-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_9/scaffold_9_1574515-1755278

-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_21639-T1
Valid prediction for GlimmerHMM_glimmerT_21650-T1
Valid prediction for snap_scaffold_9-snap.358-T1
Valid prediction for snap_scaffold_9-snap.374-T1
Valid prediction for Augustus_model.g14388.t1
Valid prediction for Augustus_model.g14386.t1
Valid prediction for GlimmerHMM_glimmerT_21648-T1
Valid prediction for GlimmerHMM_glimmerT_21646-T1
Valid prediction for GlimmerHMM_glimmerT_21634-T1
Valid prediction for snap_scaffold_9-snap.361-T1
Valid prediction for snap_scaffold_9-snap.340-T1
Valid prediction for snap_scaffold_9-snap.351-T1
Valid prediction for snap_scaffold_9-snap.350-T1
Valid prediction for GlimmerHMM_glimmerT_21642-T1
Valid prediction for snap_scaffold_9-snap.373-T1
Valid prediction for snap_scaffold_9-snap.354-T1
Valid prediction for Augustus_model.g14384.t1
Valid prediction for snap_scaffold_9-snap.355-T1
Valid prediction for snap_scaffold_9-snap.348-T1
Valid prediction for GlimmerHMM_glimmerT_21631-T1
Valid prediction for CodingQuarry_transcript_62109-T1
Valid prediction for GlimmerHMM_glimmerT_21633-T1
Valid prediction for GlimmerHMM_glimmerT_21638-T1
Valid prediction for GlimmerHMM_glimmerT_21632-T1
Valid prediction for snap_scaffold_9-snap.375-T1
Valid prediction for snap_scaffold_9-snap.345-T1
Valid prediction for snap_scaffold_9-snap.363-T1
Valid prediction for snap_scaffold_9-snap.359-T1
Valid prediction for GlimmerHMM_glimmerT_21644-T1
Valid prediction for Augustus_model.g14385.t1
Valid prediction for Augustus_model.g14389.t1
Valid prediction for snap_scaffold_9-snap.339-T1
Valid prediction for snap_scaffold_9-snap.365-T1
Valid prediction for pasa_asmbl_53828.p1
Valid prediction for snap_scaffold_9-snap.346-T1
Valid prediction for snap_scaffold_9-snap.370-T1
Valid prediction for snap_scaffold_9-snap.344-T1
Valid prediction for GlimmerHMM_glimmerT_21637-T1
Valid prediction for snap_scaffold_9-snap.353-T1
Valid prediction for snap_scaffold_9-snap.372-T1
Valid prediction for Augustus_model.g14383.t1
Valid prediction for snap_scaffold_9-snap.352-T1
Valid prediction for Augustus_model.g14390.t1
Valid prediction for snap_scaffold_9-snap.368-T1
Valid prediction for snap_scaffold_9-snap.371-T1
Valid prediction for Augustus_model.g14387.t1
Valid prediction for snap_scaffold_9-snap.376-T1
Valid prediction for GlimmerHMM_glimmerT_21640-T1
Valid prediction for GlimmerHMM_glimmerT_21653-T1
Valid prediction for GlimmerHMM_glimmerT_21652-T1
Valid prediction for snap_scaffold_9-snap.367-T1
Valid prediction for snap_scaffold_9-snap.343-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_9-snap.364-T1
Couldn't classify 68407, 68642
Couldn't classify 69298, 69401
Sorry, prediction pasa_asmbl_54832.p1 fails validation.
(GGA)	 CA	68407-68642	GT	AGG
(CGC)	 AG	68758-68813	GT	CAG
(ATC)	 AG	69298-69401	GA	TGG
-recovered pasa_asmbl_54832.p1, internal, 68758, 68813
Valid prediction for snap_scaffold_9-snap.347-T1
Couldn't classify 47705, 47790
Sorry, prediction pasa_asmbl_54841.p1 fails validation.
(ATG)	 TC	43720-43789	GT	AGG
(GGC)	 AG	45988-46105	GT	AGG
(GTA)	 AG	46399-46512	GT	AGG
(GTC)	 AG	47202-47278	GT	AGG
(CCA)	 AG	47514-47582	GT	AGG
(CGA)	 AG	47705-47790	TA	GGT
-recovered pasa_asmbl_54841.p1, initial, 43720, 43789
-recovered pasa_asmbl_54841.p1, terminal, 47202, 47278
-recovered pasa_asmbl_54841.p1, internal, 45988, 46105
-recovered pasa_asmbl_54841.p1, internal, 46399, 46512
-recovered pasa_asmbl_54841.p1, internal, 47202, 47278
-recovered pasa_asmbl_54841.p1, internal, 47514, 47582
Valid prediction for GlimmerHMM_glimmerT_21645-T1
Valid prediction for snap_scaffold_9-snap.357-T1
Valid prediction for Augustus_model.g14393.t1
Valid prediction for Augustus_model.g14394.t1
Valid prediction for CodingQuarry_transcript_62110-T1
Valid prediction for pasa_asmbl_54827.p4
Valid prediction for snap_scaffold_9-snap.362-T1
Valid prediction for GlimmerHMM_glimmerT_21630-T1
Valid prediction for GlimmerHMM_glimmerT_21651-T1
Valid prediction for GlimmerHMM_glimmerT_21643-T1
Valid prediction for HiQ_model.g14392.t1
Valid prediction for GlimmerHMM_glimmerT_21641-T1
Valid prediction for snap_scaffold_9-snap.349-T1
Valid prediction for HiQ_model.g14396.t1
Valid prediction for snap_scaffold_9-snap.341-T1
Couldn't classify 50387, 50440
Sorry, prediction pasa_asmbl_54839.p1 fails validation.
(ACT)	 AC	50387-50440	GT	AGG
(ACA)	 AG	51592-51675	GT	AGG
(ATG)	 AG	52131-52224	GT	CAG
(GTG)	 AG	52497-52552	GT	AGG
(TAT)	 AG	52776-52911	GT	AGG
(GTA)	 AG	53307-53377	GT	AGG
(GGA)	 AG	53718-53815	GT	AGG
(TAT)	 AG	54502-54601	GT	TGG
(ACG)	 AG	54956-54982	TG	GAT
-recovered pasa_asmbl_54839.p1, initial, 52131, 52224
-recovered pasa_asmbl_54839.p1, terminal, 54956, 54982
-recovered pasa_asmbl_54839.p1, internal, 51592, 51675
-recovered pasa_asmbl_54839.p1, internal, 52131, 52224
-recovered pasa_asmbl_54839.p1, internal, 52497, 52552
-recovered pasa_asmbl_54839.p1, internal, 52776, 52911
-recovered pasa_asmbl_54839.p1, internal, 53307, 53377
-recovered pasa_asmbl_54839.p1, internal, 53718, 53815
-recovered pasa_asmbl_54839.p1, internal, 54502, 54601
Valid prediction for snap_scaffold_9-snap.342-T1
Valid prediction for snap_scaffold_9-snap.360-T1
Sorry, intron length (5) is less than minimum required (10)
Valid prediction for Augustus_model.g14395.t1
Valid prediction for GlimmerHMM_glimmerT_21636-T1
Valid prediction for snap_scaffold_9-snap.366-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_9-snap.356-T1
Valid prediction for snap_scaffold_9-snap.338-T1
Valid prediction for pasa_asmbl_54821.p1
Valid prediction for snap_scaffold_9-snap.369-T1
Couldn't classify 83177, 83304
Couldn't classify 85433, 85507
Sorry, prediction pasa_asmbl_54829.p1 fails validation.
(GTG)	 AC	83177-83304	GT	CAG
(GGA)	 AG	83778-83910	GT	AGG
(GTC)	 AG	85433-85507	TA	TGT
-recovered pasa_asmbl_54829.p1, internal, 83778, 83910
Couldn't classify 33044, 33124
Couldn't classify 40108, 40154
Sorry, prediction pasa_asmbl_54842.p1 fails validation.
(GCG)	 AG	33044-33124	GT	AGG
(GGA)	 AG	33703-33882	GT	AGG
(GGT)	 AG	34178-34276	GT	AGG
(GAG)	 AG	35625-35738	GT	GGG
(TTG)	 AG	35950-36021	GT	AGG
(CTG)	 AG	36448-36567	GT	AGG
(GAT)	 AG	37232-37305	GT	AGG
(CTT)	 AG	37933-38038	GT	CCG
(TGG)	 AG	38735-38815	GT	TGG
(GAT)	 AG	39424-39515	GT	ACG
(ACA)	 AG	39741-39835	GT	CGG
(GCT)	 AG	40108-40154	GT	AGG
-recovered pasa_asmbl_54842.p1, internal, 33044, 33124
-recovered pasa_asmbl_54842.p1, internal, 33703, 33882
-recovered pasa_asmbl_54842.p1, internal, 34178, 34276
-recovered pasa_asmbl_54842.p1, internal, 35625, 35738
-recovered pasa_asmbl_54842.p1, internal, 35950, 36021
-recovered pasa_asmbl_54842.p1, internal, 36448, 36567
-recovered pasa_asmbl_54842.p1, internal, 37232, 37305
-recovered pasa_asmbl_54842.p1, internal, 37933, 38038
-recovered pasa_asmbl_54842.p1, internal, 38735, 38815
-recovered pasa_asmbl_54842.p1, internal, 39424, 39515
-recovered pasa_asmbl_54842.p1, internal, 39741, 39835
-recovered pasa_asmbl_54842.p1, internal, 40108, 40154
Couldn't classify 94707, 94740
Sorry, prediction pasa_asmbl_54823.p1 fails validation.
(TCC)	 GG	94707-94740	GT	AGG
(TCC)	 AG	95216-95285	GT	AGG
(GGA)	 AG	95409-95480	GT	AAG
(GGT)	 AG	95601-95719	GT	CAG
(AAA)	 AG	95928-96027	GT	TGG
(GTG)	 AG	96179-96261	GT	TGG
(GAA)	 AG	97149-97222	GT	AGG
(GTG)	 AG	97487-97631	GT	AGG
(CCA)	 AG	98097-98213	GT	GCG
(CTA)	 AG	98775-99349	GT	TGG
(CAT)	 AG	99667-99780	GT	AGG
(GAT)	 AG	100075-100197	GT	AGG
(AAA)	 AG	101960-102025	GT	AGG
(CTT)	 AG	102423-102488	AA	AGA
-recovered pasa_asmbl_54823.p1, terminal, 102423, 102488
-recovered pasa_asmbl_54823.p1, internal, 95216, 95285
-recovered pasa_asmbl_54823.p1, internal, 95409, 95480
-recovered pasa_asmbl_54823.p1, internal, 95601, 95719
-recovered pasa_asmbl_54823.p1, internal, 95928, 96027
-recovered pasa_asmbl_54823.p1, internal, 96179, 96261
-recovered pasa_asmbl_54823.p1, internal, 97149, 97222
-recovered pasa_asmbl_54823.p1, internal, 97487, 97631
-recovered pasa_asmbl_54823.p1, internal, 98097, 98213
-recovered pasa_asmbl_54823.p1, internal, 98775, 99349
-recovered pasa_asmbl_54823.p1, internal, 99667, 99780
-recovered pasa_asmbl_54823.p1, internal, 100075, 100197
-recovered pasa_asmbl_54823.p1, internal, 101960, 102025
Valid prediction for GlimmerHMM_glimmerT_21635-T1
Valid prediction for snap_scaffold_9-snap.377-T1
Couldn't classify 71537, 71854
Sorry, prediction pasa_asmbl_55772.p1 fails validation.
(CAC)	 CA	71537-71854	TT	TCT
Valid prediction for GlimmerHMM_glimmerT_21649-T1
Valid prediction for GlimmerHMM_glimmerT_21647-T1
Valid prediction for HiQ_model.g14391.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 18798, rend_intergenic: 14541  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20846, rend_intergenic: 18831  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35560, rend_intergenic: 30141  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40525, rend_intergenic: 36488  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84865, rend_intergenic: 78997  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93125, rend_intergenic: 87475  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100679, rend_intergenic: 96042  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110220, rend_intergenic: 103995  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110826, rend_intergenic: 110587  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116526, rend_intergenic: 111191  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121274, rend_intergenic: 116582  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126359, rend_intergenic: 125689  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167850, rend_intergenic: 126992  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 178630, rend_intergenic: 170624  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 180764
-exon list size: 371


building trellis

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4.6    
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7.0    
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10.5    
10.7    
11.0    
11.3    
11.5    
11.8    
12.1    
12.3    
12.6    
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15.3    
15.5    
15.8    
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16.4    
16.6    
16.9    
17.2    
17.4    
17.7    
18.0    
18.2    
18.5    
18.8    
19.0    
19.3    
19.6    
19.8    
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20.4    
20.6    
20.9    
21.2    
21.4    
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22.0    
22.3    
22.5    
22.8    
23.1    
23.3    
23.6    
23.9    
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25.7    
26.0    
26.3    
26.5    
26.8    
27.1    
27.3    
27.6    
27.9    
28.2    
28.4    
28.7    
29.0    
29.2    
29.5    
29.8    
30.0    
30.3    
30.6    
30.8    
31.1    
31.4    
31.6    
31.9    
32.2    
32.4    
32.7    
33.0    
33.2    
33.5    
33.8    
34.0    
34.3    
34.6    
34.9    
35.1    
35.4    
35.7    
35.9    
36.2    
36.5    
36.7    
37.0    
37.3    
37.5    
37.8    
38.1    
38.3    
38.6    
38.9    
39.1    
39.4    
39.7    
39.9    
40.2    
40.5    
40.8    
41.0    
41.3    
41.6    
41.8    
42.1    
42.4    
42.6    
42.9    
43.2    
43.4    
43.7    
44.0    
44.2    
44.5    
44.8    
45.0    
45.3    
45.6    
45.8    
46.1    
46.4    
46.6    
46.9    
47.2    
47.5    
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48.0    
48.3    
48.5    
48.8    
49.1    
49.3    
49.6    
49.9    
50.1    
50.4    
50.7    
50.9    
51.2    
51.5    
51.7    
52.0    
52.3    
52.5    
52.8    
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53.4    
53.6    
53.9    
54.2    
54.4    
54.7    
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55.8    
56.0    
56.3    
56.6    
56.8    
57.1    
57.4    
57.6    
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77.7    
78.0    
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78.6    
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79.1    
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79.6    
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82.6    
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83.4    
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86.3    
86.6    
86.9    
87.1    
87.4    
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88.2    
88.5    
88.7    
89.0    
89.3    
89.5    
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90.1    
90.3    
90.6    
90.9    
91.2    
91.4    
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92.2    
92.5    
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93.3    
93.6    
93.8    
94.1    
94.4    
94.6    
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95.4    
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96.2    
96.5    
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97.3    
97.6    
97.9    
98.1    
98.4    
98.7    
98.9    
99.2    
99.5    
99.7    
-found 31 predictions from path traversal
Error with prediction: snap lend_intergenic: 18798, rend_intergenic: 14541  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20846, rend_intergenic: 18831  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35560, rend_intergenic: 30141  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40525, rend_intergenic: 36488  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84865, rend_intergenic: 78997  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93125, rend_intergenic: 87475  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100679, rend_intergenic: 96042  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110220, rend_intergenic: 103995  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110826, rend_intergenic: 110587  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116526, rend_intergenic: 111191  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121274, rend_intergenic: 116582  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126359, rend_intergenic: 125689  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167850, rend_intergenic: 126992  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 178630, rend_intergenic: 170624  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 26 predictions persist after filtering for low support