-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_23/scaffold_23_1268404-1500266

-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.89828_t
Valid prediction for snap_scaffold_23-snap.194-T1
Valid prediction for GeneMark_model.89838_t
Valid prediction for GeneMark_model.89842_t
Valid prediction for GeneMark_model.89820_t
Valid prediction for Augustus_model.g34714.t1
Valid prediction for snap_scaffold_23-snap.208-T1
Valid prediction for GeneMark_model.89818_t
Valid prediction for GlimmerHMM_glimmerT_51676-T1
Valid prediction for GlimmerHMM_glimmerT_51678-T1
Valid prediction for pasa_asmbl_30626.p1
Valid prediction for GeneMark_model.89817_t
Valid prediction for GlimmerHMM_glimmerT_51685-T1
Valid prediction for snap_scaffold_23-snap.214-T1
Valid prediction for Augustus_model.g34715.t1
Valid prediction for GlimmerHMM_glimmerT_51668-T1
Valid prediction for snap_scaffold_23-snap.199-T1
Valid prediction for GlimmerHMM_glimmerT_51667-T1
Valid prediction for GeneMark_model.89821_t
Valid prediction for snap_scaffold_23-snap.223-T1
Valid prediction for Augustus_model.g34710.t1
Couldn't classify 226154, 226229
Sorry, prediction pasa_asmbl_30637.p1 fails validation.
(ATG)	 AC	222202-222364	GT	AGG
(GGG)	 AG	224219-224337	GT	TGG
(AAG)	 AG	224448-224556	GT	AGG
(GGG)	 AG	225127-225269	GC	AGG
(GTG)	 AG	225689-225810	GT	AAG
(GTA)	 AG	226154-226229	AT	ACA
-recovered pasa_asmbl_30637.p1, initial, 222202, 222364
-recovered pasa_asmbl_30637.p1, internal, 224219, 224337
-recovered pasa_asmbl_30637.p1, internal, 224448, 224556
-recovered pasa_asmbl_30637.p1, internal, 225127, 225269
-recovered pasa_asmbl_30637.p1, internal, 225689, 225810
Valid prediction for GlimmerHMM_glimmerT_51665-T1
Valid prediction for snap_scaffold_23-snap.198-T1
Couldn't classify 229474, 229564
Couldn't classify 231175, 231239
Sorry, prediction pasa_asmbl_30638.p1 fails validation.
(CCC)	 CC	229474-229564	GT	TGG
(GTC)	 AG	229695-229778	GT	AGG
(CGG)	 AG	229943-230038	GT	AGG
(AGA)	 AG	231175-231239	GT	TGG
-recovered pasa_asmbl_30638.p1, internal, 229695, 229778
-recovered pasa_asmbl_30638.p1, internal, 229943, 230038
-recovered pasa_asmbl_30638.p1, internal, 231175, 231239
Valid prediction for GeneMark_model.89831_t
Valid prediction for snap_scaffold_23-snap.218-T1
Couldn't classify 188892, 190868
Sorry, prediction pasa_asmbl_30632.p1 fails validation.
(TCC)	 AC	188892-190868	TT	GGT
Valid prediction for GeneMark_model.89814_t
Valid prediction for GlimmerHMM_glimmerT_51670-T1
Valid prediction for Augustus_model.g34708.t1
Valid prediction for Augustus_model.g34722.t1
Valid prediction for snap_scaffold_23-snap.200-T1
Valid prediction for GlimmerHMM_glimmerT_51674-T1
Valid prediction for GeneMark_model.89834_t
Valid prediction for Augustus_model.g34706.t1
Valid prediction for snap_scaffold_23-snap.225-T1
Valid prediction for Augustus_model.g34723.t1
Valid prediction for CodingQuarry_transcript_35479-T1
Valid prediction for snap_scaffold_23-snap.221-T1
Valid prediction for GeneMark_model.89832_t
Valid prediction for snap_scaffold_23-snap.201-T1
Valid prediction for GlimmerHMM_glimmerT_51675-T1
Valid prediction for GlimmerHMM_glimmerT_51671-T1
Valid prediction for GlimmerHMM_glimmerT_51686-T1
Valid prediction for snap_scaffold_23-snap.195-T1
Valid prediction for snap_scaffold_23-snap.224-T1
Valid prediction for GeneMark_model.89823_t
Valid prediction for HiQ_model.g34709.t1
Valid prediction for snap_scaffold_23-snap.209-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for Augustus_model.g34705.t1
Valid prediction for snap_scaffold_23-snap.206-T1
Valid prediction for Augustus_model.g34721.t1
Valid prediction for snap_scaffold_23-snap.202-T1
Valid prediction for snap_scaffold_23-snap.203-T1
Valid prediction for GeneMark_model.89840_t
Valid prediction for snap_scaffold_23-snap.210-T1
Valid prediction for HiQ_model.g34712.t1
Valid prediction for snap_scaffold_23-snap.196-T1
Valid prediction for snap_scaffold_23-snap.205-T1
Couldn't classify 197896, 198450
Sorry, prediction pasa_asmbl_30635.p1 fails validation.
(GAC)	 CC	197896-198450	CA	GAC
Valid prediction for snap_scaffold_23-snap.207-T1
Valid prediction for GeneMark_model.89811_t
Valid prediction for Augustus_model.g34720.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 GeneMark_model.89822_t
Valid prediction for snap_scaffold_23-snap.211-T1
Valid prediction for GeneMark_model.89837_t
Valid prediction for GeneMark_model.89839_t
Valid prediction for GeneMark_model.89815_t
Valid prediction for GlimmerHMM_glimmerT_51684-T1
Couldn't classify 108858, 108928
Sorry, prediction pasa_asmbl_31356.p1 fails validation.
(ATG)	 GC	104808-105273	GT	CGG
(AGT)	 AG	106297-106350	GT	TGG
(ATT)	 AG	108858-108928	GG	CAG
-recovered pasa_asmbl_31356.p1, initial, 104808, 105273
-recovered pasa_asmbl_31356.p1, internal, 106297, 106350
Valid prediction for CodingQuarry_transcript_35482-T1
Valid prediction for Augustus_model.g34724.t1
Valid prediction for snap_scaffold_23-snap.228-T1
Valid prediction for snap_scaffold_23-snap.215-T1
Valid prediction for GeneMark_model.89829_t
Valid prediction for Augustus_model.g34716.t1
Valid prediction for GeneMark_model.89810_t
Valid prediction for Augustus_model.g34718.t1
Valid prediction for Augustus_model.g34717.t1
Valid prediction for GlimmerHMM_glimmerT_51689-T1
Valid prediction for CodingQuarry_transcript_35481-T1
Valid prediction for Augustus_model.g34719.t1
Valid prediction for snap_scaffold_23-snap.213-T1
Valid prediction for GlimmerHMM_glimmerT_51681-T1
Valid prediction for GeneMark_model.89824_t
Valid prediction for GeneMark_model.89812_t
Valid prediction for GlimmerHMM_glimmerT_51688-T1
Valid prediction for Augustus_model.g34725.t1
Valid prediction for GlimmerHMM_glimmerT_51679-T1
Valid prediction for GeneMark_model.89827_t
Valid prediction for GlimmerHMM_glimmerT_51687-T1
Valid prediction for GlimmerHMM_glimmerT_51672-T1
Valid prediction for GlimmerHMM_glimmerT_51683-T1
Valid prediction for GeneMark_model.89816_t
Valid prediction for GeneMark_model.89819_t
Valid prediction for HiQ_model.g34726.t1
Valid prediction for GeneMark_model.89836_t
Valid prediction for CodingQuarry_transcript_35483-T1
Valid prediction for CodingQuarry_transcript_35484-T1
Valid prediction for Augustus_model.g34707.t1
Valid prediction for snap_scaffold_23-snap.226-T1
Valid prediction for GlimmerHMM_glimmerT_51669-T1
Valid prediction for GlimmerHMM_glimmerT_51680-T1
Valid prediction for snap_scaffold_23-snap.222-T1
Valid prediction for GeneMark_model.89833_t
Valid prediction for GeneMark_model.89825_t
Valid prediction for GlimmerHMM_glimmerT_51673-T1
Couldn't classify 66680, 66734
Sorry, prediction pasa_asmbl_31365.p1 fails validation.
(AGT)	 GC	66680-66734	GT	AAG
(TGG)	 AG	67392-67485	GT	GAG
(TCA)	 AG	68002-68135	GT	TGG
(ATA)	 AG	68606-68682	GT	GAG
-recovered pasa_asmbl_31365.p1, terminal, 68606, 68682
-recovered pasa_asmbl_31365.p1, internal, 67392, 67485
-recovered pasa_asmbl_31365.p1, internal, 68002, 68135
-recovered pasa_asmbl_31365.p1, internal, 68606, 68682
Valid prediction for Augustus_model.g34711.t1
Couldn't classify 74436, 74577
Sorry, prediction pasa_asmbl_31363.p1 fails validation.
(CTG)	 GT	74436-74577	GT	CAG
(CTG)	 AG	77250-77438	GT	AGG
(ACA)	 AG	77560-77738	GT	TGG
(GTG)	 AG	78099-78224	GT	TGG
(GTG)	 AG	79871-79984	GT	GGG
(GAT)	 AG	80092-80186	GT	AGG
(ATT)	 AG	83053-83122	CA	GAC
-recovered pasa_asmbl_31363.p1, terminal, 83053, 83122
-recovered pasa_asmbl_31363.p1, internal, 77250, 77438
-recovered pasa_asmbl_31363.p1, internal, 77560, 77738
-recovered pasa_asmbl_31363.p1, internal, 78099, 78224
-recovered pasa_asmbl_31363.p1, internal, 79871, 79984
-recovered pasa_asmbl_31363.p1, internal, 80092, 80186
Valid prediction for snap_scaffold_23-snap.217-T1
Valid prediction for snap_scaffold_23-snap.197-T1
Valid prediction for snap_scaffold_23-snap.227-T1
Valid prediction for snap_scaffold_23-snap.219-T1
Valid prediction for snap_scaffold_23-snap.220-T1
Valid prediction for pasa_asmbl_31369.p1
Valid prediction for GeneMark_model.89826_t
Valid prediction for snap_scaffold_23-snap.204-T1
Valid prediction for Augustus_model.g34713.t1
Valid prediction for GlimmerHMM_glimmerT_51677-T1
Valid prediction for GlimmerHMM_glimmerT_51682-T1
Valid prediction for GeneMark_model.89835_t
Couldn't classify 96082, 96264
Sorry, prediction pasa_asmbl_31359.p1 fails validation.
(GCC)	 AG	96082-96264	GT	TGG
(GTG)	 AG	97764-97877	GT	AGG
(AAG)	 AG	98825-98974	GT	GAG
-recovered pasa_asmbl_31359.p1, terminal, 98825, 98974
-recovered pasa_asmbl_31359.p1, internal, 96082, 96264
-recovered pasa_asmbl_31359.p1, internal, 97764, 97877
-recovered pasa_asmbl_31359.p1, internal, 98825, 98974
Valid prediction for GlimmerHMM_glimmerT_51666-T1
Valid prediction for GeneMark_model.89813_t
Valid prediction for snap_scaffold_23-snap.216-T1
Valid prediction for snap_scaffold_23-snap.212-T1
Couldn't classify 119363, 119878
Sorry, prediction pasa_asmbl_31355.p1 fails validation.
(AGT)	 TG	119363-119878	CT	AGC
Valid prediction for GeneMark_model.89830_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 161157, rend_intergenic: 160623  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 188699, rend_intergenic: 187965  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 231863
-exon list size: 361


building trellis

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31.4    
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38.0    
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38.6    
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39.4    
39.7    
39.9    
40.2    
40.5    
40.8    
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41.3    
41.6    
41.9    
42.1    
42.4    
42.7    
43.0    
43.3    
43.5    
43.8    
44.1    
44.4    
44.6    
44.9    
45.2    
45.5    
45.7    
46.0    
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46.6    
46.8    
47.1    
47.4    
47.7    
47.9    
48.2    
48.5    
48.8    
49.0    
49.3    
49.6    
49.9    
50.1    
50.4    
50.7    
51.0    
51.2    
51.5    
51.8    
52.1    
52.3    
52.6    
52.9    
53.2    
53.4    
53.7    
54.0    
54.3    
54.5    
54.8    
55.1    
55.4    
55.6    
55.9    
56.2    
56.5    
56.7    
57.0    
57.3    
57.6    
57.9    
58.1    
58.4    
58.7    
59.0    
59.2    
59.5    
59.8    
60.1    
60.3    
60.6    
60.9    
61.2    
61.4    
61.7    
62.0    
62.3    
62.5    
62.8    
63.1    
63.4    
63.6    
63.9    
64.2    
64.5    
64.7    
65.0    
65.3    
65.6    
65.8    
66.1    
66.4    
66.7    
66.9    
67.2    
67.5    
67.8    
68.0    
68.3    
68.6    
68.9    
69.1    
69.4    
69.7    
70.0    
70.2    
70.5    
70.8    
71.1    
71.3    
71.6    
71.9    
72.2    
72.5    
72.7    
73.0    
73.3    
73.6    
73.8    
74.1    
74.4    
74.7    
74.9    
75.2    
75.5    
75.8    
76.0    
76.3    
76.6    
76.9    
77.1    
77.4    
77.7    
78.0    
78.2    
78.5    
78.8    
79.1    
79.3    
79.6    
79.9    
80.2    
80.4    
80.7    
81.0    
81.3    
81.5    
81.8    
82.1    
82.4    
82.6    
82.9    
83.2    
83.5    
83.7    
84.0    
84.3    
84.6    
84.8    
85.1    
85.4    
85.7    
86.0    
86.2    
86.5    
86.8    
87.1    
87.3    
87.6    
87.9    
88.2    
88.4    
88.7    
89.0    
89.3    
89.5    
89.8    
90.1    
90.4    
90.6    
90.9    
91.2    
91.5    
91.7    
92.0    
92.3    
92.6    
92.8    
93.1    
93.4    
93.7    
93.9    
94.2    
94.5    
94.8    
95.0    
95.3    
95.6    
95.9    
96.1    
96.4    
96.7    
97.0    
97.2    
97.5    
97.8    
98.1    
98.3    
98.6    
98.9    
99.2    
99.4    
99.7    
-found 31 predictions from path traversal
Error with prediction: snap lend_intergenic: 161157, rend_intergenic: 160623  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 188699, rend_intergenic: 187965  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 29 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 15961
-exon list size: 4


building trellis

16.7    
33.3    
50.0    
66.7    
83.3    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 15770
-exon list size: 3


building trellis

20.0    
40.0    
60.0    
80.0    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support