-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_1/scaffold_1_15128110-15363913

-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_1-snap.2624-T1
Valid prediction for CodingQuarry_transcript_2938-T1
Valid prediction for snap_scaffold_1-snap.2652-T1
Valid prediction for snap_scaffold_1-snap.2658-T1
Valid prediction for snap_scaffold_1-snap.2622-T1
Valid prediction for Augustus_model.g1506.t1
Couldn't classify 2987, 3655
Sorry, prediction pasa_asmbl_2426.p1 fails validation.
(CAG)	 CC	2987-3655	TT	GAT
Valid prediction for CodingQuarry_transcript_2936-T1
Valid prediction for snap_scaffold_1-snap.2626-T1
Valid prediction for snap_scaffold_1-snap.2647-T1
Valid prediction for Augustus_model.g1490.t1
Valid prediction for snap_scaffold_1-snap.2666-T1
Valid prediction for GlimmerHMM_glimmerT_1989-T1
Valid prediction for HiQ_model.g1502.t1
Valid prediction for GlimmerHMM_glimmerT_2010-T1
Valid prediction for snap_scaffold_1-snap.2630-T1
Valid prediction for snap_scaffold_1-snap.2669-T1
Valid prediction for GlimmerHMM_glimmerT_2009-T1
Valid prediction for pasa_asmbl_2439.p1
Couldn't classify 38242, 38318
Couldn't classify 40161, 40164
Sorry, prediction pasa_asmbl_2427.p1 fails validation.
(TGT)	 TC	38242-38318	GT	AGG
(ACA)	 AG	38470-38510	GT	AGG
(GGC)	 AG	38706-38811	GT	GTG
(TTT)	 AG	39619-39765	GT	GAG
(CAC)	 AG	40161-40164	GG	CAG
-recovered pasa_asmbl_2427.p1, terminal, 38470, 38510
add_exon() Sorry, pasa_asmbl_2427.p1 39619-39765-terminal-1 is invalid.
-recovered pasa_asmbl_2427.p1, terminal, 39619, 39765
-recovered pasa_asmbl_2427.p1, internal, 38470, 38510
-recovered pasa_asmbl_2427.p1, internal, 38706, 38811
-recovered pasa_asmbl_2427.p1, internal, 39619, 39765
Valid prediction for GlimmerHMM_glimmerT_1988-T1
Valid prediction for snap_scaffold_1-snap.2633-T1
Valid prediction for snap_scaffold_1-snap.2627-T1
Valid prediction for GlimmerHMM_glimmerT_1984-T1
Valid prediction for snap_scaffold_1-snap.2639-T1
Valid prediction for snap_scaffold_1-snap.2667-T1
Valid prediction for Augustus_model.g1496.t1
Valid prediction for snap_scaffold_1-snap.2628-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for Augustus_model.g1492.t1
Valid prediction for snap_scaffold_1-snap.2629-T1
Valid prediction for snap_scaffold_1-snap.2636-T1
Valid prediction for snap_scaffold_1-snap.2654-T1
Valid prediction for CodingQuarry_transcript_2935-T1
Valid prediction for GlimmerHMM_glimmerT_1987-T1
Valid prediction for GlimmerHMM_glimmerT_1998-T1
Valid prediction for snap_scaffold_1-snap.2648-T1
Valid prediction for Augustus_model.g1491.t1
Valid prediction for Augustus_model.g1495.t1
Valid prediction for GlimmerHMM_glimmerT_2003-T1
Valid prediction for snap_scaffold_1-snap.2623-T1
Couldn't classify 137204, 137954
Couldn't classify 138251, 138648
Sorry, prediction pasa_asmbl_2435.p1 fails validation.
(TTC)	 CC	137204-137954	GT	AGG
(GAA)	 AG	138251-138648	GA	AGG
Valid prediction for snap_scaffold_1-snap.2643-T1
Couldn't classify 133621, 133737
Couldn't classify 135815, 135958
Sorry, prediction pasa_asmbl_2434.p1 fails validation.
(CAG)	 TT	133621-133737	GT	AGG
(GTG)	 AG	133933-134070	GT	AGG
(TGT)	 AG	135188-135391	GT	AGG
(ATC)	 AG	135815-135958	TC	AGT
-recovered pasa_asmbl_2434.p1, internal, 133933, 134070
-recovered pasa_asmbl_2434.p1, internal, 135188, 135391
Valid prediction for Augustus_model.g1497.t1
Valid prediction for Augustus_model.g1499.t1
Valid prediction for Augustus_model.g1507.t1
Valid prediction for GlimmerHMM_glimmerT_1997-T1
Couldn't classify 63162, 63311
Sorry, prediction pasa_asmbl_2431.p1 fails validation.
(TGC)	 CC	63162-63311	GT	CTG
(TGT)	 AG	63529-63655	GT	CTG
(GCC)	 AG	63756-63850	GT	AAG
(ATC)	 AG	64231-64325	GT	AGG
(ACT)	 AG	64472-64605	GT	CAG
(CCA)	 AG	65122-65213	GT	AGG
(GGT)	 AG	66294-66398	GT	AGG
(GAT)	 AG	67097-67186	AG	AAA
-recovered pasa_asmbl_2431.p1, terminal, 67097, 67186
-recovered pasa_asmbl_2431.p1, internal, 63529, 63655
-recovered pasa_asmbl_2431.p1, internal, 63756, 63850
-recovered pasa_asmbl_2431.p1, internal, 64231, 64325
-recovered pasa_asmbl_2431.p1, internal, 64472, 64605
-recovered pasa_asmbl_2431.p1, internal, 65122, 65213
-recovered pasa_asmbl_2431.p1, internal, 66294, 66398
Valid prediction for GlimmerHMM_glimmerT_1986-T1
Valid prediction for CodingQuarry_transcript_2937-T1
Valid prediction for pasa_asmbl_2440.p1
Valid prediction for GlimmerHMM_glimmerT_2001-T1
Valid prediction for Augustus_model.g1489.t1
Couldn't classify 46245, 46364
Couldn't classify 46951, 47007
Sorry, prediction pasa_asmbl_2428.p1 fails validation.
(GAC)	 CA	46245-46364	GT	AGG
(TGC)	 AG	46477-46641	GT	AGG
(TGC)	 AG	46951-47007	GA	GAG
-recovered pasa_asmbl_2428.p1, internal, 46477, 46641
Valid prediction for GlimmerHMM_glimmerT_2004-T1
Valid prediction for GlimmerHMM_glimmerT_1995-T1
Valid prediction for GlimmerHMM_glimmerT_2007-T1
Valid prediction for snap_scaffold_1-snap.2632-T1
Valid prediction for snap_scaffold_1-snap.2650-T1
Valid prediction for snap_scaffold_1-snap.2664-T1
Valid prediction for CodingQuarry_transcript_2934-T1
Valid prediction for snap_scaffold_1-snap.2662-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_1-snap.2642-T1
Valid prediction for Augustus_model.g1498.t1
Valid prediction for snap_scaffold_1-snap.2660-T1
Valid prediction for snap_scaffold_1-snap.2646-T1
Valid prediction for snap_scaffold_1-snap.2668-T1
Valid prediction for GlimmerHMM_glimmerT_2006-T1
Valid prediction for snap_scaffold_1-snap.2641-T1
Valid prediction for GlimmerHMM_glimmerT_1993-T1
Valid prediction for snap_scaffold_1-snap.2653-T1
Couldn't classify 17741, 17806
Sorry, prediction pasa_asmbl_957.p1 fails validation.
(CAA)	 AT	17741-17806	GT	AGG
(ATT)	 AG	20343-20478	GT	TGG
(GGC)	 AG	21131-21234	GT	AGG
(AAG)	 AG	21401-21529	GT	AGG
(ACC)	 AG	22072-22230	GT	AGG
(TCA)	 AG	23329-23459	GT	AGG
(CAC)	 AG	23669-23894	GT	AGG
(GTG)	 AG	24047-24166	GT	AGG
(ATT)	 AG	24382-24522	GT	GGG
(ATG)	 AG	24746-24871	GT	AGG
(GAC)	 AG	25125-25298	TT	AGT
-recovered pasa_asmbl_957.p1, initial, 24746, 24871
-recovered pasa_asmbl_957.p1, terminal, 25125, 25298
-recovered pasa_asmbl_957.p1, internal, 20343, 20478
-recovered pasa_asmbl_957.p1, internal, 21131, 21234
-recovered pasa_asmbl_957.p1, internal, 21401, 21529
-recovered pasa_asmbl_957.p1, internal, 22072, 22230
-recovered pasa_asmbl_957.p1, internal, 23329, 23459
-recovered pasa_asmbl_957.p1, internal, 23669, 23894
-recovered pasa_asmbl_957.p1, internal, 24047, 24166
-recovered pasa_asmbl_957.p1, internal, 24382, 24522
-recovered pasa_asmbl_957.p1, internal, 24746, 24871
Valid prediction for snap_scaffold_1-snap.2637-T1
Valid prediction for GlimmerHMM_glimmerT_1991-T1
Valid prediction for GlimmerHMM_glimmerT_2002-T1
Valid prediction for snap_scaffold_1-snap.2631-T1
Valid prediction for snap_scaffold_1-snap.2644-T1
Valid prediction for HiQ_model.g1503.t1
Valid prediction for GlimmerHMM_glimmerT_1996-T1
Valid prediction for Augustus_model.g1500.t1
Valid prediction for GlimmerHMM_glimmerT_1999-T1
Valid prediction for snap_scaffold_1-snap.2656-T1
Valid prediction for snap_scaffold_1-snap.2635-T1
Valid prediction for snap_scaffold_1-snap.2657-T1
Couldn't classify 54815, 54980
Sorry, prediction pasa_asmbl_954.p1 fails validation.
(TAC)	 AA	54815-54980	GT	TGG
(GTA)	 AG	55121-55258	GT	AGG
(CCC)	 AG	55412-55566	GT	AGG
(ATC)	 AG	55730-55868	GT	GGG
(GCA)	 AG	56099-56297	GT	AGG
(CAC)	 AG	56785-56863	GT	AGG
(AGG)	 AG	56975-57097	GT	ACG
(AAA)	 AG	57187-57328	GT	CTG
(TTA)	 AG	57490-57648	GT	AGG
(ATG)	 AG	57797-57873	GT	AGG
(GCT)	 AG	57960-58211	GT	ACG
(ATT)	 AG	58363-58587	GT	AGG
add_exon() Sorry, pasa_asmbl_954.p1 57797-57873-initial-1 is invalid.
-recovered pasa_asmbl_954.p1, initial, 57797, 57873
add_exon() Sorry, pasa_asmbl_954.p1 56099-56297-terminal-3 is invalid.
-recovered pasa_asmbl_954.p1, terminal, 56099, 56297
-recovered pasa_asmbl_954.p1, terminal, 58363, 58587
-recovered pasa_asmbl_954.p1, internal, 55121, 55258
-recovered pasa_asmbl_954.p1, internal, 55412, 55566
-recovered pasa_asmbl_954.p1, internal, 55730, 55868
-recovered pasa_asmbl_954.p1, internal, 56099, 56297
-recovered pasa_asmbl_954.p1, internal, 56785, 56863
-recovered pasa_asmbl_954.p1, internal, 56975, 57097
-recovered pasa_asmbl_954.p1, internal, 57187, 57328
-recovered pasa_asmbl_954.p1, internal, 57490, 57648
-recovered pasa_asmbl_954.p1, internal, 57797, 57873
-recovered pasa_asmbl_954.p1, internal, 57960, 58211
-recovered pasa_asmbl_954.p1, internal, 58363, 58587
Valid prediction for snap_scaffold_1-snap.2663-T1
Valid prediction for snap_scaffold_1-snap.2665-T1
Valid prediction for snap_scaffold_1-snap.2649-T1
Valid prediction for Augustus_model.g1493.t1
Valid prediction for snap_scaffold_1-snap.2634-T1
Valid prediction for HiQ_model.g1505.t1
Valid prediction for snap_scaffold_1-snap.2655-T1
Valid prediction for snap_scaffold_1-snap.2625-T1
Valid prediction for snap_scaffold_1-snap.2640-T1
Valid prediction for GlimmerHMM_glimmerT_1985-T1
Valid prediction for snap_scaffold_1-snap.2659-T1
Valid prediction for GlimmerHMM_glimmerT_1990-T1
Valid prediction for snap_scaffold_1-snap.2645-T1
Valid prediction for snap_scaffold_1-snap.2661-T1
Valid prediction for GlimmerHMM_glimmerT_1994-T1
Valid prediction for Augustus_model.g1504.t1
Valid prediction for Augustus_model.g1494.t1
Valid prediction for snap_scaffold_1-snap.2651-T1
Valid prediction for snap_scaffold_1-snap.2638-T1
Valid prediction for GlimmerHMM_glimmerT_2005-T1
Valid prediction for GlimmerHMM_glimmerT_2000-T1
Valid prediction for Augustus_model.g1501.t1
Valid prediction for GlimmerHMM_glimmerT_1992-T1
Valid prediction for GlimmerHMM_glimmerT_2008-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 17466, rend_intergenic: 10471  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53367, rend_intergenic: 48810  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91491, rend_intergenic: 88659  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102700, rend_intergenic: 96750  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114788, rend_intergenic: 106274  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122492, rend_intergenic: 117402  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136239, rend_intergenic: 132064  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154497, rend_intergenic: 151476  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 191751, rend_intergenic: 190959  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 199169, rend_intergenic: 196667  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 235804
-exon list size: 404


building trellis

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16.3    
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19.2    
19.5    
19.7    
20.0    
20.2    
20.4    
20.7    
20.9    
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21.7    
21.9    
22.2    
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22.7    
22.9    
23.2    
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23.6    
23.9    
24.1    
24.4    
24.6    
24.9    
25.1    
25.4    
25.6    
25.9    
26.1    
26.4    
26.6    
26.8    
27.1    
27.3    
27.6    
27.8    
28.1    
28.3    
28.6    
28.8    
29.1    
29.3    
29.6    
29.8    
30.0    
30.3    
30.5    
30.8    
31.0    
31.3    
31.5    
31.8    
32.0    
32.3    
32.5    
32.8    
33.0    
33.3    
33.5    
33.7    
34.0    
34.2    
34.5    
34.7    
35.0    
35.2    
35.5    
35.7    
36.0    
36.2    
36.5    
36.7    
36.9    
37.2    
37.4    
37.7    
37.9    
38.2    
38.4    
38.7    
38.9    
39.2    
39.4    
39.7    
39.9    
40.1    
40.4    
40.6    
40.9    
41.1    
41.4    
41.6    
41.9    
42.1    
42.4    
42.6    
42.9    
43.1    
43.3    
43.6    
43.8    
44.1    
44.3    
44.6    
44.8    
45.1    
45.3    
45.6    
45.8    
46.1    
46.3    
46.6    
46.8    
47.0    
47.3    
47.5    
47.8    
48.0    
48.3    
48.5    
48.8    
49.0    
49.3    
49.5    
49.8    
50.0    
50.2    
50.5    
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51.0    
51.2    
51.5    
51.7    
52.0    
52.2    
52.5    
52.7    
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53.2    
53.4    
53.7    
53.9    
54.2    
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54.7    
54.9    
55.2    
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55.9    
56.2    
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80.3    
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81.3    
81.5    
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82.0    
82.3    
82.5    
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83.0    
83.3    
83.5    
83.7    
84.0    
84.2    
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84.7    
85.0    
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86.0    
86.2    
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86.9    
87.2    
87.4    
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87.9    
88.2    
88.4    
88.7    
88.9    
89.2    
89.4    
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89.9    
90.1    
90.4    
90.6    
90.9    
91.1    
91.4    
91.6    
91.9    
92.1    
92.4    
92.6    
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93.3    
93.6    
93.8    
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94.3    
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95.1    
95.3    
95.6    
95.8    
96.1    
96.3    
96.6    
96.8    
97.0    
97.3    
97.5    
97.8    
98.0    
98.3    
98.5    
98.8    
99.0    
99.3    
99.5    
99.8    
-found 37 predictions from path traversal
Error with prediction: snap lend_intergenic: 17466, rend_intergenic: 10471  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53367, rend_intergenic: 48810  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91491, rend_intergenic: 88659  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102700, rend_intergenic: 96750  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114788, rend_intergenic: 106274  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122492, rend_intergenic: 117402  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136239, rend_intergenic: 132064  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154497, rend_intergenic: 151476  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 191751, rend_intergenic: 190959  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 199169, rend_intergenic: 196667  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