-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_17/scaffold_17_5048819-5188991

-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.70939_t
Valid prediction for GeneMark_model.70943_t
Valid prediction for Augustus_model.g27572.t1
Valid prediction for GeneMark_model.70946_t
Valid prediction for snap_scaffold_17-snap.1057-T1
Valid prediction for GeneMark_model.70936_t
Valid prediction for GlimmerHMM_glimmerT_41177-T1
Valid prediction for snap_scaffold_17-snap.1060-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_41170-T1
Valid prediction for GeneMark_model.70948_t
Valid prediction for GeneMark_model.70937_t
Valid prediction for GlimmerHMM_glimmerT_41175-T1
Valid prediction for GeneMark_model.70941_t
Valid prediction for GlimmerHMM_glimmerT_41171-T1
Couldn't classify 24955, 25014
Sorry, prediction pasa_asmbl_17932.p1 fails validation.
(ATG)	 CG	23759-23855	GT	CGG
(GTC)	 AG	24130-24224	GT	AGG
(ATT)	 AG	24334-24441	GT	CGG
(GTG)	 AG	24629-24781	GT	AGG
(ATC)	 AG	24955-25014	TA	ATT
-recovered pasa_asmbl_17932.p1, initial, 23759, 23855
-recovered pasa_asmbl_17932.p1, internal, 24130, 24224
-recovered pasa_asmbl_17932.p1, internal, 24334, 24441
-recovered pasa_asmbl_17932.p1, internal, 24629, 24781
Valid prediction for GeneMark_model.70935_t
Valid prediction for pasa_asmbl_17939.p1
Valid prediction for HiQ_model.g27580.t1
Valid prediction for Augustus_model.g27577.t1
Couldn't classify 59122, 59190
Couldn't classify 59691, 59829
Sorry, prediction pasa_asmbl_18608.p1 fails validation.
(GAG)	 CA	59122-59190	GT	AGG
(GAG)	 AG	59411-59565	GT	ACG
(GCT)	 AG	59691-59829	AT	GCA
-recovered pasa_asmbl_18608.p1, internal, 59411, 59565
Valid prediction for snap_scaffold_17-snap.1071-T1
Valid prediction for GlimmerHMM_glimmerT_41166-T1
Valid prediction for snap_scaffold_17-snap.1072-T1
Valid prediction for Augustus_model.g27575.t1
Valid prediction for GlimmerHMM_glimmerT_41173-T1
Valid prediction for GlimmerHMM_glimmerT_41167-T1
Valid prediction for pasa_asmbl_18570.p1
Valid prediction for GeneMark_model.70950_t
Valid prediction for Augustus_model.g27578.t1
Valid prediction for snap_scaffold_17-snap.1068-T1
Valid prediction for CodingQuarry_transcript_21931-T1
Valid prediction for CodingQuarry_transcript_21933-T1
Valid prediction for snap_scaffold_17-snap.1064-T1
Valid prediction for GeneMark_model.70953_t
Couldn't classify 25723, 25941
Sorry, prediction pasa_asmbl_17938.p1 fails validation.
(CAG)	 AT	25723-25941	GT	AGG
(GCC)	 AG	26153-26323	AG	AGA
-recovered pasa_asmbl_17938.p1, terminal, 26153, 26323
Valid prediction for snap_scaffold_17-snap.1066-T1
Valid prediction for CodingQuarry_transcript_21930-T1
Valid prediction for snap_scaffold_17-snap.1055-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for snap_scaffold_17-snap.1061-T1
Valid prediction for GlimmerHMM_glimmerT_41180-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 GlimmerHMM_glimmerT_41182-T1
Valid prediction for pasa_asmbl_18961.p1
Valid prediction for CodingQuarry_transcript_21934-T1
Valid prediction for GlimmerHMM_glimmerT_41165-T1
Valid prediction for GlimmerHMM_glimmerT_41164-T1
Valid prediction for snap_scaffold_17-snap.1067-T1
Valid prediction for CodingQuarry_transcript_21936-T1
Couldn't classify 89459, 89743
Sorry, prediction pasa_asmbl_18956.p1 fails validation.
(ATG)	 AG	88036-88239	GT	AGG
(GTA)	 AG	88650-88844	GT	AGG
(AGC)	 AG	89181-89327	GT	AGG
(GTG)	 AG	89459-89743	GG	GGG
-recovered pasa_asmbl_18956.p1, initial, 88036, 88239
-recovered pasa_asmbl_18956.p1, internal, 88036, 88239
-recovered pasa_asmbl_18956.p1, internal, 88650, 88844
-recovered pasa_asmbl_18956.p1, internal, 89181, 89327
Valid prediction for GeneMark_model.70944_t
Valid prediction for snap_scaffold_17-snap.1070-T1
Valid prediction for Augustus_model.g27570.t1
Valid prediction for CodingQuarry_transcript_21935-T1
Valid prediction for Augustus_model.g27581.t1
Valid prediction for CodingQuarry_transcript_21937-T1
Valid prediction for GeneMark_model.70942_t
Valid prediction for GeneMark_model.70938_t
Valid prediction for HiQ_model.g27571.t1
Valid prediction for GeneMark_model.70954_t
Valid prediction for Augustus_model.g27574.t1
Valid prediction for GeneMark_model.70955_t
Couldn't classify 97711, 97770
Sorry, prediction pasa_asmbl_18952.p1 fails validation.
(GTC)	 CA	97711-97770	GT	AGG
(TGG)	 AG	98057-98202	GT	AGG
(GAC)	 AG	98327-98473	GT	AGG
(GTC)	 AG	98583-98667	GT	AGG
(AGG)	 AG	98785-98891	GT	GGG
(GCG)	 AG	99084-99230	GT	GGG
(ACA)	 AG	99353-99449	GT	AAG
(GAC)	 AG	99630-99842	GT	AGG
(ATC)	 AG	100039-100149	GT	AGG
(GTT)	 AG	100259-100370	GT	TGG
(GAG)	 AG	100486-100604	GT	TGG
(GGC)	 AG	100762-100893	GT	AGG
(GCC)	 AG	101341-101478	GT	AGG
(AAA)	 AG	101569-101673	GT	AGG
(GTG)	 AG	101797-101932	GT	CGG
(GCC)	 AG	102036-102162	GT	CGG
(GCT)	 AG	102353-102563	GT	ATG
(TTT)	 AG	103141-103251	GT	AGG
(GTG)	 AG	103575-103793	GT	AGG
(GGC)	 AG	104440-104580	GT	TGG
(CCT)	 AG	105299-105499	GG	GAG
-recovered pasa_asmbl_18952.p1, terminal, 105299, 105499
-recovered pasa_asmbl_18952.p1, internal, 98057, 98202
-recovered pasa_asmbl_18952.p1, internal, 98327, 98473
-recovered pasa_asmbl_18952.p1, internal, 98583, 98667
-recovered pasa_asmbl_18952.p1, internal, 98785, 98891
-recovered pasa_asmbl_18952.p1, internal, 99084, 99230
-recovered pasa_asmbl_18952.p1, internal, 99353, 99449
-recovered pasa_asmbl_18952.p1, internal, 99630, 99842
-recovered pasa_asmbl_18952.p1, internal, 100039, 100149
-recovered pasa_asmbl_18952.p1, internal, 100259, 100370
-recovered pasa_asmbl_18952.p1, internal, 100486, 100604
-recovered pasa_asmbl_18952.p1, internal, 100762, 100893
-recovered pasa_asmbl_18952.p1, internal, 101341, 101478
-recovered pasa_asmbl_18952.p1, internal, 101569, 101673
-recovered pasa_asmbl_18952.p1, internal, 101797, 101932
-recovered pasa_asmbl_18952.p1, internal, 102036, 102162
-recovered pasa_asmbl_18952.p1, internal, 102353, 102563
-recovered pasa_asmbl_18952.p1, internal, 103141, 103251
-recovered pasa_asmbl_18952.p1, internal, 103575, 103793
-recovered pasa_asmbl_18952.p1, internal, 104440, 104580
Valid prediction for GeneMark_model.70933_t
Valid prediction for snap_scaffold_17-snap.1063-T1
Valid prediction for pasa_asmbl_18950.p1
Valid prediction for GlimmerHMM_glimmerT_41168-T1
Valid prediction for snap_scaffold_17-snap.1056-T1
Valid prediction for snap_scaffold_17-snap.1054-T1
Couldn't classify 131742, 132036
Couldn't classify 133500, 133748
Sorry, prediction pasa_asmbl_18945.p1 fails validation.
(GAG)	 AT	131742-132036	GT	TGG
(ACG)	 AG	132653-132906	GT	AGG
(GAG)	 AG	133500-133748	GG	AGG
-recovered pasa_asmbl_18945.p1, internal, 132653, 132906
Couldn't classify 136084, 137235
Sorry, prediction pasa_asmbl_18943.p1 fails validation.
(GGT)	 GT	136084-137235	GG	GAG
Couldn't classify 128042, 128114
Sorry, prediction pasa_asmbl_18949.p1 fails validation.
(ATG)	 CA	126339-126453	GT	TGG
(TTC)	 AG	127542-127719	GT	AGG
(TAC)	 AG	128042-128114	CG	CCC
-recovered pasa_asmbl_18949.p1, initial, 126339, 126453
-recovered pasa_asmbl_18949.p1, internal, 127542, 127719
Valid prediction for GeneMark_model.70932_t
Valid prediction for snap_scaffold_17-snap.1065-T1
Valid prediction for GeneMark_model.70940_t
Valid prediction for GlimmerHMM_glimmerT_41172-T1
Valid prediction for GlimmerHMM_glimmerT_41181-T1
Valid prediction for GeneMark_model.70952_t
Valid prediction for CodingQuarry_transcript_21932-T1
Valid prediction for GlimmerHMM_glimmerT_41176-T1
Valid prediction for snap_scaffold_17-snap.1059-T1
Couldn't classify 89750, 90520
Sorry, prediction pasa_asmbl_18955.p1 fails validation.
(GGG)	 GG	89750-90520	TG	GAT
Couldn't classify 129551, 129615
Couldn't classify 130728, 130827
Sorry, prediction pasa_asmbl_18946.p1 fails validation.
(TTC)	 CC	129551-129615	GT	AGG
(GTT)	 AG	129729-129901	GT	AGG
(GCC)	 AG	130481-130595	GT	CGG
(GGA)	 AG	130728-130827	CC	GTC
-recovered pasa_asmbl_18946.p1, internal, 129729, 129901
-recovered pasa_asmbl_18946.p1, internal, 130481, 130595
Couldn't classify 133931, 134151
Couldn't classify 134283, 135012
Sorry, prediction pasa_asmbl_19530.p1 fails validation.
(GGT)	 CA	133931-134151	GT	AGG
(GAG)	 AG	134283-135012	TC	CCT
Valid prediction for pasa_asmbl_18957.p1
Valid prediction for GeneMark_model.70951_t
Valid prediction for HiQ_model.g27576.t1
Valid prediction for snap_scaffold_17-snap.1058-T1
Valid prediction for snap_scaffold_17-snap.1069-T1
Valid prediction for CodingQuarry_transcript_21929-T1
Valid prediction for GlimmerHMM_glimmerT_41178-T1
Valid prediction for GeneMark_model.70947_t
Valid prediction for GlimmerHMM_glimmerT_41174-T1
Valid prediction for GeneMark_model.70934_t
Valid prediction for HiQ_model.g27579.t1
Valid prediction for snap_scaffold_17-snap.1062-T1
Couldn't classify 135091, 136080
Sorry, prediction pasa_asmbl_18944.p1 fails validation.
(CCC)	 AC	135091-136080	AG	CCA
Valid prediction for GlimmerHMM_glimmerT_41169-T1
Valid prediction for Augustus_model.g27573.t1
Valid prediction for GlimmerHMM_glimmerT_41179-T1
Valid prediction for GeneMark_model.70945_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 13378, rend_intergenic: 7250  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45100, rend_intergenic: 35595  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50706, rend_intergenic: 46598  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61872, rend_intergenic: 57616  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 140173
-exon list size: 354


building trellis

0.3    
0.6    
0.8    
1.1    
1.4    
1.7    
2.0    
2.2    
2.5    
2.8    
3.1    
3.4    
3.7    
3.9    
4.2    
4.5    
4.8    
5.1    
5.3    
5.6    
5.9    
6.2    
6.5    
6.7    
7.0    
7.3    
7.6    
7.9    
8.1    
8.4    
8.7    
9.0    
9.3    
9.6    
9.8    
10.1    
10.4    
10.7    
11.0    
11.2    
11.5    
11.8    
12.1    
12.4    
12.6    
12.9    
13.2    
13.5    
13.8    
14.0    
14.3    
14.6    
14.9    
15.2    
15.4    
15.7    
16.0    
16.3    
16.6    
16.9    
17.1    
17.4    
17.7    
18.0    
18.3    
18.5    
18.8    
19.1    
19.4    
19.7    
19.9    
20.2    
20.5    
20.8    
21.1    
21.3    
21.6    
21.9    
22.2    
22.5    
22.8    
23.0    
23.3    
23.6    
23.9    
24.2    
24.4    
24.7    
25.0    
25.3    
25.6    
25.8    
26.1    
26.4    
26.7    
27.0    
27.2    
27.5    
27.8    
28.1    
28.4    
28.7    
28.9    
29.2    
29.5    
29.8    
30.1    
30.3    
30.6    
30.9    
31.2    
31.5    
31.7    
32.0    
32.3    
32.6    
32.9    
33.1    
33.4    
33.7    
34.0    
34.3    
34.6    
34.8    
35.1    
35.4    
35.7    
36.0    
36.2    
36.5    
36.8    
37.1    
37.4    
37.6    
37.9    
38.2    
38.5    
38.8    
39.0    
39.3    
39.6    
39.9    
40.2    
40.4    
40.7    
41.0    
41.3    
41.6    
41.9    
42.1    
42.4    
42.7    
43.0    
43.3    
43.5    
43.8    
44.1    
44.4    
44.7    
44.9    
45.2    
45.5    
45.8    
46.1    
46.3    
46.6    
46.9    
47.2    
47.5    
47.8    
48.0    
48.3    
48.6    
48.9    
49.2    
49.4    
49.7    
50.0    
50.3    
50.6    
50.8    
51.1    
51.4    
51.7    
52.0    
52.2    
52.5    
52.8    
53.1    
53.4    
53.7    
53.9    
54.2    
54.5    
54.8    
55.1    
55.3    
55.6    
55.9    
56.2    
56.5    
56.7    
57.0    
57.3    
57.6    
57.9    
58.1    
58.4    
58.7    
59.0    
59.3    
59.6    
59.8    
60.1    
60.4    
60.7    
61.0    
61.2    
61.5    
61.8    
62.1    
62.4    
62.6    
62.9    
63.2    
63.5    
63.8    
64.0    
64.3    
64.6    
64.9    
65.2    
65.4    
65.7    
66.0    
66.3    
66.6    
66.9    
67.1    
67.4    
67.7    
68.0    
68.3    
68.5    
68.8    
69.1    
69.4    
69.7    
69.9    
70.2    
70.5    
70.8    
71.1    
71.3    
71.6    
71.9    
72.2    
72.5    
72.8    
73.0    
73.3    
73.6    
73.9    
74.2    
74.4    
74.7    
75.0    
75.3    
75.6    
75.8    
76.1    
76.4    
76.7    
77.0    
77.2    
77.5    
77.8    
78.1    
78.4    
78.7    
78.9    
79.2    
79.5    
79.8    
80.1    
80.3    
80.6    
80.9    
81.2    
81.5    
81.7    
82.0    
82.3    
82.6    
82.9    
83.1    
83.4    
83.7    
84.0    
84.3    
84.6    
84.8    
85.1    
85.4    
85.7    
86.0    
86.2    
86.5    
86.8    
87.1    
87.4    
87.6    
87.9    
88.2    
88.5    
88.8    
89.0    
89.3    
89.6    
89.9    
90.2    
90.4    
90.7    
91.0    
91.3    
91.6    
91.9    
92.1    
92.4    
92.7    
93.0    
93.3    
93.5    
93.8    
94.1    
94.4    
94.7    
94.9    
95.2    
95.5    
95.8    
96.1    
96.3    
96.6    
96.9    
97.2    
97.5    
97.8    
98.0    
98.3    
98.6    
98.9    
99.2    
99.4    
99.7    
-found 13 predictions from path traversal
Error with prediction: snap lend_intergenic: 13378, rend_intergenic: 7250  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45100, rend_intergenic: 35595  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50706, rend_intergenic: 46598  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61872, rend_intergenic: 57616  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 12 predictions persist after filtering for low support