-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_22/scaffold_22_9604916-9807708

-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 Augustus_model.g34381.t1
Valid prediction for GeneMark_model.89039_t
Valid prediction for snap_scaffold_22-snap.2032-T1
Valid prediction for Augustus_model.g34388.t1
Valid prediction for snap_scaffold_22-snap.2015-T1
Valid prediction for snap_scaffold_22-snap.2013-T1
Valid prediction for GlimmerHMM_glimmerT_51277-T1
Valid prediction for Augustus_model.g34384.t1
Valid prediction for snap_scaffold_22-snap.2006-T1
Valid prediction for GeneMark_model.89042_t
Valid prediction for snap_scaffold_22-snap.2034-T1
Couldn't classify 113015, 113094
Couldn't classify 117905, 118015
Sorry, prediction pasa_asmbl_29602.p1 fails validation.
(GGT)	 CA	113015-113094	GT	AGG
(GAT)	 AG	113305-113464	GT	AGG
(GTG)	 AG	116249-116353	GT	TGG
(GAA)	 AG	116702-116893	GT	AGG
(GAG)	 AG	117047-117154	GT	AGG
(GCC)	 AG	117520-117672	GT	AGG
(GCT)	 AG	117905-118015	CT	GCC
-recovered pasa_asmbl_29602.p1, internal, 113305, 113464
-recovered pasa_asmbl_29602.p1, internal, 116249, 116353
-recovered pasa_asmbl_29602.p1, internal, 116702, 116893
-recovered pasa_asmbl_29602.p1, internal, 117047, 117154
-recovered pasa_asmbl_29602.p1, internal, 117520, 117672
Valid prediction for snap_scaffold_22-snap.2033-T1
Valid prediction for Augustus_model.g34391.t1
Couldn't classify 119925, 120053
Couldn't classify 121228, 121437
Sorry, prediction pasa_asmbl_29603.p1 fails validation.
(CAG)	 CC	119925-120053	GT	AGG
(GGG)	 AG	120222-120364	GT	AAG
(GGA)	 AG	120442-120608	GT	AGG
(CAG)	 AG	120709-120836	GT	AGG
(GCG)	 AG	121228-121437	GG	GTG
-recovered pasa_asmbl_29603.p1, internal, 120222, 120364
-recovered pasa_asmbl_29603.p1, internal, 120442, 120608
-recovered pasa_asmbl_29603.p1, internal, 120709, 120836
Valid prediction for GeneMark_model.89040_t
Valid prediction for Augustus_model.g34377.t1
Valid prediction for snap_scaffold_22-snap.2003-T1
Couldn't classify 33846, 34001
Sorry, prediction pasa_asmbl_29814.p1 fails validation.
(ATG)	 AC	29112-29291	GT	AGG
(CGA)	 AG	29622-29855	GT	GGG
(ATG)	 AG	30434-30508	GT	TGG
(ACA)	 AG	31367-31456	GT	AGG
(GAG)	 AG	31759-31902	GT	AGG
(GTG)	 AG	32358-32446	GT	GGG
(GTT)	 AG	32735-32831	GT	AGG
(GAC)	 AG	33846-34001	AT	AGA
-recovered pasa_asmbl_29814.p1, initial, 29112, 29291
-recovered pasa_asmbl_29814.p1, initial, 30434, 30508
-recovered pasa_asmbl_29814.p1, internal, 29622, 29855
-recovered pasa_asmbl_29814.p1, internal, 30434, 30508
-recovered pasa_asmbl_29814.p1, internal, 31367, 31456
-recovered pasa_asmbl_29814.p1, internal, 31759, 31902
-recovered pasa_asmbl_29814.p1, internal, 32358, 32446
-recovered pasa_asmbl_29814.p1, internal, 32735, 32831
Valid prediction for GlimmerHMM_glimmerT_51275-T1
Valid prediction for Augustus_model.g34393.t1
Couldn't classify 188717, 188767
Sorry, prediction GeneMark_model.89079_t fails validation.
(AGA)	 AG	188717-188767	GT	GAG
(AAA)	 AG	188789-188851	GT	GAG
(AGA)	 AG	188926-189066	GT	AGG
(GAC)	 AG	189846-189969	CT	AGC
add_exon() Sorry, GeneMark_model.89079_t 188926-189066-terminal-1 is invalid.
-recovered GeneMark_model.89079_t, terminal, 188926, 189066
-recovered GeneMark_model.89079_t, terminal, 189846, 189969
-recovered GeneMark_model.89079_t, internal, 188717, 188767
-recovered GeneMark_model.89079_t, internal, 188789, 188851
-recovered GeneMark_model.89079_t, internal, 188926, 189066
Valid prediction for snap_scaffold_22-snap.2045-T1
Valid prediction for GlimmerHMM_glimmerT_51282-T1
Valid prediction for GeneMark_model.89069_t
Valid prediction for GeneMark_model.89062_t
Valid prediction for snap_scaffold_22-snap.2044-T1
Couldn't classify 176685, 176885
Couldn't classify 177284, 177490
Sorry, prediction pasa_asmbl_29752.p1 fails validation.
(CAG)	 CC	176685-176885	GT	AGG
(GAT)	 AG	177284-177490	CA	GTC
Valid prediction for snap_scaffold_22-snap.2039-T1
Valid prediction for GlimmerHMM_glimmerT_51271-T1
Valid prediction for GlimmerHMM_glimmerT_51273-T1
Valid prediction for snap_scaffold_22-snap.2037-T1
Valid prediction for GeneMark_model.89067_t
Valid prediction for GeneMark_model.89060_t
Valid prediction for GeneMark_model.89053_t
Valid prediction for GlimmerHMM_glimmerT_51279-T1
Couldn't classify 110421, 110449
Couldn't classify 113016, 113058
Sorry, prediction pasa_asmbl_29598.p2 fails validation.
(GAG)	 CG	110421-110449	GT	AGG
(GAG)	 AG	111568-111766	GT	AGG
(GAT)	 AG	112102-112304	GT	AGG
(GTT)	 AG	113016-113058	GG	GAG
-recovered pasa_asmbl_29598.p2, internal, 111568, 111766
-recovered pasa_asmbl_29598.p2, internal, 112102, 112304
Valid prediction for GeneMark_model.89051_t
Valid prediction for snap_scaffold_22-snap.2042-T1
Valid prediction for snap_scaffold_22-snap.2022-T1
Valid prediction for snap_scaffold_22-snap.2024-T1
Valid prediction for GeneMark_model.89058_t
Valid prediction for GlimmerHMM_glimmerT_51267-T1
Couldn't classify 179108, 179149
Sorry, prediction GeneMark_model.89078_t fails validation.
(ATG)	 GG	176748-176885	GT	AGG
(GAT)	 AG	177284-177488	GT	AGG
(TCT)	 AG	178544-178556	GT	AGG
(GGA)	 AG	179108-179149	GC	AGG
-recovered GeneMark_model.89078_t, initial, 176748, 176885
-recovered GeneMark_model.89078_t, internal, 177284, 177488
-recovered GeneMark_model.89078_t, internal, 178544, 178556
-recovered GeneMark_model.89078_t, internal, 179108, 179149
Valid prediction for GlimmerHMM_glimmerT_51281-T1
Valid prediction for snap_scaffold_22-snap.2002-T1
Valid prediction for Augustus_model.g34387.t1
Valid prediction for GeneMark_model.89077_t
Valid prediction for GeneMark_model.89036_t
Valid prediction for snap_scaffold_22-snap.2027-T1
Valid prediction for GeneMark_model.89045_t
Valid prediction for GeneMark_model.89074_t
Valid prediction for snap_scaffold_22-snap.2021-T1
Valid prediction for GeneMark_model.89061_t
Valid prediction for snap_scaffold_22-snap.2018-T1
Valid prediction for snap_scaffold_22-snap.2040-T1
Valid prediction for snap_scaffold_22-snap.2007-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for Augustus_model.g34392.t1
Valid prediction for GeneMark_model.89047_t
Valid prediction for snap_scaffold_22-snap.2008-T1
Valid prediction for GeneMark_model.89071_t
Valid prediction for GlimmerHMM_glimmerT_51276-T1
Valid prediction for GeneMark_model.89055_t
Valid prediction for snap_scaffold_22-snap.2029-T1
Valid prediction for GeneMark_model.89065_t
Valid prediction for snap_scaffold_22-snap.2036-T1
Valid prediction for GeneMark_model.89081_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.89056_t
Valid prediction for Augustus_model.g34385.t1
Valid prediction for GeneMark_model.89073_t
Valid prediction for GlimmerHMM_glimmerT_51270-T1
Valid prediction for snap_scaffold_22-snap.2005-T1
Valid prediction for snap_scaffold_22-snap.2026-T1
Valid prediction for GeneMark_model.89041_t
Valid prediction for Augustus_model.g34378.t1
Valid prediction for GeneMark_model.89046_t
Valid prediction for GlimmerHMM_glimmerT_51263-T1
Valid prediction for Augustus_model.g34376.t1
Valid prediction for GeneMark_model.89064_t
Valid prediction for GeneMark_model.89037_t
Valid prediction for snap_scaffold_22-snap.2043-T1
Valid prediction for snap_scaffold_22-snap.2041-T1
Valid prediction for GeneMark_model.89059_t
Valid prediction for snap_scaffold_22-snap.2016-T1
Valid prediction for GeneMark_model.89049_t
Valid prediction for GeneMark_model.89080_t
Valid prediction for snap_scaffold_22-snap.2012-T1
Valid prediction for GeneMark_model.89075_t
Valid prediction for snap_scaffold_22-snap.2028-T1
Valid prediction for CodingQuarry_transcript_34204-T1
Valid prediction for GeneMark_model.89048_t
Valid prediction for GeneMark_model.89068_t
Valid prediction for snap_scaffold_22-snap.2038-T1
Valid prediction for GeneMark_model.89063_t
Valid prediction for GeneMark_model.89054_t
Valid prediction for GlimmerHMM_glimmerT_51265-T1
Valid prediction for GlimmerHMM_glimmerT_51266-T1
Valid prediction for HiQ_model.g34375.t1
Valid prediction for GlimmerHMM_glimmerT_51269-T1
Valid prediction for Augustus_model.g34390.t1
Valid prediction for snap_scaffold_22-snap.2023-T1
Valid prediction for GlimmerHMM_glimmerT_51278-T1
Valid prediction for GeneMark_model.89044_t
Valid prediction for GlimmerHMM_glimmerT_51268-T1
Valid prediction for snap_scaffold_22-snap.2019-T1
Valid prediction for GeneMark_model.89038_t
Valid prediction for pasa_asmbl_30320.p1
Valid prediction for Augustus_model.g34382.t1
Valid prediction for snap_scaffold_22-snap.2025-T1
Valid prediction for GeneMark_model.89057_t
Valid prediction for snap_scaffold_22-snap.2035-T1
Valid prediction for Augustus_model.g34389.t1
Valid prediction for GlimmerHMM_glimmerT_51274-T1
Valid prediction for Augustus_model.g34383.t1
Valid prediction for GlimmerHMM_glimmerT_51280-T1
Valid prediction for pasa_asmbl_30325.p1
Valid prediction for snap_scaffold_22-snap.2031-T1
Valid prediction for snap_scaffold_22-snap.2017-T1
Valid prediction for snap_scaffold_22-snap.2001-T1
Valid prediction for GeneMark_model.89070_t
Valid prediction for snap_scaffold_22-snap.2009-T1
Valid prediction for Augustus_model.g34374.t1
Valid prediction for GeneMark_model.89052_t
Valid prediction for Augustus_model.g34379.t1
Valid prediction for GeneMark_model.89082_t
Valid prediction for GeneMark_model.89043_t
Valid prediction for Augustus_model.g34386.t1
Valid prediction for GeneMark_model.89072_t
Valid prediction for snap_scaffold_22-snap.2030-T1
Valid prediction for Augustus_model.g34380.t1
Valid prediction for GeneMark_model.89050_t
Valid prediction for snap_scaffold_22-snap.2004-T1
Valid prediction for snap_scaffold_22-snap.2011-T1
Valid prediction for GeneMark_model.89035_t
Valid prediction for snap_scaffold_22-snap.2020-T1
Valid prediction for GeneMark_model.89076_t
Valid prediction for snap_scaffold_22-snap.2046-T1
Valid prediction for GlimmerHMM_glimmerT_51272-T1
Valid prediction for snap_scaffold_22-snap.2014-T1
Valid prediction for GlimmerHMM_glimmerT_51264-T1
Valid prediction for GeneMark_model.89066_t
Valid prediction for snap_scaffold_22-snap.2010-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 27120, rend_intergenic: 21630  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42122, rend_intergenic: 29630  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58108, rend_intergenic: 55281  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64505, rend_intergenic: 62302  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81763, rend_intergenic: 77348  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95568, rend_intergenic: 83264  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100289, rend_intergenic: 95704  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115092, rend_intergenic: 106000  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120167, rend_intergenic: 115576  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125147, rend_intergenic: 120591  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133471, rend_intergenic: 127653  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139421, rend_intergenic: 133516  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155177, rend_intergenic: 141755  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158404, rend_intergenic: 155204  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 165024, rend_intergenic: 161692  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170689, rend_intergenic: 170049  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 190332, rend_intergenic: 170897  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 199931, rend_intergenic: 194151  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 202793
-exon list size: 870


building trellis

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58.5    
58.6    
58.7    
58.8    
58.9    
59.1    
59.2    
59.3    
59.4    
59.5    
59.6    
59.7    
59.9    
60.0    
60.1    
60.2    
60.3    
60.4    
60.6    
60.7    
60.8    
60.9    
61.0    
61.1    
61.2    
61.4    
61.5    
61.6    
61.7    
61.8    
61.9    
62.0    
62.2    
62.3    
62.4    
62.5    
62.6    
62.7    
62.8    
63.0    
63.1    
63.2    
63.3    
63.4    
63.5    
63.6    
63.8    
63.9    
64.0    
64.1    
64.2    
64.3    
64.4    
64.6    
64.7    
64.8    
64.9    
65.0    
65.1    
65.3    
65.4    
65.5    
65.6    
65.7    
65.8    
65.9    
66.1    
66.2    
66.3    
66.4    
66.5    
66.6    
66.7    
66.9    
67.0    
67.1    
67.2    
67.3    
67.4    
67.5    
67.7    
67.8    
67.9    
68.0    
68.1    
68.2    
68.3    
68.5    
68.6    
68.7    
68.8    
68.9    
69.0    
69.2    
69.3    
69.4    
69.5    
69.6    
69.7    
69.8    
70.0    
70.1    
70.2    
70.3    
70.4    
70.5    
70.6    
70.8    
70.9    
71.0    
71.1    
71.2    
71.3    
71.4    
71.6    
71.7    
71.8    
71.9    
72.0    
72.1    
72.2    
72.4    
72.5    
72.6    
72.7    
72.8    
72.9    
73.1    
73.2    
73.3    
73.4    
73.5    
73.6    
73.7    
73.9    
74.0    
74.1    
74.2    
74.3    
74.4    
74.5    
74.7    
74.8    
74.9    
75.0    
75.1    
75.2    
75.3    
75.5    
75.6    
75.7    
75.8    
75.9    
76.0    
76.1    
76.3    
76.4    
76.5    
76.6    
76.7    
76.8    
76.9    
77.1    
77.2    
77.3    
77.4    
77.5    
77.6    
77.8    
77.9    
78.0    
78.1    
78.2    
78.3    
78.4    
78.6    
78.7    
78.8    
78.9    
79.0    
79.1    
79.2    
79.4    
79.5    
79.6    
79.7    
79.8    
79.9    
80.0    
80.2    
80.3    
80.4    
80.5    
80.6    
80.7    
80.8    
81.0    
81.1    
81.2    
81.3    
81.4    
81.5    
81.7    
81.8    
81.9    
82.0    
82.1    
82.2    
82.3    
82.5    
82.6    
82.7    
82.8    
82.9    
83.0    
83.1    
83.3    
83.4    
83.5    
83.6    
83.7    
83.8    
83.9    
84.1    
84.2    
84.3    
84.4    
84.5    
84.6    
84.7    
84.9    
85.0    
85.1    
85.2    
85.3    
85.4    
85.6    
85.7    
85.8    
85.9    
86.0    
86.1    
86.2    
86.4    
86.5    
86.6    
86.7    
86.8    
86.9    
87.0    
87.2    
87.3    
87.4    
87.5    
87.6    
87.7    
87.8    
88.0    
88.1    
88.2    
88.3    
88.4    
88.5    
88.6    
88.8    
88.9    
89.0    
89.1    
89.2    
89.3    
89.4    
89.6    
89.7    
89.8    
89.9    
90.0    
90.1    
90.3    
90.4    
90.5    
90.6    
90.7    
90.8    
90.9    
91.1    
91.2    
91.3    
91.4    
91.5    
91.6    
91.7    
91.9    
92.0    
92.1    
92.2    
92.3    
92.4    
92.5    
92.7    
92.8    
92.9    
93.0    
93.1    
93.2    
93.3    
93.5    
93.6    
93.7    
93.8    
93.9    
94.0    
94.2    
94.3    
94.4    
94.5    
94.6    
94.7    
94.8    
95.0    
95.1    
95.2    
95.3    
95.4    
95.5    
95.6    
95.8    
95.9    
96.0    
96.1    
96.2    
96.3    
96.4    
96.6    
96.7    
96.8    
96.9    
97.0    
97.1    
97.2    
97.4    
97.5    
97.6    
97.7    
97.8    
97.9    
98.1    
98.2    
98.3    
98.4    
98.5    
98.6    
98.7    
98.9    
99.0    
99.1    
99.2    
99.3    
99.4    
99.5    
99.7    
99.8    
99.9    
-found 29 predictions from path traversal
Error with prediction: snap lend_intergenic: 27120, rend_intergenic: 21630  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42122, rend_intergenic: 29630  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58108, rend_intergenic: 55281  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64505, rend_intergenic: 62302  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81763, rend_intergenic: 77348  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95568, rend_intergenic: 83264  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100289, rend_intergenic: 95704  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115092, rend_intergenic: 106000  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120167, rend_intergenic: 115576  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125147, rend_intergenic: 120591  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133471, rend_intergenic: 127653  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139421, rend_intergenic: 133516  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155177, rend_intergenic: 141755  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158404, rend_intergenic: 155204  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 165024, rend_intergenic: 161692  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170689, rend_intergenic: 170049  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 190332, rend_intergenic: 170897  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 199931, rend_intergenic: 194151  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 25 predictions persist after filtering for low support