-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_14/scaffold_14_11738944-11910609

-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.60872_t
Valid prediction for GeneMark_model.60866_t
Valid prediction for GeneMark_model.60876_t
Valid prediction for GeneMark_model.60885_t
Valid prediction for GeneMark_model.60862_t
Valid prediction for GlimmerHMM_glimmerT_35513-T1
Valid prediction for Augustus_model.g23910.t1
Valid prediction for GlimmerHMM_glimmerT_35503-T1
Valid prediction for GlimmerHMM_glimmerT_35489-T1
Valid prediction for GlimmerHMM_glimmerT_35515-T1
Valid prediction for GeneMark_model.60874_t
Valid prediction for GeneMark_model.60869_t
Valid prediction for GeneMark_model.60871_t
Valid prediction for GlimmerHMM_glimmerT_35507-T1
Valid prediction for GeneMark_model.60877_t
Valid prediction for snap_scaffold_14-snap.2415-T1
Valid prediction for Augustus_model.g23906.t1
Valid prediction for Augustus_model.g23903.t1
Couldn't classify 161413, 161547
Couldn't classify 164378, 164417
Sorry, prediction pasa_asmbl_12666.p1 fails validation.
(AGT)	 AC	161413-161547	GT	AGG
(GAG)	 AG	161746-161912	GT	AGG
(GTA)	 AG	164378-164417	CT	ACC
-recovered pasa_asmbl_12666.p1, internal, 161746, 161912
Valid prediction for snap_scaffold_14-snap.2422-T1
Valid prediction for CodingQuarry_transcript_15813-T1
Valid prediction for GlimmerHMM_glimmerT_35517-T1
Valid prediction for GlimmerHMM_glimmerT_35518-T1
Valid prediction for snap_scaffold_14-snap.2429-T1
Valid prediction for snap_scaffold_14-snap.2405-T1
Valid prediction for GeneMark_model.60905_t
Valid prediction for GlimmerHMM_glimmerT_35511-T1
Valid prediction for GlimmerHMM_glimmerT_35521-T1
Valid prediction for GlimmerHMM_glimmerT_35520-T1
Valid prediction for GeneMark_model.60900_t
Valid prediction for snap_scaffold_14-snap.2438-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_35491-T1
Valid prediction for GeneMark_model.60889_t
Valid prediction for Augustus_model.g23899.t1
Valid prediction for snap_scaffold_14-snap.2444-T1
Valid prediction for snap_scaffold_14-snap.2410-T1
Valid prediction for GeneMark_model.60897_t
Valid prediction for Augustus_model.g23909.t1
Couldn't classify 148842, 148910
Couldn't classify 150218, 150328
Sorry, prediction pasa_asmbl_12689.p1 fails validation.
(CTG)	 TA	148842-148910	GT	AGG
(TCG)	 AG	149899-150015	GT	TGG
(GGC)	 AG	150218-150328	CT	CCC
-recovered pasa_asmbl_12689.p1, internal, 149899, 150015
Valid prediction for GeneMark_model.60892_t
Valid prediction for snap_scaffold_14-snap.2407-T1
Valid prediction for snap_scaffold_14-snap.2412-T1
Valid prediction for GlimmerHMM_glimmerT_35497-T1
Valid prediction for GeneMark_model.60864_t
Valid prediction for GlimmerHMM_glimmerT_35494-T1
Valid prediction for GeneMark_model.60860_t
Valid prediction for GeneMark_model.60867_t
Valid prediction for snap_scaffold_14-snap.2434-T1
Valid prediction for GeneMark_model.60883_t
Valid prediction for Augustus_model.g23892.t1
Valid prediction for HiQ_model.g23894.t1
Valid prediction for GeneMark_model.60890_t
Valid prediction for snap_scaffold_14-snap.2427-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GeneMark_model.60895_t
Valid prediction for Augustus_model.g23904.t1
Valid prediction for HiQ_model.g23897.t1
Valid prediction for GeneMark_model.60893_t
Valid prediction for GeneMark_model.60898_t
Valid prediction for GeneMark_model.60881_t
Valid prediction for snap_scaffold_14-snap.2426-T1
Couldn't classify 37301, 37343
Sorry, prediction pasa_asmbl_12385.p1 fails validation.
(AAA)	 TC	37301-37343	GT	GGG
(TAC)	 AG	37730-37899	GT	AGG
(GAG)	 AG	38040-38204	GT	AGG
(GTG)	 AG	38302-38446	GT	AGG
(GGG)	 AG	38605-38879	GG	AAG
add_exon() Sorry, pasa_asmbl_12385.p1 38302-38446-terminal-3 is invalid.
-recovered pasa_asmbl_12385.p1, terminal, 38302, 38446
-recovered pasa_asmbl_12385.p1, terminal, 38605, 38879
-recovered pasa_asmbl_12385.p1, internal, 37730, 37899
-recovered pasa_asmbl_12385.p1, internal, 38040, 38204
-recovered pasa_asmbl_12385.p1, internal, 38302, 38446
Valid prediction for snap_scaffold_14-snap.2442-T1
Valid prediction for GeneMark_model.60887_t
Valid prediction for GlimmerHMM_glimmerT_35499-T1
Valid prediction for snap_scaffold_14-snap.2413-T1
Valid prediction for GeneMark_model.60902_t
Valid prediction for snap_scaffold_14-snap.2432-T1
Valid prediction for HiQ_model.g23889.t1
Valid prediction for GlimmerHMM_glimmerT_35505-T1
Couldn't classify 16087, 16248
Sorry, prediction pasa_asmbl_12383.p1 fails validation.
(ATG)	 GA	14714-14762	GT	AGG
(CCC)	 AG	15097-15268	GT	GAG
(TGA)	 AG	15392-15554	GT	ACG
(AAA)	 AG	16087-16248	GC	CTG
-recovered pasa_asmbl_12383.p1, initial, 14714, 14762
-recovered pasa_asmbl_12383.p1, internal, 15097, 15268
-recovered pasa_asmbl_12383.p1, internal, 15392, 15554
-recovered pasa_asmbl_12383.p1, internal, 16087, 16248
Valid prediction for snap_scaffold_14-snap.2420-T1
Valid prediction for Augustus_model.g23887.t1
Valid prediction for Augustus_model.g23895.t1
Valid prediction for GeneMark_model.60909_t
Valid prediction for Augustus_model.g23907.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.60896_t
Valid prediction for pasa_asmbl_13516.p1
Valid prediction for GeneMark_model.60861_t
Valid prediction for GlimmerHMM_glimmerT_35500-T1
Valid prediction for snap_scaffold_14-snap.2424-T1
Valid prediction for Augustus_model.g23898.t1
Valid prediction for snap_scaffold_14-snap.2431-T1
Valid prediction for HiQ_model.g23890.t1
Valid prediction for snap_scaffold_14-snap.2439-T1
Valid prediction for snap_scaffold_14-snap.2419-T1
Valid prediction for snap_scaffold_14-snap.2437-T1
Valid prediction for snap_scaffold_14-snap.2436-T1
Valid prediction for GeneMark_model.60903_t
Valid prediction for GeneMark_model.60879_t
Valid prediction for snap_scaffold_14-snap.2441-T1
Valid prediction for snap_scaffold_14-snap.2417-T1
Valid prediction for snap_scaffold_14-snap.2408-T1
Valid prediction for GeneMark_model.60868_t
Valid prediction for GeneMark_model.60880_t
Valid prediction for Augustus_model.g23908.t1
Valid prediction for GlimmerHMM_glimmerT_35495-T1
Valid prediction for GlimmerHMM_glimmerT_35501-T1
Valid prediction for GlimmerHMM_glimmerT_35493-T1
Valid prediction for GeneMark_model.60886_t
Valid prediction for CodingQuarry_transcript_15818-T1
Valid prediction for GlimmerHMM_glimmerT_35509-T1
Couldn't classify 134618, 134815
Sorry, prediction pasa_asmbl_13519.p1 fails validation.
(CGT)	 TG	134618-134815	GT	AGG
(TGC)	 AG	135180-135304	GT	AAG
(GGA)	 AG	135402-135501	GT	TGG
(GAA)	 AG	135739-135792	GT	AGG
(ATT)	 AG	135877-136005	GT	ATG
(TAC)	 AG	136158-136228	GT	TGG
(GGG)	 AG	136338-136503	GA	GAG
-recovered pasa_asmbl_13519.p1, terminal, 136338, 136503
-recovered pasa_asmbl_13519.p1, internal, 135180, 135304
-recovered pasa_asmbl_13519.p1, internal, 135402, 135501
-recovered pasa_asmbl_13519.p1, internal, 135739, 135792
-recovered pasa_asmbl_13519.p1, internal, 135877, 136005
-recovered pasa_asmbl_13519.p1, internal, 136158, 136228
Valid prediction for snap_scaffold_14-snap.2435-T1
Valid prediction for GlimmerHMM_glimmerT_35514-T1
Valid prediction for GlimmerHMM_glimmerT_35519-T1
Valid prediction for snap_scaffold_14-snap.2423-T1
Valid prediction for Augustus_model.g23901.t1
Valid prediction for GeneMark_model.60907_t
Valid prediction for Augustus_model.g23900.t1
Valid prediction for snap_scaffold_14-snap.2416-T1
Valid prediction for GlimmerHMM_glimmerT_35498-T1
Valid prediction for pasa_asmbl_13511.p1
Valid prediction for Augustus_model.g23896.t1
Valid prediction for GeneMark_model.60906_t
Valid prediction for GeneMark_model.60870_t
Valid prediction for snap_scaffold_14-snap.2440-T1
Valid prediction for GlimmerHMM_glimmerT_35508-T1
Valid prediction for CodingQuarry_transcript_15816-T1
Valid prediction for snap_scaffold_14-snap.2411-T1
Valid prediction for GeneMark_model.60888_t
Valid prediction for snap_scaffold_14-snap.2406-T1
Valid prediction for GeneMark_model.60899_t
Valid prediction for GeneMark_model.60884_t
Valid prediction for GlimmerHMM_glimmerT_35502-T1
Valid prediction for GeneMark_model.60875_t
Valid prediction for snap_scaffold_14-snap.2409-T1
Valid prediction for GeneMark_model.60901_t
Valid prediction for GeneMark_model.60882_t
Valid prediction for GlimmerHMM_glimmerT_35492-T1
Valid prediction for snap_scaffold_14-snap.2443-T1
Valid prediction for GeneMark_model.60904_t
Valid prediction for GeneMark_model.60878_t
Valid prediction for snap_scaffold_14-snap.2414-T1
Valid prediction for GeneMark_model.60908_t
Valid prediction for CodingQuarry_transcript_15815-T1
Valid prediction for GlimmerHMM_glimmerT_35504-T1
Valid prediction for GlimmerHMM_glimmerT_35506-T1
Valid prediction for GlimmerHMM_glimmerT_35490-T1
Valid prediction for Augustus_model.g23888.t1
Valid prediction for GeneMark_model.60873_t
Valid prediction for GeneMark_model.60894_t
Valid prediction for snap_scaffold_14-snap.2430-T1
Valid prediction for snap_scaffold_14-snap.2428-T1
Valid prediction for Augustus_model.g23902.t1
Valid prediction for snap_scaffold_14-snap.2433-T1
Valid prediction for GeneMark_model.60863_t
Valid prediction for GeneMark_model.60891_t
Valid prediction for CodingQuarry_transcript_15812-T1
Valid prediction for snap_scaffold_14-snap.2418-T1
Valid prediction for HiQ_model.g23891.t1
Valid prediction for snap_scaffold_14-snap.2421-T1
Valid prediction for snap_scaffold_14-snap.2425-T1
Valid prediction for pasa_asmbl_13515.p1
Valid prediction for GeneMark_model.60910_t
Couldn't classify 115959, 116112
Sorry, prediction pasa_asmbl_13521.p1 fails validation.
(AGG)	 GG	115959-116112	GT	AGG
(GAA)	 AG	117414-117535	GT	AGG
(ATG)	 AG	117624-117782	GT	ACG
(ATC)	 AG	118226-118287	GT	ACG
(GCT)	 AG	118586-119378	GG	GAG
-recovered pasa_asmbl_13521.p1, initial, 117624, 117782
-recovered pasa_asmbl_13521.p1, terminal, 118586, 119378
-recovered pasa_asmbl_13521.p1, internal, 117414, 117535
-recovered pasa_asmbl_13521.p1, internal, 117624, 117782
-recovered pasa_asmbl_13521.p1, internal, 118226, 118287
Valid prediction for CodingQuarry_transcript_15814-T1
Valid prediction for GeneMark_model.60865_t
Valid prediction for GlimmerHMM_glimmerT_35516-T1
Valid prediction for Augustus_model.g23905.t1
Valid prediction for GlimmerHMM_glimmerT_35510-T1
Valid prediction for GlimmerHMM_glimmerT_35496-T1
Valid prediction for HiQ_model.g23893.t1
Valid prediction for GlimmerHMM_glimmerT_35512-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 54245, rend_intergenic: 53727  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56853, rend_intergenic: 54616  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76305, rend_intergenic: 76053  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78230, rend_intergenic: 77179  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82645, rend_intergenic: 78884  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102053, rend_intergenic: 94408  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106461, rend_intergenic: 104709  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114007, rend_intergenic: 107159  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143296, rend_intergenic: 135849  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149027, rend_intergenic: 145633  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162358, rend_intergenic: 151632  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 165497, rend_intergenic: 162521  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169157, rend_intergenic: 166373  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 171666
-exon list size: 677


building trellis

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78.2    
78.4    
78.5    
78.6    
78.8    
78.9    
79.1    
79.2    
79.4    
79.5    
79.7    
79.8    
80.0    
80.1    
80.3    
80.4    
80.6    
80.7    
80.9    
81.0    
81.1    
81.3    
81.4    
81.6    
81.7    
81.9    
82.0    
82.2    
82.3    
82.5    
82.6    
82.8    
82.9    
83.1    
83.2    
83.4    
83.5    
83.7    
83.8    
83.9    
84.1    
84.2    
84.4    
84.5    
84.7    
84.8    
85.0    
85.1    
85.3    
85.4    
85.6    
85.7    
85.9    
86.0    
86.2    
86.3    
86.5    
86.6    
86.7    
86.9    
87.0    
87.2    
87.3    
87.5    
87.6    
87.8    
87.9    
88.1    
88.2    
88.4    
88.5    
88.7    
88.8    
89.0    
89.1    
89.2    
89.4    
89.5    
89.7    
89.8    
90.0    
90.1    
90.3    
90.4    
90.6    
90.7    
90.9    
91.0    
91.2    
91.3    
91.5    
91.6    
91.8    
91.9    
92.0    
92.2    
92.3    
92.5    
92.6    
92.8    
92.9    
93.1    
93.2    
93.4    
93.5    
93.7    
93.8    
94.0    
94.1    
94.3    
94.4    
94.6    
94.7    
94.8    
95.0    
95.1    
95.3    
95.4    
95.6    
95.7    
95.9    
96.0    
96.2    
96.3    
96.5    
96.6    
96.8    
96.9    
97.1    
97.2    
97.3    
97.5    
97.6    
97.8    
97.9    
98.1    
98.2    
98.4    
98.5    
98.7    
98.8    
99.0    
99.1    
99.3    
99.4    
99.6    
99.7    
99.9    
-found 36 predictions from path traversal
Error with prediction: snap lend_intergenic: 54245, rend_intergenic: 53727  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56853, rend_intergenic: 54616  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76305, rend_intergenic: 76053  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78230, rend_intergenic: 77179  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82645, rend_intergenic: 78884  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102053, rend_intergenic: 94408  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106461, rend_intergenic: 104709  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114007, rend_intergenic: 107159  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143296, rend_intergenic: 135849  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149027, rend_intergenic: 145633  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162358, rend_intergenic: 151632  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 165497, rend_intergenic: 162521  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169157, rend_intergenic: 166373  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 24 predictions persist after filtering for low support