-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_13/scaffold_13_3979738-4197625

-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_13-snap.780-T1
Valid prediction for GeneMark_model.55099_t
Valid prediction for Augustus_model.g21550.t1
Valid prediction for snap_scaffold_13-snap.765-T1
Valid prediction for GlimmerHMM_glimmerT_32190-T1
Valid prediction for snap_scaffold_13-snap.761-T1
Valid prediction for GlimmerHMM_glimmerT_32206-T1
Valid prediction for GeneMark_model.55086_t
Valid prediction for HiQ_model.g21542.t1
Valid prediction for Augustus_model.g21539.t1
Valid prediction for GeneMark_model.55081_t
Valid prediction for GlimmerHMM_glimmerT_32202-T1
Valid prediction for snap_scaffold_13-snap.772-T1
Valid prediction for GeneMark_model.55076_t
Valid prediction for GlimmerHMM_glimmerT_32209-T1
Valid prediction for snap_scaffold_13-snap.741-T1
Valid prediction for pasa_asmbl_10742.p1
Valid prediction for Augustus_model.g21556.t1
Valid prediction for snap_scaffold_13-snap.746-T1
Valid prediction for HiQ_model.g21543.t1
Valid prediction for GeneMark_model.55113_t
Valid prediction for Augustus_model.g21546.t1
Valid prediction for HiQ_model.g21541.t1
Valid prediction for snap_scaffold_13-snap.767-T1
Valid prediction for GlimmerHMM_glimmerT_32198-T1
Valid prediction for GeneMark_model.55104_t
Valid prediction for GeneMark_model.55093_t
Couldn't classify 95507, 95614
Sorry, prediction pasa_asmbl_10736.p1 fails validation.
(GGT)	 CA	95507-95614	GT	AGG
(ATC)	 AG	95826-95925	GT	GTG
(GCT)	 AG	96147-96322	GT	TGG
(ACT)	 AG	96641-96770	GT	TGG
(CCT)	 AG	97162-97271	AT	AGA
-recovered pasa_asmbl_10736.p1, terminal, 97162, 97271
-recovered pasa_asmbl_10736.p1, internal, 95826, 95925
-recovered pasa_asmbl_10736.p1, internal, 96147, 96322
-recovered pasa_asmbl_10736.p1, internal, 96641, 96770
Valid prediction for snap_scaffold_13-snap.743-T1
Valid prediction for snap_scaffold_13-snap.786-T1
Valid prediction for GlimmerHMM_glimmerT_32183-T1
Valid prediction for snap_scaffold_13-snap.759-T1
Valid prediction for GeneMark_model.55090_t
Valid prediction for pasa_asmbl_10739.p1
Valid prediction for Augustus_model.g21534.t1
Valid prediction for snap_scaffold_13-snap.782-T1
Valid prediction for GlimmerHMM_glimmerT_32197-T1
Valid prediction for Augustus_model.g21538.t1
Valid prediction for snap_scaffold_13-snap.766-T1
Valid prediction for snap_scaffold_13-snap.788-T1
Valid prediction for GeneMark_model.55106_t
Valid prediction for GlimmerHMM_glimmerT_32193-T1
Valid prediction for GeneMark_model.55084_t
Couldn't classify 213420, 213572
Couldn't classify 216293, 216304
Sorry, prediction pasa_asmbl_10746.p1 fails validation.
(TCT)	 GC	213420-213572	GT	AGG
(GAC)	 AG	215282-215398	GT	AGG
(ATG)	 AG	215813-216031	GT	AGG
(ATT)	 AG	216293-216304	AG	AGA
-recovered pasa_asmbl_10746.p1, initial, 215813, 216031
-recovered pasa_asmbl_10746.p1, internal, 215282, 215398
-recovered pasa_asmbl_10746.p1, internal, 215813, 216031
Valid prediction for snap_scaffold_13-snap.784-T1
Valid prediction for Augustus_model.g21548.t1
Valid prediction for GlimmerHMM_glimmerT_32189-T1
Valid prediction for GlimmerHMM_glimmerT_32182-T1
Couldn't classify 34122, 34893
Sorry, prediction pasa_asmbl_10733.p1 fails validation.
(CCC)	 AC	34122-34893	GT	AGG
(CCC)	 AG	35754-35829	GT	GGG
(ATG)	 AG	36031-36369	GT	CTG
(AGA)	 AG	36499-36583	GT	TGG
(AGA)	 AG	36719-36938	GT	AGG
(GAG)	 AG	37082-37224	GT	AGG
(GGG)	 AG	37311-37511	GT	GGG
(CGG)	 AG	38330-38422	TA	GAT
add_exon() Sorry, pasa_asmbl_10733.p1 36031-36369-initial-1 is invalid.
-recovered pasa_asmbl_10733.p1, initial, 36031, 36369
-recovered pasa_asmbl_10733.p1, terminal, 38330, 38422
-recovered pasa_asmbl_10733.p1, internal, 35754, 35829
-recovered pasa_asmbl_10733.p1, internal, 36031, 36369
-recovered pasa_asmbl_10733.p1, internal, 36499, 36583
-recovered pasa_asmbl_10733.p1, internal, 36719, 36938
-recovered pasa_asmbl_10733.p1, internal, 37082, 37224
-recovered pasa_asmbl_10733.p1, internal, 37311, 37511
Valid prediction for snap_scaffold_13-snap.778-T1
Valid prediction for GeneMark_model.55101_t
Valid prediction for snap_scaffold_13-snap.783-T1
Valid prediction for GlimmerHMM_glimmerT_32200-T1
Valid prediction for GeneMark_model.55077_t
Valid prediction for snap_scaffold_13-snap.760-T1
Valid prediction for snap_scaffold_13-snap.756-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for snap_scaffold_13-snap.750-T1
Valid prediction for Augustus_model.g21555.t1
Valid prediction for GlimmerHMM_glimmerT_32194-T1
Valid prediction for snap_scaffold_13-snap.742-T1
Valid prediction for GeneMark_model.55111_t
Valid prediction for snap_scaffold_13-snap.758-T1
Valid prediction for CodingQuarry_transcript_12944-T1
Valid prediction for snap_scaffold_13-snap.744-T1
Valid prediction for GlimmerHMM_glimmerT_32192-T1
Valid prediction for snap_scaffold_13-snap.748-T1
Sorry, intron length (3) is less than minimum required (10)
Sorry, intron length (4) is less than minimum required (10)
Couldn't classify 33666, 33986
Sorry, prediction pasa_asmbl_10731.p1 fails validation.
(TTC)	 GG	33666-33986	GA	GCG
Valid prediction for snap_scaffold_13-snap.770-T1
Valid prediction for snap_scaffold_13-snap.773-T1
Valid prediction for GeneMark_model.55091_t
Valid prediction for Augustus_model.g21557.t1
Valid prediction for GeneMark_model.55087_t
Valid prediction for GlimmerHMM_glimmerT_32188-T1
Valid prediction for snap_scaffold_13-snap.769-T1
Valid prediction for GeneMark_model.55082_t
Valid prediction for snap_scaffold_13-snap.747-T1
Valid prediction for snap_scaffold_13-snap.779-T1
Valid prediction for Augustus_model.g21535.t1
Valid prediction for GeneMark_model.55085_t
Valid prediction for GeneMark_model.55116_t
Valid prediction for Augustus_model.g21540.t1
Valid prediction for GlimmerHMM_glimmerT_32195-T1
Valid prediction for Augustus_model.g21547.t1
Valid prediction for Augustus_model.g21554.t1
Valid prediction for snap_scaffold_13-snap.764-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_13-snap.752-T1
Valid prediction for GlimmerHMM_glimmerT_32208-T1
Valid prediction for snap_scaffold_13-snap.781-T1
Valid prediction for GeneMark_model.55096_t
Valid prediction for snap_scaffold_13-snap.755-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 GlimmerHMM_glimmerT_32177-T1
Valid prediction for Augustus_model.g21545.t1
Couldn't classify 197205, 197582
Sorry, prediction pasa_asmbl_9563.p1 fails validation.
(AGC)	 CC	197205-197582	GT	GGG
(GTT)	 AG	198153-198315	GT	AGG
(GCC)	 AG	198557-198703	GT	AGG
(TGG)	 AG	198923-199048	GT	AGG
(TGC)	 AG	199767-199957	GT	GGG
(GAC)	 AG	200130-200284	GT	AGG
(AGT)	 AG	200674-200789	GT	AGG
(GTT)	 AG	200893-201028	GT	AGG
(GTA)	 AG	201211-201394	GT	AAG
(GGC)	 AG	201542-201676	GT	AGG
(GTG)	 AG	201760-201849	AT	AAA
-recovered pasa_asmbl_9563.p1, terminal, 201760, 201849
-recovered pasa_asmbl_9563.p1, internal, 198153, 198315
-recovered pasa_asmbl_9563.p1, internal, 198557, 198703
-recovered pasa_asmbl_9563.p1, internal, 198923, 199048
-recovered pasa_asmbl_9563.p1, internal, 199767, 199957
-recovered pasa_asmbl_9563.p1, internal, 200130, 200284
-recovered pasa_asmbl_9563.p1, internal, 200674, 200789
-recovered pasa_asmbl_9563.p1, internal, 200893, 201028
-recovered pasa_asmbl_9563.p1, internal, 201211, 201394
-recovered pasa_asmbl_9563.p1, internal, 201542, 201676
Valid prediction for snap_scaffold_13-snap.754-T1
Couldn't classify 36219, 36320
Couldn't classify 41841, 42020
Sorry, prediction pasa_asmbl_9568.p1 fails validation.
(CAG)	 GA	36219-36320	GT	AGG
(GCC)	 AG	36845-36898	GT	TGG
(GTT)	 AG	37063-37154	GT	AGG
(TCA)	 AG	37305-37440	GT	AGG
(GTC)	 AG	37961-38072	GT	CGG
(GTC)	 AG	38162-38258	GT	AGG
(GTA)	 AG	39541-39658	GT	CTG
(CAC)	 AG	39949-40059	GT	TGG
(TTC)	 AG	41841-42020	TA	AGT
-recovered pasa_asmbl_9568.p1, internal, 36845, 36898
-recovered pasa_asmbl_9568.p1, internal, 37063, 37154
-recovered pasa_asmbl_9568.p1, internal, 37305, 37440
-recovered pasa_asmbl_9568.p1, internal, 37961, 38072
-recovered pasa_asmbl_9568.p1, internal, 38162, 38258
-recovered pasa_asmbl_9568.p1, internal, 39541, 39658
-recovered pasa_asmbl_9568.p1, internal, 39949, 40059
Valid prediction for GeneMark_model.55075_t
Valid prediction for snap_scaffold_13-snap.762-T1
Valid prediction for GlimmerHMM_glimmerT_32181-T1
Valid prediction for HiQ_model.g21532.t1
Valid prediction for CodingQuarry_transcript_12943-T1
Valid prediction for GlimmerHMM_glimmerT_32201-T1
Valid prediction for GeneMark_model.55088_t
Valid prediction for GlimmerHMM_glimmerT_32176-T1
Valid prediction for Augustus_model.g21530.t1
Valid prediction for HiQ_model.g21553.t1
Valid prediction for GeneMark_model.55079_t
Valid prediction for GeneMark_model.55107_t
Valid prediction for GeneMark_model.55083_t
Valid prediction for snap_scaffold_13-snap.739-T1
Valid prediction for snap_scaffold_13-snap.738-T1
Couldn't classify 195097, 195346
Sorry, prediction pasa_asmbl_9566.p1 fails validation.
(AAG)	 GG	195097-195346	GT	AGG
(GAG)	 AG	195475-195677	AA	GAA
-recovered pasa_asmbl_9566.p1, terminal, 195475, 195677
Valid prediction for GlimmerHMM_glimmerT_32204-T1
Valid prediction for snap_scaffold_13-snap.777-T1
Valid prediction for Augustus_model.g21531.t1
Valid prediction for GeneMark_model.55080_t
Valid prediction for snap_scaffold_13-snap.768-T1
Valid prediction for GeneMark_model.55078_t
Valid prediction for GeneMark_model.55103_t
Valid prediction for snap_scaffold_13-snap.735-T1
Valid prediction for GlimmerHMM_glimmerT_32199-T1
Valid prediction for GeneMark_model.55108_t
Valid prediction for GeneMark_model.55095_t
Valid prediction for Augustus_model.g21552.t1
Valid prediction for Augustus_model.g21536.t1
Valid prediction for Augustus_model.g21528.t1
Valid prediction for snap_scaffold_13-snap.771-T1
Valid prediction for GeneMark_model.55105_t
Valid prediction for Augustus_model.g21533.t1
Valid prediction for GeneMark_model.55100_t
Valid prediction for GlimmerHMM_glimmerT_32187-T1
Valid prediction for snap_scaffold_13-snap.740-T1
Valid prediction for Augustus_model.g21544.t1
Valid prediction for GeneMark_model.55073_t
Valid prediction for GlimmerHMM_glimmerT_32179-T1
Valid prediction for GeneMark_model.55074_t
Valid prediction for GeneMark_model.55098_t
Valid prediction for snap_scaffold_13-snap.763-T1
Valid prediction for GlimmerHMM_glimmerT_32186-T1
Valid prediction for GlimmerHMM_glimmerT_32205-T1
Valid prediction for GeneMark_model.55089_t
Valid prediction for snap_scaffold_13-snap.787-T1
Valid prediction for GeneMark_model.55112_t
Valid prediction for GlimmerHMM_glimmerT_32203-T1
Valid prediction for snap_scaffold_13-snap.749-T1
Valid prediction for GlimmerHMM_glimmerT_32185-T1
Valid prediction for snap_scaffold_13-snap.737-T1
Valid prediction for GlimmerHMM_glimmerT_32184-T1
Valid prediction for snap_scaffold_13-snap.751-T1
Valid prediction for GlimmerHMM_glimmerT_32178-T1
Valid prediction for snap_scaffold_13-snap.785-T1
Valid prediction for Augustus_model.g21537.t1
Valid prediction for GeneMark_model.55094_t
Valid prediction for GeneMark_model.55114_t
Valid prediction for snap_scaffold_13-snap.734-T1
Valid prediction for GeneMark_model.55102_t
Valid prediction for Augustus_model.g21526.t1
Valid prediction for pasa_asmbl_9561.p1
Valid prediction for GeneMark_model.55092_t
Valid prediction for snap_scaffold_13-snap.774-T1
Valid prediction for GeneMark_model.55109_t
Valid prediction for HiQ_model.g21529.t1
Valid prediction for Augustus_model.g21527.t1
Valid prediction for snap_scaffold_13-snap.757-T1
Valid prediction for snap_scaffold_13-snap.775-T1
Valid prediction for Augustus_model.g21551.t1
Valid prediction for snap_scaffold_13-snap.753-T1
Valid prediction for GeneMark_model.55110_t
Valid prediction for Augustus_model.g21549.t1
Valid prediction for snap_scaffold_13-snap.776-T1
Valid prediction for GeneMark_model.55097_t
Valid prediction for GlimmerHMM_glimmerT_32191-T1
Valid prediction for GlimmerHMM_glimmerT_32196-T1
Valid prediction for GlimmerHMM_glimmerT_32207-T1
Valid prediction for snap_scaffold_13-snap.745-T1
Valid prediction for GeneMark_model.55115_t
Valid prediction for snap_scaffold_13-snap.736-T1
Valid prediction for GlimmerHMM_glimmerT_32180-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 52140, rend_intergenic: 41501  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56656, rend_intergenic: 52968  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57838, rend_intergenic: 56965  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62745, rend_intergenic: 60169  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64130, rend_intergenic: 63397  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65918, rend_intergenic: 64164  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136940, rend_intergenic: 133903  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 209082, rend_intergenic: 207928  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 210856, rend_intergenic: 210261  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 216087, rend_intergenic: 212539  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 217888
-exon list size: 701


building trellis

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60.7    
60.9    
61.0    
61.2    
61.3    
61.5    
61.6    
61.7    
61.9    
62.0    
62.2    
62.3    
62.4    
62.6    
62.7    
62.9    
63.0    
63.2    
63.3    
63.4    
63.6    
63.7    
63.9    
64.0    
64.2    
64.3    
64.4    
64.6    
64.7    
64.9    
65.0    
65.1    
65.3    
65.4    
65.6    
65.7    
65.9    
66.0    
66.1    
66.3    
66.4    
66.6    
66.7    
66.9    
67.0    
67.1    
67.3    
67.4    
67.6    
67.7    
67.9    
68.0    
68.1    
68.3    
68.4    
68.6    
68.7    
68.8    
69.0    
69.1    
69.3    
69.4    
69.6    
69.7    
69.8    
70.0    
70.1    
70.3    
70.4    
70.6    
70.7    
70.8    
71.0    
71.1    
71.3    
71.4    
71.6    
71.7    
71.8    
72.0    
72.1    
72.3    
72.4    
72.5    
72.7    
72.8    
73.0    
73.1    
73.3    
73.4    
73.5    
73.7    
73.8    
74.0    
74.1    
74.3    
74.4    
74.5    
74.7    
74.8    
75.0    
75.1    
75.2    
75.4    
75.5    
75.7    
75.8    
76.0    
76.1    
76.2    
76.4    
76.5    
76.7    
76.8    
77.0    
77.1    
77.2    
77.4    
77.5    
77.7    
77.8    
78.0    
78.1    
78.2    
78.4    
78.5    
78.7    
78.8    
78.9    
79.1    
79.2    
79.4    
79.5    
79.7    
79.8    
79.9    
80.1    
80.2    
80.4    
80.5    
80.7    
80.8    
80.9    
81.1    
81.2    
81.4    
81.5    
81.7    
81.8    
81.9    
82.1    
82.2    
82.4    
82.5    
82.6    
82.8    
82.9    
83.1    
83.2    
83.4    
83.5    
83.6    
83.8    
83.9    
84.1    
84.2    
84.4    
84.5    
84.6    
84.8    
84.9    
85.1    
85.2    
85.3    
85.5    
85.6    
85.8    
85.9    
86.1    
86.2    
86.3    
86.5    
86.6    
86.8    
86.9    
87.1    
87.2    
87.3    
87.5    
87.6    
87.8    
87.9    
88.1    
88.2    
88.3    
88.5    
88.6    
88.8    
88.9    
89.0    
89.2    
89.3    
89.5    
89.6    
89.8    
89.9    
90.0    
90.2    
90.3    
90.5    
90.6    
90.8    
90.9    
91.0    
91.2    
91.3    
91.5    
91.6    
91.7    
91.9    
92.0    
92.2    
92.3    
92.5    
92.6    
92.7    
92.9    
93.0    
93.2    
93.3    
93.5    
93.6    
93.7    
93.9    
94.0    
94.2    
94.3    
94.5    
94.6    
94.7    
94.9    
95.0    
95.2    
95.3    
95.4    
95.6    
95.7    
95.9    
96.0    
96.2    
96.3    
96.4    
96.6    
96.7    
96.9    
97.0    
97.2    
97.3    
97.4    
97.6    
97.7    
97.9    
98.0    
98.2    
98.3    
98.4    
98.6    
98.7    
98.9    
99.0    
99.1    
99.3    
99.4    
99.6    
99.7    
99.9    
-found 40 predictions from path traversal
Error with prediction: snap lend_intergenic: 52140, rend_intergenic: 41501  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56656, rend_intergenic: 52968  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57838, rend_intergenic: 56965  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62745, rend_intergenic: 60169  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64130, rend_intergenic: 63397  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65918, rend_intergenic: 64164  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136940, rend_intergenic: 133903  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 209082, rend_intergenic: 207928  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 210856, rend_intergenic: 210261  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 216087, rend_intergenic: 212539  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 32 predictions persist after filtering for low support