-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_3/scaffold_3_10376285-10575952

-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_3-snap.2059-T1
Valid prediction for snap_scaffold_3-snap.2064-T1
Valid prediction for snap_scaffold_3-snap.2084-T1
Valid prediction for pasa_asmbl_40271.p1
Valid prediction for snap_scaffold_3-snap.2063-T1
Valid prediction for snap_scaffold_3-snap.2080-T1
Valid prediction for GlimmerHMM_glimmerT_7218-T1
Valid prediction for GlimmerHMM_glimmerT_7235-T1
Valid prediction for Augustus_model.g4701.t1
Valid prediction for snap_scaffold_3-snap.2076-T1
Valid prediction for snap_scaffold_3-snap.2061-T1
Couldn't classify 185820, 185864
Sorry, prediction pasa_asmbl_40273.p1 fails validation.
(AAA)	 TG	185820-185864	GT	AGG
(GGA)	 AG	187407-187483	GT	AGG
(AGA)	 AG	189300-189375	GT	TGG
(GTG)	 AG	190498-190633	GT	TGG
(ACC)	 AG	191024-191143	GT	AGG
(GGG)	 AG	191312-191517	GT	AGG
(GAA)	 AG	193739-193894	GA	AAG
-recovered pasa_asmbl_40273.p1, terminal, 191024, 191143
-recovered pasa_asmbl_40273.p1, terminal, 193739, 193894
-recovered pasa_asmbl_40273.p1, internal, 187407, 187483
-recovered pasa_asmbl_40273.p1, internal, 189300, 189375
-recovered pasa_asmbl_40273.p1, internal, 190498, 190633
-recovered pasa_asmbl_40273.p1, internal, 191024, 191143
-recovered pasa_asmbl_40273.p1, internal, 191312, 191517
Valid prediction for Augustus_model.g4700.t1
Couldn't classify 183598, 183633
Couldn't classify 184852, 184925
Sorry, prediction pasa_asmbl_40272.p1 fails validation.
(GCC)	 TG	183598-183633	GT	TGG
(AAT)	 AG	183775-183852	GT	CTG
(GCC)	 AG	184046-184161	GT	AGG
(GTT)	 AG	184336-184436	GT	CTG
(GTT)	 AG	184852-184925	GT	AGG
-recovered pasa_asmbl_40272.p1, internal, 183775, 183852
-recovered pasa_asmbl_40272.p1, internal, 184046, 184161
-recovered pasa_asmbl_40272.p1, internal, 184336, 184436
-recovered pasa_asmbl_40272.p1, internal, 184852, 184925
Valid prediction for snap_scaffold_3-snap.2066-T1
Valid prediction for snap_scaffold_3-snap.2053-T1
Valid prediction for GlimmerHMM_glimmerT_7221-T1
Valid prediction for GlimmerHMM_glimmerT_7232-T1
Valid prediction for snap_scaffold_3-snap.2088-T1
Valid prediction for GlimmerHMM_glimmerT_7231-T1
Valid prediction for HiQ_model.g4703.t1
Valid prediction for snap_scaffold_3-snap.2081-T1
Valid prediction for Augustus_model.g4712.t1
Valid prediction for snap_scaffold_3-snap.2070-T1
Valid prediction for snap_scaffold_3-snap.2077-T1
Valid prediction for snap_scaffold_3-snap.2083-T1
Valid prediction for snap_scaffold_3-snap.2056-T1
Valid prediction for GlimmerHMM_glimmerT_7233-T1
Valid prediction for snap_scaffold_3-snap.2075-T1
Valid prediction for GlimmerHMM_glimmerT_7222-T1
Valid prediction for snap_scaffold_3-snap.2068-T1
Valid prediction for GlimmerHMM_glimmerT_7236-T1
Couldn't classify 50190, 50240
Couldn't classify 52867, 52974
Sorry, prediction pasa_asmbl_40270.p1 fails validation.
(TTC)	 AT	50190-50240	GT	AGG
(GAA)	 AG	51566-51683	GT	TGG
(GTG)	 AG	52274-52467	GT	AGG
(CAA)	 AG	52867-52974	GT	AGG
-recovered pasa_asmbl_40270.p1, internal, 51566, 51683
-recovered pasa_asmbl_40270.p1, internal, 52274, 52467
-recovered pasa_asmbl_40270.p1, internal, 52867, 52974
Valid prediction for snap_scaffold_3-snap.2086-T1
Valid prediction for snap_scaffold_3-snap.2050-T1
Valid prediction for GlimmerHMM_glimmerT_7220-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: -)Couldn't classify 77780, 78514
Sorry, prediction pasa_asmbl_39086.p1 fails validation.
(CTG)	 AG	77780-78514	TC	CCT
Valid prediction for snap_scaffold_3-snap.2074-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_7226-T1
Valid prediction for Augustus_model.g4699.t1
Valid prediction for snap_scaffold_3-snap.2073-T1
Valid prediction for Augustus_model.g4709.t1
Valid prediction for Augustus_model.g4708.t1
Valid prediction for GlimmerHMM_glimmerT_7225-T1
Valid prediction for snap_scaffold_3-snap.2079-T1
Valid prediction for snap_scaffold_3-snap.2055-T1
Valid prediction for GlimmerHMM_glimmerT_7230-T1
Valid prediction for snap_scaffold_3-snap.2087-T1
Valid prediction for GlimmerHMM_glimmerT_7228-T1
Valid prediction for GlimmerHMM_glimmerT_7224-T1
Valid prediction for Augustus_model.g4705.t1
Valid prediction for Augustus_model.g4706.t1
Valid prediction for snap_scaffold_3-snap.2072-T1
Valid prediction for GlimmerHMM_glimmerT_7227-T1
Valid prediction for snap_scaffold_3-snap.2062-T1
Valid prediction for snap_scaffold_3-snap.2060-T1
Valid prediction for CodingQuarry_transcript_46250-T1
Valid prediction for snap_scaffold_3-snap.2082-T1
Valid prediction for GlimmerHMM_glimmerT_7223-T1
Couldn't classify 131915, 131987
Sorry, prediction pasa_asmbl_39701.p1 fails validation.
(ATG)	 GC	129227-129331	GT	TTG
(GGT)	 AG	129646-129697	GT	AGG
(GTC)	 AG	130576-130649	GT	CGG
(GCT)	 AG	131379-131458	GT	AGG
(TCC)	 AG	131915-131987	GA	GTG
-recovered pasa_asmbl_39701.p1, initial, 129227, 129331
-recovered pasa_asmbl_39701.p1, internal, 129646, 129697
-recovered pasa_asmbl_39701.p1, internal, 130576, 130649
-recovered pasa_asmbl_39701.p1, internal, 131379, 131458
Valid prediction for snap_scaffold_3-snap.2052-T1
Couldn't classify 75436, 75498
Couldn't classify 77451, 77497
Sorry, prediction pasa_asmbl_39087.p1 fails validation.
(AAA)	 AC	75436-75498	GT	AGG
(ATC)	 AG	75591-75644	GT	AGG
(TCT)	 AG	75811-75942	GT	AGG
(TGC)	 AG	76698-76956	GT	CTG
(CCG)	 AG	77451-77497	AC	AGA
-recovered pasa_asmbl_39087.p1, internal, 75591, 75644
-recovered pasa_asmbl_39087.p1, internal, 75811, 75942
-recovered pasa_asmbl_39087.p1, internal, 76698, 76956
Valid prediction for Augustus_model.g4702.t1
Valid prediction for snap_scaffold_3-snap.2049-T1
Valid prediction for Augustus_model.g4711.t1
Couldn't classify 79994, 80518
Sorry, prediction pasa_asmbl_39084.p1 fails validation.
(AAG)	 CC	79994-80518	GA	AGG
Valid prediction for GlimmerHMM_glimmerT_7217-T1
Valid prediction for snap_scaffold_3-snap.2065-T1
Valid prediction for snap_scaffold_3-snap.2085-T1
Valid prediction for snap_scaffold_3-snap.2057-T1
Valid prediction for GlimmerHMM_glimmerT_7219-T1
Couldn't classify 58605, 58731
Couldn't classify 63682, 63729
Sorry, prediction pasa_asmbl_39090.p1 fails validation.
(GGG)	 AG	58605-58731	GT	AGG
(TGG)	 AG	59035-59166	GT	ATG
(CTG)	 AG	60265-60399	GT	TGG
(GTC)	 AG	60530-60647	GT	CTG
(AGA)	 AG	60868-60978	GT	AGG
(GAG)	 AG	61130-61226	GT	AGG
(TGT)	 AG	61549-61656	GT	ACG
(ATC)	 AG	62941-63054	GT	AGG
(TGT)	 AG	63234-63368	GT	GGG
(GCG)	 AG	63682-63729	AA	ACA
-recovered pasa_asmbl_39090.p1, internal, 58605, 58731
-recovered pasa_asmbl_39090.p1, internal, 59035, 59166
-recovered pasa_asmbl_39090.p1, internal, 60265, 60399
-recovered pasa_asmbl_39090.p1, internal, 60530, 60647
-recovered pasa_asmbl_39090.p1, internal, 60868, 60978
-recovered pasa_asmbl_39090.p1, internal, 61130, 61226
-recovered pasa_asmbl_39090.p1, internal, 61549, 61656
-recovered pasa_asmbl_39090.p1, internal, 62941, 63054
-recovered pasa_asmbl_39090.p1, internal, 63234, 63368
Couldn't classify 79175, 79891
Sorry, prediction pasa_asmbl_39085.p1 fails validation.
(TCA)	 CC	79175-79891	CT	GCC
Valid prediction for snap_scaffold_3-snap.2058-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for Augustus_model.g4710.t1
Valid prediction for snap_scaffold_3-snap.2078-T1
Valid prediction for snap_scaffold_3-snap.2067-T1
Valid prediction for GlimmerHMM_glimmerT_7216-T1
Valid prediction for snap_scaffold_3-snap.2069-T1
Couldn't classify 80600, 81759
Couldn't classify 82004, 82124
Sorry, prediction pasa_asmbl_39083.p1 fails validation.
(CAG)	 AG	80600-81759	GT	AGG
(CTG)	 AG	82004-82124	AG	GCA
-recovered pasa_asmbl_39083.p1, internal, 80600, 81759
Valid prediction for snap_scaffold_3-snap.2090-T1
Couldn't classify 83862, 83917
Couldn't classify 86487, 86630
Sorry, prediction pasa_asmbl_39082.p1 fails validation.
(CTG)	 GC	83862-83917	GT	AGG
(TGA)	 AG	85271-85317	GT	CGG
(TGA)	 AG	86021-86223	GT	AGG
(CTG)	 AG	86487-86630	CG	CCC
-recovered pasa_asmbl_39082.p1, internal, 85271, 85317
-recovered pasa_asmbl_39082.p1, internal, 86021, 86223
Valid prediction for Augustus_model.g4707.t1
Valid prediction for snap_scaffold_3-snap.2051-T1
Valid prediction for snap_scaffold_3-snap.2071-T1
Valid prediction for Augustus_model.g4704.t1
Valid prediction for GlimmerHMM_glimmerT_7215-T1
Valid prediction for GlimmerHMM_glimmerT_7229-T1
Valid prediction for snap_scaffold_3-snap.2054-T1
Valid prediction for CodingQuarry_transcript_46249-T1
Valid prediction for GlimmerHMM_glimmerT_7234-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 18760, rend_intergenic: 17139  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36671, rend_intergenic: 20008  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38388, rend_intergenic: 37265  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49202, rend_intergenic: 39316  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58277, rend_intergenic: 51557  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61992, rend_intergenic: 60789  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66909, rend_intergenic: 63396  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77413, rend_intergenic: 72728  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89240, rend_intergenic: 83950  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151975, rend_intergenic: 132357  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159248, rend_intergenic: 152235  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167491, rend_intergenic: 159635  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 179405, rend_intergenic: 172869  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 186328, rend_intergenic: 179435  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 188908, rend_intergenic: 186950  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 192319, rend_intergenic: 190890  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 199668
-exon list size: 427


building trellis

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25.6    
25.9    
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26.6    
26.8    
27.0    
27.3    
27.5    
27.7    
28.0    
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28.9    
29.1    
29.4    
29.6    
29.8    
30.1    
30.3    
30.5    
30.8    
31.0    
31.2    
31.5    
31.7    
31.9    
32.2    
32.4    
32.6    
32.9    
33.1    
33.3    
33.6    
33.8    
34.0    
34.3    
34.5    
34.7    
35.0    
35.2    
35.4    
35.7    
35.9    
36.1    
36.4    
36.6    
36.8    
37.1    
37.3    
37.5    
37.8    
38.0    
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38.7    
38.9    
39.2    
39.4    
39.6    
39.9    
40.1    
40.3    
40.6    
40.8    
41.0    
41.3    
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41.7    
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43.8    
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97.9    
98.1    
98.4    
98.6    
98.8    
99.1    
99.3    
99.5    
99.8    
-found 24 predictions from path traversal
Error with prediction: snap lend_intergenic: 18760, rend_intergenic: 17139  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36671, rend_intergenic: 20008  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38388, rend_intergenic: 37265  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49202, rend_intergenic: 39316  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58277, rend_intergenic: 51557  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61992, rend_intergenic: 60789  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66909, rend_intergenic: 63396  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77413, rend_intergenic: 72728  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89240, rend_intergenic: 83950  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151975, rend_intergenic: 132357  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159248, rend_intergenic: 152235  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167491, rend_intergenic: 159635  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 179405, rend_intergenic: 172869  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 186328, rend_intergenic: 179435  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 188908, rend_intergenic: 186950  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 192319, rend_intergenic: 190890  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 15 predictions persist after filtering for low support