-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_2/scaffold_2_3636728-3763366

-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: +)Couldn't classify 78940, 79023
Couldn't classify 79587, 79716
Sorry, prediction pasa_asmbl_25474.p2 fails validation.
(GGG)	 GG	78940-79023	GT	AAG
(GGT)	 AG	79194-79351	GT	AGG
(GTT)	 AG	79587-79716	GC	GGG
-recovered pasa_asmbl_25474.p2, internal, 79194, 79351
-recovered pasa_asmbl_25474.p2, internal, 79587, 79716
Valid prediction for pasa_asmbl_24329.p1
Valid prediction for snap_scaffold_2-snap.863-T1
Valid prediction for GeneMark_model.5979_t
Couldn't classify 608, 828
Sorry, prediction pasa_asmbl_24317.p1 fails validation.
(CCC)	 GG	608-828	GT	AAG
(GGA)	 AG	942-1041	GT	AGG
(CGC)	 AG	1234-1307	GT	GAG
(GTG)	 AG	1482-1552	GT	CGG
(GTA)	 AG	1692-1899	GT	GAG
(CGA)	 AG	2039-2079	GT	AGG
(TGT)	 AG	2206-2281	GT	TGG
(GCA)	 AG	2419-2496	GT	AGG
(GGA)	 AG	4206-4286	GT	GGG
(GAC)	 AG	4372-4466	GT	AGG
(AAC)	 AG	4783-4832	CC	GAC
add_exon() Sorry, pasa_asmbl_24317.p1 1234-1307-terminal-2 is invalid.
-recovered pasa_asmbl_24317.p1, terminal, 1234, 1307
-recovered pasa_asmbl_24317.p1, terminal, 4783, 4832
-recovered pasa_asmbl_24317.p1, internal, 942, 1041
-recovered pasa_asmbl_24317.p1, internal, 1234, 1307
-recovered pasa_asmbl_24317.p1, internal, 1482, 1552
-recovered pasa_asmbl_24317.p1, internal, 1692, 1899
-recovered pasa_asmbl_24317.p1, internal, 2039, 2079
-recovered pasa_asmbl_24317.p1, internal, 2206, 2281
-recovered pasa_asmbl_24317.p1, internal, 2419, 2496
-recovered pasa_asmbl_24317.p1, internal, 4206, 4286
-recovered pasa_asmbl_24317.p1, internal, 4372, 4466
Valid prediction for GlimmerHMM_glimmerT_3640-T1
Valid prediction for GeneMark_model.5971_t
Valid prediction for GeneMark_model.5954_t
Valid prediction for snap_scaffold_2-snap.860-T1
Valid prediction for GeneMark_model.5977_t
Valid prediction for Augustus_model.g2423.t1
Valid prediction for GeneMark_model.5943_t
Valid prediction for Augustus_model.g2419.t1
Valid prediction for GeneMark_model.5969_t
Valid prediction for GeneMark_model.5944_t
Valid prediction for GeneMark_model.5986_t
Valid prediction for snap_scaffold_2-snap.864-T1
Valid prediction for CodingQuarry_transcript_28442-T1
Valid prediction for GlimmerHMM_glimmerT_3638-T1
Valid prediction for GlimmerHMM_glimmerT_3635-T1
Valid prediction for GeneMark_model.5967_t
Valid prediction for snap_scaffold_2-snap.852-T1
Valid prediction for GeneMark_model.5975_t
Couldn't classify 41498, 42028
Sorry, prediction pasa_asmbl_24320.p1 fails validation.
(GTC)	 CT	41498-42028	AA	AGA
Valid prediction for GeneMark_model.5983_t
Valid prediction for GeneMark_model.5948_t
Valid prediction for GlimmerHMM_glimmerT_3643-T1
Valid prediction for GlimmerHMM_glimmerT_3657-T1
Valid prediction for GeneMark_model.5956_t
Valid prediction for GlimmerHMM_glimmerT_3648-T1
Valid prediction for GeneMark_model.5987_t
Valid prediction for snap_scaffold_2-snap.856-T1
Valid prediction for snap_scaffold_2-snap.857-T1
Valid prediction for GlimmerHMM_glimmerT_3642-T1
Valid prediction for GeneMark_model.5985_t
Valid prediction for HiQ_model.g2421.t1
Couldn't classify 14412, 14533
Sorry, prediction pasa_asmbl_24318.p1 fails validation.
(CTA)	 AA	14412-14533	GT	CGG
(AAC)	 AG	14728-14842	GT	AGG
(ATC)	 AG	15848-16198	GT	GGG
(GTA)	 AG	16825-17045	GT	ACG
(AAC)	 AG	17341-17462	GT	AGG
(ATG)	 AG	17624-17736	GT	AGG
(GCT)	 AG	18042-18191	GT	AGG
(ATC)	 AG	18902-19038	GT	AGG
(GTT)	 AG	19467-19601	GT	AGG
(GTG)	 AG	19686-19795	GT	TGG
(GTA)	 AG	20144-20325	AC	AGA
add_exon() Sorry, pasa_asmbl_24318.p1 17624-17736-initial-1 is invalid.
-recovered pasa_asmbl_24318.p1, initial, 17624, 17736
-recovered pasa_asmbl_24318.p1, terminal, 20144, 20325
-recovered pasa_asmbl_24318.p1, internal, 14728, 14842
-recovered pasa_asmbl_24318.p1, internal, 15848, 16198
-recovered pasa_asmbl_24318.p1, internal, 16825, 17045
-recovered pasa_asmbl_24318.p1, internal, 17341, 17462
-recovered pasa_asmbl_24318.p1, internal, 17624, 17736
-recovered pasa_asmbl_24318.p1, internal, 18042, 18191
-recovered pasa_asmbl_24318.p1, internal, 18902, 19038
-recovered pasa_asmbl_24318.p1, internal, 19467, 19601
-recovered pasa_asmbl_24318.p1, internal, 19686, 19795
Valid prediction for GeneMark_model.5950_t
Valid prediction for HiQ_model.g2431.t1
Valid prediction for GeneMark_model.5964_t
Valid prediction for GeneMark_model.5973_t
Valid prediction for snap_scaffold_2-snap.873-T1
Valid prediction for GlimmerHMM_glimmerT_3636-T1
Valid prediction for snap_scaffold_2-snap.849-T1
Valid prediction for GlimmerHMM_glimmerT_3655-T1
Valid prediction for GeneMark_model.5951_t
Valid prediction for snap_scaffold_2-snap.848-T1
Valid prediction for snap_scaffold_2-snap.846-T1
Valid prediction for Augustus_model.g2422.t1
Valid prediction for GeneMark_model.5989_t
Valid prediction for snap_scaffold_2-snap.859-T1
Valid prediction for snap_scaffold_2-snap.868-T1
Valid prediction for snap_scaffold_2-snap.872-T1
Valid prediction for GeneMark_model.5946_t
Valid prediction for Augustus_model.g2434.t1
Valid prediction for GlimmerHMM_glimmerT_3650-T1
Valid prediction for snap_scaffold_2-snap.869-T1
Valid prediction for Augustus_model.g2426.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: -)Couldn't classify 18221, 18436
Sorry, prediction pasa_asmbl_23019.p1 fails validation.
(ATG)	 CG	17690-18034	GT	AGG
(ATG)	 AG	18221-18436	GC	GCG
-recovered pasa_asmbl_23019.p1, initial, 17690, 18034
-recovered pasa_asmbl_23019.p1, initial, 18221, 18436
-recovered pasa_asmbl_23019.p1, internal, 18221, 18436
Valid prediction for snap_scaffold_2-snap.874-T1
Valid prediction for GeneMark_model.5955_t
Valid prediction for snap_scaffold_2-snap.845-T1
Valid prediction for Augustus_model.g2420.t1
Couldn't classify 79792, 79857
Sorry, prediction pasa_asmbl_23012.p1 fails validation.
(TGC)	 CC	79792-79857	GT	TGG
(GGT)	 AG	79948-80133	GT	AGG
(AAG)	 AG	80229-80336	AC	AGA
-recovered pasa_asmbl_23012.p1, terminal, 80229, 80336
-recovered pasa_asmbl_23012.p1, internal, 79948, 80133
Valid prediction for GlimmerHMM_glimmerT_3649-T1
Valid prediction for GlimmerHMM_glimmerT_3652-T1
Valid prediction for GeneMark_model.5988_t
Valid prediction for GeneMark_model.5965_t
Valid prediction for snap_scaffold_2-snap.855-T1
Sorry, intron length (9) is less than minimum required (10)
Couldn't classify 19380, 19976
Sorry, prediction pasa_asmbl_23018.p1 fails validation.
(TCG)	 CC	19380-19976	TT	AGT
Valid prediction for snap_scaffold_2-snap.865-T1
Valid prediction for GlimmerHMM_glimmerT_3659-T1
Valid prediction for Augustus_model.g2432.t1
Couldn't classify 36078, 36131
Couldn't classify 39137, 39244
Sorry, prediction pasa_asmbl_24060.p1 fails validation.
(GTG)	 TA	36078-36131	GT	TGG
(GTG)	 AG	38710-38862	GT	AGG
(ATC)	 AG	39137-39244	AG	ACA
-recovered pasa_asmbl_24060.p1, internal, 38710, 38862
Valid prediction for GeneMark_model.5945_t
Valid prediction for GlimmerHMM_glimmerT_3658-T1
Valid prediction for snap_scaffold_2-snap.867-T1
Valid prediction for GlimmerHMM_glimmerT_3653-T1
Couldn't classify 73165, 73247
Couldn't classify 75162, 75190
Sorry, prediction pasa_asmbl_23014.p1 fails validation.
(GAC)	 AT	73165-73247	GT	TGG
(GTG)	 AG	73421-73517	GT	AGG
(GAC)	 AG	73602-73668	GT	TAG
(TTC)	 AG	73823-73995	GC	AGG
(ATC)	 AG	74503-74605	GT	TGG
(GAA)	 AG	74848-75051	GT	CGG
(ACA)	 AG	75162-75190	TT	TCT
-recovered pasa_asmbl_23014.p1, internal, 73421, 73517
-recovered pasa_asmbl_23014.p1, internal, 73602, 73668
-recovered pasa_asmbl_23014.p1, internal, 73823, 73995
-recovered pasa_asmbl_23014.p1, internal, 74503, 74605
-recovered pasa_asmbl_23014.p1, internal, 74848, 75051
Valid prediction for HiQ_model.g2425.t1
Valid prediction for GeneMark_model.5960_t
Valid prediction for snap_scaffold_2-snap.844-T1
Valid prediction for Augustus_model.g2427.t1
Valid prediction for GlimmerHMM_glimmerT_3651-T1
Valid prediction for snap_scaffold_2-snap.871-T1
Valid prediction for snap_scaffold_2-snap.861-T1
Valid prediction for snap_scaffold_2-snap.851-T1
Couldn't classify 54655, 54762
Sorry, prediction pasa_asmbl_23016.p1 fails validation.
(ATG)	 AA	51311-51387	GT	TGG
(GGC)	 AG	51889-51971	GT	AGG
(ACG)	 AG	54372-54529	GT	AGG
(AAC)	 AG	54655-54762	TA	AGT
-recovered pasa_asmbl_23016.p1, initial, 51311, 51387
-recovered pasa_asmbl_23016.p1, internal, 51889, 51971
-recovered pasa_asmbl_23016.p1, internal, 54372, 54529
Valid prediction for snap_scaffold_2-snap.866-T1
Valid prediction for GeneMark_model.5970_t
Valid prediction for GeneMark_model.5952_t
Valid prediction for Augustus_model.g2424.t1
Valid prediction for Augustus_model.g2428.t1
Valid prediction for GlimmerHMM_glimmerT_3637-T1
Valid prediction for GlimmerHMM_glimmerT_3645-T1
Couldn't classify 78973, 79014
Sorry, prediction pasa_asmbl_24052.p1 fails validation.
(ATG)	 GC	78260-78418	GT	AGG
(CGT)	 AG	78572-78826	GT	AGG
(TTC)	 AG	78973-79014	CA	CCC
-recovered pasa_asmbl_24052.p1, initial, 78260, 78418
-recovered pasa_asmbl_24052.p1, internal, 78572, 78826
Valid prediction for GeneMark_model.5963_t
Valid prediction for GeneMark_model.5966_t
Couldn't classify 3674, 4025
Sorry, prediction pasa_asmbl_23023.p1 fails validation.
(CAG)	 CT	3674-4025	GT	AGG
(ACC)	 AG	4201-4330	GT	AGG
(TGA)	 AG	5366-5399	AG	GAA
-recovered pasa_asmbl_23023.p1, terminal, 5366, 5399
-recovered pasa_asmbl_23023.p1, internal, 4201, 4330
Valid prediction for GeneMark_model.5980_t
Valid prediction for snap_scaffold_2-snap.850-T1
Valid prediction for Augustus_model.g2430.t1
Valid prediction for GeneMark_model.5978_t
Valid prediction for GeneMark_model.5968_t
Valid prediction for GeneMark_model.5974_t
Valid prediction for GlimmerHMM_glimmerT_3639-T1
Valid prediction for GeneMark_model.5957_t
Valid prediction for snap_scaffold_2-snap.854-T1
Valid prediction for GeneMark_model.5947_t
Valid prediction for GeneMark_model.5972_t
Valid prediction for GlimmerHMM_glimmerT_3656-T1
Valid prediction for GeneMark_model.5961_t
Valid prediction for GeneMark_model.5982_t
Valid prediction for Augustus_model.g2429.t1
Valid prediction for GeneMark_model.5976_t
Valid prediction for snap_scaffold_2-snap.853-T1
Couldn't classify 75218, 75298
Sorry, prediction pasa_asmbl_23013.p1 fails validation.
(GTT)	 AC	75218-75298	GT	AGG
(GTG)	 AG	75482-75593	GT	CCG
(GGG)	 AG	75733-75900	GT	AGG
(GTT)	 AG	76018-76106	GT	AGG
(AAA)	 AG	76344-76531	GT	AAG
(GAT)	 AG	76661-76703	GA	GAG
-recovered pasa_asmbl_23013.p1, terminal, 76661, 76703
-recovered pasa_asmbl_23013.p1, internal, 75482, 75593
-recovered pasa_asmbl_23013.p1, internal, 75733, 75900
-recovered pasa_asmbl_23013.p1, internal, 76018, 76106
-recovered pasa_asmbl_23013.p1, internal, 76344, 76531
Valid prediction for snap_scaffold_2-snap.858-T1
Valid prediction for GlimmerHMM_glimmerT_3647-T1
Valid prediction for GlimmerHMM_glimmerT_3641-T1
Valid prediction for GeneMark_model.5958_t
Valid prediction for GeneMark_model.5949_t
Valid prediction for snap_scaffold_2-snap.870-T1
Valid prediction for GeneMark_model.5981_t
Valid prediction for GlimmerHMM_glimmerT_3654-T1
Valid prediction for GlimmerHMM_glimmerT_3646-T1
Valid prediction for GeneMark_model.5990_t
Valid prediction for GlimmerHMM_glimmerT_3644-T1
Valid prediction for snap_scaffold_2-snap.847-T1
Valid prediction for GeneMark_model.5984_t
Valid prediction for GeneMark_model.5953_t
Valid prediction for HiQ_model.g2433.t1
Valid prediction for snap_scaffold_2-snap.862-T1
Valid prediction for GeneMark_model.5959_t
Valid prediction for CodingQuarry_transcript_28441-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 20325, rend_intergenic: 17628  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42153, rend_intergenic: 29135  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43994, rend_intergenic: 42426  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60863, rend_intergenic: 55057  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70403, rend_intergenic: 64118  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74364, rend_intergenic: 70919  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87163, rend_intergenic: 81501  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104111, rend_intergenic: 99319  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 126639
-exon list size: 580


building trellis

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76.8    
77.0    
77.1    
77.3    
77.5    
77.7    
77.8    
78.0    
78.2    
78.4    
78.5    
78.7    
78.9    
79.0    
79.2    
79.4    
79.6    
79.7    
79.9    
80.1    
80.2    
80.4    
80.6    
80.8    
80.9    
81.1    
81.3    
81.4    
81.6    
81.8    
82.0    
82.1    
82.3    
82.5    
82.6    
82.8    
83.0    
83.2    
83.3    
83.5    
83.7    
83.8    
84.0    
84.2    
84.4    
84.5    
84.7    
84.9    
85.1    
85.2    
85.4    
85.6    
85.7    
85.9    
86.1    
86.3    
86.4    
86.6    
86.8    
86.9    
87.1    
87.3    
87.5    
87.6    
87.8    
88.0    
88.1    
88.3    
88.5    
88.7    
88.8    
89.0    
89.2    
89.3    
89.5    
89.7    
89.9    
90.0    
90.2    
90.4    
90.5    
90.7    
90.9    
91.1    
91.2    
91.4    
91.6    
91.8    
91.9    
92.1    
92.3    
92.4    
92.6    
92.8    
93.0    
93.1    
93.3    
93.5    
93.6    
93.8    
94.0    
94.2    
94.3    
94.5    
94.7    
94.8    
95.0    
95.2    
95.4    
95.5    
95.7    
95.9    
96.0    
96.2    
96.4    
96.6    
96.7    
96.9    
97.1    
97.3    
97.4    
97.6    
97.8    
97.9    
98.1    
98.3    
98.5    
98.6    
98.8    
99.0    
99.1    
99.3    
99.5    
99.7    
99.8    
-found 29 predictions from path traversal
Error with prediction: snap lend_intergenic: 20325, rend_intergenic: 17628  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42153, rend_intergenic: 29135  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43994, rend_intergenic: 42426  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60863, rend_intergenic: 55057  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70403, rend_intergenic: 64118  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74364, rend_intergenic: 70919  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87163, rend_intergenic: 81501  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104111, rend_intergenic: 99319  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 21 predictions persist after filtering for low support