-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_2/scaffold_2_19892170-20126031

-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_2-snap.3932-T1
Valid prediction for snap_scaffold_2-snap.3959-T1
Valid prediction for GeneMark_model.9565_t
Valid prediction for snap_scaffold_2-snap.3940-T1
Valid prediction for GeneMark_model.9555_t
Valid prediction for GlimmerHMM_glimmerT_5848-T1
Valid prediction for snap_scaffold_2-snap.3927-T1
Valid prediction for GeneMark_model.9579_t
Valid prediction for GeneMark_model.9554_t
Valid prediction for snap_scaffold_2-snap.3935-T1
Valid prediction for GlimmerHMM_glimmerT_5846-T1
Valid prediction for GlimmerHMM_glimmerT_5860-T1
Valid prediction for Augustus_model.g3914.t1
Valid prediction for GeneMark_model.9540_t
Valid prediction for GeneMark_model.9578_t
Valid prediction for GeneMark_model.9544_t
Valid prediction for GeneMark_model.9594_t
Valid prediction for GlimmerHMM_glimmerT_5852-T1
Valid prediction for GlimmerHMM_glimmerT_5859-T1
Valid prediction for GeneMark_model.9563_t
Valid prediction for snap_scaffold_2-snap.3950-T1
Valid prediction for GeneMark_model.9569_t
Valid prediction for GlimmerHMM_glimmerT_5853-T1
Valid prediction for GeneMark_model.9538_t
Couldn't classify 7597, 7647
Sorry, prediction pasa_asmbl_25333.p1 fails validation.
(AAC)	 AG	7597-7647	GT	AGG
(GGC)	 AG	8310-8398	GT	GGG
(GTA)	 AG	8832-8959	GT	AGG
(TGT)	 AG	9278-9373	GT	TTG
(CCT)	 AG	9458-9617	GT	CGG
(GTC)	 AG	9708-9891	GA	AGG
-recovered pasa_asmbl_25333.p1, terminal, 9708, 9891
-recovered pasa_asmbl_25333.p1, internal, 7597, 7647
-recovered pasa_asmbl_25333.p1, internal, 8310, 8398
-recovered pasa_asmbl_25333.p1, internal, 8832, 8959
-recovered pasa_asmbl_25333.p1, internal, 9278, 9373
-recovered pasa_asmbl_25333.p1, internal, 9458, 9617
Valid prediction for Augustus_model.g3909.t1
Valid prediction for snap_scaffold_2-snap.3924-T1
Valid prediction for snap_scaffold_2-snap.3949-T1
Valid prediction for snap_scaffold_2-snap.3928-T1
Valid prediction for GlimmerHMM_glimmerT_5854-T1
Valid prediction for snap_scaffold_2-snap.3920-T1
Valid prediction for snap_scaffold_2-snap.3957-T1
Valid prediction for snap_scaffold_2-snap.3916-T1
Valid prediction for snap_scaffold_2-snap.3913-T1
Valid prediction for GeneMark_model.9580_t
Valid prediction for GeneMark_model.9571_t
Valid prediction for snap_scaffold_2-snap.3944-T1
Valid prediction for snap_scaffold_2-snap.3933-T1
Valid prediction for GlimmerHMM_glimmerT_5841-T1
Valid prediction for GeneMark_model.9553_t
Valid prediction for GlimmerHMM_glimmerT_5837-T1
Valid prediction for GeneMark_model.9547_t
Valid prediction for GeneMark_model.9585_t
Valid prediction for GlimmerHMM_glimmerT_5843-T1
Valid prediction for GlimmerHMM_glimmerT_5840-T1
Valid prediction for GeneMark_model.9591_t
Valid prediction for snap_scaffold_2-snap.3953-T1
Valid prediction for GlimmerHMM_glimmerT_5851-T1
Valid prediction for snap_scaffold_2-snap.3951-T1
Valid prediction for GeneMark_model.9583_t
Valid prediction for GeneMark_model.9556_t
Valid prediction for GlimmerHMM_glimmerT_5856-T1
Valid prediction for GeneMark_model.9575_t
Valid prediction for snap_scaffold_2-snap.3963-T1
Valid prediction for snap_scaffold_2-snap.3918-T1
Valid prediction for snap_scaffold_2-snap.3922-T1
Valid prediction for snap_scaffold_2-snap.3919-T1
Valid prediction for snap_scaffold_2-snap.3931-T1
Valid prediction for GeneMark_model.9542_t
Valid prediction for GlimmerHMM_glimmerT_5857-T1
Valid prediction for GeneMark_model.9558_t
Valid prediction for Augustus_model.g3912.t1
Valid prediction for GeneMark_model.9550_t
Valid prediction for snap_scaffold_2-snap.3942-T1
Valid prediction for GlimmerHMM_glimmerT_5855-T1
Valid prediction for snap_scaffold_2-snap.3926-T1
Valid prediction for snap_scaffold_2-snap.3929-T1
Valid prediction for GeneMark_model.9588_t
Valid prediction for GeneMark_model.9548_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 snap_scaffold_2-snap.3956-T1
Valid prediction for snap_scaffold_2-snap.3921-T1
Valid prediction for GeneMark_model.9586_t
Valid prediction for GlimmerHMM_glimmerT_5845-T1
Valid prediction for GeneMark_model.9593_t
Valid prediction for GeneMark_model.9590_t
Valid prediction for GeneMark_model.9570_t
Valid prediction for GeneMark_model.9566_t
Valid prediction for snap_scaffold_2-snap.3911-T1
Valid prediction for GeneMark_model.9581_t
Valid prediction for GeneMark_model.9552_t
Valid prediction for snap_scaffold_2-snap.3955-T1
Valid prediction for GeneMark_model.9584_t
Valid prediction for snap_scaffold_2-snap.3941-T1
Valid prediction for GlimmerHMM_glimmerT_5850-T1
Valid prediction for GeneMark_model.9546_t
Valid prediction for GeneMark_model.9582_t
Valid prediction for snap_scaffold_2-snap.3960-T1
Valid prediction for snap_scaffold_2-snap.3958-T1
Valid prediction for snap_scaffold_2-snap.3945-T1
Valid prediction for snap_scaffold_2-snap.3948-T1
Valid prediction for GlimmerHMM_glimmerT_5847-T1
Valid prediction for snap_scaffold_2-snap.3946-T1
Valid prediction for GeneMark_model.9567_t
Valid prediction for GeneMark_model.9574_t
Valid prediction for snap_scaffold_2-snap.3939-T1
Valid prediction for GeneMark_model.9562_t
Valid prediction for GeneMark_model.9549_t
Valid prediction for snap_scaffold_2-snap.3912-T1
Valid prediction for GlimmerHMM_glimmerT_5839-T1
Valid prediction for snap_scaffold_2-snap.3934-T1
Valid prediction for GeneMark_model.9587_t
Valid prediction for GeneMark_model.9551_t
Valid prediction for snap_scaffold_2-snap.3917-T1
Valid prediction for GeneMark_model.9577_t
Valid prediction for GlimmerHMM_glimmerT_5842-T1
Valid prediction for Augustus_model.g3911.t1
Valid prediction for snap_scaffold_2-snap.3962-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for snap_scaffold_2-snap.3925-T1
Valid prediction for GeneMark_model.9543_t
Valid prediction for snap_scaffold_2-snap.3923-T1
Valid prediction for snap_scaffold_2-snap.3952-T1
Valid prediction for snap_scaffold_2-snap.3930-T1
Valid prediction for snap_scaffold_2-snap.3964-T1
Valid prediction for GlimmerHMM_glimmerT_5844-T1
Valid prediction for snap_scaffold_2-snap.3954-T1
Valid prediction for GlimmerHMM_glimmerT_5838-T1
Valid prediction for GlimmerHMM_glimmerT_5849-T1
Valid prediction for GeneMark_model.9572_t
Valid prediction for GeneMark_model.9592_t
Valid prediction for snap_scaffold_2-snap.3914-T1
Valid prediction for snap_scaffold_2-snap.3937-T1
Valid prediction for Augustus_model.g3913.t1
Valid prediction for snap_scaffold_2-snap.3938-T1
Valid prediction for GeneMark_model.9545_t
Valid prediction for GeneMark_model.9541_t
Valid prediction for GeneMark_model.9557_t
Valid prediction for snap_scaffold_2-snap.3961-T1
Valid prediction for GeneMark_model.9568_t
Valid prediction for snap_scaffold_2-snap.3947-T1
Valid prediction for snap_scaffold_2-snap.3915-T1
Valid prediction for snap_scaffold_2-snap.3936-T1
Valid prediction for GeneMark_model.9564_t
Valid prediction for GeneMark_model.9573_t
Valid prediction for snap_scaffold_2-snap.3943-T1
Couldn't classify 20922, 21027
Sorry, prediction pasa_asmbl_23897.p1 fails validation.
(ATG)	 CC	19758-19864	GT	AAG
(CCA)	 AG	20053-20117	GT	AGG
(ATC)	 AG	20617-20674	GT	GAG
(CCA)	 AG	20922-21027	AT	AGA
-recovered pasa_asmbl_23897.p1, initial, 19758, 19864
add_exon() Sorry, pasa_asmbl_23897.p1 20617-20674-terminal-3 is invalid.
-recovered pasa_asmbl_23897.p1, terminal, 20617, 20674
-recovered pasa_asmbl_23897.p1, internal, 20053, 20117
-recovered pasa_asmbl_23897.p1, internal, 20617, 20674
Valid prediction for GeneMark_model.9576_t
Valid prediction for GeneMark_model.9539_t
Valid prediction for Augustus_model.g3910.t1
Valid prediction for GlimmerHMM_glimmerT_5858-T1
Valid prediction for GeneMark_model.9559_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 9891, rend_intergenic: 6533  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 16519, rend_intergenic: 11167  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34132, rend_intergenic: 18970  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44430, rend_intergenic: 38351  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63066, rend_intergenic: 56299  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83801, rend_intergenic: 83447  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86121, rend_intergenic: 84248  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117417, rend_intergenic: 105531  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134985, rend_intergenic: 119695  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156388, rend_intergenic: 136735  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158344, rend_intergenic: 157722  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159868, rend_intergenic: 158642  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162672, rend_intergenic: 159975  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181787, rend_intergenic: 172925  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 192341, rend_intergenic: 185758  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 202662, rend_intergenic: 192623  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 208519, rend_intergenic: 203571  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 224214, rend_intergenic: 215758  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 232144, rend_intergenic: 228778  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 233862
-exon list size: 785


building trellis

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84.1    
84.2    
84.4    
84.5    
84.6    
84.8    
84.9    
85.0    
85.1    
85.3    
85.4    
85.5    
85.6    
85.8    
85.9    
86.0    
86.1    
86.3    
86.4    
86.5    
86.7    
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    
88.4    
88.6    
88.7    
88.8    
88.9    
89.1    
89.2    
89.3    
89.5    
89.6    
89.7    
89.8    
90.0    
90.1    
90.2    
90.3    
90.5    
90.6    
90.7    
90.9    
91.0    
91.1    
91.2    
91.4    
91.5    
91.6    
91.7    
91.9    
92.0    
92.1    
92.2    
92.4    
92.5    
92.6    
92.8    
92.9    
93.0    
93.1    
93.3    
93.4    
93.5    
93.6    
93.8    
93.9    
94.0    
94.2    
94.3    
94.4    
94.5    
94.7    
94.8    
94.9    
95.0    
95.2    
95.3    
95.4    
95.6    
95.7    
95.8    
95.9    
96.1    
96.2    
96.3    
96.4    
96.6    
96.7    
96.8    
97.0    
97.1    
97.2    
97.3    
97.5    
97.6    
97.7    
97.8    
98.0    
98.1    
98.2    
98.3    
98.5    
98.6    
98.7    
98.9    
99.0    
99.1    
99.2    
99.4    
99.5    
99.6    
99.7    
99.9    
-found 41 predictions from path traversal
Error with prediction: snap lend_intergenic: 9891, rend_intergenic: 6533  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 16519, rend_intergenic: 11167  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34132, rend_intergenic: 18970  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44430, rend_intergenic: 38351  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63066, rend_intergenic: 56299  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83801, rend_intergenic: 83447  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86121, rend_intergenic: 84248  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117417, rend_intergenic: 105531  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134985, rend_intergenic: 119695  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156388, rend_intergenic: 136735  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158344, rend_intergenic: 157722  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159868, rend_intergenic: 158642  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162672, rend_intergenic: 159975  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181787, rend_intergenic: 172925  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 192341, rend_intergenic: 185758  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 202662, rend_intergenic: 192623  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 208519, rend_intergenic: 203571  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 224214, rend_intergenic: 215758  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 232144, rend_intergenic: 228778  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 15 predictions persist after filtering for low support