-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_2/scaffold_2_11452839-11749505

-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_4662-T1
Valid prediction for GeneMark_model.7472_t
Couldn't classify 5784, 6014
Sorry, prediction pasa_asmbl_24791.p1 fails validation.
(CCT)	 CC	5784-6014	GT	CTG
(GTC)	 AG	6169-6277	GT	AGG
(ATG)	 AG	6467-6528	CT	AGC
-recovered pasa_asmbl_24791.p1, terminal, 6467, 6528
-recovered pasa_asmbl_24791.p1, internal, 6169, 6277
Valid prediction for GlimmerHMM_glimmerT_4660-T1
Valid prediction for GeneMark_model.7459_t
Valid prediction for Augustus_model.g3126.t1
Valid prediction for snap_scaffold_2-snap.2256-T1
Valid prediction for snap_scaffold_2-snap.2243-T1
Valid prediction for GeneMark_model.7435_t
Valid prediction for GeneMark_model.7469_t
Valid prediction for GlimmerHMM_glimmerT_4658-T1
Valid prediction for snap_scaffold_2-snap.2272-T1
Valid prediction for snap_scaffold_2-snap.2265-T1
Valid prediction for snap_scaffold_2-snap.2264-T1
Valid prediction for snap_scaffold_2-snap.2258-T1
Valid prediction for GlimmerHMM_glimmerT_4665-T1
Valid prediction for GlimmerHMM_glimmerT_4656-T1
Valid prediction for CodingQuarry_transcript_28628-T1
Valid prediction for GeneMark_model.7452_t
Valid prediction for Augustus_model.g3124.t1
Valid prediction for snap_scaffold_2-snap.2282-T1
Valid prediction for snap_scaffold_2-snap.2269-T1
Valid prediction for GeneMark_model.7466_t
Valid prediction for GlimmerHMM_glimmerT_4649-T1
Valid prediction for CodingQuarry_transcript_28623-T1
Valid prediction for GlimmerHMM_glimmerT_4650-T1
Valid prediction for Augustus_model.g3129.t1
Valid prediction for CodingQuarry_transcript_28624-T1
Valid prediction for snap_scaffold_2-snap.2250-T1
Valid prediction for snap_scaffold_2-snap.2284-T1
Valid prediction for GeneMark_model.7476_t
Valid prediction for HiQ_model.g3135.t1
Valid prediction for GeneMark_model.7453_t
Valid prediction for Augustus_model.g3125.t1
Valid prediction for HiQ_model.g3137.t1
Valid prediction for Augustus_model.g3133.t1
Valid prediction for snap_scaffold_2-snap.2255-T1
Valid prediction for GlimmerHMM_glimmerT_4659-T1
Valid prediction for GeneMark_model.7455_t
Valid prediction for Augustus_model.g3127.t1
Valid prediction for GlimmerHMM_glimmerT_4651-T1
Valid prediction for snap_scaffold_2-snap.2235-T1
Valid prediction for snap_scaffold_2-snap.2251-T1
Valid prediction for GeneMark_model.7463_t
Valid prediction for snap_scaffold_2-snap.2242-T1
Valid prediction for GeneMark_model.7443_t
Valid prediction for snap_scaffold_2-snap.2259-T1
Valid prediction for snap_scaffold_2-snap.2245-T1
Valid prediction for snap_scaffold_2-snap.2244-T1
Valid prediction for GeneMark_model.7438_t
Valid prediction for pasa_asmbl_24800.p1
Valid prediction for Augustus_model.g3134.t1
Valid prediction for GeneMark_model.7456_t
Valid prediction for GlimmerHMM_glimmerT_4652-T1
Valid prediction for snap_scaffold_2-snap.2276-T1
Valid prediction for GlimmerHMM_glimmerT_4654-T1
Valid prediction for GeneMark_model.7448_t
Valid prediction for Augustus_model.g3130.t1
Valid prediction for snap_scaffold_2-snap.2273-T1
Valid prediction for GlimmerHMM_glimmerT_4648-T1
Valid prediction for GeneMark_model.7436_t
Valid prediction for Augustus_model.g3132.t1
Valid prediction for snap_scaffold_2-snap.2249-T1
Valid prediction for GeneMark_model.7446_t
Valid prediction for Augustus_model.g3123.t1
Valid prediction for snap_scaffold_2-snap.2246-T1
Valid prediction for GeneMark_model.7464_t
Valid prediction for snap_scaffold_2-snap.2261-T1
Valid prediction for snap_scaffold_2-snap.2263-T1
Valid prediction for GlimmerHMM_glimmerT_4644-T1
Valid prediction for Augustus_model.g3131.t1
Valid prediction for GeneMark_model.7461_t
Valid prediction for GeneMark_model.7444_t
Valid prediction for CodingQuarry_transcript_28627-T1
Valid prediction for snap_scaffold_2-snap.2260-T1
Valid prediction for GlimmerHMM_glimmerT_4657-T1
Valid prediction for snap_scaffold_2-snap.2247-T1
Valid prediction for snap_scaffold_2-snap.2254-T1
Valid prediction for GeneMark_model.7454_t
Valid prediction for GeneMark_model.7442_t
Valid prediction for pasa_asmbl_24795.p1
Valid prediction for GeneMark_model.7450_t
Valid prediction for GeneMark_model.7475_t
Valid prediction for snap_scaffold_2-snap.2253-T1
Valid prediction for GeneMark_model.7430_t
Valid prediction for Augustus_model.g3128.t1
Valid prediction for snap_scaffold_2-snap.2252-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 snap_scaffold_2-snap.2281-T1
Valid prediction for snap_scaffold_2-snap.2279-T1
Valid prediction for GeneMark_model.7468_t
Valid prediction for GeneMark_model.7462_t
Valid prediction for snap_scaffold_2-snap.2266-T1
Couldn't classify 46230, 46242
Sorry, prediction pasa_asmbl_23472.p1 fails validation.
(AAG)	 CA	46230-46242	GT	AGG
(AGG)	 AG	46522-46724	GT	AGG
(ATC)	 AG	47050-47253	GC	AGG
(CTC)	 AG	47491-47635	GT	AGG
(ATG)	 AG	47880-48087	GT	AAG
(GAA)	 AG	48287-48422	GT	AGG
(ATT)	 AG	48558-48728	GT	CGG
(GAA)	 AG	48870-49023	GT	AGG
(ATC)	 AG	49120-49256	GG	AAG
add_exon() Sorry, pasa_asmbl_23472.p1 47880-48087-initial-1 is invalid.
-recovered pasa_asmbl_23472.p1, initial, 47880, 48087
-recovered pasa_asmbl_23472.p1, terminal, 49120, 49256
-recovered pasa_asmbl_23472.p1, internal, 46522, 46724
-recovered pasa_asmbl_23472.p1, internal, 47050, 47253
-recovered pasa_asmbl_23472.p1, internal, 47491, 47635
-recovered pasa_asmbl_23472.p1, internal, 47880, 48087
-recovered pasa_asmbl_23472.p1, internal, 48287, 48422
-recovered pasa_asmbl_23472.p1, internal, 48558, 48728
-recovered pasa_asmbl_23472.p1, internal, 48870, 49023
Valid prediction for snap_scaffold_2-snap.2236-T1
Valid prediction for pasa_asmbl_23469.p1
Valid prediction for Augustus_model.g3138.t1
Valid prediction for snap_scaffold_2-snap.2239-T1
Valid prediction for snap_scaffold_2-snap.2240-T1
Valid prediction for Augustus_model.g3122.t1
Couldn't classify 73032, 73357
Couldn't classify 74256, 74261
Sorry, prediction pasa_asmbl_23471.p1 fails validation.
(AAG)	 AT	73032-73357	GT	ACG
(TGA)	 AG	73479-73663	GT	AGG
(GGG)	 AG	73762-74003	GT	AGG
(ACA)	 AG	74256-74261	GG	GCG
-recovered pasa_asmbl_23471.p1, internal, 73479, 73663
-recovered pasa_asmbl_23471.p1, internal, 73762, 74003
Valid prediction for snap_scaffold_2-snap.2283-T1
Valid prediction for GeneMark_model.7439_t
Valid prediction for GeneMark_model.7445_t
Valid prediction for snap_scaffold_2-snap.2275-T1
Valid prediction for GeneMark_model.7473_t
Valid prediction for snap_scaffold_2-snap.2280-T1
Valid prediction for snap_scaffold_2-snap.2257-T1
Valid prediction for snap_scaffold_2-snap.2267-T1
Valid prediction for GeneMark_model.7434_t
Valid prediction for GeneMark_model.7449_t
Valid prediction for Augustus_model.g3121.t1
Valid prediction for GlimmerHMM_glimmerT_4646-T1
Valid prediction for GeneMark_model.7432_t
Valid prediction for CodingQuarry_transcript_28626-T1
Valid prediction for Augustus_model.g3140.t1
Valid prediction for snap_scaffold_2-snap.2274-T1
Valid prediction for snap_scaffold_2-snap.2262-T1
Valid prediction for snap_scaffold_2-snap.2237-T1
Valid prediction for snap_scaffold_2-snap.2268-T1
Valid prediction for GeneMark_model.7470_t
Valid prediction for GeneMark_model.7474_t
Valid prediction for GeneMark_model.7460_t
Couldn't classify 74325, 74462
Sorry, prediction pasa_asmbl_23470.p1 fails validation.
(GCG)	 AT	74325-74462	GT	TGG
(GTG)	 AG	74650-74794	GT	GCG
(AGG)	 AG	74944-75151	GT	AGG
(TAA)	 AG	75377-75518	GT	CAG
(GTC)	 AG	75642-75818	GT	AGG
(GAC)	 AG	75969-76128	GT	AGG
(ATT)	 AG	76574-76713	AC	AAA
-recovered pasa_asmbl_23470.p1, terminal, 76574, 76713
-recovered pasa_asmbl_23470.p1, internal, 74650, 74794
-recovered pasa_asmbl_23470.p1, internal, 74944, 75151
-recovered pasa_asmbl_23470.p1, internal, 75377, 75518
-recovered pasa_asmbl_23470.p1, internal, 75642, 75818
-recovered pasa_asmbl_23470.p1, internal, 75969, 76128
Valid prediction for GeneMark_model.7457_t
Valid prediction for GeneMark_model.7465_t
Valid prediction for snap_scaffold_2-snap.2238-T1
Valid prediction for GeneMark_model.7441_t
Valid prediction for Augustus_model.g3136.t1
Valid prediction for GeneMark_model.7431_t
Valid prediction for GlimmerHMM_glimmerT_4653-T1
Valid prediction for GlimmerHMM_glimmerT_4645-T1
Valid prediction for GlimmerHMM_glimmerT_4664-T1
Valid prediction for snap_scaffold_2-snap.2241-T1
Valid prediction for snap_scaffold_2-snap.2248-T1
Valid prediction for GlimmerHMM_glimmerT_4647-T1
Valid prediction for GlimmerHMM_glimmerT_4663-T1
Valid prediction for snap_scaffold_2-snap.2277-T1
Valid prediction for GeneMark_model.7440_t
Valid prediction for CodingQuarry_transcript_28625-T1
Valid prediction for GlimmerHMM_glimmerT_4661-T1
Valid prediction for GeneMark_model.7437_t
Valid prediction for GeneMark_model.7447_t
Valid prediction for Augustus_model.g3139.t1
Couldn't classify 44724, 44733
Couldn't classify 45440, 45480
Sorry, prediction pasa_asmbl_23473.p1 fails validation.
(GAC)	 AG	44724-44733	GT	AGG
(AGT)	 AG	44931-45148	GC	AGG
(GTG)	 AG	45242-45338	GT	CTG
(CCT)	 AG	45440-45480	GA	GCG
-recovered pasa_asmbl_23473.p1, internal, 44724, 44733
-recovered pasa_asmbl_23473.p1, internal, 44931, 45148
-recovered pasa_asmbl_23473.p1, internal, 45242, 45338
Valid prediction for Augustus_model.g3120.t1
Valid prediction for GlimmerHMM_glimmerT_4655-T1
Couldn't classify 45580, 45803
Couldn't classify 46082, 46232
Sorry, prediction pasa_asmbl_23968.p2 fails validation.
(CCT)	 CC	45580-45803	GT	ATG
(GAA)	 AG	46082-46232	GA	AGG
Valid prediction for snap_scaffold_2-snap.2271-T1
Valid prediction for GeneMark_model.7458_t
Valid prediction for GeneMark_model.7451_t
Couldn't classify 277882, 277982
Couldn't classify 279069, 279214
Sorry, prediction pasa_asmbl_23974.p1 fails validation.
(GAT)	 TG	277882-277982	GT	AGG
(CAA)	 AG	278085-278122	GT	AGG
(GTG)	 AG	278632-278763	GT	TGG
(CTT)	 AG	279069-279214	CC	CGC
-recovered pasa_asmbl_23974.p1, internal, 278085, 278122
-recovered pasa_asmbl_23974.p1, internal, 278632, 278763
Valid prediction for snap_scaffold_2-snap.2278-T1
Valid prediction for snap_scaffold_2-snap.2270-T1
Valid prediction for GeneMark_model.7467_t
Valid prediction for GeneMark_model.7471_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 6528, rend_intergenic: 3897  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130867, rend_intergenic: 127417  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 184648, rend_intergenic: 182018  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 238716, rend_intergenic: 232951  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 296667
-exon list size: 661


building trellis

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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    
93.7    
93.8    
94.0    
94.1    
94.3    
94.4    
94.6    
94.7    
94.9    
95.0    
95.2    
95.3    
95.5    
95.6    
95.8    
95.9    
96.1    
96.2    
96.4    
96.5    
96.7    
96.8    
97.0    
97.1    
97.3    
97.4    
97.6    
97.7    
97.9    
98.0    
98.2    
98.3    
98.5    
98.6    
98.8    
98.9    
99.1    
99.2    
99.4    
99.5    
99.7    
99.8    
-found 28 predictions from path traversal
Error with prediction: snap lend_intergenic: 6528, rend_intergenic: 3897  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130867, rend_intergenic: 127417  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 184648, rend_intergenic: 182018  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 238716, rend_intergenic: 232951  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 24 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 285689 - 296667
-exon list size: 3


building trellis

20.0    
40.0    
60.0    
80.0    
-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

-building DP trellis

-building trellis in range 286656 - 296667
-exon list size: 1


building trellis

33.3    
66.7    
-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