-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_19/scaffold_19_13280286-13460567

-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 GlimmerHMM_glimmerT_45189-T1
Valid prediction for snap_scaffold_19-snap.2615-T1
Valid prediction for GlimmerHMM_glimmerT_45193-T1
Valid prediction for snap_scaffold_19-snap.2647-T1
Valid prediction for GlimmerHMM_glimmerT_45220-T1
Valid prediction for snap_scaffold_19-snap.2626-T1
Valid prediction for snap_scaffold_19-snap.2628-T1
Valid prediction for Augustus_model.g29998.t1
Valid prediction for snap_scaffold_19-snap.2639-T1
Couldn't classify 90261, 90265
Sorry, prediction pasa_asmbl_21872.p1 fails validation.
(ATG)	 GG	88847-89394	GT	AGG
(ACG)	 AG	89958-90043	GT	AGG
(GTA)	 AG	90261-90265	AG	TCA
-recovered pasa_asmbl_21872.p1, initial, 88847, 89394
-recovered pasa_asmbl_21872.p1, internal, 89958, 90043
Valid prediction for GlimmerHMM_glimmerT_45212-T1
Couldn't classify 169851, 170249
Sorry, prediction pasa_asmbl_22704.p1 fails validation.
(CAC)	 GC	169851-170249	TC	AAT
Valid prediction for GlimmerHMM_glimmerT_45219-T1
Valid prediction for Augustus_model.g30016.t1
Valid prediction for Augustus_model.g30020.t1
Valid prediction for GlimmerHMM_glimmerT_45218-T1
Valid prediction for Augustus_model.g29999.t1
Valid prediction for snap_scaffold_19-snap.2613-T1
Valid prediction for snap_scaffold_19-snap.2629-T1
Valid prediction for GlimmerHMM_glimmerT_45209-T1
Valid prediction for snap_scaffold_19-snap.2644-T1
Valid prediction for GlimmerHMM_glimmerT_45207-T1
Valid prediction for GlimmerHMM_glimmerT_45192-T1
Valid prediction for GlimmerHMM_glimmerT_45205-T1
Valid prediction for snap_scaffold_19-snap.2634-T1
Valid prediction for GlimmerHMM_glimmerT_45202-T1
Valid prediction for Augustus_model.g30023.t1
Valid prediction for snap_scaffold_19-snap.2627-T1
Valid prediction for snap_scaffold_19-snap.2620-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for CodingQuarry_transcript_25891-T1
Valid prediction for GlimmerHMM_glimmerT_45215-T1
Valid prediction for GlimmerHMM_glimmerT_45198-T1
Valid prediction for Augustus_model.g30012.t1
Valid prediction for Augustus_model.g30021.t1
Valid prediction for GlimmerHMM_glimmerT_45217-T1
Valid prediction for snap_scaffold_19-snap.2638-T1
Valid prediction for Augustus_model.g30004.t1
Valid prediction for snap_scaffold_19-snap.2622-T1
Couldn't classify 64153, 64585
Sorry, prediction pasa_asmbl_21869.p1 fails validation.
(GTT)	 CA	64153-64585	GT	AGG
(AGA)	 AG	64783-64826	GT	AGG
(TTT)	 AG	64942-65001	GG	AAG
-recovered pasa_asmbl_21869.p1, terminal, 64942, 65001
-recovered pasa_asmbl_21869.p1, internal, 64783, 64826
Valid prediction for Augustus_model.g30011.t1
Couldn't classify 72778, 72924
Sorry, prediction pasa_asmbl_21871.p1 fails validation.
(GCG)	 GT	72778-72924	GT	TTG
(AAC)	 AG	75001-75106	GT	TGG
(ACC)	 AG	76534-76607	GC	GAG
-recovered pasa_asmbl_21871.p1, terminal, 76534, 76607
-recovered pasa_asmbl_21871.p1, internal, 75001, 75106
-recovered pasa_asmbl_21871.p1, internal, 76534, 76607
Valid prediction for Augustus_model.g30007.t1
Valid prediction for GlimmerHMM_glimmerT_45216-T1
Valid prediction for Augustus_model.g30010.t1
Valid prediction for GlimmerHMM_glimmerT_45201-T1
Valid prediction for snap_scaffold_19-snap.2624-T1
Valid prediction for Augustus_model.g30006.t1
Valid prediction for snap_scaffold_19-snap.2643-T1
Valid prediction for Augustus_model.g30018.t1
Valid prediction for snap_scaffold_19-snap.2640-T1
Valid prediction for Augustus_model.g30009.t1
Valid prediction for GlimmerHMM_glimmerT_45208-T1
Valid prediction for snap_scaffold_19-snap.2625-T1
Valid prediction for GlimmerHMM_glimmerT_45221-T1
Couldn't classify 90281, 90371
Couldn't classify 93076, 93084
Sorry, prediction pasa_asmbl_21874.p1 fails validation.
(TCC)	 TC	90281-90371	GT	TGG
(GTG)	 AG	91641-91797	GT	AGG
(CTA)	 AG	91997-92079	GT	AGG
(GGA)	 AG	92185-92280	GT	AGG
(CAA)	 AG	92641-92729	GT	AGG
(ACC)	 AG	92904-92990	GT	AGG
(GTA)	 AG	93076-93084	CT	CCC
add_exon() Sorry, pasa_asmbl_21874.p1 92185-92280-terminal-1 is invalid.
-recovered pasa_asmbl_21874.p1, terminal, 92185, 92280
-recovered pasa_asmbl_21874.p1, internal, 91641, 91797
-recovered pasa_asmbl_21874.p1, internal, 91997, 92079
-recovered pasa_asmbl_21874.p1, internal, 92185, 92280
-recovered pasa_asmbl_21874.p1, internal, 92641, 92729
-recovered pasa_asmbl_21874.p1, internal, 92904, 92990
Valid prediction for snap_scaffold_19-snap.2630-T1
Valid prediction for Augustus_model.g30022.t1
Valid prediction for snap_scaffold_19-snap.2612-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for snap_scaffold_19-snap.2631-T1
Valid prediction for snap_scaffold_19-snap.2641-T1
Valid prediction for snap_scaffold_19-snap.2642-T1
Valid prediction for snap_scaffold_19-snap.2645-T1
Valid prediction for GlimmerHMM_glimmerT_45190-T1
Valid prediction for Augustus_model.g30013.t1
Valid prediction for GlimmerHMM_glimmerT_45204-T1
Valid prediction for Augustus_model.g30001.t1
Valid prediction for GlimmerHMM_glimmerT_45194-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 snap_scaffold_19-snap.2632-T1
Valid prediction for GlimmerHMM_glimmerT_45203-T1
Valid prediction for Augustus_model.g30008.t1
Valid prediction for GlimmerHMM_glimmerT_45196-T1
Couldn't classify 79288, 79329
Sorry, prediction pasa_asmbl_22647.p1 fails validation.
(CTG)	 TG	79288-79329	GT	CGG
(GTT)	 AG	79812-80466	GT	AGG
(GTA)	 AG	80665-80891	GA	GAG
-recovered pasa_asmbl_22647.p1, terminal, 80665, 80891
-recovered pasa_asmbl_22647.p1, internal, 79812, 80466
Valid prediction for Augustus_model.g29996.t1
Couldn't classify 54874, 54925
Couldn't classify 58397, 58552
Sorry, prediction pasa_asmbl_22652.p1 fails validation.
(TAT)	 CC	54874-54925	GT	CGG
(GTC)	 AG	55764-55856	GT	CGG
(GTT)	 AG	56006-56186	GT	GGG
(GAG)	 AG	56631-56718	GT	AGG
(GAC)	 AG	58397-58552	GC	ATG
-recovered pasa_asmbl_22652.p1, internal, 55764, 55856
-recovered pasa_asmbl_22652.p1, internal, 56006, 56186
-recovered pasa_asmbl_22652.p1, internal, 56631, 56718
-recovered pasa_asmbl_22652.p1, internal, 58397, 58552
Valid prediction for HiQ_model.g30000.t1
Valid prediction for GlimmerHMM_glimmerT_45211-T1
Valid prediction for snap_scaffold_19-snap.2617-T1
Valid prediction for snap_scaffold_19-snap.2616-T1
Valid prediction for pasa_asmbl_22640.p1
Valid prediction for snap_scaffold_19-snap.2637-T1
Valid prediction for snap_scaffold_19-snap.2614-T1
Valid prediction for Augustus_model.g30014.t1
Couldn't classify 120168, 120301
Sorry, prediction pasa_asmbl_22644.p1 fails validation.
(ATG)	 AC	118521-118563	GT	AGG
(GGC)	 AG	119345-119429	GT	GAG
(TTT)	 AG	119582-119681	GT	AGG
(GTG)	 AG	119873-120029	GT	AGG
(GTA)	 AG	120168-120301	GT	CTG
-recovered pasa_asmbl_22644.p1, initial, 118521, 118563
-recovered pasa_asmbl_22644.p1, internal, 119345, 119429
-recovered pasa_asmbl_22644.p1, internal, 119582, 119681
-recovered pasa_asmbl_22644.p1, internal, 119873, 120029
-recovered pasa_asmbl_22644.p1, internal, 120168, 120301
Valid prediction for Augustus_model.g30015.t1
Valid prediction for Augustus_model.g30003.t1
Valid prediction for CodingQuarry_transcript_25890-T1
Valid prediction for snap_scaffold_19-snap.2609-T1
Valid prediction for Augustus_model.g29997.t1
Valid prediction for GlimmerHMM_glimmerT_45200-T1
Valid prediction for GlimmerHMM_glimmerT_45188-T1
Valid prediction for GlimmerHMM_glimmerT_45195-T1
Valid prediction for snap_scaffold_19-snap.2623-T1
Valid prediction for Augustus_model.g30017.t1
Valid prediction for GlimmerHMM_glimmerT_45210-T1
Valid prediction for GlimmerHMM_glimmerT_45206-T1
Valid prediction for HiQ_model.g29994.t1
Valid prediction for GlimmerHMM_glimmerT_45191-T1
Couldn't classify 67311, 67384
Couldn't classify 72478, 72532
Sorry, prediction pasa_asmbl_22649.p1 fails validation.
(GCT)	 AG	67311-67384	GT	CGG
(ATG)	 AG	67500-67632	GT	AGG
(GGC)	 AG	67736-67912	GT	AGG
(GAG)	 AG	70384-70483	GT	AGG
(AGA)	 AG	72183-72309	GT	TGG
(GGT)	 AG	72478-72532	GG	GTG
-recovered pasa_asmbl_22649.p1, initial, 67500, 67632
-recovered pasa_asmbl_22649.p1, internal, 67311, 67384
-recovered pasa_asmbl_22649.p1, internal, 67500, 67632
-recovered pasa_asmbl_22649.p1, internal, 67736, 67912
-recovered pasa_asmbl_22649.p1, internal, 70384, 70483
-recovered pasa_asmbl_22649.p1, internal, 72183, 72309
Valid prediction for GlimmerHMM_glimmerT_45213-T1
Valid prediction for snap_scaffold_19-snap.2633-T1
Couldn't classify 137726, 137884
Sorry, prediction pasa_asmbl_22643.p1 fails validation.
(ATG)	 AC	125559-125667	GT	CTG
(CGG)	 AG	125895-126066	GT	AGG
(AGT)	 AG	126718-126951	GT	TGG
(GGA)	 AG	127596-127680	GT	AGG
(GGT)	 AG	127803-127862	GT	AGG
(GTA)	 AG	129818-129928	GT	AGG
(AAT)	 AG	130214-130350	GT	AAG
(AGA)	 AG	130503-130710	GC	AGG
(CTG)	 AG	130844-130956	GT	AGG
(CCC)	 AG	131188-131302	GT	CAG
(CCT)	 AG	131539-131685	GT	AGG
(GCC)	 AG	131854-132030	GT	AGG
(GAC)	 AG	132148-132366	GT	AGG
(GAC)	 AG	132680-132904	GT	AAG
(GAC)	 AG	133136-133354	GT	AAG
(GAC)	 AG	133638-133862	GT	AGG
(GAC)	 AG	134988-135244	GT	AGG
(GTT)	 AG	135345-135396	GT	AGG
(GTG)	 AG	135568-135777	GT	AGG
(GTT)	 AG	135913-135985	GT	AGG
(TCA)	 AG	136062-136141	GT	TGG
(AGG)	 AG	136280-136381	GT	AGG
(GTG)	 AG	136509-136664	GT	AGG
(GGT)	 AG	136817-137014	GT	AGG
(ATC)	 AG	137193-137366	GT	AGG
(GGT)	 AG	137726-137884	CG	CCC
-recovered pasa_asmbl_22643.p1, initial, 125559, 125667
-recovered pasa_asmbl_22643.p1, internal, 125895, 126066
-recovered pasa_asmbl_22643.p1, internal, 126718, 126951
-recovered pasa_asmbl_22643.p1, internal, 127596, 127680
-recovered pasa_asmbl_22643.p1, internal, 127803, 127862
-recovered pasa_asmbl_22643.p1, internal, 129818, 129928
-recovered pasa_asmbl_22643.p1, internal, 130214, 130350
-recovered pasa_asmbl_22643.p1, internal, 130503, 130710
-recovered pasa_asmbl_22643.p1, internal, 130844, 130956
-recovered pasa_asmbl_22643.p1, internal, 131188, 131302
-recovered pasa_asmbl_22643.p1, internal, 131539, 131685
-recovered pasa_asmbl_22643.p1, internal, 131854, 132030
-recovered pasa_asmbl_22643.p1, internal, 132148, 132366
-recovered pasa_asmbl_22643.p1, internal, 132680, 132904
-recovered pasa_asmbl_22643.p1, internal, 133136, 133354
-recovered pasa_asmbl_22643.p1, internal, 133638, 133862
-recovered pasa_asmbl_22643.p1, internal, 134988, 135244
-recovered pasa_asmbl_22643.p1, internal, 135345, 135396
-recovered pasa_asmbl_22643.p1, internal, 135568, 135777
-recovered pasa_asmbl_22643.p1, internal, 135913, 135985
-recovered pasa_asmbl_22643.p1, internal, 136062, 136141
-recovered pasa_asmbl_22643.p1, internal, 136280, 136381
-recovered pasa_asmbl_22643.p1, internal, 136509, 136664
-recovered pasa_asmbl_22643.p1, internal, 136817, 137014
-recovered pasa_asmbl_22643.p1, internal, 137193, 137366
Valid prediction for CodingQuarry_transcript_25892-T1
Valid prediction for pasa_asmbl_22639.p1
Valid prediction for snap_scaffold_19-snap.2636-T1
Couldn't classify 62235, 62414
Couldn't classify 64292, 64423
Sorry, prediction pasa_asmbl_22651.p1 fails validation.
(GTT)	 TG	62235-62414	GT	AGG
(TCC)	 AG	62595-62705	GT	AGG
(GAG)	 AG	62827-62961	GT	AGG
(GAG)	 AG	64292-64423	TA	GGT
-recovered pasa_asmbl_22651.p1, internal, 62595, 62705
-recovered pasa_asmbl_22651.p1, internal, 62827, 62961
Valid prediction for Augustus_model.g29995.t1
Valid prediction for snap_scaffold_19-snap.2611-T1
Valid prediction for snap_scaffold_19-snap.2619-T1
Valid prediction for snap_scaffold_19-snap.2635-T1
Valid prediction for snap_scaffold_19-snap.2646-T1
Valid prediction for HiQ_model.g30019.t1
Valid prediction for GlimmerHMM_glimmerT_45187-T1
Valid prediction for snap_scaffold_19-snap.2618-T1
Valid prediction for snap_scaffold_19-snap.2610-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_45214-T1
Valid prediction for snap_scaffold_19-snap.2621-T1
Valid prediction for HiQ_model.g30005.t1
Couldn't classify 65019, 65106
Couldn't classify 66954, 67037
Sorry, prediction pasa_asmbl_22650.p1 fails validation.
(GAC)	 GG	65019-65106	GT	TGG
(ACC)	 AG	65375-65511	GT	AGG
(GGT)	 AG	65603-65715	GT	AGG
(GGA)	 AG	65825-65987	GT	AAG
(CGT)	 AG	66112-66258	GT	TTG
(GTG)	 AG	66377-66526	GT	AGG
(GTT)	 AG	66698-66823	GT	TGG
(ATC)	 AG	66954-67037	CC	AGC
-recovered pasa_asmbl_22650.p1, internal, 65375, 65511
-recovered pasa_asmbl_22650.p1, internal, 65603, 65715
-recovered pasa_asmbl_22650.p1, internal, 65825, 65987
-recovered pasa_asmbl_22650.p1, internal, 66112, 66258
-recovered pasa_asmbl_22650.p1, internal, 66377, 66526
-recovered pasa_asmbl_22650.p1, internal, 66698, 66823
Valid prediction for GlimmerHMM_glimmerT_45199-T1
Valid prediction for GlimmerHMM_glimmerT_45197-T1
Valid prediction for HiQ_model.g30002.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 175390, rend_intergenic: 171946  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 180282
-exon list size: 436


building trellis

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87.7    
87.9    
88.1    
88.4    
88.6    
88.8    
89.0    
89.3    
89.5    
89.7    
90.0    
90.2    
90.4    
90.6    
90.9    
91.1    
91.3    
91.6    
91.8    
92.0    
92.2    
92.5    
92.7    
92.9    
93.2    
93.4    
93.6    
93.8    
94.1    
94.3    
94.5    
94.7    
95.0    
95.2    
95.4    
95.7    
95.9    
96.1    
96.3    
96.6    
96.8    
97.0    
97.3    
97.5    
97.7    
97.9    
98.2    
98.4    
98.6    
98.9    
99.1    
99.3    
99.5    
99.8    
-found 39 predictions from path traversal
Error with prediction: snap lend_intergenic: 175390, rend_intergenic: 171946  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