-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_23/scaffold_23_7047455-7229671

-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 GeneMark_model.91022_t
Valid prediction for GlimmerHMM_glimmerT_52503-T1
Valid prediction for GeneMark_model.91037_t
Couldn't classify 4279, 4485
Sorry, prediction pasa_asmbl_30964.p1 fails validation.
(ATG)	 AA	1881-2002	GT	GGG
(AGA)	 AG	2468-2636	GT	CTG
(GCT)	 AG	3488-3586	GT	AGG
(GCT)	 AG	3861-4025	GT	AGG
(GTG)	 AG	4279-4485	CT	GTC
-recovered pasa_asmbl_30964.p1, initial, 1881, 2002
-recovered pasa_asmbl_30964.p1, internal, 2468, 2636
-recovered pasa_asmbl_30964.p1, internal, 3488, 3586
-recovered pasa_asmbl_30964.p1, internal, 3861, 4025
Valid prediction for GeneMark_model.91030_t
Valid prediction for Augustus_model.g35304.t1
Valid prediction for GeneMark_model.91020_t
Valid prediction for snap_scaffold_23-snap.1299-T1
Couldn't classify 99257, 99349
Couldn't classify 102190, 102244
Sorry, prediction pasa_asmbl_30972.p1 fails validation.
(CTG)	 AC	99257-99349	GT	AGG
(GAC)	 AG	99456-99614	GT	CTG
(GTG)	 AG	101785-101882	GT	AGG
(AGA)	 AG	102190-102244	GT	AGG
-recovered pasa_asmbl_30972.p1, internal, 99456, 99614
-recovered pasa_asmbl_30972.p1, internal, 101785, 101882
-recovered pasa_asmbl_30972.p1, internal, 102190, 102244
Couldn't classify 116498, 116726
Couldn't classify 124440, 124650
Sorry, prediction pasa_asmbl_30974.p1 fails validation.
(CAG)	 TG	116498-116726	GT	AGG
(AAC)	 AG	119636-119720	GT	TGG
(CAC)	 AG	121603-121700	GT	GGG
(GTA)	 AG	122073-122211	GT	CGG
(GAT)	 AG	124440-124650	GA	GGG
-recovered pasa_asmbl_30974.p1, internal, 119636, 119720
-recovered pasa_asmbl_30974.p1, internal, 121603, 121700
-recovered pasa_asmbl_30974.p1, internal, 122073, 122211
Valid prediction for Augustus_model.g35293.t1
Valid prediction for Augustus_model.g35303.t1
Valid prediction for GeneMark_model.91035_t
Valid prediction for snap_scaffold_23-snap.1290-T1
Valid prediction for GlimmerHMM_glimmerT_52498-T1
Valid prediction for GlimmerHMM_glimmerT_52500-T1
Valid prediction for snap_scaffold_23-snap.1307-T1
Valid prediction for GeneMark_model.91041_t
Valid prediction for GlimmerHMM_glimmerT_52504-T1
Valid prediction for GeneMark_model.90994_t
Valid prediction for GeneMark_model.91032_t
Valid prediction for GlimmerHMM_glimmerT_52510-T1
Valid prediction for Augustus_model.g35291.t1
Valid prediction for GeneMark_model.91014_t
Valid prediction for snap_scaffold_23-snap.1320-T1
Sorry, intron length (5) is less than minimum required (10)
Valid prediction for HiQ_model.g35309.t1
Valid prediction for GeneMark_model.91031_t
Valid prediction for GlimmerHMM_glimmerT_52512-T1
Valid prediction for GeneMark_model.91010_t
Couldn't classify 102966, 103076
Couldn't classify 110155, 110258
Sorry, prediction pasa_asmbl_30973.p1 fails validation.
(GAG)	 CA	102966-103076	GT	CTG
(GTG)	 AG	103209-103385	GT	AGG
(ACT)	 AG	103664-103850	GT	AGG
(ACC)	 AG	104833-104963	GT	CGG
(GTG)	 AG	105056-105230	GT	AGG
(AGT)	 AG	105472-105646	GT	AGG
(TGA)	 AG	107338-107479	GT	AGG
(GTG)	 AG	109707-109755	GT	CTG
(TCT)	 AG	110155-110258	GT	AGG
-recovered pasa_asmbl_30973.p1, internal, 103209, 103385
-recovered pasa_asmbl_30973.p1, internal, 103664, 103850
-recovered pasa_asmbl_30973.p1, internal, 104833, 104963
-recovered pasa_asmbl_30973.p1, internal, 105056, 105230
-recovered pasa_asmbl_30973.p1, internal, 105472, 105646
-recovered pasa_asmbl_30973.p1, internal, 107338, 107479
-recovered pasa_asmbl_30973.p1, internal, 109707, 109755
-recovered pasa_asmbl_30973.p1, internal, 110155, 110258
Valid prediction for GlimmerHMM_glimmerT_52493-T1
Valid prediction for snap_scaffold_23-snap.1321-T1
Valid prediction for snap_scaffold_23-snap.1296-T1
Valid prediction for GlimmerHMM_glimmerT_52494-T1
Valid prediction for GeneMark_model.91026_t
Valid prediction for snap_scaffold_23-snap.1305-T1
Valid prediction for snap_scaffold_23-snap.1288-T1
Valid prediction for GeneMark_model.91011_t
Valid prediction for GlimmerHMM_glimmerT_52499-T1
Valid prediction for GeneMark_model.91007_t
Valid prediction for GlimmerHMM_glimmerT_52492-T1
Valid prediction for snap_scaffold_23-snap.1318-T1
Valid prediction for GlimmerHMM_glimmerT_52486-T1
Valid prediction for CodingQuarry_transcript_35640-T1
Valid prediction for GeneMark_model.91038_t
Valid prediction for GlimmerHMM_glimmerT_52505-T1
Valid prediction for GeneMark_model.90993_t
Valid prediction for GlimmerHMM_glimmerT_52483-T1
Valid prediction for GeneMark_model.90991_t
Valid prediction for GeneMark_model.90989_t
Valid prediction for GeneMark_model.91034_t
Valid prediction for Augustus_model.g35300.t1
Couldn't classify 32356, 32485
Sorry, prediction pasa_asmbl_30968.p1 fails validation.
(CCT)	 GC	32356-32485	GT	TGG
(GTT)	 AG	32987-33249	AT	AGA
-recovered pasa_asmbl_30968.p1, terminal, 32987, 33249
Valid prediction for snap_scaffold_23-snap.1294-T1
Valid prediction for snap_scaffold_23-snap.1317-T1
Valid prediction for GeneMark_model.91019_t
Valid prediction for Augustus_model.g35305.t1
Valid prediction for Augustus_model.g35301.t1
Valid prediction for GlimmerHMM_glimmerT_52511-T1
Valid prediction for GeneMark_model.91013_t
Valid prediction for Augustus_model.g35306.t1
Valid prediction for Augustus_model.g35296.t1
Valid prediction for snap_scaffold_23-snap.1303-T1
Valid prediction for Augustus_model.g35308.t1
Valid prediction for snap_scaffold_23-snap.1287-T1
Valid prediction for GlimmerHMM_glimmerT_52485-T1
Valid prediction for Augustus_model.g35294.t1
Valid prediction for snap_scaffold_23-snap.1315-T1
Couldn't classify 89919, 89993
Couldn't classify 93726, 93771
Sorry, prediction pasa_asmbl_30971.p1 fails validation.
(AAT)	 GG	89919-89993	GT	GGG
(TTG)	 AG	90302-90376	GT	AGG
(CTG)	 AG	92645-92740	GT	AGG
(GAC)	 AG	93279-93439	GT	AGG
(CCT)	 AG	93726-93771	CT	AGC
-recovered pasa_asmbl_30971.p1, internal, 90302, 90376
-recovered pasa_asmbl_30971.p1, internal, 92645, 92740
-recovered pasa_asmbl_30971.p1, internal, 93279, 93439
Valid prediction for GeneMark_model.91005_t
Valid prediction for Augustus_model.g35307.t1
Valid prediction for GlimmerHMM_glimmerT_52496-T1
Valid prediction for snap_scaffold_23-snap.1306-T1
Valid prediction for Augustus_model.g35297.t1
Valid prediction for HiQ_model.g35292.t1
Valid prediction for Augustus_model.g35310.t1
Valid prediction for GeneMark_model.91040_t
Valid prediction for pasa_asmbl_30965.p1
Valid prediction for GeneMark_model.91017_t
Valid prediction for GeneMark_model.91000_t
Valid prediction for snap_scaffold_23-snap.1292-T1
Valid prediction for GeneMark_model.91024_t
Valid prediction for GeneMark_model.90997_t
Couldn't classify 65218, 65637
Sorry, prediction pasa_asmbl_30969.p2 fails validation.
(ATG)	 CC	65218-65637	GG	CTG
Valid prediction for GeneMark_model.91002_t

-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.91027_t
Valid prediction for snap_scaffold_23-snap.1312-T1
Valid prediction for GeneMark_model.91003_t
Valid prediction for GeneMark_model.91039_t
Valid prediction for GlimmerHMM_glimmerT_52484-T1
Valid prediction for snap_scaffold_23-snap.1293-T1
Valid prediction for Augustus_model.g35298.t1
Valid prediction for GeneMark_model.90990_t
Valid prediction for snap_scaffold_23-snap.1295-T1
Valid prediction for GeneMark_model.91029_t
Valid prediction for GlimmerHMM_glimmerT_52501-T1
Valid prediction for GeneMark_model.91021_t
Valid prediction for snap_scaffold_23-snap.1302-T1
Valid prediction for GlimmerHMM_glimmerT_52508-T1
Valid prediction for GlimmerHMM_glimmerT_52489-T1
Valid prediction for GeneMark_model.91018_t
Valid prediction for snap_scaffold_23-snap.1316-T1
Valid prediction for GlimmerHMM_glimmerT_52502-T1
Valid prediction for GeneMark_model.91036_t
Valid prediction for Augustus_model.g35302.t1
Valid prediction for snap_scaffold_23-snap.1308-T1
Valid prediction for GeneMark_model.90996_t
Valid prediction for GeneMark_model.91012_t
Valid prediction for Augustus_model.g35299.t1
Couldn't classify 103736, 103878
Sorry, prediction pasa_asmbl_31736.p1 fails validation.
(ATG)	 CT	96886-96942	GT	AGG
(GAT)	 AG	99814-99891	GT	CGG
(GGA)	 AG	100121-100228	GT	AGG
(GAG)	 AG	101500-101611	GT	AGG
(GCA)	 AG	102198-102326	GT	GTG
(TCC)	 AG	103736-103878	CT	CCC
-recovered pasa_asmbl_31736.p1, initial, 96886, 96942
-recovered pasa_asmbl_31736.p1, internal, 99814, 99891
-recovered pasa_asmbl_31736.p1, internal, 100121, 100228
-recovered pasa_asmbl_31736.p1, internal, 101500, 101611
-recovered pasa_asmbl_31736.p1, internal, 102198, 102326
Valid prediction for snap_scaffold_23-snap.1319-T1
Valid prediction for snap_scaffold_23-snap.1310-T1
Valid prediction for snap_scaffold_23-snap.1309-T1
Valid prediction for GlimmerHMM_glimmerT_52491-T1
Valid prediction for snap_scaffold_23-snap.1298-T1
Valid prediction for GlimmerHMM_glimmerT_52497-T1
Valid prediction for snap_scaffold_23-snap.1301-T1
Valid prediction for GeneMark_model.91023_t
Valid prediction for snap_scaffold_23-snap.1314-T1
Valid prediction for CodingQuarry_transcript_35642-T1
Valid prediction for GeneMark_model.90998_t
Valid prediction for snap_scaffold_23-snap.1291-T1
Valid prediction for GeneMark_model.90992_t
Valid prediction for GlimmerHMM_glimmerT_52509-T1
Valid prediction for GeneMark_model.90995_t
Valid prediction for GlimmerHMM_glimmerT_52507-T1
Valid prediction for GlimmerHMM_glimmerT_52490-T1
Valid prediction for GeneMark_model.91008_t
Valid prediction for GeneMark_model.91016_t
Valid prediction for GeneMark_model.90999_t
Valid prediction for snap_scaffold_23-snap.1289-T1
Valid prediction for GlimmerHMM_glimmerT_52488-T1
Valid prediction for snap_scaffold_23-snap.1300-T1
Valid prediction for snap_scaffold_23-snap.1311-T1
Valid prediction for GeneMark_model.91006_t
Valid prediction for GlimmerHMM_glimmerT_52487-T1
Valid prediction for GlimmerHMM_glimmerT_52506-T1
Valid prediction for GeneMark_model.91025_t
Valid prediction for GeneMark_model.91009_t
Valid prediction for GeneMark_model.91033_t
Valid prediction for GlimmerHMM_glimmerT_52495-T1
Valid prediction for GeneMark_model.91028_t
Valid prediction for snap_scaffold_23-snap.1297-T1
Valid prediction for snap_scaffold_23-snap.1313-T1
Valid prediction for GeneMark_model.91004_t
Valid prediction for Augustus_model.g35295.t1
Valid prediction for GeneMark_model.91001_t
Valid prediction for snap_scaffold_23-snap.1304-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 17604, rend_intergenic: 13804  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34771, rend_intergenic: 22022  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47280, rend_intergenic: 42541  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58768, rend_intergenic: 53469  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62677, rend_intergenic: 59697  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74452, rend_intergenic: 63245  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83131, rend_intergenic: 80266  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89571, rend_intergenic: 88961  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129696, rend_intergenic: 98336  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150347, rend_intergenic: 147473  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 168423, rend_intergenic: 165244  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 182217
-exon list size: 695


building trellis

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77.6    
77.8    
77.9    
78.0    
78.2    
78.3    
78.5    
78.6    
78.8    
78.9    
79.1    
79.2    
79.3    
79.5    
79.6    
79.8    
79.9    
80.1    
80.2    
80.3    
80.5    
80.6    
80.8    
80.9    
81.1    
81.2    
81.3    
81.5    
81.6    
81.8    
81.9    
82.1    
82.2    
82.4    
82.5    
82.6    
82.8    
82.9    
83.1    
83.2    
83.4    
83.5    
83.6    
83.8    
83.9    
84.1    
84.2    
84.4    
84.5    
84.6    
84.8    
84.9    
85.1    
85.2    
85.4    
85.5    
85.7    
85.8    
85.9    
86.1    
86.2    
86.4    
86.5    
86.7    
86.8    
86.9    
87.1    
87.2    
87.4    
87.5    
87.7    
87.8    
87.9    
88.1    
88.2    
88.4    
88.5    
88.7    
88.8    
89.0    
89.1    
89.2    
89.4    
89.5    
89.7    
89.8    
90.0    
90.1    
90.2    
90.4    
90.5    
90.7    
90.8    
91.0    
91.1    
91.2    
91.4    
91.5    
91.7    
91.8    
92.0    
92.1    
92.3    
92.4    
92.5    
92.7    
92.8    
93.0    
93.1    
93.3    
93.4    
93.5    
93.7    
93.8    
94.0    
94.1    
94.3    
94.4    
94.5    
94.7    
94.8    
95.0    
95.1    
95.3    
95.4    
95.6    
95.7    
95.8    
96.0    
96.1    
96.3    
96.4    
96.6    
96.7    
96.8    
97.0    
97.1    
97.3    
97.4    
97.6    
97.7    
97.8    
98.0    
98.1    
98.3    
98.4    
98.6    
98.7    
98.9    
99.0    
99.1    
99.3    
99.4    
99.6    
99.7    
99.9    
-found 26 predictions from path traversal
Error with prediction: snap lend_intergenic: 17604, rend_intergenic: 13804  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34771, rend_intergenic: 22022  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47280, rend_intergenic: 42541  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58768, rend_intergenic: 53469  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62677, rend_intergenic: 59697  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74452, rend_intergenic: 63245  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83131, rend_intergenic: 80266  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89571, rend_intergenic: 88961  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129696, rend_intergenic: 98336  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150347, rend_intergenic: 147473  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 168423, rend_intergenic: 165244  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 14 predictions persist after filtering for low support