-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_28/scaffold_28_3518858-3833519

-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_28-snap.916-T1
Valid prediction for GlimmerHMM_glimmerT_58575-T1
Valid prediction for GlimmerHMM_glimmerT_58555-T1
Valid prediction for snap_scaffold_28-snap.902-T1
Valid prediction for Augustus_model.g38787.t1
Valid prediction for GlimmerHMM_glimmerT_58556-T1
Valid prediction for snap_scaffold_28-snap.888-T1
Valid prediction for snap_scaffold_28-snap.909-T1
Valid prediction for snap_scaffold_28-snap.914-T1
Valid prediction for snap_scaffold_28-snap.917-T1
Valid prediction for Augustus_model.g38794.t1
Valid prediction for pasa_asmbl_37488.p1
Valid prediction for snap_scaffold_28-snap.911-T1
Valid prediction for Augustus_model.g38784.t1
Valid prediction for GlimmerHMM_glimmerT_58579-T1
Valid prediction for snap_scaffold_28-snap.896-T1
Valid prediction for GlimmerHMM_glimmerT_58574-T1
Valid prediction for snap_scaffold_28-snap.912-T1
Couldn't classify 153738, 153788
Sorry, prediction pasa_asmbl_37491.p1 fails validation.
(TGC)	 TG	153738-153788	GT	AGG
(TTC)	 AG	154381-154449	GT	AGG
(TTC)	 AG	154863-155036	GT	TGG
(ATC)	 AG	155533-155694	GT	ATG
(TCT)	 AG	155908-156001	GT	CAG
(GAG)	 AG	156522-156562	GC	GAG
-recovered pasa_asmbl_37491.p1, terminal, 156522, 156562
-recovered pasa_asmbl_37491.p1, internal, 154381, 154449
-recovered pasa_asmbl_37491.p1, internal, 154863, 155036
-recovered pasa_asmbl_37491.p1, internal, 155533, 155694
-recovered pasa_asmbl_37491.p1, internal, 155908, 156001
-recovered pasa_asmbl_37491.p1, internal, 156522, 156562
Valid prediction for snap_scaffold_28-snap.898-T1
Valid prediction for snap_scaffold_28-snap.892-T1
Valid prediction for snap_scaffold_28-snap.922-T1
Valid prediction for Augustus_model.g38785.t1
Valid prediction for CodingQuarry_transcript_43610-T1
Couldn't classify 150465, 150500
Couldn't classify 152131, 152271
Sorry, prediction pasa_asmbl_37490.p1 fails validation.
(GGG)	 AT	150465-150500	GT	TAG
(CCT)	 AG	150668-150853	GT	CTG
(GTG)	 AG	151189-151302	GT	AGG
(CCA)	 AG	152131-152271	AG	ACA
-recovered pasa_asmbl_37490.p1, internal, 150668, 150853
-recovered pasa_asmbl_37490.p1, internal, 151189, 151302
Valid prediction for Augustus_model.g38793.t1
Valid prediction for GlimmerHMM_glimmerT_58557-T1
Valid prediction for snap_scaffold_28-snap.890-T1
Valid prediction for GlimmerHMM_glimmerT_58576-T1
Valid prediction for snap_scaffold_28-snap.889-T1
Valid prediction for GlimmerHMM_glimmerT_58577-T1
Valid prediction for snap_scaffold_28-snap.918-T1
Valid prediction for GlimmerHMM_glimmerT_58558-T1
Valid prediction for GlimmerHMM_glimmerT_58569-T1
Valid prediction for snap_scaffold_28-snap.919-T1
Valid prediction for snap_scaffold_28-snap.894-T1
Valid prediction for snap_scaffold_28-snap.905-T1
Valid prediction for Augustus_model.g38795.t1
Valid prediction for snap_scaffold_28-snap.895-T1
Valid prediction for GlimmerHMM_glimmerT_58573-T1
Valid prediction for HiQ_model.g38792.t1
Valid prediction for snap_scaffold_28-snap.901-T1
Valid prediction for GlimmerHMM_glimmerT_58562-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_58568-T1
Valid prediction for snap_scaffold_28-snap.933-T1
Valid prediction for GlimmerHMM_glimmerT_58567-T1
Valid prediction for snap_scaffold_28-snap.929-T1
Valid prediction for snap_scaffold_28-snap.923-T1
Valid prediction for snap_scaffold_28-snap.886-T1
Valid prediction for snap_scaffold_28-snap.903-T1
Valid prediction for snap_scaffold_28-snap.928-T1
Valid prediction for snap_scaffold_28-snap.906-T1
Valid prediction for GlimmerHMM_glimmerT_58572-T1
Valid prediction for GlimmerHMM_glimmerT_58566-T1
Valid prediction for snap_scaffold_28-snap.893-T1
Valid prediction for Augustus_model.g38797.t1
Valid prediction for GlimmerHMM_glimmerT_58554-T1
Valid prediction for snap_scaffold_28-snap.908-T1
Valid prediction for snap_scaffold_28-snap.904-T1
Valid prediction for HiQ_model.g38801.t1
Valid prediction for snap_scaffold_28-snap.926-T1
Valid prediction for GlimmerHMM_glimmerT_58583-T1
Valid prediction for GlimmerHMM_glimmerT_58559-T1
Valid prediction for snap_scaffold_28-snap.920-T1
Valid prediction for Augustus_model.g38786.t1
Valid prediction for pasa_asmbl_38170.p1
Valid prediction for snap_scaffold_28-snap.934-T1
Valid prediction for GlimmerHMM_glimmerT_58580-T1
Valid prediction for GlimmerHMM_glimmerT_58561-T1
Valid prediction for GlimmerHMM_glimmerT_58564-T1
Valid prediction for GlimmerHMM_glimmerT_58570-T1
Valid prediction for snap_scaffold_28-snap.900-T1
Valid prediction for GlimmerHMM_glimmerT_58582-T1
Valid prediction for Augustus_model.g38798.t1
Valid prediction for Augustus_model.g38791.t1
Valid prediction for Augustus_model.g38790.t1
Valid prediction for snap_scaffold_28-snap.921-T1
Valid prediction for CodingQuarry_transcript_43611-T1
Valid prediction for Augustus_model.g38800.t1
Valid prediction for HiQ_model.g38783.t1
Valid prediction for Augustus_model.g38799.t1
Valid prediction for pasa_asmbl_38154.p1
Valid prediction for CodingQuarry_transcript_43613-T1
Valid prediction for snap_scaffold_28-snap.913-T1
Valid prediction for Augustus_model.g38788.t1
Valid prediction for GlimmerHMM_glimmerT_58571-T1
Couldn't classify 290585, 290612
Couldn't classify 292969, 293227
Sorry, prediction pasa_asmbl_38158.p1 fails validation.
(ATC)	 AC	290585-290612	GT	TGG
(ATG)	 AG	292385-292508	GT	TGG
(CAC)	 AG	292691-292777	GT	AGG
(CGA)	 AG	292969-293227	AT	GGA
-recovered pasa_asmbl_38158.p1, initial, 292385, 292508
-recovered pasa_asmbl_38158.p1, internal, 292385, 292508
-recovered pasa_asmbl_38158.p1, internal, 292691, 292777
Valid prediction for HiQ_model.g38805.t1
Valid prediction for snap_scaffold_28-snap.927-T1
Valid prediction for snap_scaffold_28-snap.887-T1
Sorry, intron length (4) is less than minimum required (10)
Couldn't classify 51065, 51382
Sorry, prediction pasa_asmbl_38172.p1 fails validation.
(CAC)	 AG	51065-51382	TT	CGT
Valid prediction for snap_scaffold_28-snap.935-T1
Valid prediction for Augustus_model.g38796.t1
Valid prediction for Augustus_model.g38789.t1
Couldn't classify 139997, 140029
Couldn't classify 142151, 142183
Sorry, prediction pasa_asmbl_38160.p1 fails validation.
(GAT)	 CA	139997-140029	GT	TGG
(ATA)	 AG	140460-140616	GT	AGG
(GTT)	 AG	140727-140859	GT	CAG
(GTG)	 AG	141554-141761	GT	AGG
(TGC)	 AG	142151-142183	CG	AGC
-recovered pasa_asmbl_38160.p1, internal, 140460, 140616
-recovered pasa_asmbl_38160.p1, internal, 140727, 140859
-recovered pasa_asmbl_38160.p1, internal, 141554, 141761
Valid prediction for snap_scaffold_28-snap.931-T1
Valid prediction for snap_scaffold_28-snap.930-T1
Valid prediction for GlimmerHMM_glimmerT_58585-T1
Valid prediction for CodingQuarry_transcript_43612-T1
Valid prediction for snap_scaffold_28-snap.936-T1
Valid prediction for pasa_asmbl_38173.p1
Valid prediction for CodingQuarry_transcript_43614-T1
Valid prediction for CodingQuarry_transcript_43615-T1
Valid prediction for GlimmerHMM_glimmerT_58563-T1
Valid prediction for GlimmerHMM_glimmerT_58584-T1
Valid prediction for Augustus_model.g38802.t1
Valid prediction for snap_scaffold_28-snap.915-T1
Valid prediction for Augustus_model.g38803.t1
Valid prediction for snap_scaffold_28-snap.924-T1
Valid prediction for snap_scaffold_28-snap.925-T1
Valid prediction for GlimmerHMM_glimmerT_58578-T1
Valid prediction for snap_scaffold_28-snap.891-T1
Valid prediction for Augustus_model.g38804.t1
Valid prediction for snap_scaffold_28-snap.932-T1
Valid prediction for GlimmerHMM_glimmerT_58581-T1
Valid prediction for snap_scaffold_28-snap.907-T1
Valid prediction for CodingQuarry_transcript_43609-T1
Valid prediction for snap_scaffold_28-snap.897-T1
Valid prediction for snap_scaffold_28-snap.910-T1
Valid prediction for GlimmerHMM_glimmerT_58565-T1
Valid prediction for snap_scaffold_28-snap.899-T1
Valid prediction for GlimmerHMM_glimmerT_58560-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 16702, rend_intergenic: 9362  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24556, rend_intergenic: 22451  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25004, rend_intergenic: 24587  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37303, rend_intergenic: 34224  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41836, rend_intergenic: 38573  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59523, rend_intergenic: 51366  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67304, rend_intergenic: 64837  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99663, rend_intergenic: 95091  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107563, rend_intergenic: 102191  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 314662
-exon list size: 522


building trellis

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1.0    
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1.9    
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3.8    
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18.9    
19.1    
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20.8    
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22.9    
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24.2    
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24.6    
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25.0    
25.2    
25.4    
25.6    
25.8    
26.0    
26.1    
26.3    
26.5    
26.7    
26.9    
27.1    
27.3    
27.5    
27.7    
27.9    
28.1    
28.2    
28.4    
28.6    
28.8    
29.0    
29.2    
29.4    
29.6    
29.8    
30.0    
30.2    
30.3    
30.5    
30.7    
30.9    
31.1    
31.3    
31.5    
31.7    
31.9    
32.1    
32.3    
32.4    
32.6    
32.8    
33.0    
33.2    
33.4    
33.6    
33.8    
34.0    
34.2    
34.4    
34.5    
34.7    
34.9    
35.1    
35.3    
35.5    
35.7    
35.9    
36.1    
36.3    
36.5    
36.6    
36.8    
37.0    
37.2    
37.4    
37.6    
37.8    
38.0    
38.2    
38.4    
38.5    
38.7    
38.9    
39.1    
39.3    
39.5    
39.7    
39.9    
40.1    
40.3    
40.5    
40.6    
40.8    
41.0    
41.2    
41.4    
41.6    
41.8    
42.0    
42.2    
42.4    
42.6    
42.7    
42.9    
43.1    
43.3    
43.5    
43.7    
43.9    
44.1    
44.3    
44.5    
44.7    
44.8    
45.0    
45.2    
45.4    
45.6    
45.8    
46.0    
46.2    
46.4    
46.6    
46.8    
46.9    
47.1    
47.3    
47.5    
47.7    
47.9    
48.1    
48.3    
48.5    
48.7    
48.9    
49.0    
49.2    
49.4    
49.6    
49.8    
50.0    
50.2    
50.4    
50.6    
50.8    
51.0    
51.1    
51.3    
51.5    
51.7    
51.9    
52.1    
52.3    
52.5    
52.7    
52.9    
53.1    
53.2    
53.4    
53.6    
53.8    
54.0    
54.2    
54.4    
54.6    
54.8    
55.0    
55.2    
55.3    
55.5    
55.7    
55.9    
56.1    
56.3    
56.5    
56.7    
56.9    
57.1    
57.3    
57.4    
57.6    
57.8    
58.0    
58.2    
58.4    
58.6    
58.8    
59.0    
59.2    
59.4    
59.5    
59.7    
59.9    
60.1    
60.3    
60.5    
60.7    
60.9    
61.1    
61.3    
61.5    
61.6    
61.8    
62.0    
62.2    
62.4    
62.6    
62.8    
63.0    
63.2    
63.4    
63.5    
63.7    
63.9    
64.1    
64.3    
64.5    
64.7    
64.9    
65.1    
65.3    
65.5    
65.6    
65.8    
66.0    
66.2    
66.4    
66.6    
66.8    
67.0    
67.2    
67.4    
67.6    
67.7    
67.9    
68.1    
68.3    
68.5    
68.7    
68.9    
69.1    
69.3    
69.5    
69.7    
69.8    
70.0    
70.2    
70.4    
70.6    
70.8    
71.0    
71.2    
71.4    
71.6    
71.8    
71.9    
72.1    
72.3    
72.5    
72.7    
72.9    
73.1    
73.3    
73.5    
73.7    
73.9    
74.0    
74.2    
74.4    
74.6    
74.8    
75.0    
75.2    
75.4    
75.6    
75.8    
76.0    
76.1    
76.3    
76.5    
76.7    
76.9    
77.1    
77.3    
77.5    
77.7    
77.9    
78.1    
78.2    
78.4    
78.6    
78.8    
79.0    
79.2    
79.4    
79.6    
79.8    
80.0    
80.2    
80.3    
80.5    
80.7    
80.9    
81.1    
81.3    
81.5    
81.7    
81.9    
82.1    
82.3    
82.4    
82.6    
82.8    
83.0    
83.2    
83.4    
83.6    
83.8    
84.0    
84.2    
84.4    
84.5    
84.7    
84.9    
85.1    
85.3    
85.5    
85.7    
85.9    
86.1    
86.3    
86.5    
86.6    
86.8    
87.0    
87.2    
87.4    
87.6    
87.8    
88.0    
88.2    
88.4    
88.5    
88.7    
88.9    
89.1    
89.3    
89.5    
89.7    
89.9    
90.1    
90.3    
90.5    
90.6    
90.8    
91.0    
91.2    
91.4    
91.6    
91.8    
92.0    
92.2    
92.4    
92.6    
92.7    
92.9    
93.1    
93.3    
93.5    
93.7    
93.9    
94.1    
94.3    
94.5    
94.7    
94.8    
95.0    
95.2    
95.4    
95.6    
95.8    
96.0    
96.2    
96.4    
96.6    
96.8    
96.9    
97.1    
97.3    
97.5    
97.7    
97.9    
98.1    
98.3    
98.5    
98.7    
98.9    
99.0    
99.2    
99.4    
99.6    
99.8    
-found 33 predictions from path traversal
Error with prediction: snap lend_intergenic: 16702, rend_intergenic: 9362  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24556, rend_intergenic: 22451  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25004, rend_intergenic: 24587  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37303, rend_intergenic: 34224  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41836, rend_intergenic: 38573  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59523, rend_intergenic: 51366  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67304, rend_intergenic: 64837  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99663, rend_intergenic: 95091  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107563, rend_intergenic: 102191  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 29 predictions persist after filtering for low support