-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_2/scaffold_2_20283395-20470143

-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_2-snap.4013-T1
Valid prediction for snap_scaffold_2-snap.4022-T1
Valid prediction for GeneMark_model.9678_t
Valid prediction for GeneMark_model.9662_t
Valid prediction for GlimmerHMM_glimmerT_5926-T1
Couldn't classify 139752, 139974
Sorry, prediction pasa_asmbl_25361.p1 fails validation.
(GGT)	 CA	139752-139974	GT	AGG
(CTG)	 AG	140059-140213	GT	AGG
(GCT)	 AG	140476-140624	GT	AGG
(GTA)	 AG	140714-140798	GT	AGG
(ATT)	 AG	141018-141084	GT	AGG
(GTT)	 AG	141219-141266	GT	TGG
(AGG)	 AG	141436-141575	GT	CGG
(GCA)	 AG	141663-141872	AG	AAA
-recovered pasa_asmbl_25361.p1, terminal, 141018, 141084
-recovered pasa_asmbl_25361.p1, terminal, 141663, 141872
-recovered pasa_asmbl_25361.p1, internal, 140059, 140213
-recovered pasa_asmbl_25361.p1, internal, 140476, 140624
-recovered pasa_asmbl_25361.p1, internal, 140714, 140798
-recovered pasa_asmbl_25361.p1, internal, 141018, 141084
-recovered pasa_asmbl_25361.p1, internal, 141219, 141266
-recovered pasa_asmbl_25361.p1, internal, 141436, 141575
Valid prediction for GeneMark_model.9672_t
Valid prediction for GeneMark_model.9666_t
Valid prediction for GlimmerHMM_glimmerT_5903-T1
Valid prediction for GlimmerHMM_glimmerT_5920-T1
Valid prediction for snap_scaffold_2-snap.4024-T1
Valid prediction for snap_scaffold_2-snap.4028-T1
Valid prediction for GlimmerHMM_glimmerT_5918-T1
Valid prediction for snap_scaffold_2-snap.4041-T1
Valid prediction for pasa_asmbl_25353.p1
Valid prediction for snap_scaffold_2-snap.4032-T1
Valid prediction for snap_scaffold_2-snap.4029-T1
Valid prediction for GeneMark_model.9653_t
Valid prediction for GlimmerHMM_glimmerT_5924-T1
Valid prediction for GeneMark_model.9674_t
Valid prediction for GeneMark_model.9671_t
Valid prediction for GlimmerHMM_glimmerT_5923-T1
Valid prediction for CodingQuarry_transcript_28837-T1
Valid prediction for snap_scaffold_2-snap.4015-T1
Valid prediction for snap_scaffold_2-snap.4026-T1
Valid prediction for snap_scaffold_2-snap.4042-T1
Valid prediction for GlimmerHMM_glimmerT_5911-T1
Valid prediction for snap_scaffold_2-snap.4038-T1
Valid prediction for snap_scaffold_2-snap.4047-T1
Valid prediction for GlimmerHMM_glimmerT_5904-T1
Valid prediction for GlimmerHMM_glimmerT_5922-T1
Valid prediction for CodingQuarry_transcript_28833-T1
Valid prediction for GeneMark_model.9656_t
Valid prediction for GlimmerHMM_glimmerT_5921-T1
Valid prediction for snap_scaffold_2-snap.4035-T1
Valid prediction for GlimmerHMM_glimmerT_5906-T1
Valid prediction for CodingQuarry_transcript_28835-T1
Valid prediction for snap_scaffold_2-snap.4020-T1
Valid prediction for GeneMark_model.9676_t
Valid prediction for GlimmerHMM_glimmerT_5908-T1
Couldn't classify 27028, 27291
Couldn't classify 27385, 27496
Sorry, prediction CodingQuarry_transcript_28834-T1 fails validation.
(ATG)	 AG	25906-26033	GT	GGG
(ACT)	 AG	26203-26302	GT	ATG
(GTG)	 AG	26382-26505	GT	CAG
(ACT)	 AG	26613-26760	GT	AGG
(GCA)	 AG	27028-27291	GG	AAG
(GGA)	 GG	27385-27496	CA	GAC
-recovered CodingQuarry_transcript_28834-T1, initial, 25906, 26033
-recovered CodingQuarry_transcript_28834-T1, internal, 25906, 26033
-recovered CodingQuarry_transcript_28834-T1, internal, 26203, 26302
-recovered CodingQuarry_transcript_28834-T1, internal, 26382, 26505
-recovered CodingQuarry_transcript_28834-T1, internal, 26613, 26760
Valid prediction for snap_scaffold_2-snap.4017-T1
Valid prediction for snap_scaffold_2-snap.4044-T1
Valid prediction for snap_scaffold_2-snap.4016-T1
Valid prediction for GlimmerHMM_glimmerT_5916-T1
Valid prediction for GeneMark_model.9663_t
Valid prediction for GlimmerHMM_glimmerT_5929-T1
Valid prediction for GeneMark_model.9652_t
Valid prediction for GlimmerHMM_glimmerT_5905-T1
Valid prediction for GlimmerHMM_glimmerT_5919-T1
Valid prediction for snap_scaffold_2-snap.4011-T1
Valid prediction for CodingQuarry_transcript_28836-T1
Valid prediction for GlimmerHMM_glimmerT_5902-T1
Valid prediction for GlimmerHMM_glimmerT_5912-T1
Valid prediction for GeneMark_model.9669_t
Valid prediction for GeneMark_model.9654_t
Valid prediction for GlimmerHMM_glimmerT_5928-T1
Valid prediction for GlimmerHMM_glimmerT_5931-T1
Valid prediction for GeneMark_model.9648_t
Valid prediction for snap_scaffold_2-snap.4046-T1
Valid prediction for snap_scaffold_2-snap.4045-T1
Valid prediction for GeneMark_model.9660_t
Valid prediction for pasa_asmbl_25355.p1
Valid prediction for snap_scaffold_2-snap.4021-T1
Valid prediction for pasa_asmbl_25358.p1

-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 GeneMark_model.9673_t
Valid prediction for GeneMark_model.9661_t
Valid prediction for GeneMark_model.9651_t
Valid prediction for snap_scaffold_2-snap.4014-T1
Valid prediction for snap_scaffold_2-snap.4039-T1
Valid prediction for snap_scaffold_2-snap.4012-T1
Valid prediction for snap_scaffold_2-snap.4033-T1
Couldn't classify 19991, 20302
Couldn't classify 20912, 21017
Sorry, prediction pasa_asmbl_23962.p1 fails validation.
(TGC)	 AG	19991-20302	GT	AGG
(GAA)	 AG	20736-20830	GT	AGG
(CCA)	 AG	20912-21017	GC	ATG
add_exon() Sorry, pasa_asmbl_23962.p1 20736-20830-terminal-2 is invalid.
-recovered pasa_asmbl_23962.p1, terminal, 20736, 20830
-recovered pasa_asmbl_23962.p1, internal, 19991, 20302
-recovered pasa_asmbl_23962.p1, internal, 20736, 20830
-recovered pasa_asmbl_23962.p1, internal, 20912, 21017
Valid prediction for snap_scaffold_2-snap.4031-T1
Valid prediction for GlimmerHMM_glimmerT_5910-T1
Valid prediction for snap_scaffold_2-snap.4030-T1
Valid prediction for GeneMark_model.9664_t
Valid prediction for GeneMark_model.9657_t
Valid prediction for GeneMark_model.9655_t
Valid prediction for GlimmerHMM_glimmerT_5915-T1
Valid prediction for snap_scaffold_2-snap.4037-T1
Valid prediction for GeneMark_model.9677_t
Valid prediction for GeneMark_model.9667_t
Valid prediction for snap_scaffold_2-snap.4036-T1
Valid prediction for snap_scaffold_2-snap.4023-T1
Valid prediction for pasa_asmbl_23916.p1
Valid prediction for GeneMark_model.9665_t
Couldn't classify 139602, 139668
Couldn't classify 141262, 141356
Sorry, prediction pasa_asmbl_23914.p1 fails validation.
(GAG)	 AG	139602-139668	GT	GAG
(CTG)	 AG	140612-140797	GT	AGG
(ATC)	 AG	141262-141356	CC	GAC
add_exon() Sorry, pasa_asmbl_23914.p1 139602-139668-terminal-3 is invalid.
-recovered pasa_asmbl_23914.p1, terminal, 139602, 139668
-recovered pasa_asmbl_23914.p1, internal, 139602, 139668
-recovered pasa_asmbl_23914.p1, internal, 140612, 140797
Valid prediction for GlimmerHMM_glimmerT_5932-T1
Valid prediction for CodingQuarry_transcript_28839-T1
Valid prediction for snap_scaffold_2-snap.4040-T1
Valid prediction for CodingQuarry_transcript_28838-T1
Valid prediction for snap_scaffold_2-snap.4025-T1
Valid prediction for snap_scaffold_2-snap.4027-T1
Valid prediction for GlimmerHMM_glimmerT_5925-T1
Couldn't classify 39559, 39580
Sorry, prediction pasa_asmbl_23921.p1 fails validation.
(GAA)	 GG	39559-39580	GT	CAG
(ACC)	 AG	39655-39796	GT	AGG
(TAT)	 AG	39904-40087	GT	CTG
(GGT)	 AG	40260-40359	GT	AGG
(GTG)	 AG	40522-40640	GT	TGG
(AGT)	 AG	40828-40865	GT	GCG
(GCC)	 AG	40952-41064	GT	GGG
(CTG)	 AG	41199-41347	GT	AGG
(TAT)	 AG	41470-41564	GT	AGG
(TGT)	 AG	41831-41909	GT	ACG
(GAT)	 AG	42106-42214	GT	GGG
(GAA)	 AG	42520-42593	CG	GAC
-recovered pasa_asmbl_23921.p1, terminal, 42520, 42593
-recovered pasa_asmbl_23921.p1, internal, 39655, 39796
-recovered pasa_asmbl_23921.p1, internal, 39904, 40087
-recovered pasa_asmbl_23921.p1, internal, 40260, 40359
-recovered pasa_asmbl_23921.p1, internal, 40522, 40640
-recovered pasa_asmbl_23921.p1, internal, 40828, 40865
-recovered pasa_asmbl_23921.p1, internal, 40952, 41064
-recovered pasa_asmbl_23921.p1, internal, 41199, 41347
-recovered pasa_asmbl_23921.p1, internal, 41470, 41564
-recovered pasa_asmbl_23921.p1, internal, 41831, 41909
-recovered pasa_asmbl_23921.p1, internal, 42106, 42214
Valid prediction for GlimmerHMM_glimmerT_5913-T1
Valid prediction for GlimmerHMM_glimmerT_5930-T1
Couldn't classify 38337, 38366
Sorry, prediction pasa_asmbl_24038.p1 fails validation.
(ATG)	 CA	35721-35799	GT	GGG
(AGC)	 AG	36525-36740	GT	ACG
(GAC)	 AG	36845-36951	GT	GGG
(TTT)	 AG	37070-37178	GT	AGG
(AGT)	 AG	37314-37430	GT	TGG
(GTC)	 AG	37587-37648	GT	AGG
(GTT)	 AG	38337-38366	TG	ACT
-recovered pasa_asmbl_24038.p1, initial, 35721, 35799
-recovered pasa_asmbl_24038.p1, internal, 36525, 36740
-recovered pasa_asmbl_24038.p1, internal, 36845, 36951
-recovered pasa_asmbl_24038.p1, internal, 37070, 37178
-recovered pasa_asmbl_24038.p1, internal, 37314, 37430
-recovered pasa_asmbl_24038.p1, internal, 37587, 37648
Valid prediction for GlimmerHMM_glimmerT_5914-T1
Valid prediction for GeneMark_model.9670_t
Valid prediction for GeneMark_model.9675_t
Valid prediction for GeneMark_model.9668_t
Valid prediction for GlimmerHMM_glimmerT_5927-T1
Valid prediction for snap_scaffold_2-snap.4034-T1
Couldn't classify 141411, 141508
Couldn't classify 145956, 146449
Sorry, prediction pasa_asmbl_23912.p1 fails validation.
(CAG)	 CC	141411-141508	GT	AGG
(ATC)	 AG	142257-142476	GT	AGG
(CTC)	 AG	142803-142967	GT	GGG
(GTG)	 AG	143072-143210	GT	TGG
(TAG)	 AG	145956-146449	CT	GGC
-recovered pasa_asmbl_23912.p1, internal, 142257, 142476
-recovered pasa_asmbl_23912.p1, internal, 142803, 142967
-recovered pasa_asmbl_23912.p1, internal, 143072, 143210
Valid prediction for GeneMark_model.9658_t
Valid prediction for snap_scaffold_2-snap.4019-T1
Valid prediction for GeneMark_model.9649_t
Valid prediction for GlimmerHMM_glimmerT_5917-T1
Valid prediction for GlimmerHMM_glimmerT_5907-T1
Valid prediction for snap_scaffold_2-snap.4043-T1
Valid prediction for snap_scaffold_2-snap.4018-T1
Valid prediction for GeneMark_model.9659_t
Valid prediction for GlimmerHMM_glimmerT_5909-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 10454, rend_intergenic: 7246  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22069, rend_intergenic: 10497  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59668, rend_intergenic: 40159  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61809, rend_intergenic: 60842  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77685, rend_intergenic: 61912  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79093, rend_intergenic: 77693  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83214, rend_intergenic: 79282  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90530, rend_intergenic: 86264  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95765, rend_intergenic: 94434  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110068, rend_intergenic: 103356  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120110, rend_intergenic: 110487  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 168826, rend_intergenic: 165013  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 186749
-exon list size: 596


building trellis

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88.1    
88.3    
88.5    
88.6    
88.8    
89.0    
89.1    
89.3    
89.5    
89.6    
89.8    
90.0    
90.1    
90.3    
90.5    
90.6    
90.8    
91.0    
91.1    
91.3    
91.5    
91.6    
91.8    
92.0    
92.1    
92.3    
92.5    
92.6    
92.8    
93.0    
93.1    
93.3    
93.5    
93.6    
93.8    
94.0    
94.1    
94.3    
94.5    
94.6    
94.8    
95.0    
95.2    
95.3    
95.5    
95.7    
95.8    
96.0    
96.2    
96.3    
96.5    
96.7    
96.8    
97.0    
97.2    
97.3    
97.5    
97.7    
97.8    
98.0    
98.2    
98.3    
98.5    
98.7    
98.8    
99.0    
99.2    
99.3    
99.5    
99.7    
99.8    
-found 34 predictions from path traversal
Error with prediction: snap lend_intergenic: 10454, rend_intergenic: 7246  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22069, rend_intergenic: 10497  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59668, rend_intergenic: 40159  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61809, rend_intergenic: 60842  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77685, rend_intergenic: 61912  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79093, rend_intergenic: 77693  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83214, rend_intergenic: 79282  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90530, rend_intergenic: 86264  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95765, rend_intergenic: 94434  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110068, rend_intergenic: 103356  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120110, rend_intergenic: 110487  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 168826, rend_intergenic: 165013  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 28 predictions persist after filtering for low support