-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_4/scaffold_4_15915479-16137971

-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.17949_t
Valid prediction for GeneMark_model.18005_t
Valid prediction for GeneMark_model.17977_t
Valid prediction for GeneMark_model.18000_t
Valid prediction for snap_scaffold_4-snap.3226-T1
Valid prediction for GlimmerHMM_glimmerT_11041-T1
Valid prediction for GlimmerHMM_glimmerT_11030-T1
Valid prediction for GlimmerHMM_glimmerT_11035-T1
Valid prediction for GlimmerHMM_glimmerT_11051-T1
Valid prediction for GeneMark_model.18003_t
Valid prediction for snap_scaffold_4-snap.3231-T1
Valid prediction for GeneMark_model.17972_t
Valid prediction for GeneMark_model.17988_t
Valid prediction for Augustus_model.g7298.t1
Valid prediction for snap_scaffold_4-snap.3248-T1
Valid prediction for GlimmerHMM_glimmerT_11033-T1
Valid prediction for snap_scaffold_4-snap.3221-T1
Valid prediction for snap_scaffold_4-snap.3234-T1
Valid prediction for GeneMark_model.17938_t
Valid prediction for GeneMark_model.17969_t
Valid prediction for GlimmerHMM_glimmerT_11050-T1
Valid prediction for GeneMark_model.17979_t
Valid prediction for GlimmerHMM_glimmerT_11047-T1
Valid prediction for GlimmerHMM_glimmerT_11038-T1
Valid prediction for GeneMark_model.17960_t
Valid prediction for snap_scaffold_4-snap.3250-T1
Valid prediction for GeneMark_model.17950_t
Valid prediction for GeneMark_model.17987_t
Valid prediction for GeneMark_model.17946_t
Valid prediction for snap_scaffold_4-snap.3240-T1
Valid prediction for GeneMark_model.17945_t
Valid prediction for GlimmerHMM_glimmerT_11048-T1
Valid prediction for snap_scaffold_4-snap.3236-T1
Valid prediction for snap_scaffold_4-snap.3247-T1
Valid prediction for snap_scaffold_4-snap.3225-T1
Valid prediction for GeneMark_model.17982_t
Valid prediction for GeneMark_model.17962_t
Valid prediction for GeneMark_model.18002_t
Valid prediction for GlimmerHMM_glimmerT_11028-T1
Valid prediction for GeneMark_model.17984_t
Valid prediction for GeneMark_model.17961_t
Valid prediction for Augustus_model.g7292.t1
Valid prediction for GeneMark_model.17936_t
Couldn't classify 5853, 6054
Couldn't classify 6754, 6795
Sorry, prediction pasa_asmbl_43291.p1 fails validation.
(GAA)	 TG	5853-6054	GT	TGG
(AGC)	 AG	6247-6410	GT	CTG
(GAG)	 AG	6754-6795	AA	GGA
-recovered pasa_asmbl_43291.p1, internal, 6247, 6410
Valid prediction for GeneMark_model.17966_t
Valid prediction for GeneMark_model.17980_t
Valid prediction for GeneMark_model.17954_t
Valid prediction for snap_scaffold_4-snap.3244-T1
Valid prediction for snap_scaffold_4-snap.3220-T1
Valid prediction for GlimmerHMM_glimmerT_11049-T1
Valid prediction for GeneMark_model.17998_t
Valid prediction for snap_scaffold_4-snap.3222-T1
Valid prediction for snap_scaffold_4-snap.3235-T1
Valid prediction for Augustus_model.g7299.t1
Valid prediction for GeneMark_model.17999_t
Valid prediction for snap_scaffold_4-snap.3238-T1
Valid prediction for GlimmerHMM_glimmerT_11043-T1
Valid prediction for snap_scaffold_4-snap.3228-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GeneMark_model.17935_t
Valid prediction for GeneMark_model.17942_t
Valid prediction for snap_scaffold_4-snap.3216-T1
Valid prediction for GeneMark_model.17948_t
Valid prediction for GeneMark_model.17940_t
Valid prediction for GeneMark_model.17956_t
Valid prediction for Augustus_model.g7295.t1
Valid prediction for GeneMark_model.17993_t
Valid prediction for snap_scaffold_4-snap.3243-T1
Valid prediction for GeneMark_model.18006_t
Valid prediction for GeneMark_model.17974_t
Valid prediction for GeneMark_model.17934_t
Valid prediction for GeneMark_model.17994_t
Valid prediction for GeneMark_model.17986_t
Valid prediction for GeneMark_model.17992_t
Valid prediction for snap_scaffold_4-snap.3232-T1
Valid prediction for GeneMark_model.17958_t
Valid prediction for GlimmerHMM_glimmerT_11026-T1
Valid prediction for GlimmerHMM_glimmerT_11039-T1
Valid prediction for snap_scaffold_4-snap.3218-T1
Valid prediction for snap_scaffold_4-snap.3242-T1
Valid prediction for snap_scaffold_4-snap.3219-T1
Valid prediction for GeneMark_model.17952_t
Valid prediction for GeneMark_model.17968_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.17976_t
Valid prediction for GeneMark_model.17991_t
Valid prediction for snap_scaffold_4-snap.3241-T1
Valid prediction for snap_scaffold_4-snap.3254-T1
Valid prediction for snap_scaffold_4-snap.3217-T1
Valid prediction for snap_scaffold_4-snap.3246-T1
Valid prediction for pasa_asmbl_41890.p1
Valid prediction for snap_scaffold_4-snap.3233-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GeneMark_model.17989_t
Valid prediction for GeneMark_model.17951_t
Valid prediction for GeneMark_model.17955_t
Valid prediction for Augustus_model.g7302.t1
Valid prediction for GeneMark_model.17953_t
Valid prediction for snap_scaffold_4-snap.3251-T1
Valid prediction for GeneMark_model.17995_t
Valid prediction for GeneMark_model.17981_t
Valid prediction for GlimmerHMM_glimmerT_11027-T1
Valid prediction for GlimmerHMM_glimmerT_11040-T1
Valid prediction for CodingQuarry_transcript_49165-T1
Valid prediction for GeneMark_model.17978_t
Valid prediction for snap_scaffold_4-snap.3253-T1
Valid prediction for GeneMark_model.17985_t
Couldn't classify 198331, 198420
Couldn't classify 200275, 200288
Sorry, prediction pasa_asmbl_41880.p1 fails validation.
(GAT)	 CT	198331-198420	GT	AGG
(AGG)	 AG	198932-199114	GT	AGG
(GTG)	 AG	199395-199527	GT	GGG
(AGC)	 AG	199665-199855	GT	AGG
(ATG)	 AG	200026-200164	GT	CGG
(AGG)	 AG	200275-200288	AG	CCA
-recovered pasa_asmbl_41880.p1, initial, 200026, 200164
-recovered pasa_asmbl_41880.p1, internal, 198932, 199114
-recovered pasa_asmbl_41880.p1, internal, 199395, 199527
-recovered pasa_asmbl_41880.p1, internal, 199665, 199855
-recovered pasa_asmbl_41880.p1, internal, 200026, 200164
Valid prediction for GlimmerHMM_glimmerT_11042-T1
Valid prediction for Augustus_model.g7300.t1
Valid prediction for GeneMark_model.18007_t
Valid prediction for HiQ_model.g7306.t1
Valid prediction for GeneMark_model.17941_t
Valid prediction for GeneMark_model.17944_t
Valid prediction for Augustus_model.g7303.t1
Valid prediction for GeneMark_model.17963_t
Valid prediction for snap_scaffold_4-snap.3252-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for Augustus_model.g7296.t1
Valid prediction for GeneMark_model.17970_t
Valid prediction for GlimmerHMM_glimmerT_11044-T1
Valid prediction for GeneMark_model.17983_t
Couldn't classify 9945, 10300
Sorry, prediction pasa_asmbl_41888.p2 fails validation.
(CAC)	 AG	9945-10300	GT	AGG
(GTC)	 AG	10628-10634	TC	GAT
-recovered pasa_asmbl_41888.p2, terminal, 10628, 10634
-recovered pasa_asmbl_41888.p2, internal, 9945, 10300
Valid prediction for snap_scaffold_4-snap.3224-T1
Valid prediction for snap_scaffold_4-snap.3245-T1
Valid prediction for Augustus_model.g7297.t1
Valid prediction for GeneMark_model.17957_t
Valid prediction for GeneMark_model.18001_t
Valid prediction for GlimmerHMM_glimmerT_11052-T1
Valid prediction for GlimmerHMM_glimmerT_11053-T1
Valid prediction for GeneMark_model.17965_t
Valid prediction for GlimmerHMM_glimmerT_11025-T1
Valid prediction for GlimmerHMM_glimmerT_11045-T1
Valid prediction for GeneMark_model.17967_t
Valid prediction for GeneMark_model.17997_t
Valid prediction for GeneMark_model.17990_t
Valid prediction for GlimmerHMM_glimmerT_11037-T1
Couldn't classify 203737, 203977
Sorry, prediction pasa_asmbl_41878.p1 fails validation.
(CAC)	 CC	203737-203977	GT	TGG
(GGC)	 AG	204089-204360	GT	AGG
(GTG)	 AG	204487-204644	GT	AAG
(AGT)	 AG	204926-205077	GT	AGG
(ATC)	 AG	205491-205625	GT	AGG
(CGC)	 AG	205750-205908	GT	AGG
(CCC)	 AG	208025-208311	GG	GAG
-recovered pasa_asmbl_41878.p1, terminal, 208025, 208311
-recovered pasa_asmbl_41878.p1, internal, 204089, 204360
-recovered pasa_asmbl_41878.p1, internal, 204487, 204644
-recovered pasa_asmbl_41878.p1, internal, 204926, 205077
-recovered pasa_asmbl_41878.p1, internal, 205491, 205625
-recovered pasa_asmbl_41878.p1, internal, 205750, 205908
Valid prediction for GlimmerHMM_glimmerT_11036-T1
Valid prediction for CodingQuarry_transcript_49164-T1
Valid prediction for GeneMark_model.17973_t
Valid prediction for snap_scaffold_4-snap.3227-T1
Valid prediction for GlimmerHMM_glimmerT_11031-T1
Valid prediction for GlimmerHMM_glimmerT_11032-T1
Valid prediction for Augustus_model.g7294.t1
Valid prediction for GeneMark_model.17933_t
Valid prediction for Augustus_model.g7301.t1
Valid prediction for snap_scaffold_4-snap.3229-T1
Valid prediction for GlimmerHMM_glimmerT_11034-T1
Valid prediction for GeneMark_model.17937_t
Valid prediction for GeneMark_model.17939_t
Valid prediction for snap_scaffold_4-snap.3230-T1
Valid prediction for snap_scaffold_4-snap.3215-T1
Valid prediction for Augustus_model.g7305.t1
Valid prediction for Augustus_model.g7293.t1
Valid prediction for GeneMark_model.17943_t
Valid prediction for Augustus_model.g7304.t1
Valid prediction for snap_scaffold_4-snap.3237-T1
Valid prediction for GeneMark_model.17975_t
Valid prediction for GeneMark_model.17959_t
Valid prediction for snap_scaffold_4-snap.3223-T1
Valid prediction for GeneMark_model.17971_t
Couldn't classify 200801, 201569
Couldn't classify 203143, 203164
Sorry, prediction pasa_asmbl_41879.p1 fails validation.
(GGC)	 CG	200801-201569	GT	AGG
(TGC)	 AG	201942-202081	GT	AGG
(CTC)	 AG	202172-202329	GT	AGG
(GAT)	 AG	203143-203164	CC	CGC
-recovered pasa_asmbl_41879.p1, internal, 201942, 202081
-recovered pasa_asmbl_41879.p1, internal, 202172, 202329
Valid prediction for GlimmerHMM_glimmerT_11054-T1
Valid prediction for snap_scaffold_4-snap.3239-T1
Valid prediction for GlimmerHMM_glimmerT_11046-T1
Valid prediction for GeneMark_model.17996_t
Valid prediction for snap_scaffold_4-snap.3249-T1
Valid prediction for GlimmerHMM_glimmerT_11029-T1
Valid prediction for GeneMark_model.17947_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 25785, rend_intergenic: 14624  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43390, rend_intergenic: 40254  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47721, rend_intergenic: 45609  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65860, rend_intergenic: 61386  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78117, rend_intergenic: 65860  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85215, rend_intergenic: 78966  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93232, rend_intergenic: 85935  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98742, rend_intergenic: 93344  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114030, rend_intergenic: 98994  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122493, rend_intergenic: 119584  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125009, rend_intergenic: 123049  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142916, rend_intergenic: 136008  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161045, rend_intergenic: 143034  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167622, rend_intergenic: 161587  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 183699, rend_intergenic: 175625  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 187805, rend_intergenic: 186487  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 195060, rend_intergenic: 191065  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 222493
-exon list size: 916


building trellis

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59.3    
59.4    
59.5    
59.6    
59.7    
59.8    
59.9    
60.0    
60.1    
60.2    
60.3    
60.5    
60.6    
60.7    
60.8    
60.9    
61.0    
61.1    
61.2    
61.3    
61.4    
61.5    
61.7    
61.8    
61.9    
62.0    
62.1    
62.2    
62.3    
62.4    
62.5    
62.6    
62.7    
62.9    
63.0    
63.1    
63.2    
63.3    
63.4    
63.5    
63.6    
63.7    
63.8    
63.9    
64.1    
64.2    
64.3    
64.4    
64.5    
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    
66.0    
66.1    
66.2    
66.3    
66.4    
66.6    
66.7    
66.8    
66.9    
67.0    
67.1    
67.2    
67.3    
67.4    
67.5    
67.6    
67.8    
67.9    
68.0    
68.1    
68.2    
68.3    
68.4    
68.5    
68.6    
68.7    
68.8    
69.0    
69.1    
69.2    
69.3    
69.4    
69.5    
69.6    
69.7    
69.8    
69.9    
70.0    
70.2    
70.3    
70.4    
70.5    
70.6    
70.7    
70.8    
70.9    
71.0    
71.1    
71.2    
71.4    
71.5    
71.6    
71.7    
71.8    
71.9    
72.0    
72.1    
72.2    
72.3    
72.4    
72.5    
72.7    
72.8    
72.9    
73.0    
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    
74.6    
74.7    
74.8    
74.9    
75.1    
75.2    
75.3    
75.4    
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    
77.0    
77.1    
77.2    
77.3    
77.5    
77.6    
77.7    
77.8    
77.9    
78.0    
78.1    
78.2    
78.3    
78.4    
78.5    
78.6    
78.8    
78.9    
79.0    
79.1    
79.2    
79.3    
79.4    
79.5    
79.6    
79.7    
79.8    
80.0    
80.1    
80.2    
80.3    
80.4    
80.5    
80.6    
80.7    
80.8    
80.9    
81.0    
81.2    
81.3    
81.4    
81.5    
81.6    
81.7    
81.8    
81.9    
82.0    
82.1    
82.2    
82.4    
82.5    
82.6    
82.7    
82.8    
82.9    
83.0    
83.1    
83.2    
83.3    
83.4    
83.6    
83.7    
83.8    
83.9    
84.0    
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    
85.5    
85.6    
85.7    
85.8    
85.9    
86.1    
86.2    
86.3    
86.4    
86.5    
86.6    
86.7    
86.8    
86.9    
87.0    
87.1    
87.3    
87.4    
87.5    
87.6    
87.7    
87.8    
87.9    
88.0    
88.1    
88.2    
88.3    
88.5    
88.6    
88.7    
88.8    
88.9    
89.0    
89.1    
89.2    
89.3    
89.4    
89.5    
89.7    
89.8    
89.9    
90.0    
90.1    
90.2    
90.3    
90.4    
90.5    
90.6    
90.7    
90.8    
91.0    
91.1    
91.2    
91.3    
91.4    
91.5    
91.6    
91.7    
91.8    
91.9    
92.0    
92.2    
92.3    
92.4    
92.5    
92.6    
92.7    
92.8    
92.9    
93.0    
93.1    
93.2    
93.4    
93.5    
93.6    
93.7    
93.8    
93.9    
94.0    
94.1    
94.2    
94.3    
94.4    
94.6    
94.7    
94.8    
94.9    
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    
96.5    
96.6    
96.7    
96.8    
96.9    
97.1    
97.2    
97.3    
97.4    
97.5    
97.6    
97.7    
97.8    
97.9    
98.0    
98.1    
98.3    
98.4    
98.5    
98.6    
98.7    
98.8    
98.9    
99.0    
99.1    
99.2    
99.3    
99.5    
99.6    
99.7    
99.8    
99.9    
-found 50 predictions from path traversal
Error with prediction: snap lend_intergenic: 25785, rend_intergenic: 14624  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43390, rend_intergenic: 40254  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47721, rend_intergenic: 45609  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65860, rend_intergenic: 61386  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78117, rend_intergenic: 65860  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85215, rend_intergenic: 78966  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93232, rend_intergenic: 85935  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98742, rend_intergenic: 93344  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114030, rend_intergenic: 98994  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122493, rend_intergenic: 119584  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125009, rend_intergenic: 123049  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142916, rend_intergenic: 136008  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161045, rend_intergenic: 143034  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167622, rend_intergenic: 161587  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 183699, rend_intergenic: 175625  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 187805, rend_intergenic: 186487  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 195060, rend_intergenic: 191065  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 18 predictions persist after filtering for low support