-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_3/scaffold_3_19786339-19972339

-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_3-snap.3932-T1
Valid prediction for snap_scaffold_3-snap.3926-T1
Valid prediction for snap_scaffold_3-snap.3937-T1
Valid prediction for GlimmerHMM_glimmerT_8565-T1
Valid prediction for snap_scaffold_3-snap.3930-T1
Valid prediction for GlimmerHMM_glimmerT_8559-T1
Valid prediction for snap_scaffold_3-snap.3929-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for snap_scaffold_3-snap.3918-T1
Valid prediction for pasa_asmbl_40779.p1
Valid prediction for snap_scaffold_3-snap.3921-T1
Valid prediction for GlimmerHMM_glimmerT_8555-T1
Valid prediction for snap_scaffold_3-snap.3923-T1
Valid prediction for GlimmerHMM_glimmerT_8553-T1
Valid prediction for GlimmerHMM_glimmerT_8568-T1
Valid prediction for GlimmerHMM_glimmerT_8554-T1
Valid prediction for snap_scaffold_3-snap.3934-T1
Valid prediction for snap_scaffold_3-snap.3924-T1
Valid prediction for snap_scaffold_3-snap.3916-T1
Valid prediction for snap_scaffold_3-snap.3931-T1
Valid prediction for snap_scaffold_3-snap.3936-T1
Valid prediction for GlimmerHMM_glimmerT_8563-T1
Valid prediction for snap_scaffold_3-snap.3920-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: -)Couldn't classify 143635, 143745
Sorry, prediction pasa_asmbl_39663.p1 fails validation.
(ATG)	 GG	135261-135347	GT	AAG
(GAC)	 AG	135626-135828	GT	CTG
(GTT)	 AG	138040-138274	GT	CGG
(CAA)	 AG	138573-138641	GT	AAG
(ATC)	 AG	140051-140131	GT	TGG
(CTA)	 AG	140231-140360	GT	TGG
(TGT)	 AG	141007-141170	GT	AGG
(GAT)	 AG	141271-141372	GT	GGG
(CAA)	 AG	141729-141809	GT	AGG
(TGT)	 AG	143635-143745	GA	ACG
-recovered pasa_asmbl_39663.p1, initial, 135261, 135347
-recovered pasa_asmbl_39663.p1, internal, 135626, 135828
-recovered pasa_asmbl_39663.p1, internal, 138040, 138274
-recovered pasa_asmbl_39663.p1, internal, 138573, 138641
-recovered pasa_asmbl_39663.p1, internal, 140051, 140131
-recovered pasa_asmbl_39663.p1, internal, 140231, 140360
-recovered pasa_asmbl_39663.p1, internal, 141007, 141170
-recovered pasa_asmbl_39663.p1, internal, 141271, 141372
-recovered pasa_asmbl_39663.p1, internal, 141729, 141809
Valid prediction for snap_scaffold_3-snap.3925-T1
Valid prediction for snap_scaffold_3-snap.3933-T1
Valid prediction for GlimmerHMM_glimmerT_8567-T1
Valid prediction for CodingQuarry_transcript_46488-T1
Valid prediction for GlimmerHMM_glimmerT_8560-T1
Valid prediction for snap_scaffold_3-snap.3935-T1
Valid prediction for snap_scaffold_3-snap.3917-T1
Valid prediction for GlimmerHMM_glimmerT_8564-T1
Valid prediction for snap_scaffold_3-snap.3922-T1
Valid prediction for GlimmerHMM_glimmerT_8566-T1
Couldn't classify 123816, 123865
Couldn't classify 128753, 129061
Sorry, prediction pasa_asmbl_39666.p1 fails validation.
(CCT)	 AC	123816-123865	GT	AGG
(AAC)	 AG	126001-126094	GT	AGG
(GTG)	 AG	126197-126271	GT	TGG
(GTG)	 AG	127060-127170	GT	ACG
(AAG)	 AG	127604-127753	GT	ACG
(ATG)	 AG	128420-128521	GT	GGG
(GAA)	 AG	128753-129061	AG	GCA
-recovered pasa_asmbl_39666.p1, initial, 128420, 128521
-recovered pasa_asmbl_39666.p1, internal, 126001, 126094
-recovered pasa_asmbl_39666.p1, internal, 126197, 126271
-recovered pasa_asmbl_39666.p1, internal, 127060, 127170
-recovered pasa_asmbl_39666.p1, internal, 127604, 127753
-recovered pasa_asmbl_39666.p1, internal, 128420, 128521
Valid prediction for GlimmerHMM_glimmerT_8557-T1
Valid prediction for snap_scaffold_3-snap.3928-T1
Valid prediction for snap_scaffold_3-snap.3938-T1
Valid prediction for snap_scaffold_3-snap.3919-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for CodingQuarry_transcript_46489-T1
Couldn't classify 71825, 72085
Sorry, prediction pasa_asmbl_39677.p1 fails validation.
(CTA)	 AC	71825-72085	GT	CGG
(TTC)	 AG	72993-73116	GT	GGG
(GAG)	 AG	74335-74578	GT	AGG
(AGA)	 AG	74744-74839	GT	AGG
(TGG)	 AG	76709-76802	GT	TGG
(GGA)	 AG	76902-76957	GT	AGG
(GCC)	 AG	77270-77412	GT	AGG
(GCT)	 AG	78079-78273	GT	AGG
(GCT)	 AG	79616-79773	GT	AGG
(GAG)	 AG	80365-80488	GT	CTG
(TGC)	 AG	80682-80979	GT	AGG
(AAT)	 AG	81471-81678	GT	AGG
(GTG)	 AG	81879-82015	GT	AGG
(GCT)	 AG	82388-82511	GT	AGG
(GCA)	 AG	82706-83179	GT	AGG
(TGT)	 AG	83385-83576	GT	AGG
(GTT)	 AG	83880-83984	GG	GAG
-recovered pasa_asmbl_39677.p1, terminal, 83880, 83984
-recovered pasa_asmbl_39677.p1, internal, 72993, 73116
-recovered pasa_asmbl_39677.p1, internal, 74335, 74578
-recovered pasa_asmbl_39677.p1, internal, 74744, 74839
-recovered pasa_asmbl_39677.p1, internal, 76709, 76802
-recovered pasa_asmbl_39677.p1, internal, 76902, 76957
-recovered pasa_asmbl_39677.p1, internal, 77270, 77412
-recovered pasa_asmbl_39677.p1, internal, 78079, 78273
-recovered pasa_asmbl_39677.p1, internal, 79616, 79773
-recovered pasa_asmbl_39677.p1, internal, 80365, 80488
-recovered pasa_asmbl_39677.p1, internal, 80682, 80979
-recovered pasa_asmbl_39677.p1, internal, 81471, 81678
-recovered pasa_asmbl_39677.p1, internal, 81879, 82015
-recovered pasa_asmbl_39677.p1, internal, 82388, 82511
-recovered pasa_asmbl_39677.p1, internal, 82706, 83179
-recovered pasa_asmbl_39677.p1, internal, 83385, 83576
Valid prediction for GlimmerHMM_glimmerT_8558-T1
Valid prediction for GlimmerHMM_glimmerT_8556-T1
Couldn't classify 70331, 70803
Couldn't classify 71249, 71632
Sorry, prediction pasa_asmbl_39679.p1 fails validation.
(CTA)	 TC	70331-70803	GT	AGG
(AAA)	 AG	70899-70932	GT	AGG
(GCT)	 AG	71249-71632	GA	CTG
-recovered pasa_asmbl_39679.p1, internal, 70899, 70932
Valid prediction for snap_scaffold_3-snap.3939-T1
Valid prediction for pasa_asmbl_39676.p2
Valid prediction for GlimmerHMM_glimmerT_8562-T1
Valid prediction for GlimmerHMM_glimmerT_8561-T1
Valid prediction for snap_scaffold_3-snap.3927-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 32451, rend_intergenic: 21118  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52364, rend_intergenic: 44160  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77043, rend_intergenic: 56948  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86341, rend_intergenic: 78367  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130082, rend_intergenic: 102049  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137089, rend_intergenic: 131089  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147967, rend_intergenic: 139430  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166197, rend_intergenic: 153515  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 186001
-exon list size: 266


building trellis

0.4    
0.7    
1.1    
1.5    
1.9    
2.2    
2.6    
3.0    
3.4    
3.7    
4.1    
4.5    
4.9    
5.2    
5.6    
6.0    
6.3    
6.7    
7.1    
7.5    
7.8    
8.2    
8.6    
9.0    
9.3    
9.7    
10.1    
10.4    
10.8    
11.2    
11.6    
11.9    
12.3    
12.7    
13.1    
13.4    
13.8    
14.2    
14.6    
14.9    
15.3    
15.7    
16.0    
16.4    
16.8    
17.2    
17.5    
17.9    
18.3    
18.7    
19.0    
19.4    
19.8    
20.1    
20.5    
20.9    
21.3    
21.6    
22.0    
22.4    
22.8    
23.1    
23.5    
23.9    
24.3    
24.6    
25.0    
25.4    
25.7    
26.1    
26.5    
26.9    
27.2    
27.6    
28.0    
28.4    
28.7    
29.1    
29.5    
29.9    
30.2    
30.6    
31.0    
31.3    
31.7    
32.1    
32.5    
32.8    
33.2    
33.6    
34.0    
34.3    
34.7    
35.1    
35.4    
35.8    
36.2    
36.6    
36.9    
37.3    
37.7    
38.1    
38.4    
38.8    
39.2    
39.6    
39.9    
40.3    
40.7    
41.0    
41.4    
41.8    
42.2    
42.5    
42.9    
43.3    
43.7    
44.0    
44.4    
44.8    
45.1    
45.5    
45.9    
46.3    
46.6    
47.0    
47.4    
47.8    
48.1    
48.5    
48.9    
49.3    
49.6    
50.0    
50.4    
50.7    
51.1    
51.5    
51.9    
52.2    
52.6    
53.0    
53.4    
53.7    
54.1    
54.5    
54.9    
55.2    
55.6    
56.0    
56.3    
56.7    
57.1    
57.5    
57.8    
58.2    
58.6    
59.0    
59.3    
59.7    
60.1    
60.4    
60.8    
61.2    
61.6    
61.9    
62.3    
62.7    
63.1    
63.4    
63.8    
64.2    
64.6    
64.9    
65.3    
65.7    
66.0    
66.4    
66.8    
67.2    
67.5    
67.9    
68.3    
68.7    
69.0    
69.4    
69.8    
70.1    
70.5    
70.9    
71.3    
71.6    
72.0    
72.4    
72.8    
73.1    
73.5    
73.9    
74.3    
74.6    
75.0    
75.4    
75.7    
76.1    
76.5    
76.9    
77.2    
77.6    
78.0    
78.4    
78.7    
79.1    
79.5    
79.9    
80.2    
80.6    
81.0    
81.3    
81.7    
82.1    
82.5    
82.8    
83.2    
83.6    
84.0    
84.3    
84.7    
85.1    
85.4    
85.8    
86.2    
86.6    
86.9    
87.3    
87.7    
88.1    
88.4    
88.8    
89.2    
89.6    
89.9    
90.3    
90.7    
91.0    
91.4    
91.8    
92.2    
92.5    
92.9    
93.3    
93.7    
94.0    
94.4    
94.8    
95.1    
95.5    
95.9    
96.3    
96.6    
97.0    
97.4    
97.8    
98.1    
98.5    
98.9    
99.3    
99.6    
-found 12 predictions from path traversal
Error with prediction: snap lend_intergenic: 32451, rend_intergenic: 21118  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52364, rend_intergenic: 44160  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77043, rend_intergenic: 56948  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86341, rend_intergenic: 78367  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130082, rend_intergenic: 102049  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137089, rend_intergenic: 131089  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147967, rend_intergenic: 139430  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166197, rend_intergenic: 153515  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 10 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 145053 - 186001
-exon list size: 27


building trellis

3.4    
6.9    
10.3    
13.8    
17.2    
20.7    
24.1    
27.6    
31.0    
34.5    
37.9    
41.4    
44.8    
48.3    
51.7    
55.2    
58.6    
62.1    
65.5    
69.0    
72.4    
75.9    
79.3    
82.8    
86.2    
89.7    
93.1    
96.6    
-found 3 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 2 predictions persist after filtering for low support