-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_14/scaffold_14_11908917-12074938

-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.60937_t
Valid prediction for HiQ_model.g23922.t1
Valid prediction for snap_scaffold_14-snap.2446-T1
Valid prediction for GeneMark_model.60923_t
Valid prediction for GeneMark_model.60924_t
Valid prediction for GeneMark_model.60954_t
Valid prediction for GeneMark_model.60926_t
Valid prediction for Augustus_model.g23928.t1
Valid prediction for snap_scaffold_14-snap.2468-T1
Valid prediction for snap_scaffold_14-snap.2466-T1
Valid prediction for snap_scaffold_14-snap.2473-T1
Valid prediction for GeneMark_model.60956_t
Valid prediction for HiQ_model.g23914.t1
Valid prediction for GeneMark_model.60955_t
Valid prediction for GeneMark_model.60920_t
Valid prediction for GeneMark_model.60915_t
Valid prediction for snap_scaffold_14-snap.2471-T1
Valid prediction for Augustus_model.g23912.t1
Valid prediction for GeneMark_model.60922_t
Valid prediction for GlimmerHMM_glimmerT_35544-T1
Valid prediction for snap_scaffold_14-snap.2464-T1
Valid prediction for GeneMark_model.60928_t
Valid prediction for snap_scaffold_14-snap.2452-T1
Valid prediction for GeneMark_model.60942_t
Valid prediction for GlimmerHMM_glimmerT_35527-T1
Valid prediction for snap_scaffold_14-snap.2458-T1
Valid prediction for snap_scaffold_14-snap.2455-T1
Valid prediction for snap_scaffold_14-snap.2460-T1
Valid prediction for GeneMark_model.60949_t
Valid prediction for GlimmerHMM_glimmerT_35545-T1
Valid prediction for GlimmerHMM_glimmerT_35523-T1
Valid prediction for GlimmerHMM_glimmerT_35536-T1
Valid prediction for CodingQuarry_transcript_15820-T1
Valid prediction for GeneMark_model.60938_t
Valid prediction for GeneMark_model.60948_t
Valid prediction for GeneMark_model.60911_t
Valid prediction for Augustus_model.g23911.t1
Valid prediction for snap_scaffold_14-snap.2479-T1
Valid prediction for GeneMark_model.60934_t
Valid prediction for Augustus_model.g23924.t1
Valid prediction for GlimmerHMM_glimmerT_35528-T1
Valid prediction for GlimmerHMM_glimmerT_35532-T1
Valid prediction for GlimmerHMM_glimmerT_35542-T1
Valid prediction for GlimmerHMM_glimmerT_35540-T1
Valid prediction for snap_scaffold_14-snap.2463-T1
Valid prediction for GeneMark_model.60950_t
Valid prediction for GeneMark_model.60941_t
Valid prediction for GeneMark_model.60952_t
Valid prediction for snap_scaffold_14-snap.2481-T1
Valid prediction for GeneMark_model.60930_t
Valid prediction for snap_scaffold_14-snap.2470-T1
Valid prediction for snap_scaffold_14-snap.2449-T1
Valid prediction for snap_scaffold_14-snap.2450-T1
Valid prediction for GeneMark_model.60918_t
Valid prediction for Augustus_model.g23915.t1
Valid prediction for GlimmerHMM_glimmerT_35537-T1
Valid prediction for GeneMark_model.60946_t
Valid prediction for GeneMark_model.60959_t
Couldn't classify 43576, 43664
Sorry, prediction pasa_asmbl_12391.p1 fails validation.
(CAG)	 CC	43576-43664	GT	ACG
(GCA)	 AG	44496-44595	GT	AGG
(AGG)	 AG	45637-45676	GT	AGG
(TCA)	 AG	47277-47443	GT	AGG
(CTG)	 AG	47753-47860	GT	AGG
(ATC)	 AG	48050-48125	GT	TGG
(GGA)	 AG	48696-48851	GT	GGG
(GGT)	 AG	50698-50897	GT	GGG
(CTG)	 AG	52700-52865	GT	TGG
(GAA)	 AG	53126-53200	GT	TGG
(GGT)	 AG	53437-53624	GT	AGG
(GCC)	 AG	54580-54675	GT	CTG
(GCG)	 AG	54921-55077	GT	AGG
(GTC)	 AG	56241-56374	GT	AGG
(ATA)	 AG	56491-56557	GT	AGG
(ACT)	 AG	56674-56753	GT	AGG
(GGG)	 AG	58278-58412	GT	AGG
(TTG)	 AG	58785-58898	GT	AGG
(ATG)	 AG	61415-61470	GT	GCG
(GTT)	 AG	61824-61854	GA	GAG
-recovered pasa_asmbl_12391.p1, initial, 61415, 61470
add_exon() Sorry, pasa_asmbl_12391.p1 56491-56557-terminal-3 is invalid.
-recovered pasa_asmbl_12391.p1, terminal, 56491, 56557
-recovered pasa_asmbl_12391.p1, terminal, 61824, 61854
-recovered pasa_asmbl_12391.p1, internal, 44496, 44595
-recovered pasa_asmbl_12391.p1, internal, 45637, 45676
-recovered pasa_asmbl_12391.p1, internal, 47277, 47443
-recovered pasa_asmbl_12391.p1, internal, 47753, 47860
-recovered pasa_asmbl_12391.p1, internal, 48050, 48125
-recovered pasa_asmbl_12391.p1, internal, 48696, 48851
-recovered pasa_asmbl_12391.p1, internal, 50698, 50897
-recovered pasa_asmbl_12391.p1, internal, 52700, 52865
-recovered pasa_asmbl_12391.p1, internal, 53126, 53200
-recovered pasa_asmbl_12391.p1, internal, 53437, 53624
-recovered pasa_asmbl_12391.p1, internal, 54580, 54675
-recovered pasa_asmbl_12391.p1, internal, 54921, 55077
-recovered pasa_asmbl_12391.p1, internal, 56241, 56374
-recovered pasa_asmbl_12391.p1, internal, 56491, 56557
-recovered pasa_asmbl_12391.p1, internal, 56674, 56753
-recovered pasa_asmbl_12391.p1, internal, 58278, 58412
-recovered pasa_asmbl_12391.p1, internal, 58785, 58898
-recovered pasa_asmbl_12391.p1, internal, 61415, 61470
Valid prediction for pasa_asmbl_12392.p1
Couldn't classify 32597, 32684
Sorry, prediction pasa_asmbl_12388.p1 fails validation.
(GCG)	 TG	32597-32684	GT	AGG
(TGA)	 AG	33510-33611	GT	AGG
(AGC)	 AG	33791-33987	GT	AGG
(GCT)	 AG	34107-34164	GT	TGG
(GCT)	 AG	34431-34625	GT	AGG
(GGA)	 AG	34900-35044	GT	ACG
(ACC)	 AG	35178-35238	GT	AGG
(ACG)	 AG	35381-35443	GT	AGG
(GCC)	 AG	35536-35661	GT	AGG
(ATA)	 AG	35786-35821	GT	AGG
(GGG)	 AG	35912-35963	GT	CGG
(GGA)	 AG	36072-36214	GT	AGG
-recovered pasa_asmbl_12388.p1, terminal, 36072, 36214
-recovered pasa_asmbl_12388.p1, internal, 33510, 33611
-recovered pasa_asmbl_12388.p1, internal, 33791, 33987
-recovered pasa_asmbl_12388.p1, internal, 34107, 34164
-recovered pasa_asmbl_12388.p1, internal, 34431, 34625
-recovered pasa_asmbl_12388.p1, internal, 34900, 35044
-recovered pasa_asmbl_12388.p1, internal, 35178, 35238
-recovered pasa_asmbl_12388.p1, internal, 35381, 35443
-recovered pasa_asmbl_12388.p1, internal, 35536, 35661
-recovered pasa_asmbl_12388.p1, internal, 35786, 35821
-recovered pasa_asmbl_12388.p1, internal, 35912, 35963
-recovered pasa_asmbl_12388.p1, internal, 36072, 36214
Valid prediction for GlimmerHMM_glimmerT_35529-T1
Valid prediction for Augustus_model.g23916.t1
Valid prediction for snap_scaffold_14-snap.2475-T1
Valid prediction for GeneMark_model.60932_t
Valid prediction for GlimmerHMM_glimmerT_35534-T1
Valid prediction for Augustus_model.g23919.t1
Valid prediction for GlimmerHMM_glimmerT_35525-T1
Valid prediction for snap_scaffold_14-snap.2478-T1
Valid prediction for Augustus_model.g23926.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 snap_scaffold_14-snap.2467-T1
Valid prediction for snap_scaffold_14-snap.2482-T1
Valid prediction for GeneMark_model.60944_t
Valid prediction for GlimmerHMM_glimmerT_35526-T1
Couldn't classify 49284, 49470
Sorry, prediction pasa_asmbl_13532.p2 fails validation.
(CGC)	 TG	49284-49470	GT	AGG
(ACC)	 AG	49855-50105	GC	GAG
-recovered pasa_asmbl_13532.p2, terminal, 49855, 50105
-recovered pasa_asmbl_13532.p2, internal, 49855, 50105
Valid prediction for Augustus_model.g23925.t1
Valid prediction for snap_scaffold_14-snap.2472-T1
Valid prediction for snap_scaffold_14-snap.2454-T1
Valid prediction for snap_scaffold_14-snap.2477-T1
Valid prediction for snap_scaffold_14-snap.2453-T1
Valid prediction for GeneMark_model.60935_t
Valid prediction for GlimmerHMM_glimmerT_35533-T1
Valid prediction for snap_scaffold_14-snap.2462-T1
Valid prediction for GeneMark_model.60925_t
Valid prediction for GeneMark_model.60929_t
Valid prediction for Augustus_model.g23917.t1
Valid prediction for snap_scaffold_14-snap.2465-T1
Valid prediction for GeneMark_model.60951_t
Valid prediction for Augustus_model.g23929.t1
Valid prediction for GeneMark_model.60933_t
Valid prediction for snap_scaffold_14-snap.2448-T1
Valid prediction for GlimmerHMM_glimmerT_35531-T1
Valid prediction for snap_scaffold_14-snap.2457-T1
Valid prediction for Augustus_model.g23920.t1
Valid prediction for GlimmerHMM_glimmerT_35543-T1
Valid prediction for GeneMark_model.60912_t
Valid prediction for GlimmerHMM_glimmerT_35535-T1
Valid prediction for snap_scaffold_14-snap.2474-T1
Valid prediction for GeneMark_model.60947_t
Valid prediction for Augustus_model.g23918.t1
Valid prediction for GeneMark_model.60919_t
Valid prediction for GeneMark_model.60931_t
Valid prediction for snap_scaffold_14-snap.2451-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_35538-T1
Valid prediction for GlimmerHMM_glimmerT_35530-T1
Valid prediction for GeneMark_model.60945_t
Valid prediction for GeneMark_model.60940_t
Valid prediction for GeneMark_model.60943_t
Valid prediction for GlimmerHMM_glimmerT_35546-T1
Valid prediction for snap_scaffold_14-snap.2469-T1
Valid prediction for GlimmerHMM_glimmerT_35541-T1
Valid prediction for Augustus_model.g23921.t1
Valid prediction for GeneMark_model.60914_t
Valid prediction for GeneMark_model.60913_t
Valid prediction for Augustus_model.g23913.t1
Valid prediction for GeneMark_model.60939_t
Valid prediction for snap_scaffold_14-snap.2445-T1
Valid prediction for snap_scaffold_14-snap.2461-T1
Valid prediction for GlimmerHMM_glimmerT_35539-T1
Valid prediction for GeneMark_model.60916_t
Valid prediction for Augustus_model.g23927.t1
Valid prediction for snap_scaffold_14-snap.2459-T1
Valid prediction for GeneMark_model.60958_t
Valid prediction for snap_scaffold_14-snap.2480-T1
Valid prediction for GeneMark_model.60921_t
Valid prediction for snap_scaffold_14-snap.2456-T1
Valid prediction for Augustus_model.g23923.t1
Valid prediction for snap_scaffold_14-snap.2447-T1
Valid prediction for GeneMark_model.60927_t
Valid prediction for snap_scaffold_14-snap.2476-T1
Valid prediction for GeneMark_model.60953_t
Valid prediction for GeneMark_model.60957_t
Valid prediction for GlimmerHMM_glimmerT_35524-T1
Valid prediction for GeneMark_model.60917_t
Valid prediction for GeneMark_model.60936_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 10555, rend_intergenic: 3371  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 15899, rend_intergenic: 10657  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20613, rend_intergenic: 16078  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62868, rend_intergenic: 45785  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81042, rend_intergenic: 74497  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91485, rend_intergenic: 88947  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105263, rend_intergenic: 103586  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117179, rend_intergenic: 112837  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123489, rend_intergenic: 117816  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127061, rend_intergenic: 124663  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145739, rend_intergenic: 133187  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 160750, rend_intergenic: 152611  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 96389, rend_intergenic: 96386  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 166022
-exon list size: 709


building trellis

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78.6    
78.8    
78.9    
79.0    
79.2    
79.3    
79.5    
79.6    
79.7    
79.9    
80.0    
80.2    
80.3    
80.5    
80.6    
80.7    
80.9    
81.0    
81.2    
81.3    
81.4    
81.6    
81.7    
81.9    
82.0    
82.1    
82.3    
82.4    
82.6    
82.7    
82.8    
83.0    
83.1    
83.3    
83.4    
83.5    
83.7    
83.8    
84.0    
84.1    
84.2    
84.4    
84.5    
84.7    
84.8    
85.0    
85.1    
85.2    
85.4    
85.5    
85.7    
85.8    
85.9    
86.1    
86.2    
86.4    
86.5    
86.6    
86.8    
86.9    
87.1    
87.2    
87.3    
87.5    
87.6    
87.8    
87.9    
88.0    
88.2    
88.3    
88.5    
88.6    
88.7    
88.9    
89.0    
89.2    
89.3    
89.5    
89.6    
89.7    
89.9    
90.0    
90.2    
90.3    
90.4    
90.6    
90.7    
90.9    
91.0    
91.1    
91.3    
91.4    
91.6    
91.7    
91.8    
92.0    
92.1    
92.3    
92.4    
92.5    
92.7    
92.8    
93.0    
93.1    
93.2    
93.4    
93.5    
93.7    
93.8    
94.0    
94.1    
94.2    
94.4    
94.5    
94.7    
94.8    
94.9    
95.1    
95.2    
95.4    
95.5    
95.6    
95.8    
95.9    
96.1    
96.2    
96.3    
96.5    
96.6    
96.8    
96.9    
97.0    
97.2    
97.3    
97.5    
97.6    
97.7    
97.9    
98.0    
98.2    
98.3    
98.5    
98.6    
98.7    
98.9    
99.0    
99.2    
99.3    
99.4    
99.6    
99.7    
99.9    
-found 33 predictions from path traversal
Error with prediction: snap lend_intergenic: 10555, rend_intergenic: 3371  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 15899, rend_intergenic: 10657  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20613, rend_intergenic: 16078  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62868, rend_intergenic: 45785  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81042, rend_intergenic: 74497  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91485, rend_intergenic: 88947  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105263, rend_intergenic: 103586  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117179, rend_intergenic: 112837  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123489, rend_intergenic: 117816  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127061, rend_intergenic: 124663  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145739, rend_intergenic: 133187  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 160750, rend_intergenic: 152611  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 96389, rend_intergenic: 96386  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

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