-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_1/scaffold_1_20650210-20825699

-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_2761-T1
Valid prediction for CodingQuarry_transcript_3038-T1
Valid prediction for Augustus_model.g1962.t1
Valid prediction for HiQ_model.g1963.t1
Valid prediction for Augustus_model.g1964.t1
Valid prediction for snap_scaffold_1-snap.3859-T1
Valid prediction for Augustus_model.g1970.t1
Valid prediction for GlimmerHMM_glimmerT_2767-T1
Valid prediction for Augustus_model.g1972.t1
Valid prediction for snap_scaffold_1-snap.3878-T1
Valid prediction for pasa_asmbl_2651.p1
Valid prediction for CodingQuarry_transcript_3034-T1
Valid prediction for GlimmerHMM_glimmerT_2782-T1
Valid prediction for GlimmerHMM_glimmerT_2786-T1
Valid prediction for pasa_asmbl_2655.p1
Valid prediction for GlimmerHMM_glimmerT_2779-T1
Valid prediction for snap_scaffold_1-snap.3869-T1
Valid prediction for GlimmerHMM_glimmerT_2785-T1
Valid prediction for pasa_asmbl_2648.p1
Valid prediction for GlimmerHMM_glimmerT_2765-T1
Valid prediction for HiQ_model.g1974.t1
Valid prediction for snap_scaffold_1-snap.3852-T1
Valid prediction for CodingQuarry_transcript_3039-T1
Valid prediction for GlimmerHMM_glimmerT_2781-T1
Valid prediction for GlimmerHMM_glimmerT_2783-T1
Valid prediction for GlimmerHMM_glimmerT_2771-T1
Valid prediction for snap_scaffold_1-snap.3882-T1
Valid prediction for Augustus_model.g1976.t1
Couldn't classify 43058, 43309
Couldn't classify 44022, 44105
Sorry, prediction pasa_asmbl_2768.p1 fails validation.
(GAC)	 AC	43058-43309	GT	AGG
(GAT)	 AG	43426-43596	GT	TGG
(ACT)	 AG	43840-43926	GT	TGG
(GAA)	 AG	44022-44105	CT	TGC
-recovered pasa_asmbl_2768.p1, internal, 43426, 43596
-recovered pasa_asmbl_2768.p1, internal, 43840, 43926
Valid prediction for snap_scaffold_1-snap.3855-T1
Valid prediction for GlimmerHMM_glimmerT_2780-T1
Valid prediction for snap_scaffold_1-snap.3870-T1
Couldn't classify 44091, 44160
Sorry, prediction pasa_asmbl_2647.p1 fails validation.
(CTC)	 CT	44091-44160	GT	GGG
(AGC)	 AG	44636-44716	GT	CGG
(AAC)	 AG	44921-45049	GT	TGG
(TGC)	 AG	45208-45297	GT	AGG
(ATG)	 AG	45406-45578	GT	AGG
(TTG)	 AG	45975-46199	AG	GAA
add_exon() Sorry, pasa_asmbl_2647.p1 45406-45578-initial-1 is invalid.
-recovered pasa_asmbl_2647.p1, initial, 45406, 45578
-recovered pasa_asmbl_2647.p1, terminal, 45975, 46199
-recovered pasa_asmbl_2647.p1, internal, 44636, 44716
-recovered pasa_asmbl_2647.p1, internal, 44921, 45049
-recovered pasa_asmbl_2647.p1, internal, 45208, 45297
-recovered pasa_asmbl_2647.p1, internal, 45406, 45578
Valid prediction for snap_scaffold_1-snap.3868-T1
Valid prediction for Augustus_model.g1960.t1
Valid prediction for snap_scaffold_1-snap.3877-T1
Valid prediction for snap_scaffold_1-snap.3864-T1
Valid prediction for snap_scaffold_1-snap.3876-T1
Valid prediction for snap_scaffold_1-snap.3874-T1
Valid prediction for GlimmerHMM_glimmerT_2764-T1
Valid prediction for snap_scaffold_1-snap.3865-T1
Valid prediction for pasa_asmbl_2656.p1
Valid prediction for snap_scaffold_1-snap.3860-T1
Valid prediction for GlimmerHMM_glimmerT_2769-T1
Valid prediction for GlimmerHMM_glimmerT_2777-T1
Valid prediction for snap_scaffold_1-snap.3851-T1
Valid prediction for snap_scaffold_1-snap.3885-T1
Valid prediction for HiQ_model.g1973.t1
Valid prediction for snap_scaffold_1-snap.3857-T1
Valid prediction for GlimmerHMM_glimmerT_2768-T1
Valid prediction for GlimmerHMM_glimmerT_2775-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_2778-T1
Valid prediction for GlimmerHMM_glimmerT_2766-T1
Valid prediction for snap_scaffold_1-snap.3853-T1
Valid prediction for snap_scaffold_1-snap.3881-T1
Couldn't classify 135737, 135861
Sorry, prediction pasa_asmbl_1189.p1 fails validation.
(ACT)	 AC	135737-135861	GT	AGG
(CCC)	 AG	136246-136441	GT	ACG
(GTG)	 AG	136871-136937	GT	TGG
(AGG)	 AG	137243-137343	GT	CGG
(CCA)	 AG	137502-137597	CA	AAC
-recovered pasa_asmbl_1189.p1, terminal, 137502, 137597
-recovered pasa_asmbl_1189.p1, internal, 136246, 136441
-recovered pasa_asmbl_1189.p1, internal, 136871, 136937
-recovered pasa_asmbl_1189.p1, internal, 137243, 137343
Valid prediction for GlimmerHMM_glimmerT_2763-T1
Valid prediction for snap_scaffold_1-snap.3849-T1
Couldn't classify 95653, 95842
Sorry, prediction pasa_asmbl_1196.p1 fails validation.
(GCC)	 AG	95653-95842	GT	GGG
(AGG)	 AG	95935-96104	GT	AGG
(GCC)	 AG	96605-96783	GT	AGG
(GAA)	 AG	97103-97223	GT	AGG
(GTC)	 AG	97506-97619	GA	AGG
-recovered pasa_asmbl_1196.p1, terminal, 97506, 97619
-recovered pasa_asmbl_1196.p1, internal, 95653, 95842
-recovered pasa_asmbl_1196.p1, internal, 95935, 96104
-recovered pasa_asmbl_1196.p1, internal, 96605, 96783
-recovered pasa_asmbl_1196.p1, internal, 97103, 97223
Valid prediction for snap_scaffold_1-snap.3875-T1
Valid prediction for pasa_asmbl_1200.p1
Valid prediction for GlimmerHMM_glimmerT_2760-T1
Valid prediction for snap_scaffold_1-snap.3861-T1
Couldn't classify 77767, 77862
Sorry, prediction pasa_asmbl_1205.p1 fails validation.
(ATG)	 CA	73539-73821	GT	AGG
(GTG)	 AG	73948-74064	GT	CAG
(GTG)	 AG	74156-74290	GT	AGG
(GCT)	 AG	74846-74999	GT	TGG
(GTG)	 AG	75102-75212	GT	ATG
(GAG)	 AG	75903-75999	GT	AGG
(ATT)	 AG	76162-76218	GT	CGG
(CTG)	 AG	76331-76447	GT	GGG
(GTC)	 AG	77767-77862	CC	CCC
-recovered pasa_asmbl_1205.p1, initial, 73539, 73821
-recovered pasa_asmbl_1205.p1, internal, 73948, 74064
-recovered pasa_asmbl_1205.p1, internal, 74156, 74290
-recovered pasa_asmbl_1205.p1, internal, 74846, 74999
-recovered pasa_asmbl_1205.p1, internal, 75102, 75212
-recovered pasa_asmbl_1205.p1, internal, 75903, 75999
-recovered pasa_asmbl_1205.p1, internal, 76162, 76218
-recovered pasa_asmbl_1205.p1, internal, 76331, 76447
Valid prediction for Augustus_model.g1967.t1
Valid prediction for Augustus_model.g1965.t1
Valid prediction for snap_scaffold_1-snap.3872-T1
Valid prediction for GlimmerHMM_glimmerT_2774-T1
Couldn't classify 108162, 109601
Sorry, prediction pasa_asmbl_1193.p1 fails validation.
(ACC)	 CC	108162-109601	AA	CCA
Couldn't classify 161059, 161078
Sorry, prediction pasa_asmbl_1294.p1 fails validation.
(CAG)	 TT	161059-161078	GT	CGG
(GTT)	 AG	161280-161409	GT	AGG
(ATG)	 AG	162499-162603	GT	AGG
(AGG)	 AG	162875-162934	GT	AGG
(GAA)	 AG	163033-163083	GT	AGG
(GTA)	 AG	164050-164136	GA	GAG
-recovered pasa_asmbl_1294.p1, initial, 162499, 162603
-recovered pasa_asmbl_1294.p1, terminal, 164050, 164136
-recovered pasa_asmbl_1294.p1, internal, 161280, 161409
-recovered pasa_asmbl_1294.p1, internal, 162499, 162603
-recovered pasa_asmbl_1294.p1, internal, 162875, 162934
-recovered pasa_asmbl_1294.p1, internal, 163033, 163083
Valid prediction for HiQ_model.g1961.t1
Valid prediction for snap_scaffold_1-snap.3854-T1
Couldn't classify 106085, 106181
Sorry, prediction pasa_asmbl_1297.p1 fails validation.
(ATG)	 GG	105649-105738	GT	AGG
(GTG)	 AG	105838-105947	GT	AGG
(AGA)	 AG	106085-106181	GA	GAG
-recovered pasa_asmbl_1297.p1, initial, 105649, 105738
-recovered pasa_asmbl_1297.p1, internal, 105838, 105947
Valid prediction for snap_scaffold_1-snap.3848-T1
Valid prediction for GlimmerHMM_glimmerT_2773-T1
Valid prediction for snap_scaffold_1-snap.3856-T1
Couldn't classify 106485, 107912
Sorry, prediction pasa_asmbl_1194.p1 fails validation.
(GAG)	 CT	106485-107912	CA	AGC
Valid prediction for GlimmerHMM_glimmerT_2770-T1
Valid prediction for snap_scaffold_1-snap.3867-T1
Valid prediction for snap_scaffold_1-snap.3871-T1
Valid prediction for CodingQuarry_transcript_3035-T1
Valid prediction for pasa_asmbl_1187.p1
Valid prediction for CodingQuarry_transcript_3036-T1
Valid prediction for snap_scaffold_1-snap.3879-T1
Valid prediction for snap_scaffold_1-snap.3880-T1
Valid prediction for snap_scaffold_1-snap.3863-T1
Valid prediction for HiQ_model.g1975.t1
Valid prediction for GlimmerHMM_glimmerT_2784-T1
Valid prediction for pasa_asmbl_1206.p2
Valid prediction for CodingQuarry_transcript_3033-T1
Couldn't classify 95713, 95733
Sorry, prediction pasa_asmbl_1198.p1 fails validation.
(ATG)	 CC	93462-93843	GT	AGG
(AGC)	 AG	94071-94228	GT	AGG
(GGA)	 AG	95437-95652	GC	AGG
(GCC)	 AG	95713-95733	AT	ATA
-recovered pasa_asmbl_1198.p1, initial, 93462, 93843
-recovered pasa_asmbl_1198.p1, internal, 94071, 94228
-recovered pasa_asmbl_1198.p1, internal, 95437, 95652
Valid prediction for GlimmerHMM_glimmerT_2772-T1
Valid prediction for Augustus_model.g1958.t1
Valid prediction for snap_scaffold_1-snap.3873-T1
Valid prediction for snap_scaffold_1-snap.3884-T1
Couldn't classify 66750, 67271
Sorry, prediction pasa_asmbl_2781.p1 fails validation.
(ATG)	 CC	66750-67271	CT	AGC
Valid prediction for Augustus_model.g1966.t1
Valid prediction for snap_scaffold_1-snap.3858-T1
Valid prediction for HiQ_model.g1968.t1
Couldn't classify 109665, 113495
Sorry, prediction pasa_asmbl_1191.p1 fails validation.
(GCA)	 GC	109665-113495	GT	TGG
(GCT)	 AG	113651-113713	GT	CGG
(AAG)	 AG	113861-114061	GT	CAG
(GGG)	 AG	114361-114519	GT	AAG
(CCT)	 AG	114940-115071	TA	AAT
-recovered pasa_asmbl_1191.p1, terminal, 114940, 115071
-recovered pasa_asmbl_1191.p1, internal, 113651, 113713
-recovered pasa_asmbl_1191.p1, internal, 113861, 114061
-recovered pasa_asmbl_1191.p1, internal, 114361, 114519
Valid prediction for Augustus_model.g1959.t1
Valid prediction for CodingQuarry_transcript_3037-T1
Valid prediction for Augustus_model.g1969.t1
Valid prediction for snap_scaffold_1-snap.3866-T1
Valid prediction for GlimmerHMM_glimmerT_2762-T1
Valid prediction for snap_scaffold_1-snap.3883-T1
Valid prediction for snap_scaffold_1-snap.3850-T1
Valid prediction for GlimmerHMM_glimmerT_2776-T1
Valid prediction for CodingQuarry_transcript_3040-T1
Couldn't classify 78181, 78798
Sorry, prediction pasa_asmbl_1348.p1 fails validation.
(CCC)	 TG	78181-78798	TG	AAT
Valid prediction for snap_scaffold_1-snap.3862-T1
Valid prediction for Augustus_model.g1971.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 20001, rend_intergenic: 16287  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26164, rend_intergenic: 22517  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33132, rend_intergenic: 27633  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46199, rend_intergenic: 41706  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86546, rend_intergenic: 81333  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101952, rend_intergenic: 95861  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119991, rend_intergenic: 117075  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142976, rend_intergenic: 129399  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170682, rend_intergenic: 149235  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 175490
-exon list size: 428


building trellis

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98.1    
98.4    
98.6    
98.8    
99.1    
99.3    
99.5    
99.8    
-found 23 predictions from path traversal
Error with prediction: snap lend_intergenic: 20001, rend_intergenic: 16287  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26164, rend_intergenic: 22517  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33132, rend_intergenic: 27633  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46199, rend_intergenic: 41706  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86546, rend_intergenic: 81333  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101952, rend_intergenic: 95861  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119991, rend_intergenic: 117075  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142976, rend_intergenic: 129399  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170682, rend_intergenic: 149235  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 19 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 10361
-exon list size: 9


building trellis

9.1    
18.2    
27.3    
36.4    
45.5    
54.5    
63.6    
72.7    
81.8    
90.9    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 10321
-exon list size: 8


building trellis

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-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support