-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_7/scaffold_7_3575074-3778337

-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_17615-T1
Valid prediction for Augustus_model.g11803.t1
Valid prediction for snap_scaffold_7-snap.885-T1
Valid prediction for snap_scaffold_7-snap.880-T1
Valid prediction for GeneMark_model.29709_t
Valid prediction for GlimmerHMM_glimmerT_17612-T1
Valid prediction for snap_scaffold_7-snap.891-T1
Valid prediction for GeneMark_model.29696_t
Valid prediction for GeneMark_model.29722_t
Valid prediction for Augustus_model.g11793.t1
Valid prediction for snap_scaffold_7-snap.902-T1
Valid prediction for snap_scaffold_7-snap.890-T1
Valid prediction for GlimmerHMM_glimmerT_17621-T1
Valid prediction for Augustus_model.g11801.t1
Valid prediction for GlimmerHMM_glimmerT_17633-T1
Valid prediction for GeneMark_model.29729_t
Valid prediction for snap_scaffold_7-snap.872-T1
Valid prediction for GeneMark_model.29712_t
Valid prediction for snap_scaffold_7-snap.866-T1
Valid prediction for snap_scaffold_7-snap.882-T1
Valid prediction for GeneMark_model.29725_t
Valid prediction for GlimmerHMM_glimmerT_17618-T1
Valid prediction for snap_scaffold_7-snap.862-T1
Valid prediction for GeneMark_model.29718_t
Valid prediction for Augustus_model.g11797.t1
Couldn't classify 164066, 164128
Sorry, prediction pasa_asmbl_50577.p1 fails validation.
(GTG)	 CA	164066-164128	GT	CGG
(CCT)	 AG	164287-164350	GT	AGG
(ATA)	 AG	165986-166063	GT	AGG
(GTG)	 AG	166294-166469	CA	AAC
add_exon() Sorry, pasa_asmbl_50577.p1 165986-166063-terminal-1 is invalid.
-recovered pasa_asmbl_50577.p1, terminal, 165986, 166063
-recovered pasa_asmbl_50577.p1, terminal, 166294, 166469
-recovered pasa_asmbl_50577.p1, internal, 164287, 164350
-recovered pasa_asmbl_50577.p1, internal, 165986, 166063
Valid prediction for snap_scaffold_7-snap.898-T1
Valid prediction for snap_scaffold_7-snap.855-T1
Valid prediction for GeneMark_model.29697_t
Valid prediction for snap_scaffold_7-snap.887-T1
Valid prediction for snap_scaffold_7-snap.868-T1
Valid prediction for snap_scaffold_7-snap.865-T1
Valid prediction for GlimmerHMM_glimmerT_17636-T1
Valid prediction for GeneMark_model.29727_t
Valid prediction for GlimmerHMM_glimmerT_17630-T1
Couldn't classify 159635, 159801
Couldn't classify 160365, 160494
Sorry, prediction pasa_asmbl_51511.p1 fails validation.
(AAG)	 AG	159635-159801	GT	TGG
(TTC)	 AG	160365-160494	GT	ACG
-recovered pasa_asmbl_51511.p1, internal, 159635, 159801
-recovered pasa_asmbl_51511.p1, internal, 160365, 160494
Valid prediction for GeneMark_model.29708_t
Valid prediction for GlimmerHMM_glimmerT_17617-T1
Valid prediction for GeneMark_model.29714_t
Valid prediction for Augustus_model.g11795.t1
Valid prediction for snap_scaffold_7-snap.896-T1
Valid prediction for snap_scaffold_7-snap.863-T1
Valid prediction for snap_scaffold_7-snap.893-T1
Valid prediction for snap_scaffold_7-snap.861-T1
Valid prediction for snap_scaffold_7-snap.876-T1
Valid prediction for GeneMark_model.29706_t
Valid prediction for GeneMark_model.29701_t
Couldn't classify 48287, 48322
Sorry, prediction pasa_asmbl_51500.p1 fails validation.
(GCA)	 GA	48287-48322	GT	AGG
(TCC)	 AG	48440-48582	GT	GAG
(GGA)	 AG	48743-48864	GT	AGG
(CGC)	 AG	48956-49020	GT	AGG
(ATC)	 AG	49182-49344	GT	AGG
(AAG)	 AG	50381-50535	GT	AGG
(ATG)	 AG	51608-51675	GT	AGG
(GCT)	 AG	51828-51921	GT	AGG
(AGC)	 AG	52107-52265	GT	GGG
(CCC)	 AG	52550-52630	GT	AGG
(GTG)	 AG	52718-52823	GT	AGG
(AAG)	 AG	53096-53203	GT	AGG
(ACT)	 AG	53311-53468	GT	TGG
(ATG)	 AG	53557-53648	GT	GGG
(GTT)	 AG	53749-53901	GT	AGG
(TAT)	 AG	54026-54195	GT	TGG
(CCA)	 AG	54335-54439	GT	AGG
(ATA)	 AG	54547-54596	GT	CTG
(AAG)	 AG	54767-54845	GT	AGG
(CTG)	 AG	54937-55004	GT	AGG
(AAA)	 AG	55151-55233	GT	AGG
(GAA)	 AG	55391-55493	CA	GAC
-recovered pasa_asmbl_51500.p1, initial, 51608, 51675
-recovered pasa_asmbl_51500.p1, initial, 53557, 53648
-recovered pasa_asmbl_51500.p1, terminal, 55391, 55493
-recovered pasa_asmbl_51500.p1, internal, 48440, 48582
-recovered pasa_asmbl_51500.p1, internal, 48743, 48864
-recovered pasa_asmbl_51500.p1, internal, 48956, 49020
-recovered pasa_asmbl_51500.p1, internal, 49182, 49344
-recovered pasa_asmbl_51500.p1, internal, 50381, 50535
-recovered pasa_asmbl_51500.p1, internal, 51608, 51675
-recovered pasa_asmbl_51500.p1, internal, 51828, 51921
-recovered pasa_asmbl_51500.p1, internal, 52107, 52265
-recovered pasa_asmbl_51500.p1, internal, 52550, 52630
-recovered pasa_asmbl_51500.p1, internal, 52718, 52823
-recovered pasa_asmbl_51500.p1, internal, 53096, 53203
-recovered pasa_asmbl_51500.p1, internal, 53311, 53468
-recovered pasa_asmbl_51500.p1, internal, 53557, 53648
-recovered pasa_asmbl_51500.p1, internal, 53749, 53901
-recovered pasa_asmbl_51500.p1, internal, 54026, 54195
-recovered pasa_asmbl_51500.p1, internal, 54335, 54439
-recovered pasa_asmbl_51500.p1, internal, 54547, 54596
-recovered pasa_asmbl_51500.p1, internal, 54767, 54845
-recovered pasa_asmbl_51500.p1, internal, 54937, 55004
-recovered pasa_asmbl_51500.p1, internal, 55151, 55233
Valid prediction for snap_scaffold_7-snap.856-T1
Valid prediction for snap_scaffold_7-snap.875-T1
Valid prediction for GeneMark_model.29723_t
Valid prediction for snap_scaffold_7-snap.879-T1
Valid prediction for snap_scaffold_7-snap.884-T1
Valid prediction for GlimmerHMM_glimmerT_17631-T1
Couldn't classify 46202, 46252
Couldn't classify 47948, 48019
Sorry, prediction pasa_asmbl_50575.p1 fails validation.
(GTC)	 CT	46202-46252	GT	TGG
(TTG)	 AG	47190-47288	GT	CGG
(GCT)	 AG	47659-47862	GT	AGG
(ACC)	 AG	47948-48019	AA	GGA
-recovered pasa_asmbl_50575.p1, internal, 47190, 47288
-recovered pasa_asmbl_50575.p1, internal, 47659, 47862
Valid prediction for GeneMark_model.29711_t
Valid prediction for GeneMark_model.29694_t
Valid prediction for GeneMark_model.29716_t
Valid prediction for Augustus_model.g11792.t1
Valid prediction for GeneMark_model.29687_t
Valid prediction for Augustus_model.g11799.t1
Valid prediction for GeneMark_model.29700_t
Valid prediction for GlimmerHMM_glimmerT_17616-T1
Valid prediction for GlimmerHMM_glimmerT_17628-T1
Valid prediction for snap_scaffold_7-snap.894-T1
Valid prediction for snap_scaffold_7-snap.900-T1
Valid prediction for GlimmerHMM_glimmerT_17626-T1
Valid prediction for GeneMark_model.29692_t
Valid prediction for snap_scaffold_7-snap.870-T1
Valid prediction for Augustus_model.g11806.t1
Valid prediction for GeneMark_model.29704_t
Valid prediction for GlimmerHMM_glimmerT_17619-T1
Valid prediction for GeneMark_model.29693_t
Valid prediction for Augustus_model.g11794.t1
Valid prediction for snap_scaffold_7-snap.877-T1
Valid prediction for GlimmerHMM_glimmerT_17637-T1
Valid prediction for snap_scaffold_7-snap.864-T1
Sorry, intron length (8) is less than minimum required (10)

-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 snap_scaffold_7-snap.869-T1
Valid prediction for GeneMark_model.29710_t
Valid prediction for snap_scaffold_7-snap.867-T1
Valid prediction for GeneMark_model.29698_t
Valid prediction for CodingQuarry_transcript_57311-T1
Valid prediction for GlimmerHMM_glimmerT_17632-T1
Valid prediction for snap_scaffold_7-snap.878-T1
Couldn't classify 32995, 33395
Sorry, prediction pasa_asmbl_49626.p1 fails validation.
(ATG)	 AG	32612-32693	GT	GGG
(GCA)	 AG	32995-33395	CA	AGC
-recovered pasa_asmbl_49626.p1, initial, 32612, 32693
-recovered pasa_asmbl_49626.p1, internal, 32612, 32693
Valid prediction for Augustus_model.g11802.t1
Valid prediction for GlimmerHMM_glimmerT_17629-T1
Valid prediction for snap_scaffold_7-snap.857-T1
Valid prediction for snap_scaffold_7-snap.871-T1
Valid prediction for GlimmerHMM_glimmerT_17623-T1
Valid prediction for GeneMark_model.29715_t
Valid prediction for GeneMark_model.29721_t
Valid prediction for GeneMark_model.29699_t
Valid prediction for snap_scaffold_7-snap.881-T1
Valid prediction for GlimmerHMM_glimmerT_17614-T1
Valid prediction for GeneMark_model.29728_t
Valid prediction for GeneMark_model.29685_t
Valid prediction for snap_scaffold_7-snap.903-T1
Valid prediction for GlimmerHMM_glimmerT_17611-T1
Valid prediction for GlimmerHMM_glimmerT_17613-T1
Valid prediction for snap_scaffold_7-snap.899-T1
Couldn't classify 135812, 135879
Couldn't classify 139847, 139993
Sorry, prediction pasa_asmbl_49620.p1 fails validation.
(GAG)	 AT	135812-135879	GT	AGG
(GGT)	 AG	138583-138661	GT	GTG
(TTT)	 AG	139036-139131	GT	TGG
(GTC)	 AG	139374-139412	GT	CTG
(GAG)	 AG	139519-139617	GT	AGG
(GTG)	 AG	139847-139993	TG	GCT
-recovered pasa_asmbl_49620.p1, internal, 138583, 138661
-recovered pasa_asmbl_49620.p1, internal, 139036, 139131
-recovered pasa_asmbl_49620.p1, internal, 139374, 139412
-recovered pasa_asmbl_49620.p1, internal, 139519, 139617
Couldn't classify 127057, 127118
Couldn't classify 129451, 129510
Sorry, prediction pasa_asmbl_49621.p1 fails validation.
(GTG)	 GT	127057-127118	GT	AGG
(TCC)	 AG	127236-127307	GT	AGG
(ACA)	 AG	127629-127710	GT	TGG
(GCT)	 AG	128001-128031	GT	AGG
(GGA)	 AG	128122-128195	GT	AGG
(GCA)	 AG	128427-128495	GT	AGG
(CTG)	 AG	129230-129310	GT	CGG
(ATA)	 AG	129451-129510	GG	GGG
-recovered pasa_asmbl_49621.p1, internal, 127236, 127307
-recovered pasa_asmbl_49621.p1, internal, 127629, 127710
-recovered pasa_asmbl_49621.p1, internal, 128001, 128031
-recovered pasa_asmbl_49621.p1, internal, 128122, 128195
-recovered pasa_asmbl_49621.p1, internal, 128427, 128495
-recovered pasa_asmbl_49621.p1, internal, 129230, 129310
Valid prediction for snap_scaffold_7-snap.901-T1
Valid prediction for snap_scaffold_7-snap.888-T1
Valid prediction for Augustus_model.g11789.t1
Valid prediction for snap_scaffold_7-snap.886-T1
Valid prediction for snap_scaffold_7-snap.883-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for snap_scaffold_7-snap.858-T1
Valid prediction for GeneMark_model.29702_t
Couldn't classify 33618, 34072
Sorry, prediction pasa_asmbl_49624.p1 fails validation.
(CAC)	 CT	33618-34072	GT	AAG
(GCT)	 AG	34234-34453	AC	AGA
-recovered pasa_asmbl_49624.p1, terminal, 34234, 34453
Valid prediction for Augustus_model.g11790.t1
Valid prediction for GlimmerHMM_glimmerT_17634-T1
Valid prediction for GeneMark_model.29726_t
Valid prediction for Augustus_model.g11804.t1
Valid prediction for snap_scaffold_7-snap.873-T1
Valid prediction for Augustus_model.g11798.t1
Valid prediction for snap_scaffold_7-snap.889-T1
Valid prediction for GlimmerHMM_glimmerT_17620-T1
Valid prediction for Augustus_model.g11800.t1
Valid prediction for GlimmerHMM_glimmerT_17625-T1
Valid prediction for snap_scaffold_7-snap.860-T1
Valid prediction for GeneMark_model.29724_t
Valid prediction for Augustus_model.g11791.t1
Valid prediction for snap_scaffold_7-snap.904-T1
Valid prediction for GlimmerHMM_glimmerT_17627-T1
Valid prediction for GeneMark_model.29705_t
Valid prediction for GeneMark_model.29682_t
Valid prediction for GeneMark_model.29730_t
Valid prediction for GlimmerHMM_glimmerT_17624-T1
Valid prediction for GlimmerHMM_glimmerT_17635-T1
Valid prediction for Augustus_model.g11796.t1
Valid prediction for snap_scaffold_7-snap.892-T1
Valid prediction for snap_scaffold_7-snap.897-T1
Valid prediction for GeneMark_model.29686_t
Valid prediction for GeneMark_model.29695_t
Valid prediction for GeneMark_model.29703_t
Valid prediction for GeneMark_model.29719_t
Valid prediction for snap_scaffold_7-snap.895-T1
Valid prediction for Augustus_model.g11808.t1
Couldn't classify 112617, 113042
Sorry, prediction pasa_asmbl_49623.p1 fails validation.
(ACC)	 TG	112617-113042	AG	AGA
Valid prediction for snap_scaffold_7-snap.859-T1
Valid prediction for GeneMark_model.29713_t
Valid prediction for GeneMark_model.29720_t
Valid prediction for snap_scaffold_7-snap.874-T1
Valid prediction for GeneMark_model.29717_t
Valid prediction for GlimmerHMM_glimmerT_17622-T1
Valid prediction for GeneMark_model.29707_t
Valid prediction for Augustus_model.g11805.t1
Valid prediction for Augustus_model.g11807.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 50547, rend_intergenic: 47186  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55493, rend_intergenic: 53785  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64440, rend_intergenic: 58650  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76373, rend_intergenic: 70110  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92353, rend_intergenic: 92280  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94801, rend_intergenic: 92711  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103491, rend_intergenic: 95366  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108456, rend_intergenic: 106151  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151279, rend_intergenic: 129464  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 180274, rend_intergenic: 171695  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 186287, rend_intergenic: 184446  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 188655, rend_intergenic: 186640  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 201342, rend_intergenic: 190303  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 203264
-exon list size: 663


building trellis

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59.4    
59.5    
59.7    
59.8    
60.0    
60.2    
60.3    
60.5    
60.6    
60.8    
60.9    
61.1    
61.2    
61.4    
61.5    
61.7    
61.8    
62.0    
62.1    
62.3    
62.4    
62.6    
62.7    
62.9    
63.0    
63.2    
63.3    
63.5    
63.6    
63.8    
63.9    
64.1    
64.2    
64.4    
64.5    
64.7    
64.8    
65.0    
65.1    
65.3    
65.4    
65.6    
65.7    
65.9    
66.0    
66.2    
66.3    
66.5    
66.6    
66.8    
66.9    
67.1    
67.2    
67.4    
67.5    
67.7    
67.8    
68.0    
68.1    
68.3    
68.4    
68.6    
68.7    
68.9    
69.0    
69.2    
69.3    
69.5    
69.6    
69.8    
69.9    
70.1    
70.2    
70.4    
70.5    
70.7    
70.8    
71.0    
71.1    
71.3    
71.4    
71.6    
71.7    
71.9    
72.0    
72.2    
72.3    
72.5    
72.6    
72.8    
72.9    
73.1    
73.2    
73.4    
73.5    
73.7    
73.8    
74.0    
74.1    
74.3    
74.4    
74.6    
74.7    
74.9    
75.0    
75.2    
75.3    
75.5    
75.6    
75.8    
75.9    
76.1    
76.2    
76.4    
76.5    
76.7    
76.8    
77.0    
77.1    
77.3    
77.4    
77.6    
77.7    
77.9    
78.0    
78.2    
78.3    
78.5    
78.6    
78.8    
78.9    
79.1    
79.2    
79.4    
79.5    
79.7    
79.8    
80.0    
80.2    
80.3    
80.5    
80.6    
80.8    
80.9    
81.1    
81.2    
81.4    
81.5    
81.7    
81.8    
82.0    
82.1    
82.3    
82.4    
82.6    
82.7    
82.9    
83.0    
83.2    
83.3    
83.5    
83.6    
83.8    
83.9    
84.1    
84.2    
84.4    
84.5    
84.7    
84.8    
85.0    
85.1    
85.3    
85.4    
85.6    
85.7    
85.9    
86.0    
86.2    
86.3    
86.5    
86.6    
86.8    
86.9    
87.1    
87.2    
87.4    
87.5    
87.7    
87.8    
88.0    
88.1    
88.3    
88.4    
88.6    
88.7    
88.9    
89.0    
89.2    
89.3    
89.5    
89.6    
89.8    
89.9    
90.1    
90.2    
90.4    
90.5    
90.7    
90.8    
91.0    
91.1    
91.3    
91.4    
91.6    
91.7    
91.9    
92.0    
92.2    
92.3    
92.5    
92.6    
92.8    
92.9    
93.1    
93.2    
93.4    
93.5    
93.7    
93.8    
94.0    
94.1    
94.3    
94.4    
94.6    
94.7    
94.9    
95.0    
95.2    
95.3    
95.5    
95.6    
95.8    
95.9    
96.1    
96.2    
96.4    
96.5    
96.7    
96.8    
97.0    
97.1    
97.3    
97.4    
97.6    
97.7    
97.9    
98.0    
98.2    
98.3    
98.5    
98.6    
98.8    
98.9    
99.1    
99.2    
99.4    
99.5    
99.7    
99.8    
-found 44 predictions from path traversal
Error with prediction: snap lend_intergenic: 50547, rend_intergenic: 47186  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55493, rend_intergenic: 53785  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64440, rend_intergenic: 58650  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76373, rend_intergenic: 70110  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92353, rend_intergenic: 92280  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94801, rend_intergenic: 92711  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103491, rend_intergenic: 95366  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108456, rend_intergenic: 106151  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151279, rend_intergenic: 129464  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 180274, rend_intergenic: 171695  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 186287, rend_intergenic: 184446  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 188655, rend_intergenic: 186640  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 201342, rend_intergenic: 190303  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 36 predictions persist after filtering for low support