-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_1/scaffold_1_17783054-17993145

-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_2459-T1
Valid prediction for snap_scaffold_1-snap.3261-T1
Valid prediction for GeneMark_model.3617_t
Valid prediction for GlimmerHMM_glimmerT_2444-T1
Valid prediction for GeneMark_model.3629_t
Valid prediction for snap_scaffold_1-snap.3277-T1
Valid prediction for snap_scaffold_1-snap.3269-T1
Couldn't classify 131743, 131840
Sorry, prediction pasa_asmbl_2522.p1 fails validation.
(GGC)	 CA	131743-131840	GT	AGG
(TCT)	 AG	132207-132280	GT	CGG
(ACA)	 AG	132418-132494	GT	AGG
(GCG)	 AG	133023-133279	GT	GGG
(AGT)	 AG	134599-134659	GT	ATG
(GCC)	 AG	135000-135046	GT	AGG
(GTC)	 AG	135338-135446	CA	AGC
-recovered pasa_asmbl_2522.p1, terminal, 135338, 135446
-recovered pasa_asmbl_2522.p1, internal, 132207, 132280
-recovered pasa_asmbl_2522.p1, internal, 132418, 132494
-recovered pasa_asmbl_2522.p1, internal, 133023, 133279
-recovered pasa_asmbl_2522.p1, internal, 134599, 134659
-recovered pasa_asmbl_2522.p1, internal, 135000, 135046
Valid prediction for GeneMark_model.3623_t
Valid prediction for GeneMark_model.3605_t
Valid prediction for GeneMark_model.3626_t
Valid prediction for GeneMark_model.3602_t
Valid prediction for snap_scaffold_1-snap.3291-T1
Valid prediction for GeneMark_model.3583_t
Valid prediction for GlimmerHMM_glimmerT_2471-T1
Valid prediction for snap_scaffold_1-snap.3267-T1
Valid prediction for GeneMark_model.3631_t
Valid prediction for GeneMark_model.3586_t
Valid prediction for GeneMark_model.3603_t
Valid prediction for snap_scaffold_1-snap.3263-T1
Valid prediction for GlimmerHMM_glimmerT_2447-T1
Valid prediction for Augustus_model.g1769.t1
Valid prediction for GlimmerHMM_glimmerT_2462-T1
Valid prediction for snap_scaffold_1-snap.3279-T1
Valid prediction for GeneMark_model.3589_t
Valid prediction for GeneMark_model.3576_t
Valid prediction for GeneMark_model.3595_t
Valid prediction for GeneMark_model.3620_t
Valid prediction for GeneMark_model.3610_t
Valid prediction for Augustus_model.g1782.t1
Valid prediction for GeneMark_model.3597_t
Valid prediction for snap_scaffold_1-snap.3270-T1
Valid prediction for GeneMark_model.3600_t
Valid prediction for GlimmerHMM_glimmerT_2470-T1
Valid prediction for snap_scaffold_1-snap.3273-T1
Valid prediction for GeneMark_model.3614_t
Valid prediction for GeneMark_model.3591_t
Valid prediction for GeneMark_model.3578_t
Valid prediction for GlimmerHMM_glimmerT_2458-T1
Valid prediction for GeneMark_model.3608_t
Valid prediction for GeneMark_model.3593_t
Valid prediction for GlimmerHMM_glimmerT_2468-T1
Valid prediction for GeneMark_model.3581_t
Valid prediction for GlimmerHMM_glimmerT_2449-T1
Valid prediction for Augustus_model.g1774.t1
Valid prediction for snap_scaffold_1-snap.3259-T1
Valid prediction for Augustus_model.g1777.t1
Valid prediction for snap_scaffold_1-snap.3283-T1
Valid prediction for snap_scaffold_1-snap.3265-T1
Valid prediction for snap_scaffold_1-snap.3272-T1
Valid prediction for snap_scaffold_1-snap.3276-T1
Valid prediction for snap_scaffold_1-snap.3257-T1
Valid prediction for GlimmerHMM_glimmerT_2441-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_1-snap.3281-T1
Valid prediction for GlimmerHMM_glimmerT_2442-T1
Valid prediction for GlimmerHMM_glimmerT_2446-T1
Valid prediction for GeneMark_model.3590_t
Valid prediction for GeneMark_model.3594_t
Valid prediction for GeneMark_model.3609_t
Couldn't classify 16274, 16649
Couldn't classify 17455, 17529
Sorry, prediction pasa_asmbl_1073.p1 fails validation.
(GGA)	 CC	16274-16649	GT	AGG
(AGT)	 AG	17085-17248	GT	CTG
(TGT)	 AG	17455-17529	AC	TGA
-recovered pasa_asmbl_1073.p1, internal, 17085, 17248
Valid prediction for GeneMark_model.3585_t
Valid prediction for GeneMark_model.3625_t
Valid prediction for GeneMark_model.3624_t
Valid prediction for snap_scaffold_1-snap.3292-T1
Valid prediction for GeneMark_model.3592_t
Valid prediction for GeneMark_model.3584_t
Valid prediction for GlimmerHMM_glimmerT_2457-T1
Valid prediction for GeneMark_model.3599_t
Valid prediction for Augustus_model.g1775.t1
Valid prediction for Augustus_model.g1778.t1
Valid prediction for GeneMark_model.3588_t
Valid prediction for Augustus_model.g1781.t1
Valid prediction for GlimmerHMM_glimmerT_2473-T1
Valid prediction for GeneMark_model.3587_t
Valid prediction for snap_scaffold_1-snap.3278-T1
Valid prediction for Augustus_model.g1770.t1
Couldn't classify 67199, 67280
Couldn't classify 68139, 68146
Sorry, prediction pasa_asmbl_1069.p1 fails validation.
(GGG)	 GG	67199-67280	GT	AGG
(GGC)	 AG	67623-67874	GT	AGG
(ATG)	 AG	68139-68146	GT	GGG
-recovered pasa_asmbl_1069.p1, initial, 68139, 68146
-recovered pasa_asmbl_1069.p1, internal, 67623, 67874
-recovered pasa_asmbl_1069.p1, internal, 68139, 68146
Valid prediction for GlimmerHMM_glimmerT_2464-T1
Valid prediction for GlimmerHMM_glimmerT_2456-T1
Valid prediction for GlimmerHMM_glimmerT_2451-T1
Couldn't classify 58969, 59101
Couldn't classify 60030, 60271
Sorry, prediction pasa_asmbl_1070.p1 fails validation.
(GGC)	 GC	58969-59101	GT	AGG
(TGT)	 AG	59441-59576	GT	TGG
(GAA)	 AG	59768-59877	GT	TGG
(GCG)	 AG	60030-60271	GG	AGG
-recovered pasa_asmbl_1070.p1, internal, 59441, 59576
-recovered pasa_asmbl_1070.p1, internal, 59768, 59877
Valid prediction for GlimmerHMM_glimmerT_2454-T1
Valid prediction for snap_scaffold_1-snap.3284-T1
Valid prediction for snap_scaffold_1-snap.3290-T1
Valid prediction for GeneMark_model.3598_t
Valid prediction for GlimmerHMM_glimmerT_2475-T1
Valid prediction for GlimmerHMM_glimmerT_2460-T1
Valid prediction for GlimmerHMM_glimmerT_2472-T1
Valid prediction for GeneMark_model.3615_t
Valid prediction for GeneMark_model.3612_t
Valid prediction for GeneMark_model.3613_t
Valid prediction for snap_scaffold_1-snap.3293-T1
Valid prediction for GlimmerHMM_glimmerT_2453-T1
Couldn't classify 70801, 70965
Sorry, prediction pasa_asmbl_1068.p1 fails validation.
(GAG)	 CA	70801-70965	GT	CTG
(TGT)	 AG	71233-71366	GT	AGG
(GCT)	 AG	71553-71736	AT	GAA
-recovered pasa_asmbl_1068.p1, terminal, 71553, 71736
-recovered pasa_asmbl_1068.p1, internal, 71233, 71366
Valid prediction for GlimmerHMM_glimmerT_2448-T1
Valid prediction for snap_scaffold_1-snap.3282-T1
Valid prediction for GlimmerHMM_glimmerT_2452-T1
Valid prediction for snap_scaffold_1-snap.3266-T1
Valid prediction for pasa_asmbl_1063.p1
Valid prediction for Augustus_model.g1776.t1
Valid prediction for snap_scaffold_1-snap.3275-T1
Valid prediction for Augustus_model.g1784.t1
Valid prediction for snap_scaffold_1-snap.3286-T1
Couldn't classify 48581, 48680
Couldn't classify 49598, 49678
Sorry, prediction pasa_asmbl_1362.p1 fails validation.
(CTC)	 GC	48581-48680	GT	AGG
(AGT)	 AG	49057-49220	GT	CTG
(TGT)	 AG	49598-49678	TG	ACT
-recovered pasa_asmbl_1362.p1, internal, 49057, 49220
Valid prediction for snap_scaffold_1-snap.3268-T1
Valid prediction for snap_scaffold_1-snap.3285-T1
Valid prediction for GlimmerHMM_glimmerT_2450-T1
Valid prediction for HiQ_model.g1772.t1
Valid prediction for GeneMark_model.3611_t
Valid prediction for GlimmerHMM_glimmerT_2463-T1
Valid prediction for Augustus_model.g1783.t1
Valid prediction for GeneMark_model.3630_t
Valid prediction for GeneMark_model.3619_t
Valid prediction for snap_scaffold_1-snap.3264-T1
Valid prediction for snap_scaffold_1-snap.3258-T1
Couldn't classify 57621, 57816
Couldn't classify 58081, 58199
Sorry, prediction pasa_asmbl_1240.p1 fails validation.
(AAA)	 AC	57621-57816	GT	AGG
(ATG)	 AG	58081-58199	GT	AGG
add_exon() Sorry, pasa_asmbl_1240.p1 58081-58199-initial-1 is invalid.
-recovered pasa_asmbl_1240.p1, initial, 58081, 58199
-recovered pasa_asmbl_1240.p1, internal, 58081, 58199
Valid prediction for GlimmerHMM_glimmerT_2443-T1
Valid prediction for GeneMark_model.3575_t
Valid prediction for GlimmerHMM_glimmerT_2461-T1
Valid prediction for GeneMark_model.3596_t
Valid prediction for snap_scaffold_1-snap.3262-T1
Valid prediction for snap_scaffold_1-snap.3287-T1
Valid prediction for GeneMark_model.3606_t
Valid prediction for snap_scaffold_1-snap.3271-T1
Valid prediction for GeneMark_model.3621_t
Valid prediction for GeneMark_model.3580_t
Valid prediction for GlimmerHMM_glimmerT_2455-T1
Valid prediction for GeneMark_model.3577_t
Valid prediction for GeneMark_model.3579_t
Valid prediction for snap_scaffold_1-snap.3280-T1
Valid prediction for snap_scaffold_1-snap.3288-T1
Valid prediction for GeneMark_model.3601_t
Valid prediction for CodingQuarry_transcript_2973-T1
Valid prediction for GeneMark_model.3607_t
Valid prediction for GlimmerHMM_glimmerT_2466-T1
Valid prediction for GeneMark_model.3616_t
Valid prediction for GeneMark_model.3604_t
Valid prediction for GeneMark_model.3627_t
Valid prediction for GeneMark_model.3628_t
Couldn't classify 60782, 60947
Couldn't classify 61381, 61523
Sorry, prediction pasa_asmbl_1276.p1 fails validation.
(CCC)	 AG	60782-60947	GT	AGG
(AGT)	 AG	61381-61523	GA	AAG
-recovered pasa_asmbl_1276.p1, internal, 60782, 60947
Valid prediction for Augustus_model.g1771.t1
Valid prediction for GlimmerHMM_glimmerT_2474-T1
Valid prediction for GeneMark_model.3582_t
Valid prediction for GlimmerHMM_glimmerT_2445-T1
Valid prediction for GeneMark_model.3622_t
Valid prediction for GlimmerHMM_glimmerT_2469-T1
Valid prediction for snap_scaffold_1-snap.3260-T1
Valid prediction for GlimmerHMM_glimmerT_2465-T1
Valid prediction for snap_scaffold_1-snap.3289-T1
Valid prediction for GlimmerHMM_glimmerT_2467-T1
Valid prediction for snap_scaffold_1-snap.3274-T1
Valid prediction for Augustus_model.g1780.t1
Couldn't classify 60125, 60272
Couldn't classify 60471, 60634
Sorry, prediction pasa_asmbl_1325.p1 fails validation.
(GCA)	 AT	60125-60272	GT	GGG
(GCA)	 AG	60471-60634	CC	GAC
Valid prediction for pasa_asmbl_1071.p1
Valid prediction for Augustus_model.g1773.t1
Valid prediction for Augustus_model.g1779.t1
Valid prediction for pasa_asmbl_1066.p1
Valid prediction for CodingQuarry_transcript_2972-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: GlimmerHMM lend_intergenic: 37829, rend_intergenic: 37826  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 14244, rend_intergenic: 8859  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21231, rend_intergenic: 14778  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27426, rend_intergenic: 26303  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32295, rend_intergenic: 31620  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36087, rend_intergenic: 32470  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37664, rend_intergenic: 36103  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42389, rend_intergenic: 37826  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49458, rend_intergenic: 44994  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73967, rend_intergenic: 69155  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80001, rend_intergenic: 78481  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92680, rend_intergenic: 83914  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101580, rend_intergenic: 95989  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115455, rend_intergenic: 104869  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 210092
-exon list size: 753


building trellis

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71.7    
71.8    
71.9    
72.1    
72.2    
72.3    
72.5    
72.6    
72.7    
72.8    
73.0    
73.1    
73.2    
73.4    
73.5    
73.6    
73.8    
73.9    
74.0    
74.2    
74.3    
74.4    
74.6    
74.7    
74.8    
75.0    
75.1    
75.2    
75.4    
75.5    
75.6    
75.8    
75.9    
76.0    
76.2    
76.3    
76.4    
76.6    
76.7    
76.8    
77.0    
77.1    
77.2    
77.4    
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    
79.3    
79.5    
79.6    
79.7    
79.9    
80.0    
80.1    
80.3    
80.4    
80.5    
80.7    
80.8    
80.9    
81.1    
81.2    
81.3    
81.5    
81.6    
81.7    
81.9    
82.0    
82.1    
82.3    
82.4    
82.5    
82.6    
82.8    
82.9    
83.0    
83.2    
83.3    
83.4    
83.6    
83.7    
83.8    
84.0    
84.1    
84.2    
84.4    
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    
87.5    
87.7    
87.8    
87.9    
88.1    
88.2    
88.3    
88.5    
88.6    
88.7    
88.9    
89.0    
89.1    
89.3    
89.4    
89.5    
89.7    
89.8    
89.9    
90.1    
90.2    
90.3    
90.5    
90.6    
90.7    
90.9    
91.0    
91.1    
91.3    
91.4    
91.5    
91.7    
91.8    
91.9    
92.1    
92.2    
92.3    
92.5    
92.6    
92.7    
92.8    
93.0    
93.1    
93.2    
93.4    
93.5    
93.6    
93.8    
93.9    
94.0    
94.2    
94.3    
94.4    
94.6    
94.7    
94.8    
95.0    
95.1    
95.2    
95.4    
95.5    
95.6    
95.8    
95.9    
96.0    
96.2    
96.3    
96.4    
96.6    
96.7    
96.8    
97.0    
97.1    
97.2    
97.4    
97.5    
97.6    
97.7    
97.9    
98.0    
98.1    
98.3    
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 46 predictions from path traversal
Error with prediction: GlimmerHMM lend_intergenic: 37829, rend_intergenic: 37826  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 14244, rend_intergenic: 8859  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21231, rend_intergenic: 14778  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27426, rend_intergenic: 26303  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32295, rend_intergenic: 31620  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36087, rend_intergenic: 32470  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37664, rend_intergenic: 36103  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42389, rend_intergenic: 37826  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49458, rend_intergenic: 44994  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73967, rend_intergenic: 69155  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80001, rend_intergenic: 78481  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92680, rend_intergenic: 83914  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101580, rend_intergenic: 95989  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115455, rend_intergenic: 104869  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 23 predictions persist after filtering for low support