-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_13/scaffold_13_13131699-13333434

-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 CodingQuarry_transcript_13281-T1
Valid prediction for Augustus_model.g21784.t1
Valid prediction for snap_scaffold_13-snap.2523-T1
Valid prediction for snap_scaffold_13-snap.2527-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for Augustus_model.g21776.t1
Valid prediction for GlimmerHMM_glimmerT_32632-T1
Valid prediction for GlimmerHMM_glimmerT_32624-T1
Couldn't classify 146494, 146553
Sorry, prediction pasa_asmbl_11382.p1 fails validation.
(ATG)	 CA	141713-141742	GT	AGG
(GTT)	 AG	142025-142073	GT	TGG
(TGT)	 AG	142510-142565	GT	AGG
(GGC)	 AG	142757-142844	GT	AAG
(ACA)	 AG	143173-143297	GT	AGG
(GTC)	 AG	144513-144617	GT	CGG
(GCT)	 AG	144949-145094	GT	AGG
(AGC)	 AG	145383-145531	GT	CGG
(GTG)	 AG	146175-146362	GT	AGG
(GAC)	 AG	146494-146553	CA	ACC
-recovered pasa_asmbl_11382.p1, initial, 141713, 141742
-recovered pasa_asmbl_11382.p1, internal, 142025, 142073
-recovered pasa_asmbl_11382.p1, internal, 142510, 142565
-recovered pasa_asmbl_11382.p1, internal, 142757, 142844
-recovered pasa_asmbl_11382.p1, internal, 143173, 143297
-recovered pasa_asmbl_11382.p1, internal, 144513, 144617
-recovered pasa_asmbl_11382.p1, internal, 144949, 145094
-recovered pasa_asmbl_11382.p1, internal, 145383, 145531
-recovered pasa_asmbl_11382.p1, internal, 146175, 146362
Valid prediction for GlimmerHMM_glimmerT_32609-T1
Valid prediction for GlimmerHMM_glimmerT_32618-T1
Valid prediction for Augustus_model.g21780.t1
Couldn't classify 121215, 121371
Sorry, prediction pasa_asmbl_11377.p2 fails validation.
(ATG)	 AC	119286-119390	GT	AGG
(CTG)	 AG	119638-119844	GT	AGG
(AAC)	 AG	120122-120270	GT	AGG
(GAA)	 AG	121215-121371	GT	AGG
-recovered pasa_asmbl_11377.p2, initial, 119286, 119390
-recovered pasa_asmbl_11377.p2, internal, 119638, 119844
-recovered pasa_asmbl_11377.p2, internal, 120122, 120270
-recovered pasa_asmbl_11377.p2, internal, 121215, 121371
Valid prediction for HiQ_model.g21781.t1
Valid prediction for snap_scaffold_13-snap.2528-T1
Valid prediction for snap_scaffold_13-snap.2524-T1
Couldn't classify 151034, 151253
Sorry, prediction pasa_asmbl_11384.p2 fails validation.
(CAG)	 TC	151034-151253	GT	TGG
(CCA)	 AG	151609-151744	GT	AAG
(CTG)	 AG	152127-152130	AG	GAA
-recovered pasa_asmbl_11384.p2, terminal, 152127, 152130
-recovered pasa_asmbl_11384.p2, internal, 151609, 151744
Valid prediction for snap_scaffold_13-snap.2510-T1
Valid prediction for GlimmerHMM_glimmerT_32616-T1
Valid prediction for snap_scaffold_13-snap.2509-T1
Valid prediction for GlimmerHMM_glimmerT_32611-T1
Couldn't classify 125884, 125937
Sorry, prediction pasa_asmbl_11379.p1 fails validation.
(CAG)	 GC	125884-125937	GT	AGG
(GGT)	 AG	126110-126251	GT	AGG
(GCG)	 AG	127679-127985	GT	AGG
(GGA)	 AG	128092-128164	CC	AGC
-recovered pasa_asmbl_11379.p1, terminal, 128092, 128164
-recovered pasa_asmbl_11379.p1, internal, 126110, 126251
-recovered pasa_asmbl_11379.p1, internal, 127679, 127985
Valid prediction for snap_scaffold_13-snap.2500-T1
Valid prediction for snap_scaffold_13-snap.2513-T1
Valid prediction for snap_scaffold_13-snap.2507-T1
Valid prediction for snap_scaffold_13-snap.2514-T1
Valid prediction for Augustus_model.g21786.t1
Valid prediction for snap_scaffold_13-snap.2506-T1
Valid prediction for GlimmerHMM_glimmerT_32622-T1
Valid prediction for snap_scaffold_13-snap.2499-T1
Valid prediction for CodingQuarry_transcript_13278-T1
Valid prediction for GlimmerHMM_glimmerT_32623-T1
Valid prediction for Augustus_model.g21778.t1
Valid prediction for GlimmerHMM_glimmerT_32627-T1
Valid prediction for snap_scaffold_13-snap.2501-T1
Valid prediction for GlimmerHMM_glimmerT_32615-T1
Couldn't classify 123097, 123189
Couldn't classify 124108, 124504
Sorry, prediction pasa_asmbl_11378.p1 fails validation.
(CAG)	 TG	123097-123189	GT	CTG
(GCC)	 AG	123305-123453	GT	AGG
(GAT)	 AG	124108-124504	GG	CCG
-recovered pasa_asmbl_11378.p1, internal, 123305, 123453
Valid prediction for pasa_asmbl_11371.p1
Valid prediction for snap_scaffold_13-snap.2505-T1
Valid prediction for snap_scaffold_13-snap.2495-T1
Valid prediction for CodingQuarry_transcript_13279-T1
Valid prediction for Augustus_model.g21779.t1
Valid prediction for snap_scaffold_13-snap.2516-T1
Valid prediction for pasa_asmbl_11637.p1
Valid prediction for snap_scaffold_13-snap.2521-T1
Valid prediction for GlimmerHMM_glimmerT_32617-T1
Valid prediction for CodingQuarry_transcript_13280-T1
Valid prediction for GlimmerHMM_glimmerT_32621-T1
Valid prediction for snap_scaffold_13-snap.2515-T1
Valid prediction for snap_scaffold_13-snap.2503-T1
Valid prediction for HiQ_model.g21783.t1
Valid prediction for Augustus_model.g21782.t1
Couldn't classify 80260, 80437
Sorry, prediction pasa_asmbl_11691.p1 fails validation.
(ACA)	 CC	80260-80437	GT	AGG
(ACG)	 AG	80880-80921	GT	AGG
(CGT)	 AG	81756-81902	GT	AGG
(GCG)	 AG	82073-82407	GT	AGG
(GTG)	 AG	82662-82758	GT	AGG
(ACA)	 AG	83241-83282	GT	GCG
(CTA)	 AG	83866-84140	GC	GAG
-recovered pasa_asmbl_11691.p1, terminal, 83866, 84140
-recovered pasa_asmbl_11691.p1, internal, 80880, 80921
-recovered pasa_asmbl_11691.p1, internal, 81756, 81902
-recovered pasa_asmbl_11691.p1, internal, 82073, 82407
-recovered pasa_asmbl_11691.p1, internal, 82662, 82758
-recovered pasa_asmbl_11691.p1, internal, 83241, 83282
-recovered pasa_asmbl_11691.p1, internal, 83866, 84140
Valid prediction for GlimmerHMM_glimmerT_32625-T1
Valid prediction for GlimmerHMM_glimmerT_32614-T1
Valid prediction for Augustus_model.g21785.t1
Valid prediction for GlimmerHMM_glimmerT_32629-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_32608-T1
Valid prediction for GlimmerHMM_glimmerT_32619-T1
Valid prediction for GlimmerHMM_glimmerT_32613-T1
Valid prediction for GlimmerHMM_glimmerT_32631-T1
Valid prediction for GlimmerHMM_glimmerT_32628-T1
Valid prediction for snap_scaffold_13-snap.2520-T1
Valid prediction for snap_scaffold_13-snap.2511-T1
Valid prediction for snap_scaffold_13-snap.2508-T1
Valid prediction for snap_scaffold_13-snap.2512-T1
Valid prediction for GlimmerHMM_glimmerT_32610-T1
Valid prediction for GlimmerHMM_glimmerT_32633-T1
Valid prediction for snap_scaffold_13-snap.2517-T1
Valid prediction for snap_scaffold_13-snap.2518-T1
Valid prediction for Augustus_model.g21777.t1
Valid prediction for snap_scaffold_13-snap.2522-T1
Valid prediction for snap_scaffold_13-snap.2504-T1
Valid prediction for snap_scaffold_13-snap.2496-T1
Valid prediction for GlimmerHMM_glimmerT_32630-T1
Valid prediction for GlimmerHMM_glimmerT_32626-T1
Valid prediction for snap_scaffold_13-snap.2519-T1
Valid prediction for snap_scaffold_13-snap.2502-T1
Valid prediction for GlimmerHMM_glimmerT_32620-T1
Valid prediction for snap_scaffold_13-snap.2497-T1
Valid prediction for snap_scaffold_13-snap.2525-T1
Sorry, intron length (5) is less than minimum required (10)
Valid prediction for snap_scaffold_13-snap.2526-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_13-snap.2498-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_32612-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 3311, rend_intergenic: 2223  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24002, rend_intergenic: 19895  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49982, rend_intergenic: 46484  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56580, rend_intergenic: 50384  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67162, rend_intergenic: 61331  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80027, rend_intergenic: 72789  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85092, rend_intergenic: 80166  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128164, rend_intergenic: 120076  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147457, rend_intergenic: 144459  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152154, rend_intergenic: 148190  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164523, rend_intergenic: 159583  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 198665, rend_intergenic: 170199  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 201736
-exon list size: 324


building trellis

0.3    
0.6    
0.9    
1.2    
1.5    
1.8    
2.1    
2.5    
2.8    
3.1    
3.4    
3.7    
4.0    
4.3    
4.6    
4.9    
5.2    
5.5    
5.8    
6.1    
6.4    
6.7    
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    
11.0    
11.3    
11.7    
12.0    
12.3    
12.6    
12.9    
13.2    
13.5    
13.8    
14.1    
14.4    
14.7    
15.0    
15.3    
15.6    
16.0    
16.3    
16.6    
16.9    
17.2    
17.5    
17.8    
18.1    
18.4    
18.7    
19.0    
19.3    
19.6    
19.9    
20.2    
20.6    
20.9    
21.2    
21.5    
21.8    
22.1    
22.4    
22.7    
23.0    
23.3    
23.6    
23.9    
24.2    
24.5    
24.8    
25.2    
25.5    
25.8    
26.1    
26.4    
26.7    
27.0    
27.3    
27.6    
27.9    
28.2    
28.5    
28.8    
29.1    
29.4    
29.8    
30.1    
30.4    
30.7    
31.0    
31.3    
31.6    
31.9    
32.2    
32.5    
32.8    
33.1    
33.4    
33.7    
34.0    
34.4    
34.7    
35.0    
35.3    
35.6    
35.9    
36.2    
36.5    
36.8    
37.1    
37.4    
37.7    
38.0    
38.3    
38.7    
39.0    
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    
43.3    
43.6    
43.9    
44.2    
44.5    
44.8    
45.1    
45.4    
45.7    
46.0    
46.3    
46.6    
46.9    
47.2    
47.5    
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    
52.5    
52.8    
53.1    
53.4    
53.7    
54.0    
54.3    
54.6    
54.9    
55.2    
55.5    
55.8    
56.1    
56.4    
56.7    
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    
61.0    
61.3    
61.7    
62.0    
62.3    
62.6    
62.9    
63.2    
63.5    
63.8    
64.1    
64.4    
64.7    
65.0    
65.3    
65.6    
66.0    
66.3    
66.6    
66.9    
67.2    
67.5    
67.8    
68.1    
68.4    
68.7    
69.0    
69.3    
69.6    
69.9    
70.2    
70.6    
70.9    
71.2    
71.5    
71.8    
72.1    
72.4    
72.7    
73.0    
73.3    
73.6    
73.9    
74.2    
74.5    
74.8    
75.2    
75.5    
75.8    
76.1    
76.4    
76.7    
77.0    
77.3    
77.6    
77.9    
78.2    
78.5    
78.8    
79.1    
79.4    
79.8    
80.1    
80.4    
80.7    
81.0    
81.3    
81.6    
81.9    
82.2    
82.5    
82.8    
83.1    
83.4    
83.7    
84.0    
84.4    
84.7    
85.0    
85.3    
85.6    
85.9    
86.2    
86.5    
86.8    
87.1    
87.4    
87.7    
88.0    
88.3    
88.7    
89.0    
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    
93.3    
93.6    
93.9    
94.2    
94.5    
94.8    
95.1    
95.4    
95.7    
96.0    
96.3    
96.6    
96.9    
97.2    
97.5    
97.9    
98.2    
98.5    
98.8    
99.1    
99.4    
99.7    
-found 23 predictions from path traversal
Error with prediction: snap lend_intergenic: 3311, rend_intergenic: 2223  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24002, rend_intergenic: 19895  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49982, rend_intergenic: 46484  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56580, rend_intergenic: 50384  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67162, rend_intergenic: 61331  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80027, rend_intergenic: 72789  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85092, rend_intergenic: 80166  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128164, rend_intergenic: 120076  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147457, rend_intergenic: 144459  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152154, rend_intergenic: 148190  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164523, rend_intergenic: 159583  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 198665, rend_intergenic: 170199  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