-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_25/scaffold_25_3675818-3879634

-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_25-snap.748-T1
Valid prediction for Augustus_model.g35789.t1
Valid prediction for GlimmerHMM_glimmerT_53895-T1
Valid prediction for snap_scaffold_25-snap.762-T1
Couldn't classify 199811, 199948
Couldn't classify 203074, 203223
Sorry, prediction pasa_asmbl_33468.p1 fails validation.
(CCA)	 GT	199811-199948	GT	TGG
(TTT)	 AG	200491-200670	GT	AGG
(ATT)	 AG	201936-202217	GT	TGG
(TGC)	 AG	203074-203223	GA	GTG
-recovered pasa_asmbl_33468.p1, internal, 200491, 200670
-recovered pasa_asmbl_33468.p1, internal, 201936, 202217
Valid prediction for GlimmerHMM_glimmerT_53928-T1
Valid prediction for GlimmerHMM_glimmerT_53893-T1
Couldn't classify 86983, 87084
Sorry, prediction pasa_asmbl_33466.p1 fails validation.
(TTT)	 TC	86983-87084	GT	AGG
(ATC)	 AG	88453-88719	CC	GAC
-recovered pasa_asmbl_33466.p1, terminal, 88453, 88719
Valid prediction for snap_scaffold_25-snap.797-T1
Valid prediction for snap_scaffold_25-snap.766-T1
Valid prediction for GlimmerHMM_glimmerT_53924-T1
Valid prediction for snap_scaffold_25-snap.774-T1
Valid prediction for GlimmerHMM_glimmerT_53892-T1
Valid prediction for Augustus_model.g35784.t1
Valid prediction for snap_scaffold_25-snap.779-T1
Valid prediction for CodingQuarry_transcript_38689-T1
Valid prediction for HiQ_model.g35772.t1
Valid prediction for pasa_asmbl_33452.p1
Valid prediction for GlimmerHMM_glimmerT_53912-T1
Valid prediction for Augustus_model.g35786.t1
Valid prediction for pasa_asmbl_33447.p1
Valid prediction for GlimmerHMM_glimmerT_53923-T1
Valid prediction for GlimmerHMM_glimmerT_53909-T1
Valid prediction for GlimmerHMM_glimmerT_53897-T1
Valid prediction for snap_scaffold_25-snap.776-T1
Valid prediction for snap_scaffold_25-snap.792-T1
Valid prediction for snap_scaffold_25-snap.754-T1
Valid prediction for snap_scaffold_25-snap.768-T1
Valid prediction for CodingQuarry_transcript_38688-T1
Valid prediction for snap_scaffold_25-snap.747-T1
Valid prediction for snap_scaffold_25-snap.749-T1
Valid prediction for snap_scaffold_25-snap.765-T1
Valid prediction for GlimmerHMM_glimmerT_53914-T1
Couldn't classify 82164, 82325
Couldn't classify 83329, 83424
Sorry, prediction pasa_asmbl_33868.p1 fails validation.
(CAG)	 CA	82164-82325	GT	AGG
(AAC)	 AG	82612-82758	GT	AGG
(AGC)	 AG	83329-83424	GT	AGG
-recovered pasa_asmbl_33868.p1, internal, 82612, 82758
-recovered pasa_asmbl_33868.p1, internal, 83329, 83424
Valid prediction for snap_scaffold_25-snap.759-T1
Valid prediction for snap_scaffold_25-snap.791-T1
Valid prediction for GlimmerHMM_glimmerT_53908-T1
Valid prediction for HiQ_model.g35763.t1
Valid prediction for Augustus_model.g35776.t1
Valid prediction for GlimmerHMM_glimmerT_53930-T1
Valid prediction for snap_scaffold_25-snap.750-T1
Valid prediction for snap_scaffold_25-snap.753-T1
Valid prediction for snap_scaffold_25-snap.796-T1
Valid prediction for GlimmerHMM_glimmerT_53904-T1
Valid prediction for Augustus_model.g35777.t1
Valid prediction for HiQ_model.g35770.t1
Valid prediction for CodingQuarry_transcript_38683-T1
Valid prediction for pasa_asmbl_33449.p1
Valid prediction for Augustus_model.g35785.t1
Valid prediction for HiQ_model.g35765.t1
Valid prediction for snap_scaffold_25-snap.788-T1
Valid prediction for CodingQuarry_transcript_38687-T1
Valid prediction for snap_scaffold_25-snap.769-T1
Valid prediction for snap_scaffold_25-snap.784-T1
Valid prediction for snap_scaffold_25-snap.773-T1
Valid prediction for snap_scaffold_25-snap.758-T1
Valid prediction for snap_scaffold_25-snap.793-T1
Valid prediction for snap_scaffold_25-snap.777-T1
Valid prediction for GlimmerHMM_glimmerT_53922-T1
Valid prediction for GlimmerHMM_glimmerT_53894-T1
Valid prediction for HiQ_model.g35764.t1
Valid prediction for CodingQuarry_transcript_38682-T1
Valid prediction for snap_scaffold_25-snap.794-T1
Valid prediction for snap_scaffold_25-snap.778-T1
Couldn't classify 72008, 72120
Couldn't classify 79665, 79820
Sorry, prediction pasa_asmbl_33462.p1 fails validation.
(GTA)	 CA	72008-72120	GT	TGG
(GTT)	 AG	73832-74012	GT	AGG
(GAC)	 AG	75406-75630	GT	AGG
(GCC)	 AG	75897-75971	GT	AGG
(ATG)	 AG	76098-76223	GT	AGG
(GAG)	 AG	76702-76845	GT	AGG
(GGT)	 AG	77164-77253	GT	AGG
(CAC)	 AG	77385-77482	GT	AAG
(GCT)	 AG	77614-77674	GT	AGG
(AGG)	 AG	77789-77842	GT	AAG
(GAA)	 AG	79155-79187	GT	AGG
(GGA)	 AG	79665-79820	GT	CGG
-recovered pasa_asmbl_33462.p1, initial, 76098, 76223
-recovered pasa_asmbl_33462.p1, internal, 73832, 74012
-recovered pasa_asmbl_33462.p1, internal, 75406, 75630
-recovered pasa_asmbl_33462.p1, internal, 75897, 75971
-recovered pasa_asmbl_33462.p1, internal, 76098, 76223
-recovered pasa_asmbl_33462.p1, internal, 76702, 76845
-recovered pasa_asmbl_33462.p1, internal, 77164, 77253
-recovered pasa_asmbl_33462.p1, internal, 77385, 77482
-recovered pasa_asmbl_33462.p1, internal, 77614, 77674
-recovered pasa_asmbl_33462.p1, internal, 77789, 77842
-recovered pasa_asmbl_33462.p1, internal, 79155, 79187
-recovered pasa_asmbl_33462.p1, internal, 79665, 79820
Valid prediction for GlimmerHMM_glimmerT_53913-T1
Couldn't classify 197692, 197719
Couldn't classify 198775, 198903
Sorry, prediction pasa_asmbl_33467.p1 fails validation.
(CAC)	 AC	197692-197719	GT	TGG
(ATG)	 AG	197989-198272	GT	AGG
(GCC)	 AG	198775-198903	AG	ACA
add_exon() Sorry, pasa_asmbl_33467.p1 197989-198272-initial-1 is invalid.
-recovered pasa_asmbl_33467.p1, initial, 197989, 198272
-recovered pasa_asmbl_33467.p1, internal, 197989, 198272
Valid prediction for pasa_asmbl_33458.p1
Valid prediction for GlimmerHMM_glimmerT_53891-T1
Valid prediction for CodingQuarry_transcript_38684-T1
Valid prediction for snap_scaffold_25-snap.770-T1
Valid prediction for Augustus_model.g35778.t1
Valid prediction for GlimmerHMM_glimmerT_53898-T1
Valid prediction for Augustus_model.g35767.t1
Valid prediction for snap_scaffold_25-snap.782-T1
Valid prediction for GlimmerHMM_glimmerT_53902-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_53919-T1
Valid prediction for Augustus_model.g35782.t1
Valid prediction for GlimmerHMM_glimmerT_53910-T1
Valid prediction for GlimmerHMM_glimmerT_53905-T1
Valid prediction for snap_scaffold_25-snap.755-T1
Valid prediction for snap_scaffold_25-snap.761-T1
Valid prediction for GlimmerHMM_glimmerT_53926-T1
Valid prediction for Augustus_model.g35773.t1
Valid prediction for snap_scaffold_25-snap.795-T1
Valid prediction for Augustus_model.g35774.t1
Valid prediction for GlimmerHMM_glimmerT_53929-T1
Valid prediction for CodingQuarry_transcript_38694-T1
Valid prediction for pasa_asmbl_34151.p1
Valid prediction for snap_scaffold_25-snap.751-T1
Valid prediction for GlimmerHMM_glimmerT_53918-T1
Valid prediction for GlimmerHMM_glimmerT_53916-T1
Valid prediction for snap_scaffold_25-snap.781-T1
Valid prediction for GlimmerHMM_glimmerT_53917-T1
Couldn't classify 172560, 172790
Couldn't classify 173111, 173229
Sorry, prediction pasa_asmbl_34147.p1 fails validation.
(GGA)	 GA	172560-172790	GT	TTG
(CCT)	 AG	172945-173020	GT	GGG
(AGA)	 AG	173111-173229	GC	TGG
-recovered pasa_asmbl_34147.p1, internal, 172945, 173020
-recovered pasa_asmbl_34147.p1, internal, 173111, 173229
Valid prediction for GlimmerHMM_glimmerT_53906-T1
Valid prediction for snap_scaffold_25-snap.775-T1
Valid prediction for snap_scaffold_25-snap.783-T1
Valid prediction for snap_scaffold_25-snap.789-T1
Valid prediction for snap_scaffold_25-snap.763-T1
Valid prediction for snap_scaffold_25-snap.756-T1
Valid prediction for snap_scaffold_25-snap.772-T1
Valid prediction for GlimmerHMM_glimmerT_53903-T1
Valid prediction for snap_scaffold_25-snap.771-T1
Valid prediction for GlimmerHMM_glimmerT_53901-T1
Valid prediction for snap_scaffold_25-snap.764-T1
Valid prediction for Augustus_model.g35766.t1
Valid prediction for snap_scaffold_25-snap.767-T1
Valid prediction for snap_scaffold_25-snap.757-T1
Valid prediction for Augustus_model.g35781.t1
Valid prediction for GlimmerHMM_glimmerT_53925-T1
Valid prediction for GlimmerHMM_glimmerT_53899-T1
Valid prediction for CodingQuarry_transcript_38693-T1
Valid prediction for snap_scaffold_25-snap.752-T1
Valid prediction for GlimmerHMM_glimmerT_53907-T1
Valid prediction for snap_scaffold_25-snap.786-T1
Valid prediction for Augustus_model.g35780.t1
Valid prediction for HiQ_model.g35771.t1
Valid prediction for Augustus_model.g35783.t1
Valid prediction for Augustus_model.g35779.t1
Valid prediction for GlimmerHMM_glimmerT_53915-T1
Couldn't classify 56241, 56305
Sorry, prediction pasa_asmbl_34161.p1 fails validation.
(ATG)	 CC	53155-53349	GT	CAG
(GAT)	 AG	53501-53638	GT	GGG
(CCA)	 AG	53757-53895	GT	AGG
(GTG)	 AG	53984-54108	GT	AGG
(ATC)	 AG	54215-54571	GT	GGG
(AAA)	 AG	54689-54817	GT	AGG
(GAT)	 AG	54918-55145	GT	AGG
(CTG)	 AG	55250-55434	GT	ACG
(GCC)	 AG	55526-55812	GT	CCG
(AGG)	 AG	55911-56021	GT	AAG
(GTC)	 AG	56241-56305	AG	ACA
-recovered pasa_asmbl_34161.p1, initial, 53155, 53349
-recovered pasa_asmbl_34161.p1, internal, 53501, 53638
-recovered pasa_asmbl_34161.p1, internal, 53757, 53895
-recovered pasa_asmbl_34161.p1, internal, 53984, 54108
-recovered pasa_asmbl_34161.p1, internal, 54215, 54571
-recovered pasa_asmbl_34161.p1, internal, 54689, 54817
-recovered pasa_asmbl_34161.p1, internal, 54918, 55145
-recovered pasa_asmbl_34161.p1, internal, 55250, 55434
-recovered pasa_asmbl_34161.p1, internal, 55526, 55812
-recovered pasa_asmbl_34161.p1, internal, 55911, 56021
Valid prediction for GlimmerHMM_glimmerT_53900-T1
Valid prediction for snap_scaffold_25-snap.787-T1
Valid prediction for pasa_asmbl_34149.p1
Valid prediction for Augustus_model.g35768.t1
Valid prediction for snap_scaffold_25-snap.780-T1
Valid prediction for CodingQuarry_transcript_38690-T1
Valid prediction for GlimmerHMM_glimmerT_53911-T1
Valid prediction for Augustus_model.g35787.t1
Couldn't classify 173497, 173625
Sorry, prediction pasa_asmbl_34145.p2 fails validation.
(AAA)	 GG	173497-173625	GT	AGG
(CCT)	 AG	173769-173927	GT	AGG
(GGC)	 AG	174023-174138	GT	AGG
(GTT)	 AG	174244-174346	GT	AGG
(CTA)	 AG	174476-174634	CG	GAC
-recovered pasa_asmbl_34145.p2, terminal, 174476, 174634
-recovered pasa_asmbl_34145.p2, internal, 173769, 173927
-recovered pasa_asmbl_34145.p2, internal, 174023, 174138
-recovered pasa_asmbl_34145.p2, internal, 174244, 174346
Valid prediction for CodingQuarry_transcript_38686-T1
Valid prediction for GlimmerHMM_glimmerT_53927-T1
Valid prediction for GlimmerHMM_glimmerT_53896-T1
Valid prediction for snap_scaffold_25-snap.790-T1
Valid prediction for snap_scaffold_25-snap.760-T1
Valid prediction for GlimmerHMM_glimmerT_53920-T1
Valid prediction for GlimmerHMM_glimmerT_53921-T1
Valid prediction for Augustus_model.g35769.t1
Valid prediction for HiQ_model.g35775.t1
Valid prediction for snap_scaffold_25-snap.785-T1
Valid prediction for Augustus_model.g35788.t1
Couldn't classify 57964, 58090
Sorry, prediction pasa_asmbl_34157.p1 fails validation.
(CAA)	 AC	57964-58090	GT	AGG
(CCT)	 AG	58259-58600	GT	AGG
(GGT)	 AG	58804-58877	GT	AGG
(CAG)	 AG	59151-59232	GT	GAG
(CTA)	 AG	59336-59451	GT	AGG
(GAT)	 AG	59569-59765	GT	AGG
(TCT)	 AG	59877-60090	GT	CAG
(ATG)	 AG	60216-60284	AG	AAA
-recovered pasa_asmbl_34157.p1, terminal, 60216, 60284
-recovered pasa_asmbl_34157.p1, internal, 58259, 58600
-recovered pasa_asmbl_34157.p1, internal, 58804, 58877
-recovered pasa_asmbl_34157.p1, internal, 59151, 59232
-recovered pasa_asmbl_34157.p1, internal, 59336, 59451
-recovered pasa_asmbl_34157.p1, internal, 59569, 59765
-recovered pasa_asmbl_34157.p1, internal, 59877, 60090

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 56206, rend_intergenic: 54860  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60610, rend_intergenic: 58900  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83685, rend_intergenic: 77131  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126948, rend_intergenic: 123388  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131705, rend_intergenic: 129056  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 192696, rend_intergenic: 191599  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 203817
-exon list size: 513


building trellis

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88.2    
88.3    
88.5    
88.7    
88.9    
89.1    
89.3    
89.5    
89.7    
89.9    
90.1    
90.3    
90.5    
90.7    
90.9    
91.1    
91.3    
91.5    
91.7    
91.8    
92.0    
92.2    
92.4    
92.6    
92.8    
93.0    
93.2    
93.4    
93.6    
93.8    
94.0    
94.2    
94.4    
94.6    
94.8    
95.0    
95.1    
95.3    
95.5    
95.7    
95.9    
96.1    
96.3    
96.5    
96.7    
96.9    
97.1    
97.3    
97.5    
97.7    
97.9    
98.1    
98.3    
98.4    
98.6    
98.8    
99.0    
99.2    
99.4    
99.6    
99.8    
-found 40 predictions from path traversal
Error with prediction: snap lend_intergenic: 56206, rend_intergenic: 54860  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60610, rend_intergenic: 58900  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83685, rend_intergenic: 77131  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126948, rend_intergenic: 123388  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131705, rend_intergenic: 129056  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 192696, rend_intergenic: 191599  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 37 predictions persist after filtering for low support