-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_6/scaffold_6_13914505-14131655

-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 GeneMark_model.27114_t
Valid prediction for snap_scaffold_6-snap.2940-T1
Valid prediction for GeneMark_model.27136_t
Valid prediction for GlimmerHMM_glimmerT_16240-T1
Valid prediction for snap_scaffold_6-snap.2906-T1
Valid prediction for snap_scaffold_6-snap.2938-T1
Couldn't classify 204905, 205017
Couldn't classify 207139, 207229
Sorry, prediction pasa_asmbl_47519.p1 fails validation.
(AGA)	 TT	204905-205017	GT	AGG
(AGT)	 AG	205899-206009	GT	AGG
(AGT)	 AG	207139-207229	GG	AAG
-recovered pasa_asmbl_47519.p1, internal, 205899, 206009
Valid prediction for snap_scaffold_6-snap.2902-T1
Valid prediction for GeneMark_model.27143_t
Valid prediction for GlimmerHMM_glimmerT_16255-T1
Valid prediction for GlimmerHMM_glimmerT_16262-T1
Couldn't classify 104552, 104625
Couldn't classify 105346, 105423
Sorry, prediction pasa_asmbl_47860.p1 fails validation.
(GAG)	 TG	104552-104625	GT	AGG
(GTT)	 AG	104791-104962	GT	AGG
(ATT)	 AG	105346-105423	AG	AGA
-recovered pasa_asmbl_47860.p1, internal, 104791, 104962
Valid prediction for snap_scaffold_6-snap.2910-T1
Valid prediction for GeneMark_model.27123_t
Valid prediction for snap_scaffold_6-snap.2924-T1
Couldn't classify 201881, 201948
Couldn't classify 204711, 204767
Sorry, prediction pasa_asmbl_47518.p1 fails validation.
(TCT)	 TG	201881-201948	GT	AGG
(AGT)	 AG	202086-202196	GT	AGG
(AGT)	 AG	202582-202692	GT	AGG
(AGT)	 AG	202823-202933	GT	AGG
(TGC)	 AG	203114-203600	GT	AGG
(GCC)	 AG	204315-204380	GT	TGG
(AGT)	 AG	204711-204767	AG	TGA
-recovered pasa_asmbl_47518.p1, internal, 202086, 202196
-recovered pasa_asmbl_47518.p1, internal, 202582, 202692
-recovered pasa_asmbl_47518.p1, internal, 202823, 202933
-recovered pasa_asmbl_47518.p1, internal, 203114, 203600
-recovered pasa_asmbl_47518.p1, internal, 204315, 204380
Valid prediction for GeneMark_model.27121_t
Valid prediction for pasa_asmbl_47491.p1
Valid prediction for snap_scaffold_6-snap.2929-T1
Valid prediction for snap_scaffold_6-snap.2931-T1
Valid prediction for GlimmerHMM_glimmerT_16241-T1
Valid prediction for snap_scaffold_6-snap.2935-T1
Valid prediction for GlimmerHMM_glimmerT_16245-T1
Valid prediction for Augustus_model.g10963.t1
Valid prediction for CodingQuarry_transcript_55172-T1
Valid prediction for snap_scaffold_6-snap.2920-T1
Valid prediction for GlimmerHMM_glimmerT_16248-T1
Valid prediction for GlimmerHMM_glimmerT_16254-T1
Valid prediction for GlimmerHMM_glimmerT_16243-T1
Valid prediction for pasa_asmbl_47515.p1
Valid prediction for pasa_asmbl_47509.p1
Valid prediction for GeneMark_model.27142_t
Valid prediction for Augustus_model.g10967.t1
Valid prediction for snap_scaffold_6-snap.2905-T1
Valid prediction for GeneMark_model.27139_t
Valid prediction for snap_scaffold_6-snap.2909-T1
Valid prediction for GeneMark_model.27119_t
Valid prediction for snap_scaffold_6-snap.2903-T1
Couldn't classify 187276, 187408
Couldn't classify 188290, 188495
Sorry, prediction pasa_asmbl_47512.p1 fails validation.
(TCG)	 TG	187276-187408	GT	CGG
(GTC)	 AG	188290-188495	CT	CCC
Couldn't classify 161522, 161572
Couldn't classify 162652, 162687
Sorry, prediction pasa_asmbl_47505.p1 fails validation.
(GCC)	 AC	161522-161572	GT	AGG
(GTG)	 AG	161837-161980	GT	TGG
(GCT)	 AG	162274-162390	GT	AGG
(CTG)	 AG	162652-162687	CA	GAC
-recovered pasa_asmbl_47505.p1, internal, 161837, 161980
-recovered pasa_asmbl_47505.p1, internal, 162274, 162390
Valid prediction for Augustus_model.g10968.t1
Valid prediction for CodingQuarry_transcript_55171-T1
Valid prediction for HiQ_model.g10945.t1
Valid prediction for GeneMark_model.27155_t
Valid prediction for snap_scaffold_6-snap.2925-T1
Valid prediction for GlimmerHMM_glimmerT_16249-T1
Valid prediction for snap_scaffold_6-snap.2933-T1
Valid prediction for HiQ_model.g10965.t1
Valid prediction for snap_scaffold_6-snap.2937-T1
Couldn't classify 18822, 19271
Sorry, prediction pasa_asmbl_47482.p1 fails validation.
(GCT)	 CT	18822-19271	GG	GTG
Couldn't classify 158169, 159125
Sorry, prediction pasa_asmbl_47503.p1 fails validation.
(CAG)	 CT	158169-159125	GA	AGG
Valid prediction for GeneMark_model.27144_t
Valid prediction for Augustus_model.g10951.t1
Couldn't classify 159441, 159888
Couldn't classify 160986, 161126
Sorry, prediction pasa_asmbl_47504.p1 fails validation.
(AAC)	 CA	159441-159888	GT	GGG
(GTC)	 AG	160106-160267	GT	TGG
(TCT)	 AG	160478-160665	GT	AGG
(GGT)	 AG	160826-160888	GT	TGG
(GGC)	 AG	160986-161126	AT	ACA
-recovered pasa_asmbl_47504.p1, internal, 160106, 160267
-recovered pasa_asmbl_47504.p1, internal, 160478, 160665
-recovered pasa_asmbl_47504.p1, internal, 160826, 160888
Valid prediction for GeneMark_model.27151_t
Valid prediction for pasa_asmbl_47483.p1
Valid prediction for HiQ_model.g10961.t1
Valid prediction for Augustus_model.g10955.t1
Valid prediction for GeneMark_model.27132_t
Valid prediction for GeneMark_model.27146_t
Valid prediction for snap_scaffold_6-snap.2915-T1
Valid prediction for GeneMark_model.27130_t
Valid prediction for GlimmerHMM_glimmerT_16247-T1
Valid prediction for CodingQuarry_transcript_55174-T1
Valid prediction for GlimmerHMM_glimmerT_16261-T1
Valid prediction for snap_scaffold_6-snap.2922-T1
Valid prediction for snap_scaffold_6-snap.2930-T1
Valid prediction for GeneMark_model.27153_t
Valid prediction for Augustus_model.g10966.t1
Valid prediction for GeneMark_model.27127_t
Valid prediction for HiQ_model.g10947.t1
Valid prediction for Augustus_model.g10949.t1
Valid prediction for snap_scaffold_6-snap.2907-T1
Valid prediction for GlimmerHMM_glimmerT_16265-T1
Valid prediction for Augustus_model.g10962.t1
Valid prediction for pasa_asmbl_47486.p1
Valid prediction for GlimmerHMM_glimmerT_16263-T1
Valid prediction for CodingQuarry_transcript_55181-T1
Couldn't classify 193297, 193316
Couldn't classify 193655, 194090
Sorry, prediction pasa_asmbl_47514.p1 fails validation.
(TTG)	 TT	193297-193316	GT	TGG
(GGC)	 AG	193655-194090	CT	GGC
Valid prediction for snap_scaffold_6-snap.2926-T1
Valid prediction for GlimmerHMM_glimmerT_16266-T1
Valid prediction for GlimmerHMM_glimmerT_16264-T1
Valid prediction for snap_scaffold_6-snap.2927-T1
Valid prediction for Augustus_model.g10959.t1
Valid prediction for Augustus_model.g10960.t1
Valid prediction for HiQ_model.g10948.t1
Valid prediction for GlimmerHMM_glimmerT_16244-T1
Valid prediction for pasa_asmbl_47494.p1
Valid prediction for GeneMark_model.27141_t
Valid prediction for GeneMark_model.27149_t
Valid prediction for GeneMark_model.27117_t
Valid prediction for CodingQuarry_transcript_55180-T1
Valid prediction for GeneMark_model.27125_t
Valid prediction for GlimmerHMM_glimmerT_16260-T1
Couldn't classify 157011, 157430
Sorry, prediction pasa_asmbl_47502.p1 fails validation.
(TCG)	 AC	157011-157430	GC	GCG
Valid prediction for GeneMark_model.27116_t
Couldn't classify 162820, 162853
Sorry, prediction pasa_asmbl_47506.p1 fails validation.
(GAC)	 CT	162820-162853	GT	CGG
(GTC)	 AG	163377-163538	GT	CGG
(GCC)	 AG	163721-163885	GT	AGG
(AGT)	 AG	164011-164154	GT	AGG
(GGC)	 AG	164552-164644	GT	AGG
(CAA)	 AG	164991-165212	GT	AGG
(GCT)	 AG	165345-165415	GT	AGG
(ATC)	 AG	166186-166325	GT	ATG
(GTG)	 AG	166501-167065	CC	GAC
-recovered pasa_asmbl_47506.p1, terminal, 166501, 167065
-recovered pasa_asmbl_47506.p1, internal, 163377, 163538
-recovered pasa_asmbl_47506.p1, internal, 163721, 163885
-recovered pasa_asmbl_47506.p1, internal, 164011, 164154
-recovered pasa_asmbl_47506.p1, internal, 164552, 164644
-recovered pasa_asmbl_47506.p1, internal, 164991, 165212
-recovered pasa_asmbl_47506.p1, internal, 165345, 165415
-recovered pasa_asmbl_47506.p1, internal, 166186, 166325
Valid prediction for GeneMark_model.27120_t
Valid prediction for snap_scaffold_6-snap.2939-T1
Valid prediction for Augustus_model.g10958.t1
Valid prediction for Augustus_model.g10944.t1
Couldn't classify 61901, 61953
Sorry, prediction pasa_asmbl_47918.p1 fails validation.
(AGG)	 AT	61901-61953	GT	AAG
(GAC)	 AG	63671-63793	GT	GAG
(TAT)	 AG	63919-64081	GC	AGG
-recovered pasa_asmbl_47918.p1, terminal, 63919, 64081
-recovered pasa_asmbl_47918.p1, internal, 63671, 63793
-recovered pasa_asmbl_47918.p1, internal, 63919, 64081
Valid prediction for snap_scaffold_6-snap.2923-T1
Valid prediction for Augustus_model.g10964.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.27152_t
Valid prediction for HiQ_model.g10954.t1
Valid prediction for GeneMark_model.27126_t
Valid prediction for GeneMark_model.27113_t
Valid prediction for GeneMark_model.27145_t
Valid prediction for GlimmerHMM_glimmerT_16242-T1
Valid prediction for Augustus_model.g10956.t1
Valid prediction for CodingQuarry_transcript_55179-T1
Valid prediction for GeneMark_model.27124_t
Couldn't classify 212464, 212493
Sorry, prediction pasa_asmbl_48896.p1 fails validation.
(CTG)	 CT	212464-212493	GT	CGG
(TAC)	 AG	212641-212787	GT	AGG
(TGG)	 AG	213361-213439	GT	CTG
(GTA)	 AG	213565-213635	GT	ACG
(CAT)	 AG	213929-214014	GT	AAG
(GTA)	 AG	214133-214145	GT	AGG
-recovered pasa_asmbl_48896.p1, terminal, 214133, 214145
-recovered pasa_asmbl_48896.p1, internal, 212641, 212787
-recovered pasa_asmbl_48896.p1, internal, 213361, 213439
-recovered pasa_asmbl_48896.p1, internal, 213565, 213635
-recovered pasa_asmbl_48896.p1, internal, 213929, 214014
-recovered pasa_asmbl_48896.p1, internal, 214133, 214145
Valid prediction for GlimmerHMM_glimmerT_16257-T1
Valid prediction for Augustus_model.g10946.t1
Valid prediction for snap_scaffold_6-snap.2918-T1
Valid prediction for HiQ_model.g10953.t1
Valid prediction for GeneMark_model.27140_t
Valid prediction for GlimmerHMM_glimmerT_16250-T1
Valid prediction for GeneMark_model.27134_t
Valid prediction for GeneMark_model.27128_t
Couldn't classify 105138, 106040
Sorry, prediction pasa_asmbl_48917.p1 fails validation.
(ATC)	 AT	105138-106040	AC	AAA
Valid prediction for GlimmerHMM_glimmerT_16246-T1
Valid prediction for snap_scaffold_6-snap.2934-T1
Valid prediction for snap_scaffold_6-snap.2919-T1
Valid prediction for snap_scaffold_6-snap.2901-T1
Valid prediction for GeneMark_model.27115_t
Valid prediction for GlimmerHMM_glimmerT_16253-T1
Valid prediction for HiQ_model.g10950.t1
Valid prediction for GeneMark_model.27138_t
Valid prediction for GlimmerHMM_glimmerT_16251-T1
Valid prediction for GlimmerHMM_glimmerT_16252-T1
Valid prediction for Augustus_model.g10952.t1
Valid prediction for snap_scaffold_6-snap.2917-T1
Valid prediction for CodingQuarry_transcript_55176-T1
Valid prediction for GeneMark_model.27131_t
Valid prediction for CodingQuarry_transcript_55175-T1
Valid prediction for GlimmerHMM_glimmerT_16239-T1
Valid prediction for GlimmerHMM_glimmerT_16256-T1
Valid prediction for snap_scaffold_6-snap.2913-T1
Valid prediction for snap_scaffold_6-snap.2916-T1
Valid prediction for HiQ_model.g10957.t1
Valid prediction for CodingQuarry_transcript_55169-T1
Valid prediction for GeneMark_model.27129_t
Valid prediction for pasa_asmbl_48914.p1
Valid prediction for GeneMark_model.27150_t
Valid prediction for GeneMark_model.27133_t
Valid prediction for snap_scaffold_6-snap.2921-T1
Valid prediction for GlimmerHMM_glimmerT_16258-T1
Valid prediction for snap_scaffold_6-snap.2914-T1
Valid prediction for pasa_asmbl_48900.p1
Valid prediction for GeneMark_model.27154_t
Couldn't classify 103851, 104147
Sorry, prediction pasa_asmbl_49376.p1 fails validation.
(GAG)	 TT	103851-104147	AG	AGA
Valid prediction for pasa_asmbl_48905.p1
Valid prediction for CodingQuarry_transcript_55177-T1
Valid prediction for snap_scaffold_6-snap.2932-T1
Valid prediction for snap_scaffold_6-snap.2911-T1
Valid prediction for snap_scaffold_6-snap.2904-T1
Valid prediction for GeneMark_model.27137_t
Valid prediction for pasa_asmbl_48918.p1
Valid prediction for snap_scaffold_6-snap.2900-T1
Valid prediction for snap_scaffold_6-snap.2908-T1
Valid prediction for GeneMark_model.27148_t
Valid prediction for GeneMark_model.27122_t
Valid prediction for Augustus_model.g10942.t1
Valid prediction for HiQ_model.g10943.t1
Valid prediction for snap_scaffold_6-snap.2912-T1
Valid prediction for snap_scaffold_6-snap.2936-T1
Valid prediction for CodingQuarry_transcript_55170-T1
Valid prediction for GeneMark_model.27135_t
Couldn't classify 120818, 120912
Sorry, prediction pasa_asmbl_48913.p1 fails validation.
(GTG)	 GC	120818-120912	GT	CCG
(GCA)	 AG	120983-121066	GT	AGG
(TAA)	 AG	121201-121342	GT	AGG
(CCT)	 AG	121440-121580	GT	AGG
(ATG)	 AG	121836-121980	GC	TGG
(GCT)	 AG	122126-122326	GT	TGG
(GTA)	 AG	122532-122672	GT	AGG
(GAT)	 AG	122912-123097	GT	CGG
(ATT)	 AG	123213-123319	GT	AGG
(GTG)	 AG	123428-123604	AA	GAA
-recovered pasa_asmbl_48913.p1, initial, 121836, 121980
-recovered pasa_asmbl_48913.p1, terminal, 123428, 123604
-recovered pasa_asmbl_48913.p1, internal, 120983, 121066
-recovered pasa_asmbl_48913.p1, internal, 121201, 121342
-recovered pasa_asmbl_48913.p1, internal, 121440, 121580
-recovered pasa_asmbl_48913.p1, internal, 121836, 121980
-recovered pasa_asmbl_48913.p1, internal, 122126, 122326
-recovered pasa_asmbl_48913.p1, internal, 122532, 122672
-recovered pasa_asmbl_48913.p1, internal, 122912, 123097
-recovered pasa_asmbl_48913.p1, internal, 123213, 123319
Valid prediction for snap_scaffold_6-snap.2928-T1
Valid prediction for GlimmerHMM_glimmerT_16259-T1
Valid prediction for GeneMark_model.27147_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 132306, rend_intergenic: 130603  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157878, rend_intergenic: 156333  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161677, rend_intergenic: 157971  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185662, rend_intergenic: 181212  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 217151
-exon list size: 675


building trellis

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54.7    
54.8    
54.9    
55.1    
55.2    
55.4    
55.5    
55.7    
55.8    
56.0    
56.1    
56.3    
56.4    
56.6    
56.7    
56.9    
57.0    
57.2    
57.3    
57.5    
57.6    
57.8    
57.9    
58.1    
58.2    
58.3    
58.5    
58.6    
58.8    
58.9    
59.1    
59.2    
59.4    
59.5    
59.7    
59.8    
60.0    
60.1    
60.3    
60.4    
60.6    
60.7    
60.9    
61.0    
61.2    
61.3    
61.4    
61.6    
61.7    
61.9    
62.0    
62.2    
62.3    
62.5    
62.6    
62.8    
62.9    
63.1    
63.2    
63.4    
63.5    
63.7    
63.8    
64.0    
64.1    
64.3    
64.4    
64.5    
64.7    
64.8    
65.0    
65.1    
65.3    
65.4    
65.6    
65.7    
65.9    
66.0    
66.2    
66.3    
66.5    
66.6    
66.8    
66.9    
67.1    
67.2    
67.4    
67.5    
67.7    
67.8    
67.9    
68.1    
68.2    
68.4    
68.5    
68.7    
68.8    
69.0    
69.1    
69.3    
69.4    
69.6    
69.7    
69.9    
70.0    
70.2    
70.3    
70.5    
70.6    
70.8    
70.9    
71.0    
71.2    
71.3    
71.5    
71.6    
71.8    
71.9    
72.1    
72.2    
72.4    
72.5    
72.7    
72.8    
73.0    
73.1    
73.3    
73.4    
73.6    
73.7    
73.9    
74.0    
74.2    
74.3    
74.4    
74.6    
74.7    
74.9    
75.0    
75.2    
75.3    
75.5    
75.6    
75.8    
75.9    
76.1    
76.2    
76.4    
76.5    
76.7    
76.8    
77.0    
77.1    
77.3    
77.4    
77.5    
77.7    
77.8    
78.0    
78.1    
78.3    
78.4    
78.6    
78.7    
78.9    
79.0    
79.2    
79.3    
79.5    
79.6    
79.8    
79.9    
80.1    
80.2    
80.4    
80.5    
80.6    
80.8    
80.9    
81.1    
81.2    
81.4    
81.5    
81.7    
81.8    
82.0    
82.1    
82.3    
82.4    
82.6    
82.7    
82.9    
83.0    
83.2    
83.3    
83.5    
83.6    
83.8    
83.9    
84.0    
84.2    
84.3    
84.5    
84.6    
84.8    
84.9    
85.1    
85.2    
85.4    
85.5    
85.7    
85.8    
86.0    
86.1    
86.3    
86.4    
86.6    
86.7    
86.9    
87.0    
87.1    
87.3    
87.4    
87.6    
87.7    
87.9    
88.0    
88.2    
88.3    
88.5    
88.6    
88.8    
88.9    
89.1    
89.2    
89.4    
89.5    
89.7    
89.8    
90.0    
90.1    
90.3    
90.4    
90.5    
90.7    
90.8    
91.0    
91.1    
91.3    
91.4    
91.6    
91.7    
91.9    
92.0    
92.2    
92.3    
92.5    
92.6    
92.8    
92.9    
93.1    
93.2    
93.4    
93.5    
93.6    
93.8    
93.9    
94.1    
94.2    
94.4    
94.5    
94.7    
94.8    
95.0    
95.1    
95.3    
95.4    
95.6    
95.7    
95.9    
96.0    
96.2    
96.3    
96.5    
96.6    
96.8    
96.9    
97.0    
97.2    
97.3    
97.5    
97.6    
97.8    
97.9    
98.1    
98.2    
98.4    
98.5    
98.7    
98.8    
99.0    
99.1    
99.3    
99.4    
99.6    
99.7    
99.9    
-found 38 predictions from path traversal
Error with prediction: snap lend_intergenic: 132306, rend_intergenic: 130603  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157878, rend_intergenic: 156333  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161677, rend_intergenic: 157971  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185662, rend_intergenic: 181212  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