-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_15/scaffold_15_10702842-10919026

-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 pasa_asmbl_14415.p1
Valid prediction for snap_scaffold_15-snap.2205-T1
Valid prediction for CodingQuarry_transcript_18090-T1
Valid prediction for snap_scaffold_15-snap.2220-T1
Valid prediction for GeneMark_model.64899_t
Valid prediction for CodingQuarry_transcript_18088-T1
Valid prediction for GeneMark_model.64863_t
Valid prediction for Augustus_model.g25270.t1
Valid prediction for GeneMark_model.64881_t
Valid prediction for snap_scaffold_15-snap.2209-T1
Valid prediction for CodingQuarry_transcript_18089-T1
Valid prediction for CodingQuarry_transcript_18087-T1
Valid prediction for snap_scaffold_15-snap.2233-T1
Valid prediction for snap_scaffold_15-snap.2201-T1
Valid prediction for GeneMark_model.64893_t
Valid prediction for GeneMark_model.64903_t
Valid prediction for HiQ_model.g25255.t1
Valid prediction for GeneMark_model.64870_t
Valid prediction for Augustus_model.g25266.t1
Valid prediction for GlimmerHMM_glimmerT_37666-T1
Valid prediction for snap_scaffold_15-snap.2211-T1
Valid prediction for GlimmerHMM_glimmerT_37688-T1
Valid prediction for GlimmerHMM_glimmerT_37682-T1
Valid prediction for GlimmerHMM_glimmerT_37676-T1
Valid prediction for HiQ_model.g25263.t1
Valid prediction for GeneMark_model.64901_t
Valid prediction for GeneMark_model.64885_t
Valid prediction for pasa_asmbl_14405.p3
Valid prediction for GlimmerHMM_glimmerT_37685-T1
Valid prediction for GeneMark_model.64868_t
Valid prediction for GeneMark_model.64865_t
Valid prediction for pasa_asmbl_14418.p1
Valid prediction for Augustus_model.g25260.t1
Couldn't classify 70082, 70119
Sorry, prediction pasa_asmbl_14413.p1 fails validation.
(CTG)	 CG	70082-70119	GT	AGG
(CTG)	 AG	70386-70466	GT	TGG
(TGA)	 AG	70549-70729	AG	AAA
-recovered pasa_asmbl_14413.p1, terminal, 70549, 70729
-recovered pasa_asmbl_14413.p1, internal, 70386, 70466
Valid prediction for GeneMark_model.64879_t
Valid prediction for HiQ_model.g25257.t1
Valid prediction for snap_scaffold_15-snap.2218-T1
Valid prediction for snap_scaffold_15-snap.2222-T1
Valid prediction for GeneMark_model.64882_t
Valid prediction for GeneMark_model.64875_t
Valid prediction for GlimmerHMM_glimmerT_37677-T1
Couldn't classify 132145, 132162
Couldn't classify 133157, 133192
Sorry, prediction pasa_asmbl_14888.p2 fails validation.
(GTG)	 CG	132145-132162	GT	ACG
(TCT)	 AG	132257-132376	GT	TGG
(GTA)	 AG	132614-132712	GT	AGG
(GCT)	 AG	132825-132971	GT	AGG
(ACC)	 AG	133157-133192	CT	ACC
-recovered pasa_asmbl_14888.p2, internal, 132257, 132376
-recovered pasa_asmbl_14888.p2, internal, 132614, 132712
-recovered pasa_asmbl_14888.p2, internal, 132825, 132971
Valid prediction for GeneMark_model.64889_t
Valid prediction for GlimmerHMM_glimmerT_37669-T1
Valid prediction for GeneMark_model.64861_t
Valid prediction for GeneMark_model.64887_t
Valid prediction for GeneMark_model.64872_t
Valid prediction for snap_scaffold_15-snap.2230-T1
Valid prediction for snap_scaffold_15-snap.2213-T1
Valid prediction for snap_scaffold_15-snap.2229-T1
Valid prediction for snap_scaffold_15-snap.2212-T1
Valid prediction for GeneMark_model.64896_t
Valid prediction for snap_scaffold_15-snap.2235-T1
Valid prediction for snap_scaffold_15-snap.2203-T1
Valid prediction for Augustus_model.g25254.t1
Valid prediction for GeneMark_model.64900_t
Couldn't classify 192285, 192349
Sorry, prediction pasa_asmbl_14420.p1 fails validation.
(GCA)	 AC	192285-192349	GT	AAG
(GCT)	 AG	193412-193515	GT	ATG
(TTG)	 AG	193744-193793	GT	AGG
(AGA)	 AG	194052-194144	GT	AGG
(CTC)	 AG	194306-194399	GT	AGG
(TGC)	 AG	195127-195311	GT	GGG
(CAA)	 AG	195744-195926	GT	AGG
(GTC)	 AG	196337-196480	GT	AGG
(GAC)	 AG	198024-198113	AC	GAA
-recovered pasa_asmbl_14420.p1, terminal, 198024, 198113
-recovered pasa_asmbl_14420.p1, internal, 193412, 193515
-recovered pasa_asmbl_14420.p1, internal, 193744, 193793
-recovered pasa_asmbl_14420.p1, internal, 194052, 194144
-recovered pasa_asmbl_14420.p1, internal, 194306, 194399
-recovered pasa_asmbl_14420.p1, internal, 195127, 195311
-recovered pasa_asmbl_14420.p1, internal, 195744, 195926
-recovered pasa_asmbl_14420.p1, internal, 196337, 196480
Valid prediction for GeneMark_model.64905_t
Couldn't classify 135859, 135939
Sorry, prediction pasa_asmbl_14416.p1 fails validation.
(ATG)	 GC	135038-135180	GT	AGG
(GCA)	 AG	135327-135462	GT	AGG
(GAC)	 AG	135639-135719	GT	TGG
(GAG)	 AG	135859-135939	CT	AGC
-recovered pasa_asmbl_14416.p1, initial, 135038, 135180
-recovered pasa_asmbl_14416.p1, internal, 135327, 135462
-recovered pasa_asmbl_14416.p1, internal, 135639, 135719
Valid prediction for HiQ_model.g25267.t1
Valid prediction for snap_scaffold_15-snap.2228-T1
Valid prediction for snap_scaffold_15-snap.2202-T1
Valid prediction for GlimmerHMM_glimmerT_37668-T1
Valid prediction for GeneMark_model.64867_t
Valid prediction for GlimmerHMM_glimmerT_37665-T1
Valid prediction for snap_scaffold_15-snap.2232-T1
Valid prediction for GeneMark_model.64859_t
Valid prediction for snap_scaffold_15-snap.2219-T1
Valid prediction for CodingQuarry_transcript_18085-T1
Valid prediction for snap_scaffold_15-snap.2204-T1
Valid prediction for HiQ_model.g25256.t1
Valid prediction for GlimmerHMM_glimmerT_37672-T1
Couldn't classify 71348, 71383
Couldn't classify 72251, 72273
Sorry, prediction pasa_asmbl_14414.p1 fails validation.
(CCA)	 AG	71348-71383	GT	AGG
(ACT)	 AG	71583-71624	GT	AGG
(TCA)	 AG	71834-71957	GT	TGG
(TGA)	 AG	72070-72147	GT	TGG
(GTA)	 AG	72251-72273	AA	AGA
-recovered pasa_asmbl_14414.p1, internal, 71348, 71383
-recovered pasa_asmbl_14414.p1, internal, 71583, 71624
-recovered pasa_asmbl_14414.p1, internal, 71834, 71957
-recovered pasa_asmbl_14414.p1, internal, 72070, 72147
Valid prediction for snap_scaffold_15-snap.2223-T1
Valid prediction for GlimmerHMM_glimmerT_37683-T1
Valid prediction for CodingQuarry_transcript_18086-T1
Valid prediction for GeneMark_model.64895_t
Valid prediction for GlimmerHMM_glimmerT_37681-T1
Valid prediction for GlimmerHMM_glimmerT_37667-T1
Valid prediction for snap_scaffold_15-snap.2217-T1
Valid prediction for GeneMark_model.64897_t
Valid prediction for HiQ_model.g25268.t1
Valid prediction for snap_scaffold_15-snap.2210-T1
Valid prediction for GeneMark_model.64873_t
Valid prediction for GlimmerHMM_glimmerT_37684-T1
Valid prediction for snap_scaffold_15-snap.2214-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 140443, 140523
Couldn't classify 141438, 141520
Couldn't classify 141654, 141743
Sorry, prediction pasa_asmbl_15470.p1 fails validation.
(CTG)	 CC	140443-140523	GT	AGG
(GGT)	 AG	140615-140706	GT	ACG
(AGT)	 AG	140800-140857	GT	AGG
(GGT)	 AG	141018-141120	GT	AGG
(ATC)	 AG	141277-141328	GT	AGG
(TAT)	 AG	141438-141520	AT	CTA
(CAG)	 AC	141654-141743	GT	TGG
(ATT)	 AG	141832-141898	GT	GGG
(GAG)	 AG	142004-142088	CG	GAC
-recovered pasa_asmbl_15470.p1, terminal, 142004, 142088
-recovered pasa_asmbl_15470.p1, internal, 140615, 140706
-recovered pasa_asmbl_15470.p1, internal, 140800, 140857
-recovered pasa_asmbl_15470.p1, internal, 141018, 141120
-recovered pasa_asmbl_15470.p1, internal, 141277, 141328
-recovered pasa_asmbl_15470.p1, internal, 141832, 141898
Valid prediction for GeneMark_model.64884_t
Valid prediction for GeneMark_model.64860_t
Valid prediction for CodingQuarry_transcript_18091-T1
Valid prediction for GeneMark_model.64891_t
Valid prediction for CodingQuarry_transcript_18093-T1
Valid prediction for GeneMark_model.64874_t
Valid prediction for GeneMark_model.64886_t
Couldn't classify 137888, 137966
Couldn't classify 139459, 139557
Sorry, prediction pasa_asmbl_15471.p1 fails validation.
(CTC)	 CC	137888-137966	GT	AGG
(GCC)	 AG	138407-138474	GT	AGG
(ACC)	 AG	138772-138862	GT	CGG
(TGG)	 AG	139158-139279	GT	CGG
(AAG)	 AG	139459-139557	GT	ACG
-recovered pasa_asmbl_15471.p1, internal, 138407, 138474
-recovered pasa_asmbl_15471.p1, internal, 138772, 138862
-recovered pasa_asmbl_15471.p1, internal, 139158, 139279
-recovered pasa_asmbl_15471.p1, internal, 139459, 139557
Valid prediction for GlimmerHMM_glimmerT_37689-T1
Valid prediction for GeneMark_model.64858_t
Valid prediction for GlimmerHMM_glimmerT_37687-T1
Valid prediction for GeneMark_model.64880_t
Valid prediction for GlimmerHMM_glimmerT_37664-T1
Valid prediction for GeneMark_model.64904_t
Valid prediction for GeneMark_model.64862_t
Valid prediction for Augustus_model.g25269.t1
Valid prediction for Augustus_model.g25253.t1
Valid prediction for Augustus_model.g25258.t1
Valid prediction for GeneMark_model.64892_t
Valid prediction for snap_scaffold_15-snap.2225-T1
Couldn't classify 37338, 37374
Sorry, prediction pasa_asmbl_15478.p1 fails validation.
(GCC)	 CA	37338-37374	GT	GGG
(GGA)	 AG	38092-38165	GT	AGG
(TGG)	 AG	38883-38996	GT	AGG
(GTG)	 AG	40933-40994	GT	AGG
(TGA)	 AG	43127-43232	GT	ACG
(GGG)	 AG	45035-45112	GA	AAG
-recovered pasa_asmbl_15478.p1, terminal, 45035, 45112
-recovered pasa_asmbl_15478.p1, internal, 38092, 38165
-recovered pasa_asmbl_15478.p1, internal, 38883, 38996
-recovered pasa_asmbl_15478.p1, internal, 40933, 40994
-recovered pasa_asmbl_15478.p1, internal, 43127, 43232
Valid prediction for snap_scaffold_15-snap.2221-T1
Valid prediction for Augustus_model.g25271.t1
Valid prediction for Augustus_model.g25264.t1
Valid prediction for GeneMark_model.64871_t
Valid prediction for snap_scaffold_15-snap.2227-T1
Valid prediction for GeneMark_model.64869_t
Valid prediction for GlimmerHMM_glimmerT_37673-T1
Valid prediction for GeneMark_model.64890_t
Valid prediction for snap_scaffold_15-snap.2236-T1
Valid prediction for snap_scaffold_15-snap.2208-T1
Valid prediction for CodingQuarry_transcript_18092-T1
Valid prediction for GlimmerHMM_glimmerT_37674-T1
Valid prediction for GlimmerHMM_glimmerT_37686-T1
Valid prediction for Augustus_model.g25265.t1
Valid prediction for GeneMark_model.64898_t
Valid prediction for GlimmerHMM_glimmerT_37675-T1
Valid prediction for GeneMark_model.64878_t
Valid prediction for Augustus_model.g25262.t1
Valid prediction for snap_scaffold_15-snap.2207-T1
Valid prediction for snap_scaffold_15-snap.2224-T1
Valid prediction for GlimmerHMM_glimmerT_37678-T1
Valid prediction for GeneMark_model.64864_t
Valid prediction for snap_scaffold_15-snap.2231-T1
Valid prediction for GlimmerHMM_glimmerT_37680-T1
Valid prediction for Augustus_model.g25261.t1
Valid prediction for Augustus_model.g25252.t1
Valid prediction for snap_scaffold_15-snap.2206-T1
Valid prediction for snap_scaffold_15-snap.2226-T1
Valid prediction for GlimmerHMM_glimmerT_37671-T1
Valid prediction for GeneMark_model.64888_t
Valid prediction for GeneMark_model.64866_t
Valid prediction for snap_scaffold_15-snap.2216-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for GeneMark_model.64877_t
Valid prediction for GlimmerHMM_glimmerT_37679-T1
Valid prediction for Augustus_model.g25259.t1
Valid prediction for GeneMark_model.64902_t
Couldn't classify 11396, 11434
Sorry, prediction pasa_asmbl_15482.p1 fails validation.
(GAG)	 GG	11396-11434	GT	AGG
(GAG)	 AG	14200-14315	GT	GGG
(GTC)	 AG	15147-15579	AA	AAA
-recovered pasa_asmbl_15482.p1, terminal, 15147, 15579
-recovered pasa_asmbl_15482.p1, internal, 14200, 14315
Valid prediction for GeneMark_model.64883_t
Valid prediction for snap_scaffold_15-snap.2215-T1
Valid prediction for GlimmerHMM_glimmerT_37670-T1
Valid prediction for snap_scaffold_15-snap.2234-T1
Valid prediction for GeneMark_model.64894_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 22743, rend_intergenic: 20826  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53365, rend_intergenic: 41938  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101146, rend_intergenic: 88319  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 216185
-exon list size: 710


building trellis

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73.6    
73.7    
73.9    
74.0    
74.2    
74.3    
74.4    
74.6    
74.7    
74.9    
75.0    
75.1    
75.3    
75.4    
75.6    
75.7    
75.8    
76.0    
76.1    
76.3    
76.4    
76.5    
76.7    
76.8    
77.0    
77.1    
77.2    
77.4    
77.5    
77.7    
77.8    
77.9    
78.1    
78.2    
78.4    
78.5    
78.7    
78.8    
78.9    
79.1    
79.2    
79.4    
79.5    
79.6    
79.8    
79.9    
80.1    
80.2    
80.3    
80.5    
80.6    
80.8    
80.9    
81.0    
81.2    
81.3    
81.5    
81.6    
81.7    
81.9    
82.0    
82.2    
82.3    
82.4    
82.6    
82.7    
82.9    
83.0    
83.1    
83.3    
83.4    
83.6    
83.7    
83.8    
84.0    
84.1    
84.3    
84.4    
84.6    
84.7    
84.8    
85.0    
85.1    
85.3    
85.4    
85.5    
85.7    
85.8    
86.0    
86.1    
86.2    
86.4    
86.5    
86.7    
86.8    
86.9    
87.1    
87.2    
87.4    
87.5    
87.6    
87.8    
87.9    
88.1    
88.2    
88.3    
88.5    
88.6    
88.8    
88.9    
89.0    
89.2    
89.3    
89.5    
89.6    
89.7    
89.9    
90.0    
90.2    
90.3    
90.4    
90.6    
90.7    
90.9    
91.0    
91.2    
91.3    
91.4    
91.6    
91.7    
91.9    
92.0    
92.1    
92.3    
92.4    
92.6    
92.7    
92.8    
93.0    
93.1    
93.3    
93.4    
93.5    
93.7    
93.8    
94.0    
94.1    
94.2    
94.4    
94.5    
94.7    
94.8    
94.9    
95.1    
95.2    
95.4    
95.5    
95.6    
95.8    
95.9    
96.1    
96.2    
96.3    
96.5    
96.6    
96.8    
96.9    
97.1    
97.2    
97.3    
97.5    
97.6    
97.8    
97.9    
98.0    
98.2    
98.3    
98.5    
98.6    
98.7    
98.9    
99.0    
99.2    
99.3    
99.4    
99.6    
99.7    
99.9    
-found 47 predictions from path traversal
Error with prediction: snap lend_intergenic: 22743, rend_intergenic: 20826  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53365, rend_intergenic: 41938  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101146, rend_intergenic: 88319  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

-building DP trellis

-building trellis in range 205276 - 216185
-exon list size: 13


building trellis

6.7    
13.3    
20.0    
26.7    
33.3    
40.0    
46.7    
53.3    
60.0    
66.7    
73.3    
80.0    
86.7    
93.3    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support