-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_1/scaffold_1_19040295-19247629

-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 GeneMark_model.3985_t
Valid prediction for GeneMark_model.3957_t
Valid prediction for Augustus_model.g1875.t1
Couldn't classify 192931, 193536
Sorry, prediction pasa_asmbl_2572.p1 fails validation.
(CCA)	 CC	192931-193536	AA	AAA
Valid prediction for snap_scaffold_1-snap.3545-T1
Valid prediction for GeneMark_model.3989_t
Valid prediction for snap_scaffold_1-snap.3558-T1
Valid prediction for snap_scaffold_1-snap.3560-T1
Valid prediction for GlimmerHMM_glimmerT_2625-T1
Valid prediction for snap_scaffold_1-snap.3538-T1
Valid prediction for Augustus_model.g1876.t1
Valid prediction for Augustus_model.g1882.t1
Valid prediction for snap_scaffold_1-snap.3563-T1
Valid prediction for GlimmerHMM_glimmerT_2650-T1
Valid prediction for GlimmerHMM_glimmerT_2644-T1
Valid prediction for GeneMark_model.3993_t
Couldn't classify 200879, 200902
Sorry, prediction pasa_asmbl_2574.p1 fails validation.
(GAG)	 CA	200879-200902	GT	AGG
(GCC)	 AG	201520-201650	GT	AAG
(GTT)	 AG	201812-201989	GT	AGG
(GTG)	 AG	202129-202311	GT	CTG
(ATG)	 AG	202768-202844	GT	TGG
(GAG)	 AG	203051-203131	GT	AGG
(TGA)	 AG	203230-203316	GT	AGG
(TCG)	 AG	203561-203731	GT	GGG
(CAC)	 AG	204962-205439	GA	GAG
-recovered pasa_asmbl_2574.p1, initial, 202768, 202844
-recovered pasa_asmbl_2574.p1, terminal, 204962, 205439
-recovered pasa_asmbl_2574.p1, internal, 201520, 201650
-recovered pasa_asmbl_2574.p1, internal, 201812, 201989
-recovered pasa_asmbl_2574.p1, internal, 202129, 202311
-recovered pasa_asmbl_2574.p1, internal, 202768, 202844
-recovered pasa_asmbl_2574.p1, internal, 203051, 203131
-recovered pasa_asmbl_2574.p1, internal, 203230, 203316
-recovered pasa_asmbl_2574.p1, internal, 203561, 203731
Valid prediction for snap_scaffold_1-snap.3570-T1
Valid prediction for GlimmerHMM_glimmerT_2640-T1
Valid prediction for snap_scaffold_1-snap.3571-T1
Valid prediction for Augustus_model.g1884.t1
Valid prediction for GeneMark_model.3958_t
Valid prediction for snap_scaffold_1-snap.3559-T1
Valid prediction for GeneMark_model.3981_t
add_exon() Sorry, GeneMark_model.3981_t 96639-97039-terminal-1 is invalid.
Valid prediction for GlimmerHMM_glimmerT_2631-T1
Couldn't classify 136326, 136670
Sorry, prediction pasa_asmbl_1142.p1 fails validation.
(GTC)	 TT	136326-136670	AT	AGA
Valid prediction for GeneMark_model.3969_t
Valid prediction for snap_scaffold_1-snap.3550-T1
Valid prediction for GeneMark_model.3967_t
Valid prediction for GeneMark_model.3956_t
Valid prediction for snap_scaffold_1-snap.3542-T1
Valid prediction for snap_scaffold_1-snap.3564-T1
Valid prediction for GeneMark_model.3977_t
Valid prediction for snap_scaffold_1-snap.3535-T1
Valid prediction for snap_scaffold_1-snap.3565-T1
Valid prediction for GeneMark_model.3999_t
Couldn't classify 185829, 185960
Couldn't classify 188382, 188457
Sorry, prediction pasa_asmbl_2570.p1 fails validation.
(CAT)	 AG	185829-185960	GT	AGG
(ATC)	 AG	186126-186338	GT	GGG
(GCC)	 AG	186521-186639	GT	AGG
(CCA)	 AG	188382-188457	TA	ACT
-recovered pasa_asmbl_2570.p1, internal, 185829, 185960
-recovered pasa_asmbl_2570.p1, internal, 186126, 186338
-recovered pasa_asmbl_2570.p1, internal, 186521, 186639
Valid prediction for GlimmerHMM_glimmerT_2643-T1
Valid prediction for GeneMark_model.3980_t
Valid prediction for GeneMark_model.3979_t
Valid prediction for Augustus_model.g1889.t1
Valid prediction for GeneMark_model.4000_t
Couldn't classify 198080, 198123
Couldn't classify 199067, 199113
Sorry, prediction pasa_asmbl_2573.p2 fails validation.
(CAG)	 CC	198080-198123	GT	TGG
(GCA)	 AG	198256-198322	GT	AGG
(ATC)	 AG	198508-198829	GT	GGG
(GCA)	 AG	199067-199113	AG	CCA
-recovered pasa_asmbl_2573.p2, internal, 198256, 198322
-recovered pasa_asmbl_2573.p2, internal, 198508, 198829
Valid prediction for GeneMark_model.3991_t
Valid prediction for snap_scaffold_1-snap.3569-T1
Valid prediction for GeneMark_model.3995_t
Valid prediction for GlimmerHMM_glimmerT_2634-T1
Valid prediction for Augustus_model.g1891.t1
Valid prediction for snap_scaffold_1-snap.3536-T1
Valid prediction for GeneMark_model.3963_t
Valid prediction for GlimmerHMM_glimmerT_2624-T1
Valid prediction for GeneMark_model.3971_t
Valid prediction for snap_scaffold_1-snap.3561-T1
Valid prediction for snap_scaffold_1-snap.3547-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GeneMark_model.3974_t
Valid prediction for GeneMark_model.4002_t
Couldn't classify 188894, 188925
Couldn't classify 190045, 190224
Sorry, prediction pasa_asmbl_2571.p1 fails validation.
(AGC)	 AC	188894-188925	GT	AGG
(GGC)	 AG	189314-189519	GT	TGG
(ACC)	 AG	189617-189792	GT	AGG
(CCA)	 AG	190045-190224	TT	CCT
-recovered pasa_asmbl_2571.p1, internal, 189314, 189519
-recovered pasa_asmbl_2571.p1, internal, 189617, 189792
Valid prediction for snap_scaffold_1-snap.3575-T1
Valid prediction for GeneMark_model.3987_t
Valid prediction for GlimmerHMM_glimmerT_2639-T1
Valid prediction for GeneMark_model.3984_t
Valid prediction for GlimmerHMM_glimmerT_2642-T1
Valid prediction for GlimmerHMM_glimmerT_2648-T1
Valid prediction for GeneMark_model.3997_t
Valid prediction for GeneMark_model.3960_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.g1880.t1
Valid prediction for GeneMark_model.3983_t
Valid prediction for GeneMark_model.3973_t
Valid prediction for Augustus_model.g1878.t1
Valid prediction for CodingQuarry_transcript_3002-T1
Valid prediction for snap_scaffold_1-snap.3543-T1
Valid prediction for snap_scaffold_1-snap.3551-T1
Couldn't classify 158340, 158478
Sorry, prediction pasa_asmbl_1139.p1 fails validation.
(ATG)	 CC	156879-156975	GT	AGG
(GCT)	 AG	157102-157274	GT	AGG
(AAA)	 AG	157441-157569	GT	CTG
(TAC)	 AG	157660-157845	GT	AGG
(GAA)	 AG	157961-158205	GT	ACG
(GTA)	 AG	158340-158478	AC	ATA
-recovered pasa_asmbl_1139.p1, initial, 156879, 156975
-recovered pasa_asmbl_1139.p1, internal, 157102, 157274
-recovered pasa_asmbl_1139.p1, internal, 157441, 157569
-recovered pasa_asmbl_1139.p1, internal, 157660, 157845
-recovered pasa_asmbl_1139.p1, internal, 157961, 158205
Valid prediction for snap_scaffold_1-snap.3546-T1
Valid prediction for snap_scaffold_1-snap.3566-T1
Valid prediction for snap_scaffold_1-snap.3576-T1
Valid prediction for Augustus_model.g1890.t1
Valid prediction for snap_scaffold_1-snap.3553-T1
Valid prediction for Augustus_model.g1886.t1
Valid prediction for GeneMark_model.3972_t
Valid prediction for GeneMark_model.3994_t
Couldn't classify 150379, 150505
Sorry, prediction pasa_asmbl_1141.p1 fails validation.
(GAC)	 AG	150379-150505	GT	GTG
(TGC)	 AG	150640-150770	GT	AGG
(GAC)	 AG	150866-151009	GT	ATG
(AAC)	 AG	151275-151490	GT	AGG
-recovered pasa_asmbl_1141.p1, terminal, 151275, 151490
-recovered pasa_asmbl_1141.p1, internal, 150379, 150505
-recovered pasa_asmbl_1141.p1, internal, 150640, 150770
-recovered pasa_asmbl_1141.p1, internal, 150866, 151009
-recovered pasa_asmbl_1141.p1, internal, 151275, 151490
Couldn't classify 146163, 146368
Sorry, prediction GeneMark_model.3975_t fails validation.
(GTC)	 AG	146163-146368	GT	AGG
(TAA)	 AG	147992-148233	GT	TGG
(GAG)	 AG	148522-148772	TG	GAT
-recovered GeneMark_model.3975_t, terminal, 148522, 148772
-recovered GeneMark_model.3975_t, internal, 146163, 146368
-recovered GeneMark_model.3975_t, internal, 147992, 148233
Valid prediction for GlimmerHMM_glimmerT_2632-T1
Valid prediction for Augustus_model.g1883.t1
Valid prediction for GeneMark_model.3988_t
Valid prediction for GeneMark_model.3998_t
Valid prediction for snap_scaffold_1-snap.3562-T1
Valid prediction for CodingQuarry_transcript_3001-T1
Valid prediction for snap_scaffold_1-snap.3554-T1
Valid prediction for snap_scaffold_1-snap.3567-T1
Valid prediction for GlimmerHMM_glimmerT_2633-T1
Valid prediction for GeneMark_model.3986_t
Valid prediction for snap_scaffold_1-snap.3540-T1
Valid prediction for GlimmerHMM_glimmerT_2649-T1
Valid prediction for GlimmerHMM_glimmerT_2641-T1
Valid prediction for GeneMark_model.3966_t
Valid prediction for GlimmerHMM_glimmerT_2626-T1
Valid prediction for snap_scaffold_1-snap.3573-T1
Valid prediction for GeneMark_model.3964_t
Valid prediction for snap_scaffold_1-snap.3577-T1
Valid prediction for GlimmerHMM_glimmerT_2646-T1
Valid prediction for GlimmerHMM_glimmerT_2628-T1
Valid prediction for snap_scaffold_1-snap.3552-T1
Valid prediction for GlimmerHMM_glimmerT_2637-T1
Valid prediction for snap_scaffold_1-snap.3537-T1
Valid prediction for GeneMark_model.3990_t
Valid prediction for GeneMark_model.3996_t
Valid prediction for GeneMark_model.3962_t
Valid prediction for Augustus_model.g1881.t1
Couldn't classify 158740, 158893
Sorry, prediction pasa_asmbl_1138.p1 fails validation.
(ATT)	 TC	158740-158893	GT	CCG
(AGA)	 AG	159103-159321	GT	GTG
(TGC)	 AG	159456-159586	GT	AGG
(GAC)	 AG	159682-159825	GT	ATG
(AAC)	 AG	160091-160306	GT	AGG
-recovered pasa_asmbl_1138.p1, terminal, 160091, 160306
-recovered pasa_asmbl_1138.p1, internal, 159103, 159321
-recovered pasa_asmbl_1138.p1, internal, 159456, 159586
-recovered pasa_asmbl_1138.p1, internal, 159682, 159825
-recovered pasa_asmbl_1138.p1, internal, 160091, 160306
Valid prediction for snap_scaffold_1-snap.3544-T1
Valid prediction for GlimmerHMM_glimmerT_2635-T1
Valid prediction for HiQ_model.g1888.t1
Valid prediction for snap_scaffold_1-snap.3541-T1
Valid prediction for GlimmerHMM_glimmerT_2629-T1
Valid prediction for GeneMark_model.3982_t
Valid prediction for snap_scaffold_1-snap.3572-T1
Valid prediction for GeneMark_model.3992_t
Valid prediction for snap_scaffold_1-snap.3574-T1
Valid prediction for Augustus_model.g1887.t1
Valid prediction for snap_scaffold_1-snap.3556-T1
Valid prediction for GlimmerHMM_glimmerT_2638-T1
Valid prediction for HiQ_model.g1877.t1
Valid prediction for GlimmerHMM_glimmerT_2647-T1
Valid prediction for pasa_asmbl_1143.p1
Valid prediction for GeneMark_model.3968_t
Valid prediction for GeneMark_model.3978_t
Valid prediction for GlimmerHMM_glimmerT_2627-T1
Valid prediction for GeneMark_model.3959_t
Valid prediction for Augustus_model.g1879.t1
Valid prediction for Augustus_model.g1885.t1
Valid prediction for GeneMark_model.3965_t
Valid prediction for snap_scaffold_1-snap.3555-T1
Valid prediction for GeneMark_model.3976_t
Valid prediction for GlimmerHMM_glimmerT_2636-T1
Valid prediction for snap_scaffold_1-snap.3548-T1
Valid prediction for GeneMark_model.3970_t
Valid prediction for snap_scaffold_1-snap.3539-T1
Valid prediction for GlimmerHMM_glimmerT_2645-T1
Valid prediction for snap_scaffold_1-snap.3557-T1
Valid prediction for GlimmerHMM_glimmerT_2630-T1
Valid prediction for snap_scaffold_1-snap.3549-T1
Valid prediction for snap_scaffold_1-snap.3568-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 10750, rend_intergenic: 10015  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29648, rend_intergenic: 27206  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34226, rend_intergenic: 30118  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44992, rend_intergenic: 34426  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61162, rend_intergenic: 55846  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70334, rend_intergenic: 61454  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97039, rend_intergenic: 73957  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133068, rend_intergenic: 124412  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140933, rend_intergenic: 140325  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156713, rend_intergenic: 140944  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162466, rend_intergenic: 156972  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174503, rend_intergenic: 166457  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 193536, rend_intergenic: 180188  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 205819, rend_intergenic: 199564  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 207335
-exon list size: 671


building trellis

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70.0    
70.1    
70.3    
70.4    
70.6    
70.7    
70.9    
71.0    
71.2    
71.3    
71.5    
71.6    
71.8    
71.9    
72.1    
72.2    
72.4    
72.5    
72.7    
72.8    
73.0    
73.1    
73.3    
73.4    
73.6    
73.7    
73.8    
74.0    
74.1    
74.3    
74.4    
74.6    
74.7    
74.9    
75.0    
75.2    
75.3    
75.5    
75.6    
75.8    
75.9    
76.1    
76.2    
76.4    
76.5    
76.7    
76.8    
77.0    
77.1    
77.3    
77.4    
77.6    
77.7    
77.9    
78.0    
78.2    
78.3    
78.5    
78.6    
78.8    
78.9    
79.0    
79.2    
79.3    
79.5    
79.6    
79.8    
79.9    
80.1    
80.2    
80.4    
80.5    
80.7    
80.8    
81.0    
81.1    
81.3    
81.4    
81.6    
81.7    
81.9    
82.0    
82.2    
82.3    
82.5    
82.6    
82.8    
82.9    
83.1    
83.2    
83.4    
83.5    
83.7    
83.8    
84.0    
84.1    
84.2    
84.4    
84.5    
84.7    
84.8    
85.0    
85.1    
85.3    
85.4    
85.6    
85.7    
85.9    
86.0    
86.2    
86.3    
86.5    
86.6    
86.8    
86.9    
87.1    
87.2    
87.4    
87.5    
87.7    
87.8    
88.0    
88.1    
88.3    
88.4    
88.6    
88.7    
88.9    
89.0    
89.2    
89.3    
89.5    
89.6    
89.7    
89.9    
90.0    
90.2    
90.3    
90.5    
90.6    
90.8    
90.9    
91.1    
91.2    
91.4    
91.5    
91.7    
91.8    
92.0    
92.1    
92.3    
92.4    
92.6    
92.7    
92.9    
93.0    
93.2    
93.3    
93.5    
93.6    
93.8    
93.9    
94.1    
94.2    
94.4    
94.5    
94.7    
94.8    
94.9    
95.1    
95.2    
95.4    
95.5    
95.7    
95.8    
96.0    
96.1    
96.3    
96.4    
96.6    
96.7    
96.9    
97.0    
97.2    
97.3    
97.5    
97.6    
97.8    
97.9    
98.1    
98.2    
98.4    
98.5    
98.7    
98.8    
99.0    
99.1    
99.3    
99.4    
99.6    
99.7    
99.9    
-found 33 predictions from path traversal
Error with prediction: snap lend_intergenic: 10750, rend_intergenic: 10015  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29648, rend_intergenic: 27206  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34226, rend_intergenic: 30118  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44992, rend_intergenic: 34426  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61162, rend_intergenic: 55846  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70334, rend_intergenic: 61454  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97039, rend_intergenic: 73957  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133068, rend_intergenic: 124412  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140933, rend_intergenic: 140325  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156713, rend_intergenic: 140944  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162466, rend_intergenic: 156972  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174503, rend_intergenic: 166457  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 193536, rend_intergenic: 180188  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 205819, rend_intergenic: 199564  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

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