-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_5/scaffold_5_15682736-15851719

-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_5-snap.2939-T1
Valid prediction for GeneMark_model.22746_t
Valid prediction for GlimmerHMM_glimmerT_13559-T1
Valid prediction for CodingQuarry_transcript_52269-T1
Valid prediction for GeneMark_model.22750_t
Valid prediction for GeneMark_model.22787_t
Valid prediction for snap_scaffold_5-snap.2910-T1
Valid prediction for GlimmerHMM_glimmerT_13558-T1
Valid prediction for GlimmerHMM_glimmerT_13563-T1
Valid prediction for GeneMark_model.22760_t
Valid prediction for GeneMark_model.22795_t
Valid prediction for snap_scaffold_5-snap.2913-T1
Couldn't classify 20730, 20885
Sorry, prediction pasa_asmbl_44675.p1 fails validation.
(TTG)	 GC	20730-20885	GT	TGG
(ACA)	 AG	23350-23476	GT	TGG
(ACA)	 AG	23632-23807	GT	AGG
(GAG)	 AG	24752-24901	GG	GAG
-recovered pasa_asmbl_44675.p1, terminal, 24752, 24901
-recovered pasa_asmbl_44675.p1, internal, 23350, 23476
-recovered pasa_asmbl_44675.p1, internal, 23632, 23807
Valid prediction for GeneMark_model.22785_t
Valid prediction for snap_scaffold_5-snap.2918-T1
Valid prediction for snap_scaffold_5-snap.2925-T1
Valid prediction for GlimmerHMM_glimmerT_13560-T1
Valid prediction for GlimmerHMM_glimmerT_13564-T1
Valid prediction for HiQ_model.g9072.t1
Valid prediction for GeneMark_model.22767_t
Valid prediction for GlimmerHMM_glimmerT_13562-T1
Valid prediction for GeneMark_model.22773_t
Valid prediction for Augustus_model.g9073.t1
Valid prediction for snap_scaffold_5-snap.2904-T1
Valid prediction for GeneMark_model.22772_t
Valid prediction for CodingQuarry_transcript_52268-T1
Valid prediction for GeneMark_model.22771_t
Valid prediction for snap_scaffold_5-snap.2906-T1
Valid prediction for snap_scaffold_5-snap.2934-T1
Valid prediction for GeneMark_model.22774_t
Valid prediction for snap_scaffold_5-snap.2914-T1
Valid prediction for GlimmerHMM_glimmerT_13547-T1
Valid prediction for GlimmerHMM_glimmerT_13553-T1
Valid prediction for GeneMark_model.22763_t
Valid prediction for snap_scaffold_5-snap.2923-T1
Valid prediction for GlimmerHMM_glimmerT_13567-T1
Valid prediction for GlimmerHMM_glimmerT_13569-T1
Valid prediction for snap_scaffold_5-snap.2924-T1
Valid prediction for GeneMark_model.22790_t
Valid prediction for GeneMark_model.22792_t
Valid prediction for GlimmerHMM_glimmerT_13565-T1
Valid prediction for pasa_asmbl_44673.p1
Valid prediction for GeneMark_model.22761_t
Valid prediction for GlimmerHMM_glimmerT_13566-T1
Valid prediction for GlimmerHMM_glimmerT_13549-T1
Valid prediction for GeneMark_model.22744_t
Valid prediction for snap_scaffold_5-snap.2901-T1
Valid prediction for GeneMark_model.22765_t
Valid prediction for Augustus_model.g9069.t1
Valid prediction for snap_scaffold_5-snap.2936-T1
Valid prediction for GeneMark_model.22781_t
Valid prediction for snap_scaffold_5-snap.2912-T1
Valid prediction for GlimmerHMM_glimmerT_13546-T1
Valid prediction for GeneMark_model.22793_t
Valid prediction for Augustus_model.g9068.t1
Valid prediction for GeneMark_model.22783_t
Valid prediction for GeneMark_model.22752_t
Valid prediction for pasa_asmbl_44677.p1
Valid prediction for GeneMark_model.22759_t
Valid prediction for Augustus_model.g9064.t1
Valid prediction for GlimmerHMM_glimmerT_13550-T1
Valid prediction for snap_scaffold_5-snap.2937-T1
Valid prediction for CodingQuarry_transcript_52270-T1
Valid prediction for GeneMark_model.22770_t
Valid prediction for GeneMark_model.22743_t
Valid prediction for GeneMark_model.22754_t
Valid prediction for snap_scaffold_5-snap.2917-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_5-snap.2926-T1
Valid prediction for Augustus_model.g9062.t1
Valid prediction for GeneMark_model.22779_t
Valid prediction for snap_scaffold_5-snap.2921-T1
Valid prediction for Augustus_model.g9074.t1
Valid prediction for GeneMark_model.22749_t

-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 Augustus_model.g9076.t1
Valid prediction for Augustus_model.g9082.t1
Valid prediction for snap_scaffold_5-snap.2933-T1
Valid prediction for GeneMark_model.22756_t
Valid prediction for GeneMark_model.22748_t
Valid prediction for GlimmerHMM_glimmerT_13557-T1
Valid prediction for snap_scaffold_5-snap.2899-T1
Valid prediction for GlimmerHMM_glimmerT_13551-T1
Couldn't classify 137571, 137610
Sorry, prediction pasa_asmbl_46098.p1 fails validation.
(CTA)	 CT	137571-137610	GT	AGG
(CCG)	 AG	138303-138476	GT	CGG
(GAC)	 AG	138579-138806	GT	CCG
(GAG)	 AG	139011-139129	GT	AGG
(TTT)	 AG	139481-139609	GT	TGG
(GTC)	 AG	139853-140024	GT	AGG
(TCT)	 AG	140346-140475	GT	TGG
(GAA)	 AG	140648-140751	GT	GGG
(GTG)	 AG	140846-141088	GT	AGG
(GCT)	 AG	141289-141564	GT	GGG
(AGA)	 AG	141724-141884	GT	ATG
(ATC)	 AG	142105-142241	GT	GTG
(GAT)	 AG	142434-142581	CA	GAC
-recovered pasa_asmbl_46098.p1, terminal, 142434, 142581
-recovered pasa_asmbl_46098.p1, internal, 138303, 138476
-recovered pasa_asmbl_46098.p1, internal, 138579, 138806
-recovered pasa_asmbl_46098.p1, internal, 139011, 139129
-recovered pasa_asmbl_46098.p1, internal, 139481, 139609
-recovered pasa_asmbl_46098.p1, internal, 139853, 140024
-recovered pasa_asmbl_46098.p1, internal, 140346, 140475
-recovered pasa_asmbl_46098.p1, internal, 140648, 140751
-recovered pasa_asmbl_46098.p1, internal, 140846, 141088
-recovered pasa_asmbl_46098.p1, internal, 141289, 141564
-recovered pasa_asmbl_46098.p1, internal, 141724, 141884
-recovered pasa_asmbl_46098.p1, internal, 142105, 142241
Couldn't classify 95847, 95993
Sorry, prediction pasa_asmbl_46102.p1 fails validation.
(GAG)	 AG	95847-95993	GT	GGG
(GAC)	 AG	96079-96131	GT	ACG
(GCT)	 AG	96250-96316	GT	CAG
(GCG)	 AG	96560-96631	TT	GAT
-recovered pasa_asmbl_46102.p1, terminal, 96560, 96631
-recovered pasa_asmbl_46102.p1, internal, 95847, 95993
-recovered pasa_asmbl_46102.p1, internal, 96079, 96131
-recovered pasa_asmbl_46102.p1, internal, 96250, 96316
Valid prediction for snap_scaffold_5-snap.2931-T1
Valid prediction for GeneMark_model.22776_t
Valid prediction for GeneMark_model.22784_t
Valid prediction for HiQ_model.g9065.t1
Valid prediction for snap_scaffold_5-snap.2903-T1
Valid prediction for snap_scaffold_5-snap.2941-T1
Valid prediction for GeneMark_model.22789_t
Valid prediction for GlimmerHMM_glimmerT_13555-T1
Valid prediction for Augustus_model.g9063.t1
Valid prediction for snap_scaffold_5-snap.2922-T1
Couldn't classify 155369, 155405
Sorry, prediction pasa_asmbl_46097.p1 fails validation.
(CAA)	 TG	155369-155405	GT	GGG
(GTG)	 AG	156023-156110	GT	AGG
(TGT)	 AG	156371-156590	CG	AAC
-recovered pasa_asmbl_46097.p1, terminal, 156371, 156590
-recovered pasa_asmbl_46097.p1, internal, 156023, 156110
Valid prediction for GlimmerHMM_glimmerT_13573-T1
Valid prediction for snap_scaffold_5-snap.2915-T1
Valid prediction for GeneMark_model.22778_t
Valid prediction for snap_scaffold_5-snap.2902-T1
Valid prediction for snap_scaffold_5-snap.2908-T1
Valid prediction for GeneMark_model.22788_t
Valid prediction for GeneMark_model.22757_t
Valid prediction for GeneMark_model.22745_t
Valid prediction for GeneMark_model.22762_t
Valid prediction for snap_scaffold_5-snap.2900-T1
Valid prediction for Augustus_model.g9071.t1
Valid prediction for GeneMark_model.22753_t
Valid prediction for snap_scaffold_5-snap.2920-T1
Couldn't classify 40940, 41125
Couldn't classify 42125, 42217
Sorry, prediction pasa_asmbl_46113.p1 fails validation.
(GGT)	 CA	40940-41125	GT	AGG
(CAC)	 AG	41416-41508	GT	CGG
(TCC)	 AG	42125-42217	GC	CCG
-recovered pasa_asmbl_46113.p1, internal, 41416, 41508
-recovered pasa_asmbl_46113.p1, internal, 42125, 42217
Valid prediction for GeneMark_model.22791_t
Valid prediction for GlimmerHMM_glimmerT_13575-T1
Valid prediction for snap_scaffold_5-snap.2919-T1
Valid prediction for snap_scaffold_5-snap.2916-T1
Valid prediction for HiQ_model.g9078.t1
Valid prediction for snap_scaffold_5-snap.2909-T1
Valid prediction for GeneMark_model.22782_t
Valid prediction for GlimmerHMM_glimmerT_13571-T1
Valid prediction for GlimmerHMM_glimmerT_13574-T1
Valid prediction for pasa_asmbl_46110.p1
Valid prediction for GeneMark_model.22764_t
Valid prediction for snap_scaffold_5-snap.2938-T1
Valid prediction for CodingQuarry_transcript_52271-T1
Valid prediction for GlimmerHMM_glimmerT_13570-T1
Valid prediction for Augustus_model.g9081.t1
Couldn't classify 60195, 60231
Sorry, prediction pasa_asmbl_46103.p1 fails validation.
(GCC)	 AC	60195-60231	GT	TGG
(GCA)	 AG	60355-60430	GT	GAG
(GAT)	 AG	60566-60632	GT	AGG
(ATT)	 AG	60853-60978	GT	ACG
(GTC)	 AG	61090-61194	AA	GAA
add_exon() Sorry, pasa_asmbl_46103.p1 60355-60430-terminal-3 is invalid.
-recovered pasa_asmbl_46103.p1, terminal, 60355, 60430
-recovered pasa_asmbl_46103.p1, terminal, 61090, 61194
-recovered pasa_asmbl_46103.p1, internal, 60355, 60430
-recovered pasa_asmbl_46103.p1, internal, 60566, 60632
-recovered pasa_asmbl_46103.p1, internal, 60853, 60978
Valid prediction for GeneMark_model.22769_t
Valid prediction for CodingQuarry_transcript_52272-T1
Valid prediction for GeneMark_model.22786_t
Valid prediction for GeneMark_model.22775_t
Valid prediction for GeneMark_model.22766_t
Valid prediction for GeneMark_model.22768_t
Valid prediction for snap_scaffold_5-snap.2935-T1
Valid prediction for snap_scaffold_5-snap.2905-T1
Valid prediction for GeneMark_model.22751_t
Valid prediction for Augustus_model.g9077.t1
Valid prediction for GeneMark_model.22794_t
Valid prediction for GlimmerHMM_glimmerT_13576-T1
Valid prediction for GeneMark_model.22758_t
Valid prediction for GlimmerHMM_glimmerT_13556-T1
Valid prediction for GeneMark_model.22777_t
Valid prediction for GeneMark_model.22780_t
Valid prediction for Augustus_model.g9083.t1
Valid prediction for snap_scaffold_5-snap.2930-T1
Valid prediction for GlimmerHMM_glimmerT_13554-T1
Valid prediction for snap_scaffold_5-snap.2907-T1
Valid prediction for Augustus_model.g9080.t1
Valid prediction for snap_scaffold_5-snap.2932-T1
Valid prediction for Augustus_model.g9075.t1
Valid prediction for GlimmerHMM_glimmerT_13561-T1
Valid prediction for Augustus_model.g9067.t1
Valid prediction for snap_scaffold_5-snap.2929-T1
Valid prediction for CodingQuarry_transcript_52273-T1
Valid prediction for Augustus_model.g9066.t1
Valid prediction for GlimmerHMM_glimmerT_13572-T1
Valid prediction for Augustus_model.g9070.t1
Valid prediction for Augustus_model.g9079.t1
Couldn't classify 59193, 59498
Couldn't classify 60108, 60125
Sorry, prediction pasa_asmbl_46104.p1 fails validation.
(ACT)	 GG	59193-59498	GT	AGG
(GTT)	 AG	59599-59643	GT	AGG
(TGG)	 AG	59723-59779	GT	AGG
(ATG)	 AG	59877-60020	GT	AGG
(GTC)	 AG	60108-60125	CC	CAC
-recovered pasa_asmbl_46104.p1, initial, 59877, 60020
-recovered pasa_asmbl_46104.p1, internal, 59599, 59643
-recovered pasa_asmbl_46104.p1, internal, 59723, 59779
-recovered pasa_asmbl_46104.p1, internal, 59877, 60020
Valid prediction for snap_scaffold_5-snap.2928-T1
Valid prediction for snap_scaffold_5-snap.2911-T1
Valid prediction for snap_scaffold_5-snap.2927-T1
Valid prediction for GlimmerHMM_glimmerT_13568-T1
Valid prediction for GeneMark_model.22755_t
Valid prediction for GlimmerHMM_glimmerT_13548-T1
Valid prediction for GlimmerHMM_glimmerT_13552-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 7323, rend_intergenic: 6658  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 14290, rend_intergenic: 12395  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24901, rend_intergenic: 20697  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30686, rend_intergenic: 26404  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39947, rend_intergenic: 36703  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42517, rend_intergenic: 40215  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48961, rend_intergenic: 42559  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55032, rend_intergenic: 50666  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65105, rend_intergenic: 59715  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66137, rend_intergenic: 65767  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79158, rend_intergenic: 75276  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128635, rend_intergenic: 126708  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131457, rend_intergenic: 130827  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142670, rend_intergenic: 131946  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143365, rend_intergenic: 143314  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162949, rend_intergenic: 146193  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 168984
-exon list size: 739


building trellis

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59.0    
59.1    
59.2    
59.4    
59.5    
59.6    
59.8    
59.9    
60.1    
60.2    
60.3    
60.5    
60.6    
60.7    
60.9    
61.0    
61.1    
61.3    
61.4    
61.5    
61.7    
61.8    
61.9    
62.1    
62.2    
62.3    
62.5    
62.6    
62.8    
62.9    
63.0    
63.2    
63.3    
63.4    
63.6    
63.7    
63.8    
64.0    
64.1    
64.2    
64.4    
64.5    
64.6    
64.8    
64.9    
65.0    
65.2    
65.3    
65.5    
65.6    
65.7    
65.9    
66.0    
66.1    
66.3    
66.4    
66.5    
66.7    
66.8    
66.9    
67.1    
67.2    
67.3    
67.5    
67.6    
67.7    
67.9    
68.0    
68.2    
68.3    
68.4    
68.6    
68.7    
68.8    
69.0    
69.1    
69.2    
69.4    
69.5    
69.6    
69.8    
69.9    
70.0    
70.2    
70.3    
70.4    
70.6    
70.7    
70.9    
71.0    
71.1    
71.3    
71.4    
71.5    
71.7    
71.8    
71.9    
72.1    
72.2    
72.3    
72.5    
72.6    
72.7    
72.9    
73.0    
73.1    
73.3    
73.4    
73.5    
73.7    
73.8    
74.0    
74.1    
74.2    
74.4    
74.5    
74.6    
74.8    
74.9    
75.0    
75.2    
75.3    
75.4    
75.6    
75.7    
75.8    
76.0    
76.1    
76.2    
76.4    
76.5    
76.7    
76.8    
76.9    
77.1    
77.2    
77.3    
77.5    
77.6    
77.7    
77.9    
78.0    
78.1    
78.3    
78.4    
78.5    
78.7    
78.8    
78.9    
79.1    
79.2    
79.4    
79.5    
79.6    
79.8    
79.9    
80.0    
80.2    
80.3    
80.4    
80.6    
80.7    
80.8    
81.0    
81.1    
81.2    
81.4    
81.5    
81.6    
81.8    
81.9    
82.1    
82.2    
82.3    
82.5    
82.6    
82.7    
82.9    
83.0    
83.1    
83.3    
83.4    
83.5    
83.7    
83.8    
83.9    
84.1    
84.2    
84.3    
84.5    
84.6    
84.8    
84.9    
85.0    
85.2    
85.3    
85.4    
85.6    
85.7    
85.8    
86.0    
86.1    
86.2    
86.4    
86.5    
86.6    
86.8    
86.9    
87.0    
87.2    
87.3    
87.4    
87.6    
87.7    
87.9    
88.0    
88.1    
88.3    
88.4    
88.5    
88.7    
88.8    
88.9    
89.1    
89.2    
89.3    
89.5    
89.6    
89.7    
89.9    
90.0    
90.1    
90.3    
90.4    
90.6    
90.7    
90.8    
91.0    
91.1    
91.2    
91.4    
91.5    
91.6    
91.8    
91.9    
92.0    
92.2    
92.3    
92.4    
92.6    
92.7    
92.8    
93.0    
93.1    
93.3    
93.4    
93.5    
93.7    
93.8    
93.9    
94.1    
94.2    
94.3    
94.5    
94.6    
94.7    
94.9    
95.0    
95.1    
95.3    
95.4    
95.5    
95.7    
95.8    
96.0    
96.1    
96.2    
96.4    
96.5    
96.6    
96.8    
96.9    
97.0    
97.2    
97.3    
97.4    
97.6    
97.7    
97.8    
98.0    
98.1    
98.2    
98.4    
98.5    
98.7    
98.8    
98.9    
99.1    
99.2    
99.3    
99.5    
99.6    
99.7    
99.9    
-found 37 predictions from path traversal
Error with prediction: snap lend_intergenic: 7323, rend_intergenic: 6658  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 14290, rend_intergenic: 12395  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24901, rend_intergenic: 20697  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30686, rend_intergenic: 26404  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39947, rend_intergenic: 36703  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42517, rend_intergenic: 40215  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48961, rend_intergenic: 42559  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55032, rend_intergenic: 50666  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65105, rend_intergenic: 59715  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66137, rend_intergenic: 65767  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79158, rend_intergenic: 75276  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128635, rend_intergenic: 126708  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131457, rend_intergenic: 130827  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142670, rend_intergenic: 131946  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143365, rend_intergenic: 143314  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162949, rend_intergenic: 146193  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 27 predictions persist after filtering for low support