-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_18/scaffold_18_1704564-1935654

-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_41834-T1
Valid prediction for Augustus_model.g27834.t1
Valid prediction for GlimmerHMM_glimmerT_41821-T1
Valid prediction for Augustus_model.g27842.t1
Valid prediction for snap_scaffold_18-snap.392-T1
Valid prediction for snap_scaffold_18-snap.399-T1
Valid prediction for snap_scaffold_18-snap.402-T1
Valid prediction for snap_scaffold_18-snap.383-T1
Valid prediction for snap_scaffold_18-snap.368-T1
Valid prediction for snap_scaffold_18-snap.357-T1
Valid prediction for GlimmerHMM_glimmerT_41848-T1
Valid prediction for Augustus_model.g27852.t1
Valid prediction for Augustus_model.g27829.t1
Valid prediction for CodingQuarry_transcript_23671-T1
Couldn't classify 168711, 169211
Sorry, prediction pasa_asmbl_20387.p1 fails validation.
(GCT)	 TG	168711-169211	AG	ACA
Valid prediction for GlimmerHMM_glimmerT_41831-T1
Valid prediction for Augustus_model.g27847.t1
Valid prediction for snap_scaffold_18-snap.378-T1
Valid prediction for snap_scaffold_18-snap.380-T1
Couldn't classify 131089, 131131
Sorry, prediction pasa_asmbl_20382.p1 fails validation.
(GGG)	 TC	131089-131131	GT	AGG
(AGG)	 AG	131710-132011	AC	GAA
-recovered pasa_asmbl_20382.p1, terminal, 131710, 132011
Couldn't classify 105875, 105915
Sorry, prediction pasa_asmbl_20381.p1 fails validation.
(TAC)	 AG	105875-105915	GT	CCG
(GGA)	 AG	106026-106095	GT	AGG
(GAA)	 AG	106223-106279	GT	CGG
(GTC)	 AG	106388-106483	GT	AGG
(TAC)	 AG	107113-107246	GT	GGG
(GAA)	 AG	107370-107485	GT	TGG
(GTG)	 AG	107749-107792	AA	AAA
-recovered pasa_asmbl_20381.p1, terminal, 107749, 107792
-recovered pasa_asmbl_20381.p1, internal, 105875, 105915
-recovered pasa_asmbl_20381.p1, internal, 106026, 106095
-recovered pasa_asmbl_20381.p1, internal, 106223, 106279
-recovered pasa_asmbl_20381.p1, internal, 106388, 106483
-recovered pasa_asmbl_20381.p1, internal, 107113, 107246
-recovered pasa_asmbl_20381.p1, internal, 107370, 107485
Valid prediction for snap_scaffold_18-snap.384-T1
Valid prediction for CodingQuarry_transcript_23669-T1
Valid prediction for snap_scaffold_18-snap.361-T1
Valid prediction for GlimmerHMM_glimmerT_41841-T1
Valid prediction for pasa_asmbl_20384.p1
Valid prediction for snap_scaffold_18-snap.389-T1
Valid prediction for pasa_asmbl_20393.p1
Valid prediction for snap_scaffold_18-snap.365-T1
Valid prediction for snap_scaffold_18-snap.388-T1
Valid prediction for GlimmerHMM_glimmerT_41849-T1
Valid prediction for Augustus_model.g27830.t1
Valid prediction for snap_scaffold_18-snap.375-T1
Valid prediction for snap_scaffold_18-snap.398-T1
Valid prediction for snap_scaffold_18-snap.366-T1
Valid prediction for Augustus_model.g27837.t1
Valid prediction for Augustus_model.g27841.t1
Valid prediction for Augustus_model.g27850.t1
Valid prediction for CodingQuarry_transcript_23680-T1
Valid prediction for Augustus_model.g27835.t1
Valid prediction for snap_scaffold_18-snap.382-T1
Valid prediction for GlimmerHMM_glimmerT_41819-T1
Couldn't classify 162661, 162775
Couldn't classify 163085, 163219
Sorry, prediction pasa_asmbl_21097.p1 fails validation.
(GAG)	 AG	162661-162775	GT	TGG
(CTG)	 AG	162902-162966	GT	TGG
(ACA)	 AG	163085-163219	GT	AGG
-recovered pasa_asmbl_21097.p1, internal, 162661, 162775
-recovered pasa_asmbl_21097.p1, internal, 162902, 162966
-recovered pasa_asmbl_21097.p1, internal, 163085, 163219
Valid prediction for HiQ_model.g27858.t1
Valid prediction for snap_scaffold_18-snap.370-T1
Valid prediction for HiQ_model.g27833.t1
Valid prediction for GlimmerHMM_glimmerT_41833-T1
Valid prediction for snap_scaffold_18-snap.360-T1
Couldn't classify 166984, 167130
Couldn't classify 167776, 167816
Sorry, prediction pasa_asmbl_21140.p1 fails validation.
(TTC)	 GC	166984-167130	GT	AGG
(GAT)	 AG	167267-167437	GT	AGG
(GTT)	 AG	167563-167686	GT	GGG
(GAG)	 AG	167776-167816	GG	CAG
-recovered pasa_asmbl_21140.p1, internal, 167267, 167437
-recovered pasa_asmbl_21140.p1, internal, 167563, 167686
Valid prediction for CodingQuarry_transcript_23670-T1
Valid prediction for GlimmerHMM_glimmerT_41822-T1
Valid prediction for snap_scaffold_18-snap.364-T1
Valid prediction for snap_scaffold_18-snap.377-T1
Valid prediction for GlimmerHMM_glimmerT_41828-T1
Valid prediction for Augustus_model.g27859.t1
Valid prediction for GlimmerHMM_glimmerT_41827-T1
Valid prediction for GlimmerHMM_glimmerT_41832-T1
Valid prediction for Augustus_model.g27843.t1
Valid prediction for GlimmerHMM_glimmerT_41824-T1
Valid prediction for GlimmerHMM_glimmerT_41837-T1
Valid prediction for Augustus_model.g27845.t1
Valid prediction for snap_scaffold_18-snap.373-T1
Valid prediction for GlimmerHMM_glimmerT_41840-T1
Couldn't classify 169533, 169591
Couldn't classify 170699, 170771
Sorry, prediction pasa_asmbl_20388.p1 fails validation.
(GTC)	 AA	169533-169591	GT	ATG
(GTT)	 AG	169727-169946	GT	AGG
(GAT)	 AG	170096-170209	GT	TGG
(CCT)	 AG	170318-170403	GT	AAG
(GTT)	 AG	170489-170587	GT	AGG
(GAA)	 AG	170699-170771	GA	GGG
-recovered pasa_asmbl_20388.p1, terminal, 170318, 170403
-recovered pasa_asmbl_20388.p1, internal, 169727, 169946
-recovered pasa_asmbl_20388.p1, internal, 170096, 170209
-recovered pasa_asmbl_20388.p1, internal, 170318, 170403
-recovered pasa_asmbl_20388.p1, internal, 170489, 170587
Valid prediction for snap_scaffold_18-snap.403-T1
Valid prediction for GlimmerHMM_glimmerT_41817-T1
Valid prediction for snap_scaffold_18-snap.376-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 HiQ_model.g27853.t1
Valid prediction for CodingQuarry_transcript_23673-T1
Valid prediction for Augustus_model.g27840.t1
Couldn't classify 110632, 110727
Sorry, prediction pasa_asmbl_19646.p1 fails validation.
(ATG)	 CA	108241-108396	GT	AGG
(GAG)	 AG	108491-108615	GT	AGG
(ATT)	 AG	110046-110118	GT	AGG
(GTT)	 AG	110632-110727	TC	GGT
-recovered pasa_asmbl_19646.p1, initial, 108241, 108396
-recovered pasa_asmbl_19646.p1, internal, 108491, 108615
-recovered pasa_asmbl_19646.p1, internal, 110046, 110118
Valid prediction for GlimmerHMM_glimmerT_41847-T1
Valid prediction for snap_scaffold_18-snap.386-T1
Valid prediction for GlimmerHMM_glimmerT_41839-T1
Valid prediction for GlimmerHMM_glimmerT_41838-T1
Valid prediction for GlimmerHMM_glimmerT_41850-T1
Valid prediction for snap_scaffold_18-snap.393-T1
Valid prediction for Augustus_model.g27849.t1
Valid prediction for CodingQuarry_transcript_23672-T1
Valid prediction for snap_scaffold_18-snap.371-T1
Valid prediction for snap_scaffold_18-snap.372-T1
Valid prediction for snap_scaffold_18-snap.396-T1
Valid prediction for snap_scaffold_18-snap.362-T1
Valid prediction for snap_scaffold_18-snap.381-T1
Valid prediction for HiQ_model.g27831.t1
Valid prediction for CodingQuarry_transcript_23666-T1
Valid prediction for snap_scaffold_18-snap.358-T1
Valid prediction for pasa_asmbl_19652.p1
Valid prediction for Augustus_model.g27851.t1
Valid prediction for CodingQuarry_transcript_23667-T1
Valid prediction for GlimmerHMM_glimmerT_41825-T1
Valid prediction for HiQ_model.g27836.t1
Valid prediction for GlimmerHMM_glimmerT_41845-T1
Couldn't classify 21049, 21145
Sorry, prediction pasa_asmbl_19667.p1 fails validation.
(CTG)	 AT	21049-21145	GT	AGG
(GTC)	 AG	21248-21759	AC	AAA
-recovered pasa_asmbl_19667.p1, terminal, 21248, 21759
Valid prediction for CodingQuarry_transcript_23678-T1
Valid prediction for snap_scaffold_18-snap.369-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_18-snap.400-T1
Valid prediction for Augustus_model.g27844.t1
Valid prediction for snap_scaffold_18-snap.387-T1
Valid prediction for Augustus_model.g27832.t1
Valid prediction for GlimmerHMM_glimmerT_41826-T1
Valid prediction for Augustus_model.g27860.t1
Valid prediction for GlimmerHMM_glimmerT_41842-T1
Valid prediction for snap_scaffold_18-snap.379-T1
Valid prediction for Augustus_model.g27839.t1
Valid prediction for Augustus_model.g27848.t1
Valid prediction for snap_scaffold_18-snap.394-T1
Valid prediction for Augustus_model.g27846.t1
Valid prediction for GlimmerHMM_glimmerT_41820-T1
Valid prediction for snap_scaffold_18-snap.359-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_41836-T1
Valid prediction for Augustus_model.g27857.t1
Valid prediction for snap_scaffold_18-snap.374-T1
Valid prediction for GlimmerHMM_glimmerT_41823-T1
Valid prediction for CodingQuarry_transcript_23668-T1
Valid prediction for snap_scaffold_18-snap.395-T1
Valid prediction for GlimmerHMM_glimmerT_41818-T1
Valid prediction for snap_scaffold_18-snap.363-T1
Valid prediction for snap_scaffold_18-snap.385-T1
Valid prediction for GlimmerHMM_glimmerT_41846-T1
Couldn't classify 218452, 218533
Sorry, prediction pasa_asmbl_19641.p1 fails validation.
(TCA)	 AA	218452-218533	GT	TGG
(GGG)	 AG	218631-218727	GT	AGG
(GTC)	 AG	218815-218916	GT	AGG
(TTT)	 AG	218999-219125	GT	AGG
(GAG)	 AG	219269-219447	GT	AGG
(GTT)	 AG	219548-219710	GT	AGG
(GGA)	 AG	219831-219899	GG	AAG
add_exon() Sorry, pasa_asmbl_19641.p1 218631-218727-terminal-3 is invalid.
-recovered pasa_asmbl_19641.p1, terminal, 218631, 218727
-recovered pasa_asmbl_19641.p1, terminal, 219831, 219899
-recovered pasa_asmbl_19641.p1, internal, 218631, 218727
-recovered pasa_asmbl_19641.p1, internal, 218815, 218916
-recovered pasa_asmbl_19641.p1, internal, 218999, 219125
-recovered pasa_asmbl_19641.p1, internal, 219269, 219447
-recovered pasa_asmbl_19641.p1, internal, 219548, 219710
Valid prediction for GlimmerHMM_glimmerT_41830-T1
Valid prediction for HiQ_model.g27854.t1
Valid prediction for GlimmerHMM_glimmerT_41829-T1
Valid prediction for CodingQuarry_transcript_23676-T1
Valid prediction for pasa_asmbl_19638.p1
Couldn't classify 46922, 47055
Sorry, prediction pasa_asmbl_19660.p1 fails validation.
(ATG)	 CC	35870-35888	GT	AGG
(TGT)	 AG	36642-36752	GT	GGG
(GTG)	 AG	36896-37044	GT	AGG
(ATA)	 AG	37121-37238	GT	AGG
(AAG)	 AG	37372-37423	GT	AGG
(CAG)	 AG	38121-38177	GT	AGG
(AAT)	 AG	38718-38726	GT	AGG
(GGA)	 AG	40309-40472	GT	AGG
(CTT)	 AG	40810-40942	GT	AAG
(TCA)	 AG	42003-42011	GT	AAG
(GTA)	 AG	42372-42496	GT	AGG
(AGC)	 AG	42606-42711	GT	TGG
(GAT)	 AG	42867-43033	GT	ATG
(TGA)	 AG	43189-43354	GT	AAG
(GAA)	 AG	43494-43600	GT	CGG
(ACC)	 AG	43700-43836	GT	GGG
(GTA)	 AG	43959-44118	GT	TGG
(ATA)	 AG	44217-44321	GT	GGG
(GCT)	 AG	44413-44601	GT	GGG
(CTG)	 AG	45228-45362	GT	AAG
(CTG)	 AG	45463-45630	GT	AGG
(AAC)	 AG	45714-45802	GT	TGG
(GGG)	 AG	45891-46086	GT	TGG
(ACC)	 AG	46228-46367	GT	TGG
(GAA)	 AG	46453-46612	GT	AGG
(GCA)	 AG	46922-47055	AG	CGA
-recovered pasa_asmbl_19660.p1, initial, 35870, 35888
add_exon() Sorry, pasa_asmbl_19660.p1 38121-38177-terminal-1 is invalid.
-recovered pasa_asmbl_19660.p1, terminal, 38121, 38177
add_exon() Sorry, pasa_asmbl_19660.p1 45463-45630-terminal-1 is invalid.
-recovered pasa_asmbl_19660.p1, terminal, 45463, 45630
-recovered pasa_asmbl_19660.p1, internal, 36642, 36752
-recovered pasa_asmbl_19660.p1, internal, 36896, 37044
-recovered pasa_asmbl_19660.p1, internal, 37121, 37238
-recovered pasa_asmbl_19660.p1, internal, 37372, 37423
-recovered pasa_asmbl_19660.p1, internal, 38121, 38177
-recovered pasa_asmbl_19660.p1, internal, 38718, 38726
-recovered pasa_asmbl_19660.p1, internal, 40309, 40472
-recovered pasa_asmbl_19660.p1, internal, 40810, 40942
-recovered pasa_asmbl_19660.p1, internal, 42003, 42011
-recovered pasa_asmbl_19660.p1, internal, 42372, 42496
-recovered pasa_asmbl_19660.p1, internal, 42606, 42711
-recovered pasa_asmbl_19660.p1, internal, 42867, 43033
-recovered pasa_asmbl_19660.p1, internal, 43189, 43354
-recovered pasa_asmbl_19660.p1, internal, 43494, 43600
-recovered pasa_asmbl_19660.p1, internal, 43700, 43836
-recovered pasa_asmbl_19660.p1, internal, 43959, 44118
-recovered pasa_asmbl_19660.p1, internal, 44217, 44321
-recovered pasa_asmbl_19660.p1, internal, 44413, 44601
-recovered pasa_asmbl_19660.p1, internal, 45228, 45362
-recovered pasa_asmbl_19660.p1, internal, 45463, 45630
-recovered pasa_asmbl_19660.p1, internal, 45714, 45802
-recovered pasa_asmbl_19660.p1, internal, 45891, 46086
-recovered pasa_asmbl_19660.p1, internal, 46228, 46367
-recovered pasa_asmbl_19660.p1, internal, 46453, 46612
Valid prediction for snap_scaffold_18-snap.390-T1
Valid prediction for GlimmerHMM_glimmerT_41843-T1
Valid prediction for CodingQuarry_transcript_23675-T1
Valid prediction for Augustus_model.g27855.t1
Valid prediction for snap_scaffold_18-snap.391-T1
Valid prediction for GlimmerHMM_glimmerT_41844-T1
Valid prediction for snap_scaffold_18-snap.397-T1
Valid prediction for pasa_asmbl_19645.p1
Valid prediction for Augustus_model.g27856.t1
Valid prediction for GlimmerHMM_glimmerT_41835-T1
Valid prediction for CodingQuarry_transcript_23674-T1
Valid prediction for snap_scaffold_18-snap.367-T1
Valid prediction for CodingQuarry_transcript_23677-T1
Valid prediction for snap_scaffold_18-snap.401-T1
Valid prediction for snap_scaffold_18-snap.404-T1
Valid prediction for pasa_asmbl_19642.p1
Valid prediction for Augustus_model.g27838.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 17581, rend_intergenic: 12648  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37879, rend_intergenic: 36338  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65064, rend_intergenic: 63674  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68830, rend_intergenic: 66547  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86227, rend_intergenic: 77539  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88858, rend_intergenic: 87044  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 225403, rend_intergenic: 224976  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 231091
-exon list size: 541


building trellis

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62.4    
62.6    
62.8    
63.0    
63.2    
63.4    
63.5    
63.7    
63.9    
64.1    
64.3    
64.5    
64.6    
64.8    
65.0    
65.2    
65.4    
65.6    
65.7    
65.9    
66.1    
66.3    
66.5    
66.7    
66.9    
67.0    
67.2    
67.4    
67.6    
67.8    
68.0    
68.1    
68.3    
68.5    
68.7    
68.9    
69.1    
69.2    
69.4    
69.6    
69.8    
70.0    
70.2    
70.3    
70.5    
70.7    
70.9    
71.1    
71.3    
71.5    
71.6    
71.8    
72.0    
72.2    
72.4    
72.6    
72.7    
72.9    
73.1    
73.3    
73.5    
73.7    
73.8    
74.0    
74.2    
74.4    
74.6    
74.8    
75.0    
75.1    
75.3    
75.5    
75.7    
75.9    
76.1    
76.2    
76.4    
76.6    
76.8    
77.0    
77.2    
77.3    
77.5    
77.7    
77.9    
78.1    
78.3    
78.5    
78.6    
78.8    
79.0    
79.2    
79.4    
79.6    
79.7    
79.9    
80.1    
80.3    
80.5    
80.7    
80.8    
81.0    
81.2    
81.4    
81.6    
81.8    
82.0    
82.1    
82.3    
82.5    
82.7    
82.9    
83.1    
83.2    
83.4    
83.6    
83.8    
84.0    
84.2    
84.3    
84.5    
84.7    
84.9    
85.1    
85.3    
85.5    
85.6    
85.8    
86.0    
86.2    
86.4    
86.6    
86.7    
86.9    
87.1    
87.3    
87.5    
87.7    
87.8    
88.0    
88.2    
88.4    
88.6    
88.8    
89.0    
89.1    
89.3    
89.5    
89.7    
89.9    
90.1    
90.2    
90.4    
90.6    
90.8    
91.0    
91.2    
91.3    
91.5    
91.7    
91.9    
92.1    
92.3    
92.4    
92.6    
92.8    
93.0    
93.2    
93.4    
93.6    
93.7    
93.9    
94.1    
94.3    
94.5    
94.7    
94.8    
95.0    
95.2    
95.4    
95.6    
95.8    
95.9    
96.1    
96.3    
96.5    
96.7    
96.9    
97.1    
97.2    
97.4    
97.6    
97.8    
98.0    
98.2    
98.3    
98.5    
98.7    
98.9    
99.1    
99.3    
99.4    
99.6    
99.8    
-found 38 predictions from path traversal
Error with prediction: snap lend_intergenic: 17581, rend_intergenic: 12648  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37879, rend_intergenic: 36338  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65064, rend_intergenic: 63674  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68830, rend_intergenic: 66547  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86227, rend_intergenic: 77539  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88858, rend_intergenic: 87044  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 225403, rend_intergenic: 224976  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 33 predictions persist after filtering for low support