-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_9/scaffold_9_13949704-14123057

-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_9-snap.2794-T1
Valid prediction for snap_scaffold_9-snap.2808-T1
Valid prediction for GlimmerHMM_glimmerT_23267-T1
Valid prediction for snap_scaffold_9-snap.2815-T1
Valid prediction for snap_scaffold_9-snap.2775-T1
Couldn't classify 65648, 65998
Sorry, prediction pasa_asmbl_54516.p1 fails validation.
(GTA)	 GT	65648-65998	GC	GGG
Valid prediction for GlimmerHMM_glimmerT_23277-T1
Valid prediction for snap_scaffold_9-snap.2796-T1
Valid prediction for CodingQuarry_transcript_62399-T1
Valid prediction for snap_scaffold_9-snap.2773-T1
Valid prediction for snap_scaffold_9-snap.2778-T1
Valid prediction for Augustus_model.g15504.t1
Valid prediction for snap_scaffold_9-snap.2803-T1
Valid prediction for Augustus_model.g15509.t1
Valid prediction for snap_scaffold_9-snap.2798-T1
Valid prediction for snap_scaffold_9-snap.2816-T1
Valid prediction for HiQ_model.g15506.t1
Couldn't classify 86239, 86360
Sorry, prediction pasa_asmbl_54725.p1 fails validation.
(ATG)	 CC	83107-83259	GT	AGG
(GAA)	 AG	84141-84302	GT	AGG
(CAC)	 AG	84990-85136	GT	AGG
(GTG)	 AG	85735-85854	GT	GGG
(AGC)	 AG	85989-86091	GT	AGG
(GTC)	 AG	86239-86360	CC	CCC
-recovered pasa_asmbl_54725.p1, initial, 83107, 83259
-recovered pasa_asmbl_54725.p1, internal, 84141, 84302
-recovered pasa_asmbl_54725.p1, internal, 84990, 85136
-recovered pasa_asmbl_54725.p1, internal, 85735, 85854
-recovered pasa_asmbl_54725.p1, internal, 85989, 86091
Valid prediction for GlimmerHMM_glimmerT_23265-T1
Valid prediction for snap_scaffold_9-snap.2804-T1
Valid prediction for GlimmerHMM_glimmerT_23268-T1
Valid prediction for snap_scaffold_9-snap.2810-T1
Valid prediction for Augustus_model.g15512.t1
Valid prediction for snap_scaffold_9-snap.2779-T1
Valid prediction for GlimmerHMM_glimmerT_23262-T1
Valid prediction for GlimmerHMM_glimmerT_23271-T1
Valid prediction for snap_scaffold_9-snap.2784-T1
Valid prediction for snap_scaffold_9-snap.2787-T1
Valid prediction for snap_scaffold_9-snap.2776-T1
Valid prediction for GlimmerHMM_glimmerT_23276-T1
Valid prediction for GlimmerHMM_glimmerT_23281-T1
Valid prediction for snap_scaffold_9-snap.2793-T1
Valid prediction for snap_scaffold_9-snap.2789-T1
Valid prediction for CodingQuarry_transcript_62398-T1
Couldn't classify 64559, 65482
Sorry, prediction pasa_asmbl_54515.p1 fails validation.
(ATG)	 TT	64559-65482	CG	CCC
Valid prediction for Augustus_model.g15508.t1
Valid prediction for Augustus_model.g15503.t1
Valid prediction for GlimmerHMM_glimmerT_23272-T1
Valid prediction for snap_scaffold_9-snap.2806-T1
Valid prediction for snap_scaffold_9-snap.2780-T1
Valid prediction for GlimmerHMM_glimmerT_23274-T1
Valid prediction for GlimmerHMM_glimmerT_23278-T1
Valid prediction for snap_scaffold_9-snap.2786-T1
Valid prediction for snap_scaffold_9-snap.2799-T1
Valid prediction for Augustus_model.g15510.t1
Valid prediction for GlimmerHMM_glimmerT_23264-T1
Valid prediction for pasa_asmbl_54514.p1
Valid prediction for snap_scaffold_9-snap.2812-T1
Valid prediction for GlimmerHMM_glimmerT_23270-T1
Valid prediction for GlimmerHMM_glimmerT_23269-T1
Valid prediction for GlimmerHMM_glimmerT_23261-T1
Valid prediction for snap_scaffold_9-snap.2811-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.g15511.t1
Valid prediction for snap_scaffold_9-snap.2814-T1
Valid prediction for snap_scaffold_9-snap.2774-T1
Valid prediction for GlimmerHMM_glimmerT_23260-T1
Valid prediction for snap_scaffold_9-snap.2807-T1
Valid prediction for snap_scaffold_9-snap.2802-T1
Valid prediction for Augustus_model.g15507.t1
Valid prediction for snap_scaffold_9-snap.2777-T1
Valid prediction for snap_scaffold_9-snap.2788-T1
Valid prediction for snap_scaffold_9-snap.2801-T1
Valid prediction for snap_scaffold_9-snap.2797-T1
Valid prediction for snap_scaffold_9-snap.2781-T1
Valid prediction for Augustus_model.g15502.t1
Valid prediction for HiQ_model.g15505.t1
Valid prediction for snap_scaffold_9-snap.2790-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_9-snap.2785-T1
Valid prediction for snap_scaffold_9-snap.2782-T1
Valid prediction for GlimmerHMM_glimmerT_23259-T1
Valid prediction for snap_scaffold_9-snap.2809-T1
Valid prediction for snap_scaffold_9-snap.2783-T1
Valid prediction for snap_scaffold_9-snap.2805-T1
Couldn't classify 169849, 170073
Sorry, prediction pasa_asmbl_55469.p1 fails validation.
(ATG)	 CA	168685-168802	GT	AGG
(ACC)	 AG	169038-169654	GT	AGG
(GCC)	 AG	169849-170073	CA	GCC
-recovered pasa_asmbl_55469.p1, initial, 168685, 168802
-recovered pasa_asmbl_55469.p1, internal, 169038, 169654
Valid prediction for GlimmerHMM_glimmerT_23280-T1
Valid prediction for snap_scaffold_9-snap.2800-T1
Valid prediction for GlimmerHMM_glimmerT_23266-T1
Valid prediction for GlimmerHMM_glimmerT_23279-T1
Valid prediction for snap_scaffold_9-snap.2792-T1
Valid prediction for snap_scaffold_9-snap.2791-T1
Valid prediction for pasa_asmbl_55475.p1
Valid prediction for snap_scaffold_9-snap.2813-T1
Valid prediction for GlimmerHMM_glimmerT_23275-T1
Valid prediction for snap_scaffold_9-snap.2795-T1
Couldn't classify 146961, 147047
Sorry, prediction pasa_asmbl_55471.p1 fails validation.
(ATG)	 AC	142189-142212	GT	AGG
(GAT)	 AG	143287-143340	GT	AGG
(TTG)	 AG	143594-143666	GT	TGG
(TTG)	 AG	143917-143966	GT	AGG
(ATT)	 AG	144177-144232	GT	GAG
(GGT)	 AG	145176-145253	GT	AGG
(GCG)	 AG	145604-145681	GT	AGG
(TGT)	 AG	145776-145851	GT	TTG
(AGA)	 AG	145971-146084	GT	AGG
(ATA)	 AG	146196-146234	GT	AAG
(GGT)	 AG	146319-146438	GT	TGG
(GAG)	 AG	146606-146659	GT	AGG
(CTG)	 AG	146961-147047	GT	AGG
-recovered pasa_asmbl_55471.p1, initial, 142189, 142212
-recovered pasa_asmbl_55471.p1, internal, 143287, 143340
-recovered pasa_asmbl_55471.p1, internal, 143594, 143666
-recovered pasa_asmbl_55471.p1, internal, 143917, 143966
-recovered pasa_asmbl_55471.p1, internal, 144177, 144232
-recovered pasa_asmbl_55471.p1, internal, 145176, 145253
-recovered pasa_asmbl_55471.p1, internal, 145604, 145681
-recovered pasa_asmbl_55471.p1, internal, 145776, 145851
-recovered pasa_asmbl_55471.p1, internal, 145971, 146084
-recovered pasa_asmbl_55471.p1, internal, 146196, 146234
-recovered pasa_asmbl_55471.p1, internal, 146319, 146438
-recovered pasa_asmbl_55471.p1, internal, 146606, 146659
-recovered pasa_asmbl_55471.p1, internal, 146961, 147047
Valid prediction for GlimmerHMM_glimmerT_23263-T1
Valid prediction for GlimmerHMM_glimmerT_23273-T1
Valid prediction for Augustus_model.g15501.t1
Valid prediction for snap_scaffold_9-snap.2772-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 16558, rend_intergenic: 8434  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27408, rend_intergenic: 25755  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45929, rend_intergenic: 38696  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47526, rend_intergenic: 46730  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50622, rend_intergenic: 47638  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54526, rend_intergenic: 50714  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62492, rend_intergenic: 58108  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82219, rend_intergenic: 65101  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93434, rend_intergenic: 90914  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102975, rend_intergenic: 97332  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110730, rend_intergenic: 106641  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133198, rend_intergenic: 116649  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135486, rend_intergenic: 133479  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136852, rend_intergenic: 135774  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137101, rend_intergenic: 136964  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139803, rend_intergenic: 137517  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141588, rend_intergenic: 141248  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149969, rend_intergenic: 141612  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171069, rend_intergenic: 161915  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 173354
-exon list size: 336


building trellis

0.3    
0.6    
0.9    
1.2    
1.5    
1.8    
2.1    
2.4    
2.7    
3.0    
3.3    
3.6    
3.8    
4.1    
4.4    
4.7    
5.0    
5.3    
5.6    
5.9    
6.2    
6.5    
6.8    
7.1    
7.4    
7.7    
8.0    
8.3    
8.6    
8.9    
9.2    
9.5    
9.8    
10.1    
10.4    
10.7    
10.9    
11.2    
11.5    
11.8    
12.1    
12.4    
12.7    
13.0    
13.3    
13.6    
13.9    
14.2    
14.5    
14.8    
15.1    
15.4    
15.7    
16.0    
16.3    
16.6    
16.9    
17.2    
17.5    
17.8    
18.0    
18.3    
18.6    
18.9    
19.2    
19.5    
19.8    
20.1    
20.4    
20.7    
21.0    
21.3    
21.6    
21.9    
22.2    
22.5    
22.8    
23.1    
23.4    
23.7    
24.0    
24.3    
24.6    
24.9    
25.1    
25.4    
25.7    
26.0    
26.3    
26.6    
26.9    
27.2    
27.5    
27.8    
28.1    
28.4    
28.7    
29.0    
29.3    
29.6    
29.9    
30.2    
30.5    
30.8    
31.1    
31.4    
31.7    
32.0    
32.2    
32.5    
32.8    
33.1    
33.4    
33.7    
34.0    
34.3    
34.6    
34.9    
35.2    
35.5    
35.8    
36.1    
36.4    
36.7    
37.0    
37.3    
37.6    
37.9    
38.2    
38.5    
38.8    
39.1    
39.3    
39.6    
39.9    
40.2    
40.5    
40.8    
41.1    
41.4    
41.7    
42.0    
42.3    
42.6    
42.9    
43.2    
43.5    
43.8    
44.1    
44.4    
44.7    
45.0    
45.3    
45.6    
45.9    
46.2    
46.4    
46.7    
47.0    
47.3    
47.6    
47.9    
48.2    
48.5    
48.8    
49.1    
49.4    
49.7    
50.0    
50.3    
50.6    
50.9    
51.2    
51.5    
51.8    
52.1    
52.4    
52.7    
53.0    
53.3    
53.6    
53.8    
54.1    
54.4    
54.7    
55.0    
55.3    
55.6    
55.9    
56.2    
56.5    
56.8    
57.1    
57.4    
57.7    
58.0    
58.3    
58.6    
58.9    
59.2    
59.5    
59.8    
60.1    
60.4    
60.7    
60.9    
61.2    
61.5    
61.8    
62.1    
62.4    
62.7    
63.0    
63.3    
63.6    
63.9    
64.2    
64.5    
64.8    
65.1    
65.4    
65.7    
66.0    
66.3    
66.6    
66.9    
67.2    
67.5    
67.8    
68.0    
68.3    
68.6    
68.9    
69.2    
69.5    
69.8    
70.1    
70.4    
70.7    
71.0    
71.3    
71.6    
71.9    
72.2    
72.5    
72.8    
73.1    
73.4    
73.7    
74.0    
74.3    
74.6    
74.9    
75.1    
75.4    
75.7    
76.0    
76.3    
76.6    
76.9    
77.2    
77.5    
77.8    
78.1    
78.4    
78.7    
79.0    
79.3    
79.6    
79.9    
80.2    
80.5    
80.8    
81.1    
81.4    
81.7    
82.0    
82.2    
82.5    
82.8    
83.1    
83.4    
83.7    
84.0    
84.3    
84.6    
84.9    
85.2    
85.5    
85.8    
86.1    
86.4    
86.7    
87.0    
87.3    
87.6    
87.9    
88.2    
88.5    
88.8    
89.1    
89.3    
89.6    
89.9    
90.2    
90.5    
90.8    
91.1    
91.4    
91.7    
92.0    
92.3    
92.6    
92.9    
93.2    
93.5    
93.8    
94.1    
94.4    
94.7    
95.0    
95.3    
95.6    
95.9    
96.2    
96.4    
96.7    
97.0    
97.3    
97.6    
97.9    
98.2    
98.5    
98.8    
99.1    
99.4    
99.7    
-found 29 predictions from path traversal
Error with prediction: snap lend_intergenic: 16558, rend_intergenic: 8434  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27408, rend_intergenic: 25755  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45929, rend_intergenic: 38696  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47526, rend_intergenic: 46730  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50622, rend_intergenic: 47638  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54526, rend_intergenic: 50714  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62492, rend_intergenic: 58108  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82219, rend_intergenic: 65101  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93434, rend_intergenic: 90914  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102975, rend_intergenic: 97332  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110730, rend_intergenic: 106641  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133198, rend_intergenic: 116649  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135486, rend_intergenic: 133479  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136852, rend_intergenic: 135774  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137101, rend_intergenic: 136964  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139803, rend_intergenic: 137517  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141588, rend_intergenic: 141248  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149969, rend_intergenic: 141612  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171069, rend_intergenic: 161915  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 16 predictions persist after filtering for low support