-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_1/scaffold_1_20606915-20762334

-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_1-snap.3891-T1
Valid prediction for GeneMark_model.4399_t
Valid prediction for snap_scaffold_1-snap.3895-T1
Valid prediction for snap_scaffold_1-snap.3881-T1
Valid prediction for GlimmerHMM_glimmerT_2832-T1
Valid prediction for Augustus_model.g1993.t1
Valid prediction for GeneMark_model.4431_t
Valid prediction for GeneMark_model.4401_t
Valid prediction for GeneMark_model.4398_t
Valid prediction for Augustus_model.g1987.t1
Valid prediction for GlimmerHMM_glimmerT_2827-T1
Valid prediction for GeneMark_model.4420_t
Valid prediction for GlimmerHMM_glimmerT_2825-T1
Valid prediction for GlimmerHMM_glimmerT_2826-T1
Valid prediction for snap_scaffold_1-snap.3899-T1
Valid prediction for GlimmerHMM_glimmerT_2834-T1
Valid prediction for snap_scaffold_1-snap.3901-T1
Valid prediction for GeneMark_model.4410_t
Valid prediction for snap_scaffold_1-snap.3885-T1
Valid prediction for GlimmerHMM_glimmerT_2823-T1
Couldn't classify 86353, 86604
Couldn't classify 87317, 87400
Sorry, prediction pasa_asmbl_2779.p1 fails validation.
(GAC)	 AC	86353-86604	GT	AGG
(GAT)	 AG	86721-86891	GT	TGG
(ACT)	 AG	87135-87221	GT	TGG
(GAA)	 AG	87317-87400	CT	TGC
-recovered pasa_asmbl_2779.p1, internal, 86721, 86891
-recovered pasa_asmbl_2779.p1, internal, 87135, 87221
Valid prediction for pasa_asmbl_2639.p1
Valid prediction for GlimmerHMM_glimmerT_2841-T1
Valid prediction for Augustus_model.g1980.t1
Valid prediction for GeneMark_model.4435_t
Couldn't classify 87386, 87455
Sorry, prediction pasa_asmbl_2635.p1 fails validation.
(CTC)	 CT	87386-87455	GT	GGG
(AGC)	 AG	87931-88011	GT	CGG
(AAC)	 AG	88216-88344	GT	TGG
(TGC)	 AG	88503-88592	GT	AGG
(ATG)	 AG	88701-88873	GT	AGG
(TTG)	 AG	89270-89494	AG	GAA
add_exon() Sorry, pasa_asmbl_2635.p1 88701-88873-initial-1 is invalid.
-recovered pasa_asmbl_2635.p1, initial, 88701, 88873
-recovered pasa_asmbl_2635.p1, terminal, 89270, 89494
-recovered pasa_asmbl_2635.p1, internal, 87931, 88011
-recovered pasa_asmbl_2635.p1, internal, 88216, 88344
-recovered pasa_asmbl_2635.p1, internal, 88503, 88592
-recovered pasa_asmbl_2635.p1, internal, 88701, 88873
Valid prediction for Augustus_model.g1979.t1
Valid prediction for CodingQuarry_transcript_3029-T1
Valid prediction for GeneMark_model.4411_t
Valid prediction for GeneMark_model.4413_t
Valid prediction for GeneMark_model.4403_t
Valid prediction for Augustus_model.g1983.t1
Valid prediction for pasa_asmbl_2637.p1
Valid prediction for Augustus_model.g1985.t1
Valid prediction for GlimmerHMM_glimmerT_2831-T1
Valid prediction for GeneMark_model.4396_t
Valid prediction for GeneMark_model.4429_t
Valid prediction for GlimmerHMM_glimmerT_2835-T1
Valid prediction for CodingQuarry_transcript_3033-T1
Valid prediction for GlimmerHMM_glimmerT_2842-T1
Valid prediction for GeneMark_model.4424_t
Valid prediction for snap_scaffold_1-snap.3887-T1
Valid prediction for snap_scaffold_1-snap.3893-T1
Valid prediction for HiQ_model.g1986.t1
Valid prediction for snap_scaffold_1-snap.3897-T1
Valid prediction for GeneMark_model.4418_t
Valid prediction for GlimmerHMM_glimmerT_2836-T1
Valid prediction for GeneMark_model.4409_t
Valid prediction for snap_scaffold_1-snap.3911-T1
Valid prediction for GlimmerHMM_glimmerT_2828-T1
Valid prediction for GeneMark_model.4426_t
Valid prediction for GeneMark_model.4434_t
Valid prediction for snap_scaffold_1-snap.3878-T1
Valid prediction for GeneMark_model.4415_t
Valid prediction for snap_scaffold_1-snap.3880-T1
Valid prediction for GeneMark_model.4417_t
Valid prediction for snap_scaffold_1-snap.3908-T1
Valid prediction for snap_scaffold_1-snap.3909-T1
Valid prediction for Augustus_model.g1978.t1
Valid prediction for GeneMark_model.4407_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 CodingQuarry_transcript_3031-T1
Couldn't classify 43120, 44547
Sorry, prediction pasa_asmbl_1192.p1 fails validation.
(GAG)	 CT	43120-44547	CA	AGC
Valid prediction for GlimmerHMM_glimmerT_2824-T1
Valid prediction for GeneMark_model.4416_t
Valid prediction for Augustus_model.g1992.t1
Valid prediction for Augustus_model.g1989.t1
Valid prediction for GeneMark_model.4404_t
Valid prediction for snap_scaffold_1-snap.3902-T1
Valid prediction for snap_scaffold_1-snap.3883-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for snap_scaffold_1-snap.3892-T1
Valid prediction for snap_scaffold_1-snap.3894-T1
Couldn't classify 14402, 14497
Sorry, prediction pasa_asmbl_1203.p1 fails validation.
(ATG)	 CA	10174-10456	GT	AGG
(GTG)	 AG	10583-10699	GT	CAG
(GTG)	 AG	10791-10925	GT	AGG
(GCT)	 AG	11481-11634	GT	TGG
(GTG)	 AG	11737-11847	GT	ATG
(GAG)	 AG	12538-12634	GT	AGG
(ATT)	 AG	12797-12853	GT	CGG
(CTG)	 AG	12966-13082	GT	GGG
(GTC)	 AG	14402-14497	CC	CCC
-recovered pasa_asmbl_1203.p1, initial, 10174, 10456
-recovered pasa_asmbl_1203.p1, internal, 10583, 10699
-recovered pasa_asmbl_1203.p1, internal, 10791, 10925
-recovered pasa_asmbl_1203.p1, internal, 11481, 11634
-recovered pasa_asmbl_1203.p1, internal, 11737, 11847
-recovered pasa_asmbl_1203.p1, internal, 12538, 12634
-recovered pasa_asmbl_1203.p1, internal, 12797, 12853
-recovered pasa_asmbl_1203.p1, internal, 12966, 13082
Valid prediction for snap_scaffold_1-snap.3907-T1
Couldn't classify 32348, 32368
Sorry, prediction pasa_asmbl_1196.p1 fails validation.
(ATG)	 CC	30097-30478	GT	AGG
(AGC)	 AG	30706-30863	GT	AGG
(GGA)	 AG	32072-32287	GC	AGG
(GCC)	 AG	32348-32368	AT	ATA
-recovered pasa_asmbl_1196.p1, initial, 30097, 30478
-recovered pasa_asmbl_1196.p1, internal, 30706, 30863
-recovered pasa_asmbl_1196.p1, internal, 32072, 32287
Couldn't classify 42260, 42373
Couldn't classify 42720, 42816
Sorry, prediction pasa_asmbl_1366.p1 fails validation.
(GTT)	 AG	42260-42373	GT	AGG
(GTG)	 AG	42473-42582	GT	AGG
(AGA)	 AG	42720-42816	GA	GAG
-recovered pasa_asmbl_1366.p1, internal, 42260, 42373
-recovered pasa_asmbl_1366.p1, internal, 42473, 42582
Couldn't classify 72372, 72496
Sorry, prediction pasa_asmbl_1187.p1 fails validation.
(ACT)	 AC	72372-72496	GT	AGG
(CCC)	 AG	72881-73076	GT	ACG
(GTG)	 AG	73506-73572	GT	TGG
(AGG)	 AG	73878-73978	GT	CGG
(CCA)	 AG	74137-74232	CA	AAC
-recovered pasa_asmbl_1187.p1, terminal, 74137, 74232
-recovered pasa_asmbl_1187.p1, internal, 72881, 73076
-recovered pasa_asmbl_1187.p1, internal, 73506, 73572
-recovered pasa_asmbl_1187.p1, internal, 73878, 73978
Valid prediction for snap_scaffold_1-snap.3905-T1
Valid prediction for snap_scaffold_1-snap.3884-T1
Valid prediction for snap_scaffold_1-snap.3906-T1
Valid prediction for GeneMark_model.4408_t
Valid prediction for Augustus_model.g1988.t1
Valid prediction for GeneMark_model.4433_t
Valid prediction for GeneMark_model.4419_t
Valid prediction for GeneMark_model.4427_t
Valid prediction for GeneMark_model.4421_t
Valid prediction for snap_scaffold_1-snap.3904-T1
Valid prediction for GeneMark_model.4414_t
Valid prediction for HiQ_model.g1991.t1
Valid prediction for Augustus_model.g1981.t1
Valid prediction for snap_scaffold_1-snap.3912-T1
Couldn't classify 46300, 50130
Sorry, prediction pasa_asmbl_1189.p1 fails validation.
(GCA)	 GC	46300-50130	GT	TGG
(GCT)	 AG	50286-50348	GT	CGG
(AAG)	 AG	50496-50696	GT	CAG
(GGG)	 AG	50996-51154	GT	AAG
(CCT)	 AG	51575-51706	TA	AAT
-recovered pasa_asmbl_1189.p1, terminal, 51575, 51706
-recovered pasa_asmbl_1189.p1, internal, 50286, 50348
-recovered pasa_asmbl_1189.p1, internal, 50496, 50696
-recovered pasa_asmbl_1189.p1, internal, 50996, 51154
Valid prediction for GlimmerHMM_glimmerT_2840-T1
Valid prediction for GlimmerHMM_glimmerT_2829-T1
Valid prediction for GeneMark_model.4402_t
Valid prediction for snap_scaffold_1-snap.3898-T1
Couldn't classify 85219, 85626
Couldn't classify 86850, 86876
Sorry, prediction pasa_asmbl_1340.p1 fails validation.
(CGG)	 GA	85219-85626	GT	AGG
(GTG)	 AG	86122-86250	GC	AGG
(GTG)	 AG	86850-86876	AA	ACA
-recovered pasa_asmbl_1340.p1, internal, 86122, 86250
Valid prediction for GlimmerHMM_glimmerT_2837-T1
Valid prediction for GeneMark_model.4428_t
Valid prediction for Augustus_model.g1990.t1
Valid prediction for GeneMark_model.4432_t
Valid prediction for snap_scaffold_1-snap.3910-T1
Valid prediction for snap_scaffold_1-snap.3890-T1
Valid prediction for Augustus_model.g1982.t1
Valid prediction for snap_scaffold_1-snap.3900-T1
Valid prediction for GeneMark_model.4405_t
Valid prediction for GlimmerHMM_glimmerT_2830-T1
Valid prediction for pasa_asmbl_1198.p1
Valid prediction for GeneMark_model.4430_t
Couldn't classify 44797, 46236
Sorry, prediction pasa_asmbl_1191.p1 fails validation.
(ACC)	 CC	44797-46236	AA	CCA
Valid prediction for snap_scaffold_1-snap.3877-T1
Couldn't classify 32288, 32477
Sorry, prediction pasa_asmbl_1194.p1 fails validation.
(GCC)	 AG	32288-32477	GT	GGG
(AGG)	 AG	32570-32739	GT	AGG
(GCC)	 AG	33240-33418	GT	AGG
(GAA)	 AG	33738-33858	GT	AGG
(GTC)	 AG	34141-34254	GA	AGG
-recovered pasa_asmbl_1194.p1, terminal, 34141, 34254
-recovered pasa_asmbl_1194.p1, internal, 32288, 32477
-recovered pasa_asmbl_1194.p1, internal, 32570, 32739
-recovered pasa_asmbl_1194.p1, internal, 33240, 33418
-recovered pasa_asmbl_1194.p1, internal, 33738, 33858
Valid prediction for GeneMark_model.4400_t
Valid prediction for GeneMark_model.4425_t
Valid prediction for GlimmerHMM_glimmerT_2833-T1
Valid prediction for snap_scaffold_1-snap.3888-T1
Couldn't classify 3385, 3906
Sorry, prediction pasa_asmbl_2771.p1 fails validation.
(ATG)	 CC	3385-3906	CT	AGC
Valid prediction for GeneMark_model.4397_t
Valid prediction for HiQ_model.g1984.t1
Couldn't classify 97694, 97713
Sorry, prediction pasa_asmbl_1257.p1 fails validation.
(CAG)	 TT	97694-97713	GT	CGG
(GTT)	 AG	97915-98044	GT	AGG
(ATG)	 AG	99134-99238	GT	AGG
(AGG)	 AG	99510-99569	GT	AGG
(GAA)	 AG	99668-99718	GT	AGG
(GTA)	 AG	100685-100771	GA	GAG
-recovered pasa_asmbl_1257.p1, initial, 99134, 99238
-recovered pasa_asmbl_1257.p1, terminal, 100685, 100771
-recovered pasa_asmbl_1257.p1, internal, 97915, 98044
-recovered pasa_asmbl_1257.p1, internal, 99134, 99238
-recovered pasa_asmbl_1257.p1, internal, 99510, 99569
-recovered pasa_asmbl_1257.p1, internal, 99668, 99718
Valid prediction for snap_scaffold_1-snap.3882-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for CodingQuarry_transcript_3028-T1
Valid prediction for CodingQuarry_transcript_3030-T1
Valid prediction for GlimmerHMM_glimmerT_2839-T1
Valid prediction for GlimmerHMM_glimmerT_2838-T1
Valid prediction for snap_scaffold_1-snap.3889-T1
Couldn't classify 89088, 89609
Sorry, prediction pasa_asmbl_1186.p1 fails validation.
(GAG)	 AA	89088-89609	AC	AGA
Valid prediction for snap_scaffold_1-snap.3903-T1
Valid prediction for GeneMark_model.4406_t
Valid prediction for GeneMark_model.4423_t
Couldn't classify 14804, 15433
Sorry, prediction pasa_asmbl_1202.p1 fails validation.
(CAC)	 CC	14804-15433	TG	AAT
Valid prediction for snap_scaffold_1-snap.3896-T1
Valid prediction for GlimmerHMM_glimmerT_2822-T1
Valid prediction for GeneMark_model.4412_t
Valid prediction for snap_scaffold_1-snap.3886-T1
Valid prediction for snap_scaffold_1-snap.3879-T1
Valid prediction for CodingQuarry_transcript_3032-T1
Valid prediction for GeneMark_model.4395_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 12501, rend_intergenic: 6524  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 16615, rend_intergenic: 14101  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23762, rend_intergenic: 22129  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28673, rend_intergenic: 24003  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43295, rend_intergenic: 38648  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47377, rend_intergenic: 45310  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63296, rend_intergenic: 59582  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69911, rend_intergenic: 65882  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76427, rend_intergenic: 70928  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89494, rend_intergenic: 85001  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97224, rend_intergenic: 93602  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145247, rend_intergenic: 139156  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 155420
-exon list size: 597


building trellis

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72.5    
72.6    
72.8    
73.0    
73.1    
73.3    
73.5    
73.6    
73.8    
74.0    
74.1    
74.3    
74.5    
74.6    
74.8    
75.0    
75.1    
75.3    
75.5    
75.6    
75.8    
76.0    
76.1    
76.3    
76.5    
76.6    
76.8    
77.0    
77.1    
77.3    
77.5    
77.6    
77.8    
78.0    
78.1    
78.3    
78.5    
78.6    
78.8    
79.0    
79.1    
79.3    
79.5    
79.6    
79.8    
80.0    
80.1    
80.3    
80.5    
80.6    
80.8    
81.0    
81.1    
81.3    
81.5    
81.6    
81.8    
82.0    
82.1    
82.3    
82.5    
82.6    
82.8    
83.0    
83.1    
83.3    
83.5    
83.6    
83.8    
84.0    
84.1    
84.3    
84.5    
84.6    
84.8    
85.0    
85.1    
85.3    
85.5    
85.6    
85.8    
86.0    
86.1    
86.3    
86.5    
86.6    
86.8    
87.0    
87.1    
87.3    
87.5    
87.6    
87.8    
88.0    
88.1    
88.3    
88.5    
88.6    
88.8    
89.0    
89.1    
89.3    
89.5    
89.6    
89.8    
90.0    
90.2    
90.3    
90.5    
90.7    
90.8    
91.0    
91.2    
91.3    
91.5    
91.7    
91.8    
92.0    
92.2    
92.3    
92.5    
92.7    
92.8    
93.0    
93.2    
93.3    
93.5    
93.7    
93.8    
94.0    
94.2    
94.3    
94.5    
94.7    
94.8    
95.0    
95.2    
95.3    
95.5    
95.7    
95.8    
96.0    
96.2    
96.3    
96.5    
96.7    
96.8    
97.0    
97.2    
97.3    
97.5    
97.7    
97.8    
98.0    
98.2    
98.3    
98.5    
98.7    
98.8    
99.0    
99.2    
99.3    
99.5    
99.7    
99.8    
-found 28 predictions from path traversal
Error with prediction: snap lend_intergenic: 12501, rend_intergenic: 6524  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 16615, rend_intergenic: 14101  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23762, rend_intergenic: 22129  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28673, rend_intergenic: 24003  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43295, rend_intergenic: 38648  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47377, rend_intergenic: 45310  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63296, rend_intergenic: 59582  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69911, rend_intergenic: 65882  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76427, rend_intergenic: 70928  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89494, rend_intergenic: 85001  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97224, rend_intergenic: 93602  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145247, rend_intergenic: 139156  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 18 predictions persist after filtering for low support