-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_15/scaffold_15_13720238-13923860

-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_15-snap.2770-T1
Valid prediction for snap_scaffold_15-snap.2760-T1
Valid prediction for snap_scaffold_15-snap.2754-T1
Valid prediction for Augustus_model.g24837.t1
Valid prediction for Augustus_model.g24839.t1
Valid prediction for snap_scaffold_15-snap.2756-T1
Valid prediction for snap_scaffold_15-snap.2762-T1
Valid prediction for snap_scaffold_15-snap.2751-T1
Valid prediction for Augustus_model.g24850.t1
Valid prediction for GlimmerHMM_glimmerT_37294-T1
Valid prediction for GlimmerHMM_glimmerT_37277-T1
Valid prediction for GlimmerHMM_glimmerT_37300-T1
Valid prediction for snap_scaffold_15-snap.2766-T1
Valid prediction for snap_scaffold_15-snap.2758-T1
Couldn't classify 194579, 195337
Sorry, prediction pasa_asmbl_15657.p1 fails validation.
(AGC)	 GC	194579-195337	CC	AGC
Valid prediction for Augustus_model.g24852.t1
Valid prediction for GlimmerHMM_glimmerT_37275-T1
Valid prediction for GlimmerHMM_glimmerT_37299-T1
Valid prediction for snap_scaffold_15-snap.2765-T1
Valid prediction for snap_scaffold_15-snap.2775-T1
Valid prediction for snap_scaffold_15-snap.2773-T1
Valid prediction for Augustus_model.g24847.t1
Valid prediction for snap_scaffold_15-snap.2771-T1
Valid prediction for snap_scaffold_15-snap.2752-T1
Valid prediction for snap_scaffold_15-snap.2777-T1
Valid prediction for snap_scaffold_15-snap.2761-T1
Valid prediction for GlimmerHMM_glimmerT_37283-T1
Valid prediction for snap_scaffold_15-snap.2744-T1
Valid prediction for snap_scaffold_15-snap.2763-T1
Valid prediction for Augustus_model.g24842.t1
Valid prediction for Augustus_model.g24848.t1
Valid prediction for GlimmerHMM_glimmerT_37297-T1
Valid prediction for snap_scaffold_15-snap.2747-T1
Valid prediction for snap_scaffold_15-snap.2749-T1
Valid prediction for snap_scaffold_15-snap.2745-T1
Valid prediction for GlimmerHMM_glimmerT_37293-T1
Valid prediction for GlimmerHMM_glimmerT_37281-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 Augustus_model.g24846.t1
Couldn't classify 106516, 106517
Sorry, prediction CodingQuarry_transcript_18213-T1 fails validation.
(ATG)	 CG	106516-106517	GT	ATG
(GAT)	 AG	107399-107593	GT	AGG
(CGA)	 AG	107794-107854	GG	GAG
-recovered CodingQuarry_transcript_18213-T1, terminal, 107794, 107854
-recovered CodingQuarry_transcript_18213-T1, internal, 107399, 107593
Valid prediction for GlimmerHMM_glimmerT_37279-T1
Valid prediction for Augustus_model.g24851.t1
Valid prediction for GlimmerHMM_glimmerT_37289-T1
Valid prediction for snap_scaffold_15-snap.2757-T1
Valid prediction for Augustus_model.g24835.t1
Valid prediction for snap_scaffold_15-snap.2769-T1
Valid prediction for GlimmerHMM_glimmerT_37298-T1
Couldn't classify 137476, 137607
Sorry, prediction GlimmerHMM_glimmerT_37282-T1 fails validation.
(ATG)	 AC	127399-127576	GT	AGG
(AAG)	 AG	128203-128356	GT	TGG
(GCT)	 AG	128524-128647	GT	AGG
(ATC)	 AG	129971-130084	GT	AGG
(GTG)	 AG	130213-130262	GT	AGG
(TCT)	 AG	130433-130592	GT	AGG
(ATT)	 AG	131048-131189	GT	ATG
(ATG)	 AG	131325-131434	GT	AGG
(CCG)	 AG	131536-131653	GT	CGG
(GCT)	 AG	132313-132435	GT	AGG
(ATG)	 AG	133037-133237	GT	AGG
(GAG)	 AG	133460-134017	GT	TGG
(GTT)	 AG	134189-134386	GT	CGG
(CCC)	 AG	134685-134858	GT	TGG
(CCC)	 AN	137476-137607	GT	CTG
(TGC)	 AG	141324-141578	GT	AGG
(GTT)	 AG	143716-143752	GT	ATG
(GCA)	 AG	150835-150916	AC	GAA
-recovered GlimmerHMM_glimmerT_37282-T1, initial, 127399, 127576
add_exon() Sorry, GlimmerHMM_glimmerT_37282-T1 131325-131434-initial-1 is invalid.
-recovered GlimmerHMM_glimmerT_37282-T1, initial, 131325, 131434
add_exon() Sorry, GlimmerHMM_glimmerT_37282-T1 133037-133237-initial-1 is invalid.
-recovered GlimmerHMM_glimmerT_37282-T1, initial, 133037, 133237
-recovered GlimmerHMM_glimmerT_37282-T1, terminal, 150835, 150916
-recovered GlimmerHMM_glimmerT_37282-T1, internal, 128203, 128356
-recovered GlimmerHMM_glimmerT_37282-T1, internal, 128524, 128647
-recovered GlimmerHMM_glimmerT_37282-T1, internal, 129971, 130084
-recovered GlimmerHMM_glimmerT_37282-T1, internal, 130213, 130262
-recovered GlimmerHMM_glimmerT_37282-T1, internal, 130433, 130592
-recovered GlimmerHMM_glimmerT_37282-T1, internal, 131048, 131189
-recovered GlimmerHMM_glimmerT_37282-T1, internal, 131325, 131434
-recovered GlimmerHMM_glimmerT_37282-T1, internal, 131536, 131653
-recovered GlimmerHMM_glimmerT_37282-T1, internal, 132313, 132435
-recovered GlimmerHMM_glimmerT_37282-T1, internal, 133037, 133237
-recovered GlimmerHMM_glimmerT_37282-T1, internal, 133460, 134017
-recovered GlimmerHMM_glimmerT_37282-T1, internal, 134189, 134386
-recovered GlimmerHMM_glimmerT_37282-T1, internal, 134685, 134858
-recovered GlimmerHMM_glimmerT_37282-T1, internal, 141324, 141578
-recovered GlimmerHMM_glimmerT_37282-T1, internal, 143716, 143752
Valid prediction for Augustus_model.g24834.t1
Valid prediction for GlimmerHMM_glimmerT_37280-T1
Couldn't classify 81770, 81861
Couldn't classify 91285, 91310
Sorry, prediction pasa_asmbl_14677.p1 fails validation.
(TCC)	 GT	81770-81861	GT	GGG
(AAG)	 AG	84175-84244	GT	AGG
(AGC)	 AG	84357-84442	GT	AGG
(GTC)	 AG	85311-85372	GT	CTG
(CCG)	 AG	86680-86885	GT	AGG
(AAG)	 AG	89472-89617	GT	AAG
(GTA)	 AG	91056-91150	GT	AGG
(AGG)	 AG	91285-91310	GC	GCG
add_exon() Sorry, pasa_asmbl_14677.p1 91056-91150-terminal-2 is invalid.
-recovered pasa_asmbl_14677.p1, terminal, 91056, 91150
-recovered pasa_asmbl_14677.p1, internal, 84175, 84244
-recovered pasa_asmbl_14677.p1, internal, 84357, 84442
-recovered pasa_asmbl_14677.p1, internal, 85311, 85372
-recovered pasa_asmbl_14677.p1, internal, 86680, 86885
-recovered pasa_asmbl_14677.p1, internal, 89472, 89617
-recovered pasa_asmbl_14677.p1, internal, 91056, 91150
-recovered pasa_asmbl_14677.p1, internal, 91285, 91310
Valid prediction for GlimmerHMM_glimmerT_37296-T1
Valid prediction for Augustus_model.g24849.t1
Valid prediction for GlimmerHMM_glimmerT_37285-T1
Valid prediction for pasa_asmbl_14662.p1
Valid prediction for GlimmerHMM_glimmerT_37295-T1
Valid prediction for CodingQuarry_transcript_18211-T1
Valid prediction for snap_scaffold_15-snap.2743-T1
Valid prediction for snap_scaffold_15-snap.2746-T1
Valid prediction for GlimmerHMM_glimmerT_37284-T1
Couldn't classify 78318, 78419
Couldn't classify 81319, 81371
Sorry, prediction pasa_asmbl_14940.p1 fails validation.
(ATC)	 TA	78318-78419	GT	GGG
(CAA)	 AG	79417-79504	GT	AGG
(GAA)	 AG	79653-79814	GT	AGG
(ATG)	 AG	81319-81371	AC	TCA
-recovered pasa_asmbl_14940.p1, internal, 79417, 79504
-recovered pasa_asmbl_14940.p1, internal, 79653, 79814
Valid prediction for GlimmerHMM_glimmerT_37276-T1
Valid prediction for snap_scaffold_15-snap.2764-T1
Valid prediction for CodingQuarry_transcript_18210-T1
Valid prediction for snap_scaffold_15-snap.2774-T1
Valid prediction for Augustus_model.g24838.t1
Couldn't classify 92503, 92701
Couldn't classify 95257, 95337
Sorry, prediction pasa_asmbl_14676.p1 fails validation.
(GAG)	 AG	92503-92701	GT	AGG
(GCT)	 AG	93692-93795	GT	TGG
(GCA)	 AG	95257-95337	GT	AGG
-recovered pasa_asmbl_14676.p1, internal, 92503, 92701
-recovered pasa_asmbl_14676.p1, internal, 93692, 93795
-recovered pasa_asmbl_14676.p1, internal, 95257, 95337
Valid prediction for GlimmerHMM_glimmerT_37292-T1
Valid prediction for snap_scaffold_15-snap.2755-T1
Couldn't classify 113020, 113322
Sorry, prediction pasa_asmbl_14672.p1 fails validation.
(CAG)	 CC	113020-113322	GC	CCG
Valid prediction for GlimmerHMM_glimmerT_37287-T1
Couldn't classify 181797, 181807
Sorry, prediction pasa_asmbl_14661.p1 fails validation.
(ATG)	 AA	178353-178425	GT	CGG
(ATG)	 AG	181191-181409	GT	TGG
(ACC)	 AG	181797-181807	GG	GAG
-recovered pasa_asmbl_14661.p1, initial, 178353, 178425
add_exon() Sorry, pasa_asmbl_14661.p1 181191-181409-initial-1 is invalid.
-recovered pasa_asmbl_14661.p1, initial, 181191, 181409
-recovered pasa_asmbl_14661.p1, internal, 181191, 181409
Valid prediction for snap_scaffold_15-snap.2753-T1
Valid prediction for snap_scaffold_15-snap.2778-T1
Valid prediction for Augustus_model.g24853.t1
Valid prediction for GlimmerHMM_glimmerT_37288-T1
Couldn't classify 107794, 108501
Sorry, prediction pasa_asmbl_14675.p1 fails validation.
(ATG)	 AC	103885-103887	GT	TGG
(GAC)	 AG	104178-104251	GT	AGG
(GGC)	 AG	105537-105655	GT	GGG
(CCT)	 AG	105944-106141	GT	CAG
(ACC)	 AG	106426-106517	GT	ATG
(GAT)	 AG	107399-107593	GT	AGG
(CGA)	 AG	107794-108501	CC	CCC
-recovered pasa_asmbl_14675.p1, initial, 103885, 103887
-recovered pasa_asmbl_14675.p1, internal, 104178, 104251
-recovered pasa_asmbl_14675.p1, internal, 105537, 105655
-recovered pasa_asmbl_14675.p1, internal, 105944, 106141
-recovered pasa_asmbl_14675.p1, internal, 106426, 106517
-recovered pasa_asmbl_14675.p1, internal, 107399, 107593
Valid prediction for snap_scaffold_15-snap.2772-T1
Couldn't classify 190353, 190436
Sorry, prediction pasa_asmbl_14660.p1 fails validation.
(TTC)	 AC	190353-190436	GT	TGG
(GTG)	 AG	190625-190772	GT	AGG
(TCA)	 AG	191217-191321	GT	AGG
(TGA)	 AG	191413-191497	GT	AAG
(GAA)	 AG	191664-191710	GT	AGG
(GTT)	 AG	193484-193603	GT	AGG
(AGT)	 AG	193727-194283	TC	GAT
add_exon() Sorry, pasa_asmbl_14660.p1 191217-191321-terminal-1 is invalid.
-recovered pasa_asmbl_14660.p1, terminal, 191217, 191321
-recovered pasa_asmbl_14660.p1, terminal, 193727, 194283
-recovered pasa_asmbl_14660.p1, internal, 190625, 190772
-recovered pasa_asmbl_14660.p1, internal, 191217, 191321
-recovered pasa_asmbl_14660.p1, internal, 191413, 191497
-recovered pasa_asmbl_14660.p1, internal, 191664, 191710
-recovered pasa_asmbl_14660.p1, internal, 193484, 193603
Couldn't classify 74390, 74585
Couldn't classify 76628, 76787
Sorry, prediction pasa_asmbl_14679.p1 fails validation.
(GAC)	 AG	74390-74585	GT	GGG
(AGC)	 AG	75203-75312	GT	AGG
(AAG)	 AG	75933-76093	GT	AGG
(GGA)	 AG	76628-76787	GG	CAG
-recovered pasa_asmbl_14679.p1, internal, 74390, 74585
-recovered pasa_asmbl_14679.p1, internal, 75203, 75312
-recovered pasa_asmbl_14679.p1, internal, 75933, 76093
Valid prediction for snap_scaffold_15-snap.2750-T1
Valid prediction for snap_scaffold_15-snap.2748-T1
Valid prediction for Augustus_model.g24844.t1
Valid prediction for snap_scaffold_15-snap.2767-T1
Valid prediction for snap_scaffold_15-snap.2759-T1
Valid prediction for Augustus_model.g24840.t1
Valid prediction for GlimmerHMM_glimmerT_37278-T1
Valid prediction for Augustus_model.g24841.t1
Couldn't classify 108565, 108707
Couldn't classify 112828, 112968
Sorry, prediction pasa_asmbl_14673.p1 fails validation.
(CCC)	 CC	108565-108707	GT	AGG
(CAA)	 AG	108918-109047	GT	AGG
(GCC)	 AG	109251-109430	GT	GGG
(TTG)	 AG	111479-111613	GT	AGG
(AGG)	 AG	112828-112968	CC	CCC
-recovered pasa_asmbl_14673.p1, internal, 108918, 109047
-recovered pasa_asmbl_14673.p1, internal, 109251, 109430
-recovered pasa_asmbl_14673.p1, internal, 111479, 111613
Valid prediction for GlimmerHMM_glimmerT_37290-T1
Valid prediction for GlimmerHMM_glimmerT_37291-T1
Valid prediction for snap_scaffold_15-snap.2742-T1
Valid prediction for snap_scaffold_15-snap.2776-T1
Valid prediction for snap_scaffold_15-snap.2768-T1
Valid prediction for GlimmerHMM_glimmerT_37286-T1
Valid prediction for GlimmerHMM_glimmerT_37301-T1
Valid prediction for Augustus_model.g24843.t1
Valid prediction for CodingQuarry_transcript_18212-T1
Valid prediction for Augustus_model.g24845.t1
Valid prediction for Augustus_model.g24836.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 25271, rend_intergenic: 13748  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37790, rend_intergenic: 36044  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40495, rend_intergenic: 38728  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51447, rend_intergenic: 50117  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93967, rend_intergenic: 88477  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106195, rend_intergenic: 96035  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107348, rend_intergenic: 106663  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125285, rend_intergenic: 107411  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130101, rend_intergenic: 125341  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141808, rend_intergenic: 130678  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150736, rend_intergenic: 143171  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162660, rend_intergenic: 158298  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175808, rend_intergenic: 172776  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 188466, rend_intergenic: 185348  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 203623
-exon list size: 444


building trellis

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80.7    
80.9    
81.2    
81.4    
81.6    
81.8    
82.1    
82.3    
82.5    
82.7    
83.0    
83.2    
83.4    
83.6    
83.9    
84.1    
84.3    
84.5    
84.8    
85.0    
85.2    
85.4    
85.7    
85.9    
86.1    
86.3    
86.5    
86.8    
87.0    
87.2    
87.4    
87.7    
87.9    
88.1    
88.3    
88.6    
88.8    
89.0    
89.2    
89.5    
89.7    
89.9    
90.1    
90.4    
90.6    
90.8    
91.0    
91.3    
91.5    
91.7    
91.9    
92.2    
92.4    
92.6    
92.8    
93.0    
93.3    
93.5    
93.7    
93.9    
94.2    
94.4    
94.6    
94.8    
95.1    
95.3    
95.5    
95.7    
96.0    
96.2    
96.4    
96.6    
96.9    
97.1    
97.3    
97.5    
97.8    
98.0    
98.2    
98.4    
98.7    
98.9    
99.1    
99.3    
99.6    
99.8    
-found 28 predictions from path traversal
Error with prediction: snap lend_intergenic: 25271, rend_intergenic: 13748  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37790, rend_intergenic: 36044  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40495, rend_intergenic: 38728  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51447, rend_intergenic: 50117  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93967, rend_intergenic: 88477  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106195, rend_intergenic: 96035  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107348, rend_intergenic: 106663  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125285, rend_intergenic: 107411  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130101, rend_intergenic: 125341  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141808, rend_intergenic: 130678  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150736, rend_intergenic: 143171  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162660, rend_intergenic: 158298  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175808, rend_intergenic: 172776  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 188466, rend_intergenic: 185348  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 20 predictions persist after filtering for low support