4    
21.6    
21.9    
22.2    
22.4    
22.7    
23.0    
23.2    
23.5    
23.7    
24.0    
24.3    
24.5    
24.8    
25.1    
25.3    
25.6    
25.9    
26.1    
26.4    
26.6    
26.9    
27.2    
27.4    
27.7    
28.0    
28.2    
28.5    
28.8    
29.0    
29.3    
29.6    
29.8    
30.1    
30.3    
30.6    
30.9    
31.1    
31.4    
31.7    
31.9    
32.2    
32.5    
32.7    
33.0    
33.2    
33.5    
33.8    
34.0    
34.3    
34.6    
34.8    
35.1    
35.4    
35.6    
35.9    
36.1    
36.4    
36.7    
36.9    
37.2    
37.5    
37.7    
38.0    
38.3    
38.5    
38.8    
39.1    
39.3    
39.6    
39.8    
40.1    
40.4    
40.6    
40.9    
41.2    
41.4    
41.7    
42.0    
42.2    
42.5    
42.7    
43.0    
43.3    
43.5    
43.8    
44.1    
44.3    
44.6    
44.9    
45.1    
45.4    
45.6    
45.9    
46.2    
46.4    
46.7    
47.0    
47.2    
47.5    
47.8    
48.0    
48.3    
48.5    
48.8    
49.1    
49.3    
49.6    
49.9    
50.1    
50.4    
50.7    
50.9    
51.2    
51.5    
51.7    
52.0    
52.2    
52.5    
52.8    
53.0    
53.3    
53.6    
53.8    
54.1    
54.4    
54.6    
54.9    
55.1    
55.4    
55.7    
55.9    
56.2    
56.5    
56.7    
57.0    
57.3    
57.5    
57.8    
58.0    
58.3    
58.6    
58.8    
59.1    
59.4    
59.6    
59.9    
60.2    
60.4    
60.7    
60.9    
61.2    
61.5    
61.7    
62.0    
62.3    
62.5    
62.8    
63.1    
63.3    
63.6    
63.9    
64.1    
64.4    
64.6    
64.9    
65.2    
65.4    
65.7    
66.0    
66.2    
66.5    
66.8    
67.0    
67.3    
67.5    
67.8    
68.1    
68.3    
68.6    
68.9    
69.1    
69.4    
69.7    
69.9    
70.2    
70.4    
70.7    
71.0    
71.2    
71.5    
71.8    
72.0    
72.3    
72.6    
72.8    
73.1    
73.4    
73.6    
73.9    
74.1    
74.4    
74.7    
74.9    
75.2    
75.5    
75.7    
76.0    
76.3    
76.5    
76.8    
77.0    
77.3    
77.6    
77.8    
78.1    
78.4    
78.6    
78.9    
79.2    
79.4    
79.7    
79.9    
80.2    
80.5    
80.7    
81.0    
81.3    
81.5    
81.8    
82.1    
82.3    
82.6    
82.8    
83.1    
83.4    
83.6    
83.9    
84.2    
84.4    
84.7    
85.0    
85.2    
85.5    
85.8    
86.0    
86.3    
86.5    
86.8    
87.1    
87.3    
87.6    
87.9    
88.1    
88.4    
88.7    
88.9    
89.2    
89.4    
89.7    
90.0    
90.2    
90.5    
90.8    
91.0    
91.3    
91.6    
91.8    
92.1    
92.3    
92.6    
92.9    
93.1    
93.4    
93.7    
93.9    
94.2    
94.5    
94.7    
95.0    
95.3    
95.5    
95.8    
96.0    
96.3    
96.6    
96.8    
97.1    
97.4    
97.6    
97.9    
98.2    
98.4    
98.7    
98.9    
99.2    
99.5    
99.7    
-found 35 predictions from path traversal
Error with prediction: snap lend_intergenic: 92383, rend_intergenic: 88998  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95875, rend_intergenic: 94608  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97156, rend_intergenic: 96370  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140148, rend_intergenic: 138833  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156829, rend_intergenic: 147812  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 183260, rend_intergenic: 172298  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 206281, rend_intergenic: 204615  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 28 predictions persist after filtering for low support