-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_15826893-16032126

-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 Augustus_model.g12582.t1
Valid prediction for snap_scaffold_7-snap.3000-T1
Valid prediction for snap_scaffold_7-snap.2985-T1
Valid prediction for GlimmerHMM_glimmerT_18675-T1
Valid prediction for GlimmerHMM_glimmerT_18684-T1
Valid prediction for snap_scaffold_7-snap.2995-T1
Valid prediction for snap_scaffold_7-snap.3009-T1
Valid prediction for snap_scaffold_7-snap.2997-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_18673-T1
Valid prediction for snap_scaffold_7-snap.2991-T1
Valid prediction for Augustus_model.g12583.t1
Valid prediction for snap_scaffold_7-snap.2983-T1
Valid prediction for snap_scaffold_7-snap.3013-T1
Valid prediction for snap_scaffold_7-snap.3006-T1
Valid prediction for snap_scaffold_7-snap.2993-T1
Valid prediction for GlimmerHMM_glimmerT_18678-T1
Valid prediction for snap_scaffold_7-snap.3005-T1
Valid prediction for snap_scaffold_7-snap.3004-T1
Valid prediction for GlimmerHMM_glimmerT_18667-T1
Valid prediction for snap_scaffold_7-snap.2984-T1
Valid prediction for snap_scaffold_7-snap.2999-T1
Valid prediction for Augustus_model.g12585.t1
Valid prediction for GlimmerHMM_glimmerT_18664-T1
Valid prediction for snap_scaffold_7-snap.2998-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for snap_scaffold_7-snap.2988-T1
Valid prediction for GlimmerHMM_glimmerT_18666-T1
Valid prediction for snap_scaffold_7-snap.3007-T1
Valid prediction for snap_scaffold_7-snap.3003-T1
Valid prediction for GlimmerHMM_glimmerT_18682-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.3008-T1
Valid prediction for Augustus_model.g12579.t1
Valid prediction for CodingQuarry_transcript_57734-T1
Valid prediction for Augustus_model.g12584.t1
Valid prediction for snap_scaffold_7-snap.2992-T1
Valid prediction for Augustus_model.g12578.t1
Couldn't classify 85317, 85847
Sorry, prediction pasa_asmbl_51395.p1 fails validation.
(GAA)	 TG	85317-85847	CA	GAC
Valid prediction for snap_scaffold_7-snap.2982-T1
Valid prediction for snap_scaffold_7-snap.3001-T1
Valid prediction for Augustus_model.g12580.t1
Couldn't classify 104289, 104334
Sorry, prediction pasa_asmbl_51394.p1 fails validation.
(GTG)	 AG	104289-104334	GT	CGG
(TCA)	 AG	106214-106311	GT	CTG
(GTT)	 AG	106414-106545	GT	AGG
(CAG)	 AG	106768-106914	GT	TGG
(ATG)	 AG	107539-107607	GT	TGG
(GAA)	 AG	108436-108500	GT	AGG
(TGA)	 AG	108933-109086	GT	CGG
(GAC)	 AG	111679-112035	TC	GAT
-recovered pasa_asmbl_51394.p1, initial, 107539, 107607
-recovered pasa_asmbl_51394.p1, terminal, 111679, 112035
-recovered pasa_asmbl_51394.p1, internal, 104289, 104334
-recovered pasa_asmbl_51394.p1, internal, 106214, 106311
-recovered pasa_asmbl_51394.p1, internal, 106414, 106545
-recovered pasa_asmbl_51394.p1, internal, 106768, 106914
-recovered pasa_asmbl_51394.p1, internal, 107539, 107607
-recovered pasa_asmbl_51394.p1, internal, 108436, 108500
-recovered pasa_asmbl_51394.p1, internal, 108933, 109086
Valid prediction for Augustus_model.g12581.t1
Valid prediction for snap_scaffold_7-snap.2990-T1
Couldn't classify 136818, 137248
Couldn't classify 142786, 142894
Sorry, prediction pasa_asmbl_51389.p1 fails validation.
(ACA)	 GT	136818-137248	GT	CGG
(GTT)	 AG	137575-137879	GT	AGG
(ATG)	 AG	138205-138335	GT	AGG
(TCT)	 AG	138566-138661	GT	CGG
(GCC)	 AG	138851-139018	GT	AGG
(TTG)	 AG	139212-139348	GT	AGG
(TAT)	 AG	140752-140863	GT	CTG
(AAC)	 AG	141208-141438	GT	CGG
(TCG)	 AG	141628-141739	GT	AGG
(TGA)	 AG	141977-142074	GT	GTG
(GTG)	 AG	142230-142306	GT	AGG
(AGG)	 AG	142786-142894	AA	GCA
add_exon() Sorry, pasa_asmbl_51389.p1 138205-138335-initial-1 is invalid.
-recovered pasa_asmbl_51389.p1, initial, 138205, 138335
-recovered pasa_asmbl_51389.p1, internal, 137575, 137879
-recovered pasa_asmbl_51389.p1, internal, 138205, 138335
-recovered pasa_asmbl_51389.p1, internal, 138566, 138661
-recovered pasa_asmbl_51389.p1, internal, 138851, 139018
-recovered pasa_asmbl_51389.p1, internal, 139212, 139348
-recovered pasa_asmbl_51389.p1, internal, 140752, 140863
-recovered pasa_asmbl_51389.p1, internal, 141208, 141438
-recovered pasa_asmbl_51389.p1, internal, 141628, 141739
-recovered pasa_asmbl_51389.p1, internal, 141977, 142074
-recovered pasa_asmbl_51389.p1, internal, 142230, 142306
Valid prediction for snap_scaffold_7-snap.2994-T1
Valid prediction for GlimmerHMM_glimmerT_18680-T1
Valid prediction for GlimmerHMM_glimmerT_18668-T1
Couldn't classify 135848, 136165
Sorry, prediction pasa_asmbl_51390.p1 fails validation.
(ATG)	 GC	135848-136165	AG	GGA
Valid prediction for GlimmerHMM_glimmerT_18665-T1
Valid prediction for GlimmerHMM_glimmerT_18677-T1
Valid prediction for GlimmerHMM_glimmerT_18674-T1
Valid prediction for Augustus_model.g12575.t1
Valid prediction for GlimmerHMM_glimmerT_18672-T1
Valid prediction for snap_scaffold_7-snap.2996-T1
Valid prediction for GlimmerHMM_glimmerT_18676-T1
Valid prediction for GlimmerHMM_glimmerT_18679-T1
Valid prediction for snap_scaffold_7-snap.3002-T1
Valid prediction for snap_scaffold_7-snap.3014-T1
Valid prediction for GlimmerHMM_glimmerT_18671-T1
Valid prediction for Augustus_model.g12577.t1
Valid prediction for pasa_asmbl_51391.p1
Valid prediction for snap_scaffold_7-snap.3011-T1
Valid prediction for GlimmerHMM_glimmerT_18681-T1
Valid prediction for snap_scaffold_7-snap.2989-T1
Valid prediction for GlimmerHMM_glimmerT_18669-T1
Valid prediction for snap_scaffold_7-snap.3012-T1
Valid prediction for snap_scaffold_7-snap.2987-T1
Valid prediction for GlimmerHMM_glimmerT_18670-T1
Valid prediction for snap_scaffold_7-snap.2986-T1
Valid prediction for GlimmerHMM_glimmerT_18683-T1
Couldn't classify 121747, 121847
Couldn't classify 122578, 122782
Sorry, prediction pasa_asmbl_51589.p2 fails validation.
(GCA)	 CA	121747-121847	GT	AAG
(GAT)	 AG	122578-122782	GT	CGG
-recovered pasa_asmbl_51589.p2, internal, 122578, 122782
Valid prediction for Augustus_model.g12576.t1
Couldn't classify 143660, 143920
Sorry, prediction pasa_asmbl_51388.p1 fails validation.
(GGC)	 AG	143660-143920	GT	AGG
(TTC)	 AG	144302-144515	GT	AGG
(CTC)	 AG	144675-144763	GT	AGG
(GTG)	 AG	145103-145198	GT	CGG
(TGT)	 AG	145442-145507	CG	AGC
-recovered pasa_asmbl_51388.p1, terminal, 145442, 145507
-recovered pasa_asmbl_51388.p1, internal, 143660, 143920
-recovered pasa_asmbl_51388.p1, internal, 144302, 144515
-recovered pasa_asmbl_51388.p1, internal, 144675, 144763
-recovered pasa_asmbl_51388.p1, internal, 145103, 145198
Valid prediction for snap_scaffold_7-snap.3010-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 7487, rend_intergenic: 5511  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57155, rend_intergenic: 52168  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69387, rend_intergenic: 58898  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75485, rend_intergenic: 74130  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89604, rend_intergenic: 77515  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103476, rend_intergenic: 94636  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 202859, rend_intergenic: 200569  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 205234
-exon list size: 269


building trellis

0.4    
0.7    
1.1    
1.5    
1.8    
2.2    
2.6    
3.0    
3.3    
3.7    
4.1    
4.4    
4.8    
5.2    
5.5    
5.9    
6.3    
6.6    
7.0    
7.4    
7.7    
8.1    
8.5    
8.9    
9.2    
9.6    
10.0    
10.3    
10.7    
11.1    
11.4    
11.8    
12.2    
12.5    
12.9    
13.3    
13.7    
14.0    
14.4    
14.8    
15.1    
15.5    
15.9    
16.2    
16.6    
17.0    
17.3    
17.7    
18.1    
18.5    
18.8    
19.2    
19.6    
19.9    
20.3    
20.7    
21.0    
21.4    
21.8    
22.1    
22.5    
22.9    
23.2    
23.6    
24.0    
24.4    
24.7    
25.1    
25.5    
25.8    
26.2    
26.6    
26.9    
27.3    
27.7    
28.0    
28.4    
28.8    
29.2    
29.5    
29.9    
30.3    
30.6    
31.0    
31.4    
31.7    
32.1    
32.5    
32.8    
33.2    
33.6    
33.9    
34.3    
34.7    
35.1    
35.4    
35.8    
36.2    
36.5    
36.9    
37.3    
37.6    
38.0    
38.4    
38.7    
39.1    
39.5    
39.9    
40.2    
40.6    
41.0    
41.3    
41.7    
42.1    
42.4    
42.8    
43.2    
43.5    
43.9    
44.3    
44.6    
45.0    
45.4    
45.8    
46.1    
46.5    
46.9    
47.2    
47.6    
48.0    
48.3    
48.7    
49.1    
49.4    
49.8    
50.2    
50.6    
50.9    
51.3    
51.7    
52.0    
52.4    
52.8    
53.1    
53.5    
53.9    
54.2    
54.6    
55.0    
55.4    
55.7    
56.1    
56.5    
56.8    
57.2    
57.6    
57.9    
58.3    
58.7    
59.0    
59.4    
59.8    
60.1    
60.5    
60.9    
61.3    
61.6    
62.0    
62.4    
62.7    
63.1    
63.5    
63.8    
64.2    
64.6    
64.9    
65.3    
65.7    
66.1    
66.4    
66.8    
67.2    
67.5    
67.9    
68.3    
68.6    
69.0    
69.4    
69.7    
70.1    
70.5    
70.8    
71.2    
71.6    
72.0    
72.3    
72.7    
73.1    
73.4    
73.8    
74.2    
74.5    
74.9    
75.3    
75.6    
76.0    
76.4    
76.8    
77.1    
77.5    
77.9    
78.2    
78.6    
79.0    
79.3    
79.7    
80.1    
80.4    
80.8    
81.2    
81.5    
81.9    
82.3    
82.7    
83.0    
83.4    
83.8    
84.1    
84.5    
84.9    
85.2    
85.6    
86.0    
86.3    
86.7    
87.1    
87.5    
87.8    
88.2    
88.6    
88.9    
89.3    
89.7    
90.0    
90.4    
90.8    
91.1    
91.5    
91.9    
92.3    
92.6    
93.0    
93.4    
93.7    
94.1    
94.5    
94.8    
95.2    
95.6    
95.9    
96.3    
96.7    
97.0    
97.4    
97.8    
98.2    
98.5    
98.9    
99.3    
99.6    
-found 22 predictions from path traversal
Error with prediction: snap lend_intergenic: 7487, rend_intergenic: 5511  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57155, rend_intergenic: 52168  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69387, rend_intergenic: 58898  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75485, rend_intergenic: 74130  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89604, rend_intergenic: 77515  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103476, rend_intergenic: 94636  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 202859, rend_intergenic: 200569  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

-building DP trellis

-building trellis in range 1 - 15132
-exon list size: 10


building trellis

8.3    
16.7    
25.0    
33.3    
41.7    
50.0    
58.3    
66.7    
75.0    
83.3    
91.7    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 14653
-exon list size: 9


building trellis

9.1    
18.2    
27.3    
36.4    
45.5    
54.5    
63.6    
72.7    
81.8    
90.9    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support