-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_7/scaffold_7_167360-324361

-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_7-snap.75-T1
Valid prediction for Augustus_model.g11179.t1
Valid prediction for GlimmerHMM_glimmerT_16696-T1
Valid prediction for CodingQuarry_transcript_57419-T1
Valid prediction for Augustus_model.g11174.t1
Couldn't classify 131759, 133658
Sorry, prediction pasa_asmbl_49553.p1 fails validation.
(CTC)	 GA	131759-133658	GT	GGG
(CAG)	 AG	134023-134225	GT	AGG
(GTG)	 AG	134415-134480	GG	AAG
-recovered pasa_asmbl_49553.p1, terminal, 134415, 134480
-recovered pasa_asmbl_49553.p1, internal, 134023, 134225
Valid prediction for snap_scaffold_7-snap.55-T1
Valid prediction for GlimmerHMM_glimmerT_16701-T1
Valid prediction for snap_scaffold_7-snap.72-T1
Valid prediction for snap_scaffold_7-snap.47-T1
Valid prediction for Augustus_model.g11177.t1
Valid prediction for snap_scaffold_7-snap.63-T1
Valid prediction for GlimmerHMM_glimmerT_16707-T1
Valid prediction for snap_scaffold_7-snap.56-T1
Valid prediction for snap_scaffold_7-snap.73-T1
Valid prediction for HiQ_model.g11178.t1
Valid prediction for snap_scaffold_7-snap.54-T1
Valid prediction for snap_scaffold_7-snap.67-T1
Valid prediction for snap_scaffold_7-snap.60-T1
Valid prediction for snap_scaffold_7-snap.70-T1
Valid prediction for snap_scaffold_7-snap.52-T1
Valid prediction for snap_scaffold_7-snap.74-T1
Valid prediction for pasa_asmbl_49550.p1
Valid prediction for GlimmerHMM_glimmerT_16697-T1
Valid prediction for GlimmerHMM_glimmerT_16705-T1
Valid prediction for GlimmerHMM_glimmerT_16716-T1
Valid prediction for snap_scaffold_7-snap.57-T1
Couldn't classify 49415, 50762
Sorry, prediction pasa_asmbl_49540.p1 fails validation.
(CGC)	 CT	49415-50762	GT	GGG
(ACG)	 AG	51460-51755	GT	AGG
(TGT)	 AG	51855-51972	GT	TGG
(GTG)	 AG	52179-52268	GT	GGG
(GCA)	 AG	52391-52545	GT	TGG
(GCC)	 AG	52652-52851	GT	AAG
(GAA)	 AG	54533-54614	GA	AGG
-recovered pasa_asmbl_49540.p1, terminal, 54533, 54614
-recovered pasa_asmbl_49540.p1, internal, 51460, 51755
-recovered pasa_asmbl_49540.p1, internal, 51855, 51972
-recovered pasa_asmbl_49540.p1, internal, 52179, 52268
-recovered pasa_asmbl_49540.p1, internal, 52391, 52545
-recovered pasa_asmbl_49540.p1, internal, 52652, 52851
Valid prediction for snap_scaffold_7-snap.65-T1
Valid prediction for Augustus_model.g11168.t1
Valid prediction for snap_scaffold_7-snap.80-T1
Valid prediction for GlimmerHMM_glimmerT_16715-T1
Valid prediction for GlimmerHMM_glimmerT_16713-T1
Valid prediction for snap_scaffold_7-snap.69-T1
Couldn't classify 47749, 47895
Couldn't classify 48038, 48343
Sorry, prediction pasa_asmbl_49539.p1 fails validation.
(GTG)	 AG	47749-47895	GT	AGG
(CTG)	 AG	48038-48343	AA	CCA
-recovered pasa_asmbl_49539.p1, internal, 47749, 47895
Valid prediction for GlimmerHMM_glimmerT_16708-T1
Valid prediction for snap_scaffold_7-snap.49-T1
Valid prediction for CodingQuarry_transcript_57420-T1
Valid prediction for GlimmerHMM_glimmerT_16710-T1
Valid prediction for GlimmerHMM_glimmerT_16699-T1
Valid prediction for GlimmerHMM_glimmerT_16711-T1
Couldn't classify 118712, 118981
Sorry, prediction pasa_asmbl_49552.p1 fails validation.
(CTC)	 GT	118712-118981	GT	TGG
(GTT)	 AG	119073-119108	GT	AGG
(GTT)	 AG	119219-119335	GT	AGG
(TGT)	 AG	120170-120268	GT	AGG
(GAT)	 AG	120632-120760	GT	AGG
(GGA)	 AG	120917-120946	GA	AGG
-recovered pasa_asmbl_49552.p1, terminal, 120917, 120946
-recovered pasa_asmbl_49552.p1, internal, 119073, 119108
-recovered pasa_asmbl_49552.p1, internal, 119219, 119335
-recovered pasa_asmbl_49552.p1, internal, 120170, 120268
-recovered pasa_asmbl_49552.p1, internal, 120632, 120760
Valid prediction for snap_scaffold_7-snap.62-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_7-snap.61-T1
Valid prediction for Augustus_model.g11172.t1
Valid prediction for snap_scaffold_7-snap.48-T1
Valid prediction for snap_scaffold_7-snap.71-T1
Valid prediction for snap_scaffold_7-snap.51-T1
Valid prediction for Augustus_model.g11176.t1
Valid prediction for GlimmerHMM_glimmerT_16702-T1
Valid prediction for GlimmerHMM_glimmerT_16718-T1
Couldn't classify 96534, 96680
Sorry, prediction pasa_asmbl_50679.p1 fails validation.
(GTA)	 GG	96534-96680	GT	TGG
(CAT)	 AG	97041-97163	GT	AGG
(GTG)	 AG	97242-97327	GT	AGG
(GAC)	 AG	97412-97488	GT	AGG
(GTT)	 AG	97764-97907	GT	AGG
(GAG)	 AG	98839-98949	GT	AGG
(GTA)	 AG	99920-100027	GT	AGG
(ATA)	 AG	100200-100308	GT	AGG
(GTG)	 AG	100396-100494	GT	AGG
(GTT)	 AG	100905-101034	GC	AGG
-recovered pasa_asmbl_50679.p1, terminal, 100905, 101034
-recovered pasa_asmbl_50679.p1, internal, 97041, 97163
-recovered pasa_asmbl_50679.p1, internal, 97242, 97327
-recovered pasa_asmbl_50679.p1, internal, 97412, 97488
-recovered pasa_asmbl_50679.p1, internal, 97764, 97907
-recovered pasa_asmbl_50679.p1, internal, 98839, 98949
-recovered pasa_asmbl_50679.p1, internal, 99920, 100027
-recovered pasa_asmbl_50679.p1, internal, 100200, 100308
-recovered pasa_asmbl_50679.p1, internal, 100396, 100494
-recovered pasa_asmbl_50679.p1, internal, 100905, 101034
Valid prediction for Augustus_model.g11170.t1
Valid prediction for GlimmerHMM_glimmerT_16717-T1
Valid prediction for GlimmerHMM_glimmerT_16712-T1
Valid prediction for Augustus_model.g11173.t1
Valid prediction for snap_scaffold_7-snap.76-T1
Valid prediction for snap_scaffold_7-snap.81-T1
Valid prediction for snap_scaffold_7-snap.78-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_7-snap.58-T1
Valid prediction for Augustus_model.g11169.t1
Valid prediction for GlimmerHMM_glimmerT_16704-T1
Valid prediction for GlimmerHMM_glimmerT_16714-T1
Valid prediction for Augustus_model.g11181.t1
Valid prediction for GlimmerHMM_glimmerT_16700-T1
Valid prediction for Augustus_model.g11180.t1
Valid prediction for GlimmerHMM_glimmerT_16706-T1
Valid prediction for HiQ_model.g11175.t1
Valid prediction for snap_scaffold_7-snap.53-T1
Valid prediction for GlimmerHMM_glimmerT_16698-T1
Valid prediction for snap_scaffold_7-snap.77-T1
Valid prediction for CodingQuarry_transcript_57416-T1
Valid prediction for snap_scaffold_7-snap.68-T1
Valid prediction for snap_scaffold_7-snap.66-T1
Valid prediction for GlimmerHMM_glimmerT_16709-T1
Valid prediction for snap_scaffold_7-snap.59-T1
Valid prediction for snap_scaffold_7-snap.50-T1
Valid prediction for GlimmerHMM_glimmerT_16703-T1
Valid prediction for Augustus_model.g11171.t1
Valid prediction for GlimmerHMM_glimmerT_16719-T1
Valid prediction for snap_scaffold_7-snap.64-T1
Sorry, intron length (6) is less than minimum required (10)
Valid prediction for snap_scaffold_7-snap.79-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 10104, rend_intergenic: 8400  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 14676, rend_intergenic: 13332  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25441, rend_intergenic: 19389  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53637, rend_intergenic: 51549  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64945, rend_intergenic: 56446  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80504, rend_intergenic: 77322  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85100, rend_intergenic: 80537  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98059, rend_intergenic: 86820  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102171, rend_intergenic: 101838  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120946, rend_intergenic: 112925  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142504, rend_intergenic: 137374  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153964, rend_intergenic: 151887  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155345, rend_intergenic: 154235  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 157002
-exon list size: 313


building trellis

0.3    
0.6    
1.0    
1.3    
1.6    
1.9    
2.2    
2.5    
2.9    
3.2    
3.5    
3.8    
4.1    
4.4    
4.8    
5.1    
5.4    
5.7    
6.0    
6.3    
6.7    
7.0    
7.3    
7.6    
7.9    
8.3    
8.6    
8.9    
9.2    
9.5    
9.8    
10.2    
10.5    
10.8    
11.1    
11.4    
11.7    
12.1    
12.4    
12.7    
13.0    
13.3    
13.7    
14.0    
14.3    
14.6    
14.9    
15.2    
15.6    
15.9    
16.2    
16.5    
16.8    
17.1    
17.5    
17.8    
18.1    
18.4    
18.7    
19.0    
19.4    
19.7    
20.0    
20.3    
20.6    
21.0    
21.3    
21.6    
21.9    
22.2    
22.5    
22.9    
23.2    
23.5    
23.8    
24.1    
24.4    
24.8    
25.1    
25.4    
25.7    
26.0    
26.3    
26.7    
27.0    
27.3    
27.6    
27.9    
28.3    
28.6    
28.9    
29.2    
29.5    
29.8    
30.2    
30.5    
30.8    
31.1    
31.4    
31.7    
32.1    
32.4    
32.7    
33.0    
33.3    
33.7    
34.0    
34.3    
34.6    
34.9    
35.2    
35.6    
35.9    
36.2    
36.5    
36.8    
37.1    
37.5    
37.8    
38.1    
38.4    
38.7    
39.0    
39.4    
39.7    
40.0    
40.3    
40.6    
41.0    
41.3    
41.6    
41.9    
42.2    
42.5    
42.9    
43.2    
43.5    
43.8    
44.1    
44.4    
44.8    
45.1    
45.4    
45.7    
46.0    
46.3    
46.7    
47.0    
47.3    
47.6    
47.9    
48.3    
48.6    
48.9    
49.2    
49.5    
49.8    
50.2    
50.5    
50.8    
51.1    
51.4    
51.7    
52.1    
52.4    
52.7    
53.0    
53.3    
53.7    
54.0    
54.3    
54.6    
54.9    
55.2    
55.6    
55.9    
56.2    
56.5    
56.8    
57.1    
57.5    
57.8    
58.1    
58.4    
58.7    
59.0    
59.4    
59.7    
60.0    
60.3    
60.6    
61.0    
61.3    
61.6    
61.9    
62.2    
62.5    
62.9    
63.2    
63.5    
63.8    
64.1    
64.4    
64.8    
65.1    
65.4    
65.7    
66.0    
66.3    
66.7    
67.0    
67.3    
67.6    
67.9    
68.3    
68.6    
68.9    
69.2    
69.5    
69.8    
70.2    
70.5    
70.8    
71.1    
71.4    
71.7    
72.1    
72.4    
72.7    
73.0    
73.3    
73.7    
74.0    
74.3    
74.6    
74.9    
75.2    
75.6    
75.9    
76.2    
76.5    
76.8    
77.1    
77.5    
77.8    
78.1    
78.4    
78.7    
79.0    
79.4    
79.7    
80.0    
80.3    
80.6    
81.0    
81.3    
81.6    
81.9    
82.2    
82.5    
82.9    
83.2    
83.5    
83.8    
84.1    
84.4    
84.8    
85.1    
85.4    
85.7    
86.0    
86.3    
86.7    
87.0    
87.3    
87.6    
87.9    
88.3    
88.6    
88.9    
89.2    
89.5    
89.8    
90.2    
90.5    
90.8    
91.1    
91.4    
91.7    
92.1    
92.4    
92.7    
93.0    
93.3    
93.7    
94.0    
94.3    
94.6    
94.9    
95.2    
95.6    
95.9    
96.2    
96.5    
96.8    
97.1    
97.5    
97.8    
98.1    
98.4    
98.7    
99.0    
99.4    
99.7    
-found 27 predictions from path traversal
Error with prediction: snap lend_intergenic: 10104, rend_intergenic: 8400  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 14676, rend_intergenic: 13332  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25441, rend_intergenic: 19389  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53637, rend_intergenic: 51549  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64945, rend_intergenic: 56446  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80504, rend_intergenic: 77322  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85100, rend_intergenic: 80537  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98059, rend_intergenic: 86820  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102171, rend_intergenic: 101838  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120946, rend_intergenic: 112925  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142504, rend_intergenic: 137374  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153964, rend_intergenic: 151887  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155345, rend_intergenic: 154235  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 25 predictions persist after filtering for low support