-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_14/scaffold_14_2181942-2328554

-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 HiQ_model.g22961.t1
Valid prediction for Augustus_model.g22968.t1
Valid prediction for Augustus_model.g22956.t1
Valid prediction for Augustus_model.g22955.t1
Valid prediction for GlimmerHMM_glimmerT_34130-T1
Valid prediction for HiQ_model.g22967.t1
Valid prediction for Augustus_model.g22969.t1
Valid prediction for GeneMark_model.58385_t
Valid prediction for GlimmerHMM_glimmerT_34141-T1
Valid prediction for GeneMark_model.58407_t
Valid prediction for GlimmerHMM_glimmerT_34134-T1
Valid prediction for HiQ_model.g22965.t1
Valid prediction for GlimmerHMM_glimmerT_34135-T1
Valid prediction for GeneMark_model.58412_t
Valid prediction for GlimmerHMM_glimmerT_34146-T1
Valid prediction for GeneMark_model.58379_t
Valid prediction for HiQ_model.g22959.t1
Valid prediction for snap_scaffold_14-snap.384-T1
Valid prediction for snap_scaffold_14-snap.379-T1
Valid prediction for snap_scaffold_14-snap.374-T1
Valid prediction for snap_scaffold_14-snap.383-T1
Valid prediction for GlimmerHMM_glimmerT_34129-T1
Valid prediction for GeneMark_model.58392_t
Valid prediction for snap_scaffold_14-snap.387-T1
Valid prediction for GeneMark_model.58405_t
Valid prediction for GlimmerHMM_glimmerT_34138-T1
Valid prediction for GeneMark_model.58383_t
Valid prediction for GeneMark_model.58398_t
Valid prediction for GeneMark_model.58397_t
Valid prediction for snap_scaffold_14-snap.359-T1
Valid prediction for Augustus_model.g22966.t1
Valid prediction for GeneMark_model.58395_t
Valid prediction for snap_scaffold_14-snap.377-T1
Valid prediction for HiQ_model.g22957.t1
Valid prediction for GlimmerHMM_glimmerT_34132-T1
Valid prediction for GlimmerHMM_glimmerT_34139-T1
Valid prediction for pasa_asmbl_11824.p1
Valid prediction for snap_scaffold_14-snap.362-T1
Valid prediction for GeneMark_model.58387_t
Valid prediction for snap_scaffold_14-snap.376-T1
Valid prediction for GlimmerHMM_glimmerT_34148-T1
Valid prediction for CodingQuarry_transcript_15530-T1
Valid prediction for CodingQuarry_transcript_15531-T1
Valid prediction for snap_scaffold_14-snap.369-T1
Valid prediction for GlimmerHMM_glimmerT_34131-T1
Valid prediction for snap_scaffold_14-snap.365-T1
Valid prediction for snap_scaffold_14-snap.390-T1
Valid prediction for CodingQuarry_transcript_15535-T1
Valid prediction for snap_scaffold_14-snap.360-T1
Valid prediction for pasa_asmbl_11825.p1
Valid prediction for GeneMark_model.58399_t
Valid prediction for GeneMark_model.58391_t
Valid prediction for snap_scaffold_14-snap.382-T1
Valid prediction for snap_scaffold_14-snap.364-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for CodingQuarry_transcript_15529-T1
Valid prediction for pasa_asmbl_11823.p1
Valid prediction for GlimmerHMM_glimmerT_34144-T1
Valid prediction for GeneMark_model.58389_t
Valid prediction for GeneMark_model.58393_t
Valid prediction for GeneMark_model.58381_t
Valid prediction for GeneMark_model.58403_t
Valid prediction for GeneMark_model.58414_t
Valid prediction for snap_scaffold_14-snap.368-T1
Valid prediction for GeneMark_model.58411_t
Couldn't classify 54859, 54981
Sorry, prediction pasa_asmbl_11821.p1 fails validation.
(ATG)	 AA	50149-50236	GT	AGG
(ATG)	 AG	51505-51656	GT	AGG
(GGA)	 AG	51805-51886	GT	AGG
(CAC)	 AG	52108-52249	GT	TGG
(GAA)	 AG	52448-52577	GT	TGG
(TAT)	 AG	52763-52846	GT	TGG
(TAC)	 AG	52948-53080	GT	AGG
(CTC)	 AG	53189-53295	GT	GGG
(TTC)	 AG	53483-53594	GT	AGG
(TGG)	 AG	53715-53821	GT	AGG
(GGT)	 AG	53943-54080	GT	TGG
(GGC)	 AG	54256-54473	GT	CGG
(GGG)	 AG	54586-54766	GT	TGG
(CAT)	 AG	54859-54981	GT	AGG
-recovered pasa_asmbl_11821.p1, initial, 50149, 50236
-recovered pasa_asmbl_11821.p1, initial, 51505, 51656
-recovered pasa_asmbl_11821.p1, internal, 51505, 51656
-recovered pasa_asmbl_11821.p1, internal, 51805, 51886
-recovered pasa_asmbl_11821.p1, internal, 52108, 52249
-recovered pasa_asmbl_11821.p1, internal, 52448, 52577
-recovered pasa_asmbl_11821.p1, internal, 52763, 52846
-recovered pasa_asmbl_11821.p1, internal, 52948, 53080
-recovered pasa_asmbl_11821.p1, internal, 53189, 53295
-recovered pasa_asmbl_11821.p1, internal, 53483, 53594
-recovered pasa_asmbl_11821.p1, internal, 53715, 53821
-recovered pasa_asmbl_11821.p1, internal, 53943, 54080
-recovered pasa_asmbl_11821.p1, internal, 54256, 54473
-recovered pasa_asmbl_11821.p1, internal, 54586, 54766
-recovered pasa_asmbl_11821.p1, internal, 54859, 54981
Valid prediction for snap_scaffold_14-snap.380-T1
Valid prediction for GlimmerHMM_glimmerT_34133-T1
Valid prediction for GeneMark_model.58408_t
Valid prediction for CodingQuarry_transcript_15533-T1
Valid prediction for snap_scaffold_14-snap.371-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 GeneMark_model.58402_t
Valid prediction for GeneMark_model.58400_t
Valid prediction for snap_scaffold_14-snap.392-T1
Valid prediction for CodingQuarry_transcript_15532-T1
Valid prediction for GeneMark_model.58401_t
Valid prediction for GeneMark_model.58413_t
Valid prediction for Augustus_model.g22964.t1
Valid prediction for GlimmerHMM_glimmerT_34136-T1
Valid prediction for GeneMark_model.58380_t
Valid prediction for HiQ_model.g22962.t1
Couldn't classify 76213, 76432
Couldn't classify 77108, 77188
Sorry, prediction pasa_asmbl_12907.p1 fails validation.
(GGA)	 CG	76213-76432	GT	TGG
(GAA)	 AG	76765-76913	GT	AGG
(GCA)	 AG	77108-77188	GC	GTG
-recovered pasa_asmbl_12907.p1, internal, 76765, 76913
-recovered pasa_asmbl_12907.p1, internal, 77108, 77188
Valid prediction for GeneMark_model.58410_t
Valid prediction for GeneMark_model.58378_t
Valid prediction for GeneMark_model.58416_t
Valid prediction for snap_scaffold_14-snap.381-T1
Valid prediction for pasa_asmbl_12908.p1
Valid prediction for pasa_asmbl_12910.p1
Valid prediction for GlimmerHMM_glimmerT_34143-T1
Valid prediction for snap_scaffold_14-snap.363-T1
Valid prediction for snap_scaffold_14-snap.361-T1
Valid prediction for snap_scaffold_14-snap.367-T1
Valid prediction for GeneMark_model.58388_t
Valid prediction for GeneMark_model.58396_t
Valid prediction for GeneMark_model.58386_t
Valid prediction for snap_scaffold_14-snap.388-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for Augustus_model.g22958.t1
Valid prediction for GeneMark_model.58406_t
Valid prediction for snap_scaffold_14-snap.393-T1
Valid prediction for GlimmerHMM_glimmerT_34142-T1
Valid prediction for GeneMark_model.58404_t
Couldn't classify 77777, 77929
Couldn't classify 78282, 78297
Sorry, prediction pasa_asmbl_13818.p1 fails validation.
(CAG)	 TT	77777-77929	GT	AGG
(GGT)	 AG	78027-78160	GT	AGG
(ACT)	 AG	78282-78297	AG	AGA
-recovered pasa_asmbl_13818.p1, internal, 78027, 78160
Valid prediction for GlimmerHMM_glimmerT_34137-T1
Valid prediction for snap_scaffold_14-snap.358-T1
Valid prediction for snap_scaffold_14-snap.373-T1
Valid prediction for GlimmerHMM_glimmerT_34140-T1
Valid prediction for snap_scaffold_14-snap.386-T1
Valid prediction for snap_scaffold_14-snap.389-T1
Valid prediction for GeneMark_model.58394_t
Valid prediction for snap_scaffold_14-snap.366-T1
Valid prediction for GeneMark_model.58382_t
Valid prediction for HiQ_model.g22960.t1
Valid prediction for snap_scaffold_14-snap.385-T1
Valid prediction for snap_scaffold_14-snap.375-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_14-snap.378-T1
Valid prediction for snap_scaffold_14-snap.372-T1
Valid prediction for CodingQuarry_transcript_15534-T1
Valid prediction for GeneMark_model.58384_t
Valid prediction for GlimmerHMM_glimmerT_34149-T1
Valid prediction for GlimmerHMM_glimmerT_34145-T1
Valid prediction for HiQ_model.g22963.t1
Valid prediction for snap_scaffold_14-snap.370-T1
Valid prediction for GlimmerHMM_glimmerT_34147-T1
Valid prediction for GeneMark_model.58390_t
Valid prediction for GeneMark_model.58409_t
Couldn't classify 78967, 78994
Sorry, prediction pasa_asmbl_12903.p1 fails validation.
(GTC)	 CT	78967-78994	GT	GGG
(GTT)	 AG	79307-79457	GT	AGG
(TAA)	 AG	79929-80026	GT	AGG
(GTT)	 AG	80112-80354	GT	AGG
(GGC)	 AG	80433-80637	GT	CGG
(TTC)	 AG	80977-81224	GT	AGG
(GCG)	 AG	81320-81486	GT	AGG
(GAG)	 AG	81872-82033	GT	AGG
-recovered pasa_asmbl_12903.p1, terminal, 81872, 82033
-recovered pasa_asmbl_12903.p1, internal, 79307, 79457
-recovered pasa_asmbl_12903.p1, internal, 79929, 80026
-recovered pasa_asmbl_12903.p1, internal, 80112, 80354
-recovered pasa_asmbl_12903.p1, internal, 80433, 80637
-recovered pasa_asmbl_12903.p1, internal, 80977, 81224
-recovered pasa_asmbl_12903.p1, internal, 81320, 81486
-recovered pasa_asmbl_12903.p1, internal, 81872, 82033

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 15953, rend_intergenic: 8886  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24422, rend_intergenic: 20700  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36737, rend_intergenic: 26393  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55357, rend_intergenic: 52074  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63064, rend_intergenic: 60420  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70389, rend_intergenic: 65138  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74206, rend_intergenic: 73265  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106903, rend_intergenic: 97963  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125072, rend_intergenic: 112906  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 146613
-exon list size: 533


building trellis

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11.8    
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26.2    
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27.9    
28.0    
28.2    
28.4    
28.6    
28.8    
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29.5    
29.7    
29.9    
30.1    
30.3    
30.5    
30.7    
30.8    
31.0    
31.2    
31.4    
31.6    
31.8    
32.0    
32.1    
32.3    
32.5    
32.7    
32.9    
33.1    
33.3    
33.5    
33.6    
33.8    
34.0    
34.2    
34.4    
34.6    
34.8    
35.0    
35.1    
35.3    
35.5    
35.7    
35.9    
36.1    
36.3    
36.4    
36.6    
36.8    
37.0    
37.2    
37.4    
37.6    
37.8    
37.9    
38.1    
38.3    
38.5    
38.7    
38.9    
39.1    
39.3    
39.4    
39.6    
39.8    
40.0    
40.2    
40.4    
40.6    
40.7    
40.9    
41.1    
41.3    
41.5    
41.7    
41.9    
42.1    
42.2    
42.4    
42.6    
42.8    
43.0    
43.2    
43.4    
43.6    
43.7    
43.9    
44.1    
44.3    
44.5    
44.7    
44.9    
45.0    
45.2    
45.4    
45.6    
45.8    
46.0    
46.2    
46.4    
46.5    
46.7    
46.9    
47.1    
47.3    
47.5    
47.7    
47.9    
48.0    
48.2    
48.4    
48.6    
48.8    
49.0    
49.2    
49.3    
49.5    
49.7    
49.9    
50.1    
50.3    
50.5    
50.7    
50.8    
51.0    
51.2    
51.4    
51.6    
51.8    
52.0    
52.1    
52.3    
52.5    
52.7    
52.9    
53.1    
53.3    
53.5    
53.6    
53.8    
54.0    
54.2    
54.4    
54.6    
54.8    
55.0    
55.1    
55.3    
55.5    
55.7    
55.9    
56.1    
56.3    
56.4    
56.6    
56.8    
57.0    
57.2    
57.4    
57.6    
57.8    
57.9    
58.1    
58.3    
58.5    
58.7    
58.9    
59.1    
59.3    
59.4    
59.6    
59.8    
60.0    
60.2    
60.4    
60.6    
60.7    
60.9    
61.1    
61.3    
61.5    
61.7    
61.9    
62.1    
62.2    
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62.6    
62.8    
63.0    
63.2    
63.4    
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64.1    
64.3    
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65.2    
65.4    
65.6    
65.8    
66.0    
66.2    
66.4    
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66.7    
66.9    
67.1    
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68.0    
68.2    
68.4    
68.6    
68.8    
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69.2    
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71.2    
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71.6    
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72.3    
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73.3    
73.5    
73.6    
73.8    
74.0    
74.2    
74.4    
74.6    
74.8    
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75.1    
75.3    
75.5    
75.7    
75.9    
76.1    
76.3    
76.4    
76.6    
76.8    
77.0    
77.2    
77.4    
77.6    
77.8    
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78.1    
78.3    
78.5    
78.7    
78.9    
79.1    
79.3    
79.4    
79.6    
79.8    
80.0    
80.2    
80.4    
80.6    
80.7    
80.9    
81.1    
81.3    
81.5    
81.7    
81.9    
82.1    
82.2    
82.4    
82.6    
82.8    
83.0    
83.2    
83.4    
83.6    
83.7    
83.9    
84.1    
84.3    
84.5    
84.7    
84.9    
85.0    
85.2    
85.4    
85.6    
85.8    
86.0    
86.2    
86.4    
86.5    
86.7    
86.9    
87.1    
87.3    
87.5    
87.7    
87.9    
88.0    
88.2    
88.4    
88.6    
88.8    
89.0    
89.2    
89.3    
89.5    
89.7    
89.9    
90.1    
90.3    
90.5    
90.7    
90.8    
91.0    
91.2    
91.4    
91.6    
91.8    
92.0    
92.1    
92.3    
92.5    
92.7    
92.9    
93.1    
93.3    
93.5    
93.6    
93.8    
94.0    
94.2    
94.4    
94.6    
94.8    
95.0    
95.1    
95.3    
95.5    
95.7    
95.9    
96.1    
96.3    
96.4    
96.6    
96.8    
97.0    
97.2    
97.4    
97.6    
97.8    
97.9    
98.1    
98.3    
98.5    
98.7    
98.9    
99.1    
99.3    
99.4    
99.6    
99.8    
-found 30 predictions from path traversal
Error with prediction: snap lend_intergenic: 15953, rend_intergenic: 8886  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24422, rend_intergenic: 20700  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36737, rend_intergenic: 26393  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55357, rend_intergenic: 52074  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63064, rend_intergenic: 60420  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70389, rend_intergenic: 65138  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74206, rend_intergenic: 73265  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106903, rend_intergenic: 97963  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125072, rend_intergenic: 112906  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 22 predictions persist after filtering for low support