-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_22/scaffold_22_613669-803825

-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 HiQ_model.g33594.t1
Valid prediction for GeneMark_model.86701_t
Valid prediction for snap_scaffold_22-snap.140-T1
Valid prediction for GlimmerHMM_glimmerT_50088-T1
Valid prediction for snap_scaffold_22-snap.146-T1
Valid prediction for GlimmerHMM_glimmerT_50062-T1
Valid prediction for snap_scaffold_22-snap.162-T1
Valid prediction for GeneMark_model.86707_t
Valid prediction for GlimmerHMM_glimmerT_50068-T1
Valid prediction for GeneMark_model.86709_t
Valid prediction for GlimmerHMM_glimmerT_50075-T1
Valid prediction for Augustus_model.g33599.t1
Couldn't classify 388, 484
Sorry, prediction pasa_asmbl_29168.p1 fails validation.
(CAG)	 GG	388-484	GT	CGG
(GTA)	 AG	978-1085	GT	GGG
(ATG)	 AG	1487-1631	GT	AGG
(GAT)	 AG	1943-2055	GT	CGG
(GTA)	 AG	2285-2444	GT	CAG
(ATT)	 AG	2723-2927	GG	GAG
-recovered pasa_asmbl_29168.p1, initial, 1487, 1631
add_exon() Sorry, pasa_asmbl_29168.p1 1487-1631-terminal-3 is invalid.
-recovered pasa_asmbl_29168.p1, terminal, 1487, 1631
-recovered pasa_asmbl_29168.p1, terminal, 2723, 2927
-recovered pasa_asmbl_29168.p1, internal, 978, 1085
-recovered pasa_asmbl_29168.p1, internal, 1487, 1631
-recovered pasa_asmbl_29168.p1, internal, 1943, 2055
-recovered pasa_asmbl_29168.p1, internal, 2285, 2444
Valid prediction for GlimmerHMM_glimmerT_50082-T1
Valid prediction for CodingQuarry_transcript_34034-T1
Valid prediction for snap_scaffold_22-snap.144-T1
Valid prediction for HiQ_model.g33611.t1
Valid prediction for GlimmerHMM_glimmerT_50085-T1
Couldn't classify 113765, 113845
Sorry, prediction pasa_asmbl_29179.p1 fails validation.
(GAT)	 AT	113765-113845	GT	AAG
(CCG)	 AG	114409-114583	GT	AGG
(ACT)	 AG	114809-114933	GG	GAG
-recovered pasa_asmbl_29179.p1, terminal, 114809, 114933
-recovered pasa_asmbl_29179.p1, internal, 114409, 114583
Valid prediction for GeneMark_model.86694_t
Valid prediction for GlimmerHMM_glimmerT_50069-T1
Valid prediction for GeneMark_model.86685_t
Valid prediction for Augustus_model.g33614.t1
Valid prediction for snap_scaffold_22-snap.145-T1
Valid prediction for GlimmerHMM_glimmerT_50080-T1
Valid prediction for GeneMark_model.86686_t
Valid prediction for GlimmerHMM_glimmerT_50086-T1
Valid prediction for GeneMark_model.86703_t
Valid prediction for snap_scaffold_22-snap.133-T1
Valid prediction for GeneMark_model.86706_t
Valid prediction for snap_scaffold_22-snap.159-T1
Valid prediction for snap_scaffold_22-snap.164-T1
Valid prediction for HiQ_model.g33604.t1
Valid prediction for GlimmerHMM_glimmerT_50070-T1
Valid prediction for snap_scaffold_22-snap.142-T1
Valid prediction for snap_scaffold_22-snap.130-T1
Valid prediction for snap_scaffold_22-snap.161-T1
Valid prediction for pasa_asmbl_29183.p1
Valid prediction for HiQ_model.g33600.t1
Couldn't classify 76534, 76590
Sorry, prediction pasa_asmbl_29176.p1 fails validation.
(CGA)	 GG	76534-76590	GT	AGG
(GTG)	 AG	77932-78013	GT	TGG
(GGA)	 AG	79466-79522	GT	AAG
(TTA)	 AG	79651-79689	GT	AGG
(TGG)	 AG	79815-79945	GT	AGG
(GTG)	 AG	80092-80352	GA	GAG
-recovered pasa_asmbl_29176.p1, terminal, 80092, 80352
-recovered pasa_asmbl_29176.p1, internal, 77932, 78013
-recovered pasa_asmbl_29176.p1, internal, 79466, 79522
-recovered pasa_asmbl_29176.p1, internal, 79651, 79689
-recovered pasa_asmbl_29176.p1, internal, 79815, 79945
Valid prediction for CodingQuarry_transcript_34033-T1
Valid prediction for CodingQuarry_transcript_34030-T1
Valid prediction for Augustus_model.g33597.t1
Valid prediction for Augustus_model.g33613.t1
Valid prediction for GeneMark_model.86699_t
Valid prediction for HiQ_model.g33609.t1
Valid prediction for GlimmerHMM_glimmerT_50065-T1
Valid prediction for GeneMark_model.86696_t
Valid prediction for GeneMark_model.86692_t
Valid prediction for snap_scaffold_22-snap.152-T1
Valid prediction for CodingQuarry_transcript_34032-T1
Couldn't classify 26934, 27400
Sorry, prediction pasa_asmbl_29169.p1 fails validation.
(ATG)	 AC	25170-25602	GT	AGG
(AGC)	 AG	26934-27400	GA	CGG
-recovered pasa_asmbl_29169.p1, initial, 25170, 25602
Couldn't classify 27782, 27833
Sorry, prediction pasa_asmbl_29170.p1 fails validation.
(GAC)	 GA	27782-27833	GT	AGG
(AAC)	 AG	28298-28349	GT	AAG
(ATG)	 AG	28459-28514	GT	CGG
(AAC)	 AG	28839-29062	GT	AGG
(AGT)	 AG	29581-29741	GT	AGG
(GTT)	 AG	29937-30089	GT	ATG
(AAA)	 AG	30237-30366	GT	AGG
(AAC)	 AG	30983-31057	GT	AGG
(ATC)	 AG	31692-31784	GT	AGG
(GCT)	 AG	31958-32112	GT	GGG
(CCC)	 AG	32505-32672	GT	CAG
(GTC)	 AG	33850-33935	GT	GGG
(ACT)	 AG	34094-34198	GT	GGG
(GGT)	 AG	34544-34704	TC	GAT
add_exon() Sorry, pasa_asmbl_29170.p1 28459-28514-initial-1 is invalid.
-recovered pasa_asmbl_29170.p1, initial, 28459, 28514
-recovered pasa_asmbl_29170.p1, terminal, 34544, 34704
-recovered pasa_asmbl_29170.p1, internal, 28298, 28349
-recovered pasa_asmbl_29170.p1, internal, 28459, 28514
-recovered pasa_asmbl_29170.p1, internal, 28839, 29062
-recovered pasa_asmbl_29170.p1, internal, 29581, 29741
-recovered pasa_asmbl_29170.p1, internal, 29937, 30089
-recovered pasa_asmbl_29170.p1, internal, 30237, 30366
-recovered pasa_asmbl_29170.p1, internal, 30983, 31057
-recovered pasa_asmbl_29170.p1, internal, 31692, 31784
-recovered pasa_asmbl_29170.p1, internal, 31958, 32112
-recovered pasa_asmbl_29170.p1, internal, 32505, 32672
-recovered pasa_asmbl_29170.p1, internal, 33850, 33935
-recovered pasa_asmbl_29170.p1, internal, 34094, 34198
Valid prediction for GeneMark_model.86689_t
Valid prediction for CodingQuarry_transcript_34029-T1
Couldn't classify 146906, 147084
Sorry, prediction pasa_asmbl_29185.p1 fails validation.
(ATG)	 GA	146396-146804	GT	GGG
(GTA)	 AG	146906-147084	AA	ACA
-recovered pasa_asmbl_29185.p1, initial, 146396, 146804
Valid prediction for snap_scaffold_22-snap.143-T1
Valid prediction for CodingQuarry_transcript_34037-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 snap_scaffold_22-snap.160-T1
Valid prediction for GeneMark_model.86693_t
Valid prediction for snap_scaffold_22-snap.147-T1
Valid prediction for GlimmerHMM_glimmerT_50074-T1
Valid prediction for snap_scaffold_22-snap.137-T1
Valid prediction for snap_scaffold_22-snap.154-T1
Valid prediction for HiQ_model.g33607.t1
Valid prediction for snap_scaffold_22-snap.156-T1
Valid prediction for GeneMark_model.86700_t
Valid prediction for snap_scaffold_22-snap.139-T1
Valid prediction for Augustus_model.g33616.t1
Valid prediction for snap_scaffold_22-snap.155-T1
Valid prediction for pasa_asmbl_29887.p1
Valid prediction for GlimmerHMM_glimmerT_50081-T1
Valid prediction for HiQ_model.g33598.t1
Valid prediction for CodingQuarry_transcript_34036-T1
Valid prediction for GeneMark_model.86704_t
Valid prediction for GlimmerHMM_glimmerT_50079-T1
Valid prediction for GeneMark_model.86695_t
Valid prediction for snap_scaffold_22-snap.151-T1
Valid prediction for GeneMark_model.86710_t
Valid prediction for snap_scaffold_22-snap.158-T1
Valid prediction for GlimmerHMM_glimmerT_50064-T1
Valid prediction for snap_scaffold_22-snap.136-T1
Valid prediction for GeneMark_model.86711_t
Valid prediction for GlimmerHMM_glimmerT_50089-T1
Valid prediction for GlimmerHMM_glimmerT_50077-T1
Valid prediction for GeneMark_model.86690_t
Valid prediction for GlimmerHMM_glimmerT_50063-T1
Valid prediction for GlimmerHMM_glimmerT_50072-T1
Valid prediction for Augustus_model.g33592.t1
Valid prediction for Augustus_model.g33617.t1
Valid prediction for GlimmerHMM_glimmerT_50087-T1
Valid prediction for snap_scaffold_22-snap.129-T1
Couldn't classify 84976, 85146
Sorry, prediction pasa_asmbl_29885.p1 fails validation.
(ATG)	 TA	80290-80455	GT	AGG
(AGG)	 AG	82389-82522	GT	TCG
(GAC)	 AG	82655-82837	GT	AGG
(CCT)	 AG	82968-83092	GT	AGG
(GCC)	 AG	83345-83583	GT	AGG
(GCC)	 AG	83748-83881	GT	CAG
(AGT)	 AG	84175-84304	GT	AAG
(CAA)	 AG	84530-84705	GT	GCG
(GAG)	 AG	84976-85146	GG	GAG
-recovered pasa_asmbl_29885.p1, initial, 80290, 80455
-recovered pasa_asmbl_29885.p1, internal, 82389, 82522
-recovered pasa_asmbl_29885.p1, internal, 82655, 82837
-recovered pasa_asmbl_29885.p1, internal, 82968, 83092
-recovered pasa_asmbl_29885.p1, internal, 83345, 83583
-recovered pasa_asmbl_29885.p1, internal, 83748, 83881
-recovered pasa_asmbl_29885.p1, internal, 84175, 84304
-recovered pasa_asmbl_29885.p1, internal, 84530, 84705
Valid prediction for snap_scaffold_22-snap.166-T1
Valid prediction for GeneMark_model.86715_t
Valid prediction for GeneMark_model.86688_t
Valid prediction for Augustus_model.g33608.t1
Valid prediction for GlimmerHMM_glimmerT_50060-T1
Valid prediction for pasa_asmbl_29892.p1
Valid prediction for Augustus_model.g33612.t1
Valid prediction for snap_scaffold_22-snap.157-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for Augustus_model.g33606.t1
Valid prediction for snap_scaffold_22-snap.153-T1
Valid prediction for GlimmerHMM_glimmerT_50061-T1
Valid prediction for snap_scaffold_22-snap.148-T1
Valid prediction for GlimmerHMM_glimmerT_50078-T1
Couldn't classify 150811, 150988
Sorry, prediction pasa_asmbl_29876.p1 fails validation.
(ATC)	 AG	150811-150988	GT	GAG
(GTT)	 AG	151070-151320	GG	GAG
-recovered pasa_asmbl_29876.p1, terminal, 151070, 151320
-recovered pasa_asmbl_29876.p1, internal, 150811, 150988
Valid prediction for GlimmerHMM_glimmerT_50073-T1
Valid prediction for snap_scaffold_22-snap.138-T1
Valid prediction for HiQ_model.g33605.t1
Valid prediction for snap_scaffold_22-snap.163-T1
Valid prediction for Augustus_model.g33601.t1
Valid prediction for GeneMark_model.86687_t
Valid prediction for GlimmerHMM_glimmerT_50066-T1
Valid prediction for snap_scaffold_22-snap.165-T1
Valid prediction for GeneMark_model.86705_t
Valid prediction for Augustus_model.g33593.t1
Valid prediction for GeneMark_model.86702_t
Valid prediction for GlimmerHMM_glimmerT_50091-T1
Valid prediction for Augustus_model.g33610.t1
Valid prediction for Augustus_model.g33596.t1
Valid prediction for GlimmerHMM_glimmerT_50084-T1
Valid prediction for GlimmerHMM_glimmerT_50083-T1
Valid prediction for snap_scaffold_22-snap.134-T1
Valid prediction for GeneMark_model.86714_t
Valid prediction for Augustus_model.g33595.t1
Valid prediction for HiQ_model.g33602.t1
Valid prediction for Augustus_model.g33603.t1
Valid prediction for GeneMark_model.86691_t
Valid prediction for snap_scaffold_22-snap.135-T1
Valid prediction for GlimmerHMM_glimmerT_50067-T1
Valid prediction for GeneMark_model.86698_t
Valid prediction for snap_scaffold_22-snap.149-T1
Valid prediction for GlimmerHMM_glimmerT_50090-T1
Valid prediction for CodingQuarry_transcript_34035-T1
Valid prediction for snap_scaffold_22-snap.131-T1
Valid prediction for snap_scaffold_22-snap.132-T1
Couldn't classify 85464, 85562
Couldn't classify 101751, 101905
Sorry, prediction pasa_asmbl_29882.p1 fails validation.
(CCT)	 CA	85464-85562	GT	AGG
(TTG)	 AG	85794-86011	GT	AGG
(TCT)	 AG	86233-86364	GT	AGG
(GAA)	 AG	86514-86610	GT	ACG
(CCG)	 AG	86820-87011	GT	AGG
(GGT)	 AG	87386-87586	GT	GGG
(AGA)	 AG	87827-87964	GT	AGG
(TTC)	 AG	88046-88167	GT	AAG
(CAA)	 AG	88299-88472	GT	AAG
(GAA)	 AG	88924-89065	GT	TGG
(GAA)	 AG	89529-89660	GT	AGG
(ATG)	 AG	89976-90093	GT	CGG
(CCC)	 AG	90615-90739	GT	AGG
(GCG)	 AG	91038-91269	GT	AGG
(GTT)	 AG	91447-91500	GT	CAG
(TGG)	 AG	91740-91909	GT	AGG
(ATC)	 AG	92155-92332	GT	AGG
(ATA)	 AG	92848-92913	GT	AGG
(GTC)	 AG	93266-93351	GT	AGG
(GTA)	 AG	93473-93606	GT	AAG
(GGC)	 AG	93754-93898	GT	AGG
(ATC)	 AG	94063-94225	GT	AGG
(CCA)	 AG	94378-94490	GT	AGG
(CCG)	 AG	94864-95083	GT	AGG
(CAG)	 AG	95237-95371	GT	AGG
(AGG)	 AG	95485-95616	GT	AGG
(AGC)	 AG	96095-96203	GT	CTG
(TCA)	 AG	96408-96540	GT	AGG
(TTG)	 AG	97509-97704	GT	GGG
(TGT)	 AG	98826-98989	GT	CGG
(CAC)	 AG	99221-99347	GT	AGG
(AAG)	 AG	101751-101905	CG	ACC
-recovered pasa_asmbl_29882.p1, initial, 89976, 90093
-recovered pasa_asmbl_29882.p1, internal, 85794, 86011
-recovered pasa_asmbl_29882.p1, internal, 86233, 86364
-recovered pasa_asmbl_29882.p1, internal, 86514, 86610
-recovered pasa_asmbl_29882.p1, internal, 86820, 87011
-recovered pasa_asmbl_29882.p1, internal, 87386, 87586
-recovered pasa_asmbl_29882.p1, internal, 87827, 87964
-recovered pasa_asmbl_29882.p1, internal, 88046, 88167
-recovered pasa_asmbl_29882.p1, internal, 88299, 88472
-recovered pasa_asmbl_29882.p1, internal, 88924, 89065
-recovered pasa_asmbl_29882.p1, internal, 89529, 89660
-recovered pasa_asmbl_29882.p1, internal, 89976, 90093
-recovered pasa_asmbl_29882.p1, internal, 90615, 90739
-recovered pasa_asmbl_29882.p1, internal, 91038, 91269
-recovered pasa_asmbl_29882.p1, internal, 91447, 91500
-recovered pasa_asmbl_29882.p1, internal, 91740, 91909
-recovered pasa_asmbl_29882.p1, internal, 92155, 92332
-recovered pasa_asmbl_29882.p1, internal, 92848, 92913
-recovered pasa_asmbl_29882.p1, internal, 93266, 93351
-recovered pasa_asmbl_29882.p1, internal, 93473, 93606
-recovered pasa_asmbl_29882.p1, internal, 93754, 93898
-recovered pasa_asmbl_29882.p1, internal, 94063, 94225
-recovered pasa_asmbl_29882.p1, internal, 94378, 94490
-recovered pasa_asmbl_29882.p1, internal, 94864, 95083
-recovered pasa_asmbl_29882.p1, internal, 95237, 95371
-recovered pasa_asmbl_29882.p1, internal, 95485, 95616
-recovered pasa_asmbl_29882.p1, internal, 96095, 96203
-recovered pasa_asmbl_29882.p1, internal, 96408, 96540
-recovered pasa_asmbl_29882.p1, internal, 97509, 97704
-recovered pasa_asmbl_29882.p1, internal, 98826, 98989
-recovered pasa_asmbl_29882.p1, internal, 99221, 99347
Valid prediction for GlimmerHMM_glimmerT_50071-T1
Valid prediction for Augustus_model.g33615.t1
Valid prediction for snap_scaffold_22-snap.141-T1
Valid prediction for GeneMark_model.86697_t
Valid prediction for snap_scaffold_22-snap.150-T1
Valid prediction for GlimmerHMM_glimmerT_50076-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 11314, rend_intergenic: 9694  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 13426, rend_intergenic: 11732  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34704, rend_intergenic: 26612  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 190157
-exon list size: 500


building trellis

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59.8    
60.0    
60.2    
60.4    
60.6    
60.8    
61.0    
61.2    
61.4    
61.6    
61.8    
62.0    
62.2    
62.4    
62.5    
62.7    
62.9    
63.1    
63.3    
63.5    
63.7    
63.9    
64.1    
64.3    
64.5    
64.7    
64.9    
65.1    
65.3    
65.5    
65.7    
65.9    
66.1    
66.3    
66.5    
66.7    
66.9    
67.1    
67.3    
67.5    
67.7    
67.9    
68.1    
68.3    
68.5    
68.7    
68.9    
69.1    
69.3    
69.5    
69.7    
69.9    
70.1    
70.3    
70.5    
70.7    
70.9    
71.1    
71.3    
71.5    
71.7    
71.9    
72.1    
72.3    
72.5    
72.7    
72.9    
73.1    
73.3    
73.5    
73.7    
73.9    
74.1    
74.3    
74.5    
74.7    
74.9    
75.1    
75.3    
75.5    
75.7    
75.9    
76.1    
76.3    
76.5    
76.7    
76.9    
77.1    
77.3    
77.5    
77.7    
77.9    
78.1    
78.3    
78.5    
78.7    
78.9    
79.1    
79.3    
79.5    
79.7    
79.9    
80.1    
80.3    
80.5    
80.7    
80.9    
81.1    
81.3    
81.5    
81.7    
81.9    
82.1    
82.3    
82.5    
82.7    
82.9    
83.1    
83.3    
83.5    
83.7    
83.9    
84.1    
84.3    
84.5    
84.7    
84.9    
85.1    
85.3    
85.5    
85.7    
85.9    
86.1    
86.3    
86.5    
86.7    
86.9    
87.1    
87.3    
87.5    
87.6    
87.8    
88.0    
88.2    
88.4    
88.6    
88.8    
89.0    
89.2    
89.4    
89.6    
89.8    
90.0    
90.2    
90.4    
90.6    
90.8    
91.0    
91.2    
91.4    
91.6    
91.8    
92.0    
92.2    
92.4    
92.6    
92.8    
93.0    
93.2    
93.4    
93.6    
93.8    
94.0    
94.2    
94.4    
94.6    
94.8    
95.0    
95.2    
95.4    
95.6    
95.8    
96.0    
96.2    
96.4    
96.6    
96.8    
97.0    
97.2    
97.4    
97.6    
97.8    
98.0    
98.2    
98.4    
98.6    
98.8    
99.0    
99.2    
99.4    
99.6    
99.8    
-found 32 predictions from path traversal
Error with prediction: snap lend_intergenic: 11314, rend_intergenic: 9694  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 13426, rend_intergenic: 11732  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34704, rend_intergenic: 26612  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 31 predictions persist after filtering for low support