-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_23/scaffold_23_9332126-9491774

-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.91740_t
Valid prediction for GeneMark_model.91710_t
Couldn't classify 88688, 88978
Couldn't classify 89499, 90239
Sorry, prediction pasa_asmbl_31089.p1 fails validation.
(AAC)	 CG	88688-88978	GT	AGG
(GTA)	 AG	89499-90239	AT	AGA
Valid prediction for GeneMark_model.91706_t
Valid prediction for snap_scaffold_23-snap.1807-T1
Valid prediction for GeneMark_model.91723_t
Valid prediction for GlimmerHMM_glimmerT_52874-T1
Valid prediction for GeneMark_model.91725_t
Valid prediction for GlimmerHMM_glimmerT_52861-T1
Valid prediction for GeneMark_model.91746_t
Valid prediction for GlimmerHMM_glimmerT_52849-T1
Valid prediction for snap_scaffold_23-snap.1834-T1
Valid prediction for snap_scaffold_23-snap.1841-T1
Valid prediction for snap_scaffold_23-snap.1814-T1
Valid prediction for snap_scaffold_23-snap.1805-T1
Valid prediction for GeneMark_model.91744_t
Valid prediction for snap_scaffold_23-snap.1817-T1
Valid prediction for GeneMark_model.91726_t
Valid prediction for snap_scaffold_23-snap.1837-T1
Valid prediction for snap_scaffold_23-snap.1821-T1
Valid prediction for GeneMark_model.91737_t
Valid prediction for snap_scaffold_23-snap.1822-T1
Valid prediction for GeneMark_model.91716_t
Valid prediction for snap_scaffold_23-snap.1803-T1
Valid prediction for GeneMark_model.91732_t
Valid prediction for snap_scaffold_23-snap.1806-T1
Valid prediction for snap_scaffold_23-snap.1842-T1
Valid prediction for GlimmerHMM_glimmerT_52851-T1
Valid prediction for Augustus_model.g35514.t1
Valid prediction for Augustus_model.g35518.t1
Valid prediction for GeneMark_model.91701_t
Valid prediction for GlimmerHMM_glimmerT_52850-T1
Valid prediction for Augustus_model.g35510.t1
Valid prediction for snap_scaffold_23-snap.1812-T1
Valid prediction for GlimmerHMM_glimmerT_52867-T1
Valid prediction for GeneMark_model.91742_t
Valid prediction for GeneMark_model.91736_t
Valid prediction for snap_scaffold_23-snap.1809-T1
Valid prediction for snap_scaffold_23-snap.1826-T1
Valid prediction for snap_scaffold_23-snap.1831-T1
Valid prediction for GlimmerHMM_glimmerT_52863-T1
Valid prediction for snap_scaffold_23-snap.1839-T1
Valid prediction for GlimmerHMM_glimmerT_52871-T1
Valid prediction for snap_scaffold_23-snap.1816-T1
Valid prediction for GlimmerHMM_glimmerT_52859-T1
Valid prediction for GlimmerHMM_glimmerT_52869-T1
Valid prediction for snap_scaffold_23-snap.1819-T1
Valid prediction for snap_scaffold_23-snap.1838-T1
Valid prediction for GlimmerHMM_glimmerT_52856-T1
Valid prediction for GlimmerHMM_glimmerT_52854-T1
Valid prediction for GeneMark_model.91730_t
Valid prediction for GeneMark_model.91708_t
Valid prediction for GeneMark_model.91748_t
Valid prediction for GeneMark_model.91700_t
Valid prediction for HiQ_model.g35517.t1
Valid prediction for Augustus_model.g35512.t1
Valid prediction for snap_scaffold_23-snap.1811-T1
Valid prediction for GeneMark_model.91714_t
Valid prediction for GlimmerHMM_glimmerT_52862-T1
Valid prediction for GlimmerHMM_glimmerT_52872-T1
Valid prediction for GeneMark_model.91717_t
Couldn't classify 90354, 91247
Sorry, prediction pasa_asmbl_31090.p1 fails validation.
(TCC)	 TC	90354-91247	GT	AGG
(GTG)	 AG	91520-91650	GT	AGG
(GTG)	 AG	92775-92863	GT	GGG
(ACC)	 AG	93125-93189	AA	AGA
-recovered pasa_asmbl_31090.p1, terminal, 93125, 93189
-recovered pasa_asmbl_31090.p1, internal, 91520, 91650
-recovered pasa_asmbl_31090.p1, internal, 92775, 92863
Valid prediction for GlimmerHMM_glimmerT_52857-T1
Valid prediction for GlimmerHMM_glimmerT_52860-T1
Valid prediction for snap_scaffold_23-snap.1823-T1
Valid prediction for GeneMark_model.91734_t
Valid prediction for snap_scaffold_23-snap.1825-T1
Couldn't classify 63255, 63322
Sorry, prediction GeneMark_model.91719_t fails validation.
(TTA)	 AG	63255-63322	GT	GAG
(TCC)	 AG	63343-63494	GT	CTG
(GCG)	 AG	63551-63666	GT	CGG
(GGT)	 AG	64184-64230	GT	GAG
(GAG)	 AG	64255-64323	GT	GTG
(GGA)	 AG	64346-64429	GT	CAG
(GGG)	 AG	64477-64506	GT	GGG
(AGG)	 AG	64536-64559	GT	GAG
(AGA)	 AG	64591-64826	GT	AGG
(ACG)	 AG	67801-67813	GT	AGG
(ACT)	 AG	67836-67844	GT	ATG
(AGG)	 AG	68561-68656	GT	GAG
(AGG)	 AG	68678-68683	GT	ATG
(CAT)	 AG	68721-68735	GT	GGG
(AGA)	 AG	68759-68797	GT	GGG
(AGA)	 AG	71093-71498	CC	AAC
add_exon() Sorry, GeneMark_model.91719_t 63255-63322-terminal-2 is invalid.
-recovered GeneMark_model.91719_t, terminal, 63255, 63322
-recovered GeneMark_model.91719_t, terminal, 68561, 68656
-recovered GeneMark_model.91719_t, terminal, 71093, 71498
-recovered GeneMark_model.91719_t, internal, 63255, 63322
-recovered GeneMark_model.91719_t, internal, 63343, 63494
-recovered GeneMark_model.91719_t, internal, 63551, 63666
-recovered GeneMark_model.91719_t, internal, 64184, 64230
-recovered GeneMark_model.91719_t, internal, 64255, 64323
-recovered GeneMark_model.91719_t, internal, 64346, 64429
-recovered GeneMark_model.91719_t, internal, 64477, 64506
-recovered GeneMark_model.91719_t, internal, 64536, 64559
-recovered GeneMark_model.91719_t, internal, 64591, 64826
-recovered GeneMark_model.91719_t, internal, 67801, 67813
-recovered GeneMark_model.91719_t, internal, 67836, 67844
-recovered GeneMark_model.91719_t, internal, 68561, 68656
-recovered GeneMark_model.91719_t, internal, 68678, 68683
-recovered GeneMark_model.91719_t, internal, 68721, 68735
-recovered GeneMark_model.91719_t, internal, 68759, 68797
Valid prediction for GeneMark_model.91728_t
Valid prediction for GeneMark_model.91720_t
Valid prediction for GlimmerHMM_glimmerT_52866-T1
Valid prediction for GeneMark_model.91702_t
Valid prediction for GeneMark_model.91721_t
Valid prediction for Augustus_model.g35516.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.91743_t
Valid prediction for GlimmerHMM_glimmerT_52848-T1
Valid prediction for GeneMark_model.91747_t
Valid prediction for snap_scaffold_23-snap.1813-T1
Valid prediction for snap_scaffold_23-snap.1827-T1
Couldn't classify 20789, 21004
Couldn't classify 23937, 24099
Sorry, prediction pasa_asmbl_31813.p1 fails validation.
(TGT)	 TG	20789-21004	GT	AGG
(AGT)	 AG	21290-21400	GT	AGG
(CTG)	 AG	21997-22119	GT	AGG
(GAG)	 AG	22360-22547	GT	AGG
(GGC)	 AG	23445-23609	GT	AGG
(CGT)	 AG	23937-24099	CC	CCC
-recovered pasa_asmbl_31813.p1, internal, 21290, 21400
-recovered pasa_asmbl_31813.p1, internal, 21997, 22119
-recovered pasa_asmbl_31813.p1, internal, 22360, 22547
-recovered pasa_asmbl_31813.p1, internal, 23445, 23609
Valid prediction for Augustus_model.g35520.t1
Valid prediction for GeneMark_model.91738_t
Valid prediction for GlimmerHMM_glimmerT_52873-T1
Valid prediction for Augustus_model.g35511.t1
Valid prediction for snap_scaffold_23-snap.1804-T1
Valid prediction for GeneMark_model.91704_t
Valid prediction for Augustus_model.g35515.t1
Valid prediction for GeneMark_model.91699_t
Valid prediction for snap_scaffold_23-snap.1828-T1
Valid prediction for GeneMark_model.91729_t
Valid prediction for GlimmerHMM_glimmerT_52855-T1
Valid prediction for GeneMark_model.91735_t
Valid prediction for snap_scaffold_23-snap.1820-T1
Valid prediction for snap_scaffold_23-snap.1836-T1
Valid prediction for GeneMark_model.91712_t
Couldn't classify 17609, 17965
Sorry, prediction pasa_asmbl_31815.p1 fails validation.
(GCC)	 CA	17609-17965	CC	ACC
Valid prediction for GeneMark_model.91749_t
Valid prediction for Augustus_model.g35521.t1
Valid prediction for Augustus_model.g35519.t1
Valid prediction for pasa_asmbl_31940.p1
Valid prediction for snap_scaffold_23-snap.1829-T1
Valid prediction for snap_scaffold_23-snap.1815-T1
Valid prediction for GeneMark_model.91731_t
Valid prediction for Augustus_model.g35513.t1
Valid prediction for GlimmerHMM_glimmerT_52868-T1
Valid prediction for GlimmerHMM_glimmerT_52864-T1
Valid prediction for GeneMark_model.91709_t
Valid prediction for GeneMark_model.91711_t
Valid prediction for snap_scaffold_23-snap.1835-T1
Valid prediction for GlimmerHMM_glimmerT_52876-T1
Valid prediction for CodingQuarry_transcript_35702-T1
Valid prediction for GeneMark_model.91741_t
Valid prediction for GeneMark_model.91718_t
add_exon() Sorry, GeneMark_model.91718_t 103874-104023-internal-1 is invalid.
add_exon() Sorry, GeneMark_model.91718_t 104486-104575-terminal-2 is invalid.
Valid prediction for snap_scaffold_23-snap.1830-T1
Valid prediction for snap_scaffold_23-snap.1840-T1
Couldn't classify 5035, 5185
Couldn't classify 12143, 12256
Sorry, prediction pasa_asmbl_31968.p1 fails validation.
(AGC)	 GC	5035-5185	GT	AGG
(AGC)	 AG	5582-5685	GT	AGG
(CAT)	 AG	5909-6061	GT	AGG
(ACG)	 AG	6515-6659	GT	AGG
(GAC)	 AG	7265-7419	GT	AGG
(CCG)	 AG	7504-7577	GT	AGG
(ATG)	 AG	8465-8643	GT	TGG
(GAA)	 AG	8888-9000	GT	AGG
(AAC)	 AG	10051-10216	GT	AGG
(GTG)	 AG	11795-11910	GT	AGG
(GAG)	 AG	12143-12256	GG	CAG
add_exon() Sorry, pasa_asmbl_31968.p1 8465-8643-initial-1 is invalid.
-recovered pasa_asmbl_31968.p1, initial, 8465, 8643
-recovered pasa_asmbl_31968.p1, internal, 5582, 5685
-recovered pasa_asmbl_31968.p1, internal, 5909, 6061
-recovered pasa_asmbl_31968.p1, internal, 6515, 6659
-recovered pasa_asmbl_31968.p1, internal, 7265, 7419
-recovered pasa_asmbl_31968.p1, internal, 7504, 7577
-recovered pasa_asmbl_31968.p1, internal, 8465, 8643
-recovered pasa_asmbl_31968.p1, internal, 8888, 9000
-recovered pasa_asmbl_31968.p1, internal, 10051, 10216
-recovered pasa_asmbl_31968.p1, internal, 11795, 11910
Valid prediction for snap_scaffold_23-snap.1833-T1
Valid prediction for snap_scaffold_23-snap.1824-T1
Valid prediction for GlimmerHMM_glimmerT_52875-T1
Valid prediction for GlimmerHMM_glimmerT_52852-T1
Valid prediction for GeneMark_model.91745_t
Valid prediction for GeneMark_model.91707_t
Valid prediction for Augustus_model.g35509.t1
Valid prediction for GlimmerHMM_glimmerT_52865-T1
Valid prediction for snap_scaffold_23-snap.1832-T1
Valid prediction for GlimmerHMM_glimmerT_52870-T1
Valid prediction for GeneMark_model.91739_t
Couldn't classify 26908, 26991
Couldn't classify 27022, 27297
Sorry, prediction CodingQuarry_transcript_35703-T1 fails validation.
(ATG)	 CA	26908-26991	CT	ACC
(CTG)	 AC	27022-27297	AA	AAA
Valid prediction for GeneMark_model.91713_t
Valid prediction for GeneMark_model.91727_t
Valid prediction for GeneMark_model.91715_t
Valid prediction for GeneMark_model.91722_t
Valid prediction for GeneMark_model.91733_t
Valid prediction for GeneMark_model.91705_t
Valid prediction for GlimmerHMM_glimmerT_52853-T1
Valid prediction for GlimmerHMM_glimmerT_52877-T1
Valid prediction for GeneMark_model.91724_t
Valid prediction for GlimmerHMM_glimmerT_52858-T1
Valid prediction for snap_scaffold_23-snap.1810-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_23-snap.1808-T1
Valid prediction for snap_scaffold_23-snap.1818-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 5320, rend_intergenic: 5008  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 10084, rend_intergenic: 5567  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29684, rend_intergenic: 21745  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32151, rend_intergenic: 29860  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41833, rend_intergenic: 32366  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63689, rend_intergenic: 54721  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74824, rend_intergenic: 69476  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78573, rend_intergenic: 77941  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80168, rend_intergenic: 78804  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84779, rend_intergenic: 81375  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93189, rend_intergenic: 89451  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114776, rend_intergenic: 101075  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115967, rend_intergenic: 114779  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121311, rend_intergenic: 116052  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126534, rend_intergenic: 123043  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128637, rend_intergenic: 126624  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148322, rend_intergenic: 130936  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157082, rend_intergenic: 149499  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 159649
-exon list size: 730


building trellis

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58.3    
58.5    
58.6    
58.7    
58.9    
59.0    
59.2    
59.3    
59.4    
59.6    
59.7    
59.8    
60.0    
60.1    
60.2    
60.4    
60.5    
60.7    
60.8    
60.9    
61.1    
61.2    
61.3    
61.5    
61.6    
61.7    
61.9    
62.0    
62.2    
62.3    
62.4    
62.6    
62.7    
62.8    
63.0    
63.1    
63.3    
63.4    
63.5    
63.7    
63.8    
63.9    
64.1    
64.2    
64.3    
64.5    
64.6    
64.8    
64.9    
65.0    
65.2    
65.3    
65.4    
65.6    
65.7    
65.8    
66.0    
66.1    
66.3    
66.4    
66.5    
66.7    
66.8    
66.9    
67.1    
67.2    
67.3    
67.5    
67.6    
67.8    
67.9    
68.0    
68.2    
68.3    
68.4    
68.6    
68.7    
68.9    
69.0    
69.1    
69.3    
69.4    
69.5    
69.7    
69.8    
69.9    
70.1    
70.2    
70.4    
70.5    
70.6    
70.8    
70.9    
71.0    
71.2    
71.3    
71.4    
71.6    
71.7    
71.9    
72.0    
72.1    
72.3    
72.4    
72.5    
72.7    
72.8    
73.0    
73.1    
73.2    
73.4    
73.5    
73.6    
73.8    
73.9    
74.0    
74.2    
74.3    
74.5    
74.6    
74.7    
74.9    
75.0    
75.1    
75.3    
75.4    
75.5    
75.7    
75.8    
76.0    
76.1    
76.2    
76.4    
76.5    
76.6    
76.8    
76.9    
77.0    
77.2    
77.3    
77.5    
77.6    
77.7    
77.9    
78.0    
78.1    
78.3    
78.4    
78.6    
78.7    
78.8    
79.0    
79.1    
79.2    
79.4    
79.5    
79.6    
79.8    
79.9    
80.1    
80.2    
80.3    
80.5    
80.6    
80.7    
80.9    
81.0    
81.1    
81.3    
81.4    
81.6    
81.7    
81.8    
82.0    
82.1    
82.2    
82.4    
82.5    
82.7    
82.8    
82.9    
83.1    
83.2    
83.3    
83.5    
83.6    
83.7    
83.9    
84.0    
84.2    
84.3    
84.4    
84.6    
84.7    
84.8    
85.0    
85.1    
85.2    
85.4    
85.5    
85.7    
85.8    
85.9    
86.1    
86.2    
86.3    
86.5    
86.6    
86.7    
86.9    
87.0    
87.2    
87.3    
87.4    
87.6    
87.7    
87.8    
88.0    
88.1    
88.3    
88.4    
88.5    
88.7    
88.8    
88.9    
89.1    
89.2    
89.3    
89.5    
89.6    
89.8    
89.9    
90.0    
90.2    
90.3    
90.4    
90.6    
90.7    
90.8    
91.0    
91.1    
91.3    
91.4    
91.5    
91.7    
91.8    
91.9    
92.1    
92.2    
92.3    
92.5    
92.6    
92.8    
92.9    
93.0    
93.2    
93.3    
93.4    
93.6    
93.7    
93.9    
94.0    
94.1    
94.3    
94.4    
94.5    
94.7    
94.8    
94.9    
95.1    
95.2    
95.4    
95.5    
95.6    
95.8    
95.9    
96.0    
96.2    
96.3    
96.4    
96.6    
96.7    
96.9    
97.0    
97.1    
97.3    
97.4    
97.5    
97.7    
97.8    
98.0    
98.1    
98.2    
98.4    
98.5    
98.6    
98.8    
98.9    
99.0    
99.2    
99.3    
99.5    
99.6    
99.7    
99.9    
-found 32 predictions from path traversal
Error with prediction: snap lend_intergenic: 5320, rend_intergenic: 5008  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 10084, rend_intergenic: 5567  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29684, rend_intergenic: 21745  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32151, rend_intergenic: 29860  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41833, rend_intergenic: 32366  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63689, rend_intergenic: 54721  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74824, rend_intergenic: 69476  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78573, rend_intergenic: 77941  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80168, rend_intergenic: 78804  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84779, rend_intergenic: 81375  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93189, rend_intergenic: 89451  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114776, rend_intergenic: 101075  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115967, rend_intergenic: 114779  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121311, rend_intergenic: 116052  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126534, rend_intergenic: 123043  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128637, rend_intergenic: 126624  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148322, rend_intergenic: 130936  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157082, rend_intergenic: 149499  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 16 predictions persist after filtering for low support