-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_2/scaffold_2_5341117-5520536

-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 GlimmerHMM_glimmerT_3805-T1
Valid prediction for snap_scaffold_2-snap.1217-T1
Valid prediction for Augustus_model.g2549.t1
Valid prediction for snap_scaffold_2-snap.1235-T1
Valid prediction for snap_scaffold_2-snap.1212-T1
Valid prediction for snap_scaffold_2-snap.1240-T1
Valid prediction for GlimmerHMM_glimmerT_3823-T1
Valid prediction for Augustus_model.g2543.t1
Valid prediction for pasa_asmbl_24414.p1
Valid prediction for GlimmerHMM_glimmerT_3813-T1
Valid prediction for Augustus_model.g2557.t1
Valid prediction for pasa_asmbl_24416.p1
Valid prediction for Augustus_model.g2546.t1
Valid prediction for snap_scaffold_2-snap.1208-T1
Valid prediction for snap_scaffold_2-snap.1232-T1
Valid prediction for snap_scaffold_2-snap.1220-T1
Valid prediction for HiQ_model.g2545.t1
Valid prediction for snap_scaffold_2-snap.1216-T1
Valid prediction for GlimmerHMM_glimmerT_3809-T1
Valid prediction for GlimmerHMM_glimmerT_3812-T1
Valid prediction for snap_scaffold_2-snap.1209-T1
Valid prediction for GlimmerHMM_glimmerT_3815-T1
Valid prediction for snap_scaffold_2-snap.1237-T1
Valid prediction for GlimmerHMM_glimmerT_3833-T1
Valid prediction for GlimmerHMM_glimmerT_3827-T1
Valid prediction for GlimmerHMM_glimmerT_3810-T1
Valid prediction for snap_scaffold_2-snap.1210-T1
Valid prediction for Augustus_model.g2558.t1
Valid prediction for GlimmerHMM_glimmerT_3830-T1
Valid prediction for snap_scaffold_2-snap.1238-T1
Valid prediction for GlimmerHMM_glimmerT_3811-T1
Valid prediction for Augustus_model.g2548.t1
Valid prediction for Augustus_model.g2554.t1
Couldn't classify 106571, 106744
Sorry, prediction pasa_asmbl_24420.p1 fails validation.
(ATG)	 GA	99447-100685	GT	AGG
(ATC)	 AG	101494-101643	GT	AGG
(GAG)	 AG	102313-102464	GT	AGG
(AGG)	 AG	102584-102678	GT	AGG
(GTG)	 AG	104933-105104	GT	AAG
(AGA)	 AG	105960-106017	GT	AGG
(GTG)	 AG	106571-106744	GG	TGG
-recovered pasa_asmbl_24420.p1, initial, 99447, 100685
-recovered pasa_asmbl_24420.p1, internal, 101494, 101643
-recovered pasa_asmbl_24420.p1, internal, 102313, 102464
-recovered pasa_asmbl_24420.p1, internal, 102584, 102678
-recovered pasa_asmbl_24420.p1, internal, 104933, 105104
-recovered pasa_asmbl_24420.p1, internal, 105960, 106017
Valid prediction for snap_scaffold_2-snap.1230-T1
Valid prediction for Augustus_model.g2564.t1
Valid prediction for GlimmerHMM_glimmerT_3822-T1
Valid prediction for snap_scaffold_2-snap.1245-T1
Valid prediction for GlimmerHMM_glimmerT_3807-T1
Couldn't classify 178440, 178506
Sorry, prediction pasa_asmbl_24428.p1 fails validation.
(ATG)	 CT	175546-175675	GT	AGG
(TGA)	 AG	175823-175901	GT	AGG
(TGA)	 AG	178440-178506	GA	GCG
-recovered pasa_asmbl_24428.p1, initial, 175546, 175675
-recovered pasa_asmbl_24428.p1, internal, 175823, 175901
Valid prediction for GlimmerHMM_glimmerT_3817-T1
Couldn't classify 48186, 48226
Sorry, prediction pasa_asmbl_24417.p1 fails validation.
(CAG)	 TA	48186-48226	GT	TTG
(AAT)	 AG	48435-48602	GT	AGG
(ATA)	 AG	49003-49143	GT	GAG
(GTA)	 AG	49553-49634	GT	AGG
(CTG)	 AG	50085-50234	AG	GAA
-recovered pasa_asmbl_24417.p1, terminal, 50085, 50234
-recovered pasa_asmbl_24417.p1, internal, 48435, 48602
-recovered pasa_asmbl_24417.p1, internal, 49003, 49143
-recovered pasa_asmbl_24417.p1, internal, 49553, 49634
Couldn't classify 161901, 162051
Couldn't classify 163711, 163751
Sorry, prediction pasa_asmbl_24426.p1 fails validation.
(GAC)	 TG	161901-162051	GT	CAG
(AGT)	 AG	162618-162740	GT	CAG
(ACT)	 AG	162957-163127	GT	CCG
(TGG)	 AG	163711-163751	AC	GCA
-recovered pasa_asmbl_24426.p1, internal, 162618, 162740
-recovered pasa_asmbl_24426.p1, internal, 162957, 163127
Valid prediction for GlimmerHMM_glimmerT_3828-T1
Valid prediction for GlimmerHMM_glimmerT_3831-T1
Valid prediction for Augustus_model.g2555.t1
Valid prediction for snap_scaffold_2-snap.1236-T1
Valid prediction for snap_scaffold_2-snap.1224-T1
Valid prediction for snap_scaffold_2-snap.1223-T1
Valid prediction for snap_scaffold_2-snap.1211-T1
Valid prediction for Augustus_model.g2561.t1
Valid prediction for snap_scaffold_2-snap.1229-T1
Valid prediction for GlimmerHMM_glimmerT_3821-T1
Valid prediction for snap_scaffold_2-snap.1234-T1
Couldn't classify 169440, 169478
Couldn't classify 170973, 171094
Sorry, prediction pasa_asmbl_24427.p1 fails validation.
(CAT)	 GT	169440-169478	GT	AGG
(CCA)	 AG	169773-169998	GT	CCG
(TGC)	 AG	170277-170392	GT	AGG
(TTG)	 AG	170600-170804	GT	AGG
(TTC)	 AG	170973-171094	GG	CAG
-recovered pasa_asmbl_24427.p1, internal, 169773, 169998
-recovered pasa_asmbl_24427.p1, internal, 170277, 170392
-recovered pasa_asmbl_24427.p1, internal, 170600, 170804
Valid prediction for snap_scaffold_2-snap.1227-T1
Valid prediction for GlimmerHMM_glimmerT_3834-T1
Valid prediction for GlimmerHMM_glimmerT_3804-T1
Valid prediction for Augustus_model.g2544.t1
Valid prediction for Augustus_model.g2560.t1
Valid prediction for snap_scaffold_2-snap.1243-T1
Valid prediction for snap_scaffold_2-snap.1231-T1
Valid prediction for snap_scaffold_2-snap.1242-T1
Valid prediction for GlimmerHMM_glimmerT_3824-T1
Valid prediction for snap_scaffold_2-snap.1239-T1
Valid prediction for GlimmerHMM_glimmerT_3806-T1
Couldn't classify 115368, 115569
Sorry, prediction pasa_asmbl_24424.p1 fails validation.
(CAG)	 TG	115368-115569	GT	GGG
(AGG)	 AG	116837-117117	AC	GAA
-recovered pasa_asmbl_24424.p1, terminal, 116837, 117117
Valid prediction for GlimmerHMM_glimmerT_3826-T1
Valid prediction for GlimmerHMM_glimmerT_3829-T1
Valid prediction for Augustus_model.g2563.t1
Valid prediction for GlimmerHMM_glimmerT_3803-T1
Valid prediction for GlimmerHMM_glimmerT_3835-T1
Couldn't classify 86729, 87217
Sorry, prediction pasa_asmbl_23998.p1 fails validation.
(GCC)	 AA	86729-87217	GC	GTG
Valid prediction for Augustus_model.g2556.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_3819-T1
Valid prediction for snap_scaffold_2-snap.1219-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_3814-T1
Valid prediction for snap_scaffold_2-snap.1233-T1
Valid prediction for Augustus_model.g2562.t1
Valid prediction for CodingQuarry_transcript_28556-T1
Couldn't classify 127085, 127254
Sorry, prediction pasa_asmbl_23147.p1 fails validation.
(AGC)	 GA	127085-127254	GT	CGG
(AGG)	 AG	127620-127695	GT	AGG
(GTG)	 AG	127816-127948	GT	CAG
(AAG)	 AG	128046-128252	GT	CTG
(ACT)	 AG	128381-128547	GT	GGG
(GAT)	 AG	128685-128693	GG	AAG
-recovered pasa_asmbl_23147.p1, terminal, 128685, 128693
-recovered pasa_asmbl_23147.p1, internal, 127620, 127695
-recovered pasa_asmbl_23147.p1, internal, 127816, 127948
-recovered pasa_asmbl_23147.p1, internal, 128046, 128252
-recovered pasa_asmbl_23147.p1, internal, 128381, 128547
Valid prediction for GlimmerHMM_glimmerT_3820-T1
Valid prediction for snap_scaffold_2-snap.1241-T1
Valid prediction for snap_scaffold_2-snap.1244-T1
Valid prediction for snap_scaffold_2-snap.1214-T1
Valid prediction for Augustus_model.g2559.t1
Couldn't classify 113197, 113571
Sorry, prediction pasa_asmbl_23151.p4 fails validation.
(ATG)	 AC	113197-113571	GG	AAG
Valid prediction for snap_scaffold_2-snap.1221-T1
Valid prediction for GlimmerHMM_glimmerT_3832-T1
Valid prediction for snap_scaffold_2-snap.1225-T1
Valid prediction for Augustus_model.g2551.t1
Valid prediction for HiQ_model.g2547.t1
Valid prediction for HiQ_model.g2550.t1
Valid prediction for GlimmerHMM_glimmerT_3818-T1
Valid prediction for pasa_asmbl_23143.p1
Valid prediction for GlimmerHMM_glimmerT_3816-T1
Valid prediction for snap_scaffold_2-snap.1222-T1
Valid prediction for GlimmerHMM_glimmerT_3808-T1
Valid prediction for snap_scaffold_2-snap.1218-T1
Valid prediction for CodingQuarry_transcript_28555-T1
Valid prediction for snap_scaffold_2-snap.1213-T1
Valid prediction for CodingQuarry_transcript_28554-T1
Valid prediction for snap_scaffold_2-snap.1228-T1
Valid prediction for snap_scaffold_2-snap.1215-T1
Valid prediction for Augustus_model.g2552.t1
Valid prediction for snap_scaffold_2-snap.1226-T1
Valid prediction for GlimmerHMM_glimmerT_3825-T1
Valid prediction for Augustus_model.g2553.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 22560, rend_intergenic: 21034  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96234, rend_intergenic: 95319  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97683, rend_intergenic: 96652  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110153, rend_intergenic: 108717  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 176103, rend_intergenic: 161498  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 179420
-exon list size: 343


building trellis

0.3    
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11.9    
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12.5    
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18.8    
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20.9    
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24.6    
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26.4    
26.7    
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27.2    
27.5    
27.8    
28.1    
28.4    
28.7    
29.0    
29.3    
29.6    
29.9    
30.1    
30.4    
30.7    
31.0    
31.3    
31.6    
31.9    
32.2    
32.5    
32.8    
33.0    
33.3    
33.6    
33.9    
34.2    
34.5    
34.8    
35.1    
35.4    
35.7    
35.9    
36.2    
36.5    
36.8    
37.1    
37.4    
37.7    
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38.3    
38.6    
38.8    
39.1    
39.4    
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40.3    
40.6    
40.9    
41.2    
41.4    
41.7    
42.0    
42.3    
42.6    
42.9    
43.2    
43.5    
43.8    
44.1    
44.3    
44.6    
44.9    
45.2    
45.5    
45.8    
46.1    
46.4    
46.7    
47.0    
47.2    
47.5    
47.8    
48.1    
48.4    
48.7    
49.0    
49.3    
49.6    
49.9    
50.1    
50.4    
50.7    
51.0    
51.3    
51.6    
51.9    
52.2    
52.5    
52.8    
53.0    
53.3    
53.6    
53.9    
54.2    
54.5    
54.8    
55.1    
55.4    
55.7    
55.9    
56.2    
56.5    
56.8    
57.1    
57.4    
57.7    
58.0    
58.3    
58.6    
58.8    
59.1    
59.4    
59.7    
60.0    
60.3    
60.6    
60.9    
61.2    
61.4    
61.7    
62.0    
62.3    
62.6    
62.9    
63.2    
63.5    
63.8    
64.1    
64.3    
64.6    
64.9    
65.2    
65.5    
65.8    
66.1    
66.4    
66.7    
67.0    
67.2    
67.5    
67.8    
68.1    
68.4    
68.7    
69.0    
69.3    
69.6    
69.9    
70.1    
70.4    
70.7    
71.0    
71.3    
71.6    
71.9    
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72.5    
72.8    
73.0    
73.3    
73.6    
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75.1    
75.4    
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75.9    
76.2    
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76.8    
77.1    
77.4    
77.7    
78.0    
78.3    
78.6    
78.8    
79.1    
79.4    
79.7    
80.0    
80.3    
80.6    
80.9    
81.2    
81.4    
81.7    
82.0    
82.3    
82.6    
82.9    
83.2    
83.5    
83.8    
84.1    
84.3    
84.6    
84.9    
85.2    
85.5    
85.8    
86.1    
86.4    
86.7    
87.0    
87.2    
87.5    
87.8    
88.1    
88.4    
88.7    
89.0    
89.3    
89.6    
89.9    
90.1    
90.4    
90.7    
91.0    
91.3    
91.6    
91.9    
92.2    
92.5    
92.8    
93.0    
93.3    
93.6    
93.9    
94.2    
94.5    
94.8    
95.1    
95.4    
95.7    
95.9    
96.2    
96.5    
96.8    
97.1    
97.4    
97.7    
98.0    
98.3    
98.6    
98.8    
99.1    
99.4    
99.7    
-found 31 predictions from path traversal
Error with prediction: snap lend_intergenic: 22560, rend_intergenic: 21034  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96234, rend_intergenic: 95319  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97683, rend_intergenic: 96652  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110153, rend_intergenic: 108717  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 176103, rend_intergenic: 161498  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 27 predictions persist after filtering for low support