-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_14/scaffold_14_5786605-5993124

-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: +)Couldn't classify 118581, 118619
Sorry, prediction pasa_asmbl_12017.p1 fails validation.
(ATC)	 CC	118581-118619	GT	AGG
(GTC)	 AG	118834-119063	GT	AAG
(ACA)	 AG	119152-119293	AC	GAA
-recovered pasa_asmbl_12017.p1, terminal, 119152, 119293
-recovered pasa_asmbl_12017.p1, internal, 118834, 119063
Valid prediction for snap_scaffold_14-snap.1209-T1
Valid prediction for Augustus_model.g23321.t1
Valid prediction for GlimmerHMM_glimmerT_34690-T1
Valid prediction for snap_scaffold_14-snap.1210-T1
Valid prediction for GeneMark_model.59375_t
Valid prediction for snap_scaffold_14-snap.1195-T1
Valid prediction for GeneMark_model.59425_t
Valid prediction for GeneMark_model.59413_t
Valid prediction for GeneMark_model.59402_t
Valid prediction for GeneMark_model.59393_t
Valid prediction for snap_scaffold_14-snap.1187-T1
Valid prediction for GlimmerHMM_glimmerT_34681-T1
Valid prediction for GeneMark_model.59429_t
Valid prediction for HiQ_model.g23317.t1
Valid prediction for Augustus_model.g23326.t1
Valid prediction for GeneMark_model.59388_t
Valid prediction for GeneMark_model.59421_t
Valid prediction for snap_scaffold_14-snap.1190-T1
Valid prediction for snap_scaffold_14-snap.1205-T1
Valid prediction for GeneMark_model.59411_t
Valid prediction for Augustus_model.g23314.t1
Valid prediction for pasa_asmbl_12015.p1
Valid prediction for GeneMark_model.59410_t
Valid prediction for HiQ_model.g23324.t1
Valid prediction for GeneMark_model.59405_t
Valid prediction for snap_scaffold_14-snap.1202-T1
Valid prediction for GlimmerHMM_glimmerT_34688-T1
Valid prediction for snap_scaffold_14-snap.1201-T1
Valid prediction for GeneMark_model.59407_t
Valid prediction for GeneMark_model.59376_t
Valid prediction for GeneMark_model.59403_t
Valid prediction for snap_scaffold_14-snap.1196-T1
Valid prediction for GeneMark_model.59377_t
Valid prediction for snap_scaffold_14-snap.1185-T1
Valid prediction for snap_scaffold_14-snap.1174-T1
Valid prediction for GeneMark_model.59399_t
Valid prediction for CodingQuarry_transcript_15606-T1
Valid prediction for GeneMark_model.59417_t
Valid prediction for GeneMark_model.59382_t
Valid prediction for GlimmerHMM_glimmerT_34696-T1
Valid prediction for GeneMark_model.59396_t
Valid prediction for snap_scaffold_14-snap.1178-T1
Valid prediction for GeneMark_model.59419_t
Valid prediction for GeneMark_model.59415_t
Valid prediction for GeneMark_model.59383_t
Valid prediction for GeneMark_model.59381_t
Valid prediction for GeneMark_model.59391_t
Valid prediction for GlimmerHMM_glimmerT_34701-T1
Valid prediction for GlimmerHMM_glimmerT_34698-T1
Valid prediction for GlimmerHMM_glimmerT_34679-T1
Valid prediction for Augustus_model.g23320.t1
Valid prediction for snap_scaffold_14-snap.1214-T1
Valid prediction for GeneMark_model.59409_t
Valid prediction for snap_scaffold_14-snap.1212-T1
Valid prediction for snap_scaffold_14-snap.1200-T1
Valid prediction for snap_scaffold_14-snap.1176-T1
Valid prediction for GlimmerHMM_glimmerT_34687-T1
Valid prediction for GlimmerHMM_glimmerT_34693-T1
Valid prediction for GeneMark_model.59432_t
Valid prediction for pasa_asmbl_12021.p1
Valid prediction for GeneMark_model.59387_t
Valid prediction for GeneMark_model.59395_t
Valid prediction for snap_scaffold_14-snap.1198-T1
Valid prediction for GlimmerHMM_glimmerT_34700-T1
Valid prediction for GeneMark_model.59435_t
Valid prediction for GeneMark_model.59385_t
Valid prediction for snap_scaffold_14-snap.1204-T1
Valid prediction for GeneMark_model.59423_t
Valid prediction for CodingQuarry_transcript_15607-T1
Valid prediction for GeneMark_model.59386_t
Valid prediction for snap_scaffold_14-snap.1193-T1
Valid prediction for Augustus_model.g23318.t1
Valid prediction for GeneMark_model.59379_t
Valid prediction for snap_scaffold_14-snap.1182-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 GlimmerHMM_glimmerT_34691-T1
Valid prediction for GlimmerHMM_glimmerT_34699-T1
Valid prediction for HiQ_model.g23319.t1
Valid prediction for Augustus_model.g23313.t1
Valid prediction for pasa_asmbl_13080.p1
Valid prediction for snap_scaffold_14-snap.1181-T1
Valid prediction for GeneMark_model.59400_t
Valid prediction for snap_scaffold_14-snap.1180-T1
Valid prediction for GlimmerHMM_glimmerT_34684-T1
Valid prediction for Augustus_model.g23312.t1
Valid prediction for snap_scaffold_14-snap.1189-T1
Couldn't classify 104550, 104716
Sorry, prediction pasa_asmbl_13078.p2 fails validation.
(ATC)	 TG	104550-104716	GT	AGG
(GTC)	 AG	105356-105473	GT	AGG
(CTG)	 AG	106543-106696	GT	GTG
(ACT)	 AG	106997-107163	GT	AGG
(GTT)	 AG	107457-107636	TG	GAT
-recovered pasa_asmbl_13078.p2, terminal, 107457, 107636
-recovered pasa_asmbl_13078.p2, internal, 105356, 105473
-recovered pasa_asmbl_13078.p2, internal, 106543, 106696
-recovered pasa_asmbl_13078.p2, internal, 106997, 107163
Valid prediction for snap_scaffold_14-snap.1208-T1
Valid prediction for pasa_asmbl_13088.p1
Couldn't classify 45277, 45437
Sorry, prediction pasa_asmbl_13086.p1 fails validation.
(ATG)	 GC	43497-43614	GT	AGG
(GAG)	 AG	43928-44033	GT	AGG
(CTT)	 AG	44439-44584	GT	AGG
(CAG)	 AG	45277-45437	TG	CCT
-recovered pasa_asmbl_13086.p1, initial, 43497, 43614
-recovered pasa_asmbl_13086.p1, internal, 43928, 44033
-recovered pasa_asmbl_13086.p1, internal, 44439, 44584
Valid prediction for snap_scaffold_14-snap.1194-T1
Valid prediction for CodingQuarry_transcript_15608-T1
Valid prediction for snap_scaffold_14-snap.1192-T1
Valid prediction for GeneMark_model.59404_t
Valid prediction for GlimmerHMM_glimmerT_34685-T1
Valid prediction for GlimmerHMM_glimmerT_34692-T1
Valid prediction for GlimmerHMM_glimmerT_34678-T1
Valid prediction for GeneMark_model.59398_t
Valid prediction for GeneMark_model.59414_t
Valid prediction for snap_scaffold_14-snap.1184-T1
Valid prediction for GeneMark_model.59416_t
Valid prediction for HiQ_model.g23325.t1
Valid prediction for snap_scaffold_14-snap.1173-T1
Valid prediction for snap_scaffold_14-snap.1186-T1
Valid prediction for GeneMark_model.59422_t
Valid prediction for Augustus_model.g23329.t1
Valid prediction for HiQ_model.g23327.t1
Valid prediction for snap_scaffold_14-snap.1213-T1
Valid prediction for GlimmerHMM_glimmerT_34675-T1
Valid prediction for GlimmerHMM_glimmerT_34694-T1
Valid prediction for Augustus_model.g23323.t1
Valid prediction for GeneMark_model.59424_t
Valid prediction for GlimmerHMM_glimmerT_34702-T1
Valid prediction for GlimmerHMM_glimmerT_34704-T1
Valid prediction for snap_scaffold_14-snap.1211-T1
Valid prediction for HiQ_model.g23316.t1
Valid prediction for GlimmerHMM_glimmerT_34697-T1
Valid prediction for GeneMark_model.59412_t
Valid prediction for Augustus_model.g23328.t1
Valid prediction for GlimmerHMM_glimmerT_34686-T1
Valid prediction for GeneMark_model.59397_t
Valid prediction for GeneMark_model.59392_t
Valid prediction for GeneMark_model.59434_t
Valid prediction for snap_scaffold_14-snap.1177-T1
Valid prediction for GeneMark_model.59430_t
Valid prediction for Augustus_model.g23322.t1
Valid prediction for GeneMark_model.59408_t
Valid prediction for GeneMark_model.59426_t
Valid prediction for snap_scaffold_14-snap.1179-T1
Valid prediction for snap_scaffold_14-snap.1199-T1
Valid prediction for GeneMark_model.59374_t
Valid prediction for GeneMark_model.59389_t
Valid prediction for GeneMark_model.59378_t
Valid prediction for snap_scaffold_14-snap.1183-T1
Valid prediction for snap_scaffold_14-snap.1207-T1
Valid prediction for CodingQuarry_transcript_15605-T1
Valid prediction for GeneMark_model.59406_t
Valid prediction for snap_scaffold_14-snap.1206-T1
Valid prediction for GeneMark_model.59433_t
Valid prediction for Augustus_model.g23309.t1
Valid prediction for Augustus_model.g23311.t1
Valid prediction for GlimmerHMM_glimmerT_34682-T1
Valid prediction for GlimmerHMM_glimmerT_34672-T1
Valid prediction for HiQ_model.g23308.t1
Valid prediction for snap_scaffold_14-snap.1191-T1
Valid prediction for snap_scaffold_14-snap.1215-T1
Valid prediction for pasa_asmbl_13082.p1
Valid prediction for GlimmerHMM_glimmerT_34703-T1
Valid prediction for GeneMark_model.59394_t
Valid prediction for GeneMark_model.59428_t
Valid prediction for snap_scaffold_14-snap.1175-T1
Valid prediction for GeneMark_model.59384_t
Valid prediction for GlimmerHMM_glimmerT_34677-T1
Valid prediction for snap_scaffold_14-snap.1188-T1
Valid prediction for GeneMark_model.59380_t
Valid prediction for GeneMark_model.59418_t
Valid prediction for pasa_asmbl_13090.p1
Valid prediction for GlimmerHMM_glimmerT_34673-T1
Valid prediction for pasa_asmbl_13074.p1
Valid prediction for GlimmerHMM_glimmerT_34674-T1
Valid prediction for GeneMark_model.59431_t
Valid prediction for GeneMark_model.59420_t
Valid prediction for GlimmerHMM_glimmerT_34683-T1
Valid prediction for GlimmerHMM_glimmerT_34676-T1
Valid prediction for GlimmerHMM_glimmerT_34689-T1
Valid prediction for snap_scaffold_14-snap.1216-T1
Valid prediction for CodingQuarry_transcript_15610-T1
Valid prediction for CodingQuarry_transcript_15609-T1
Valid prediction for GlimmerHMM_glimmerT_34695-T1
Valid prediction for snap_scaffold_14-snap.1197-T1
Valid prediction for snap_scaffold_14-snap.1203-T1
Valid prediction for Augustus_model.g23315.t1
Valid prediction for Augustus_model.g23310.t1
Valid prediction for GeneMark_model.59390_t
Couldn't classify 53263, 53434
Sorry, prediction pasa_asmbl_13085.p1 fails validation.
(ATA)	 TG	53263-53434	GT	AGG
(AGT)	 AG	54293-54468	GT	AGG
(GTG)	 AG	56292-56444	GG	GAG
-recovered pasa_asmbl_13085.p1, terminal, 56292, 56444
-recovered pasa_asmbl_13085.p1, internal, 54293, 54468
Valid prediction for GlimmerHMM_glimmerT_34680-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 6936, rend_intergenic: 6560  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 13379, rend_intergenic: 8581  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 14063, rend_intergenic: 13451  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 15958, rend_intergenic: 14076  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23441, rend_intergenic: 19200  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48779, rend_intergenic: 23641  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51645, rend_intergenic: 49492  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58863, rend_intergenic: 52409  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65443, rend_intergenic: 60752  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81355, rend_intergenic: 69210  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92205, rend_intergenic: 88653  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94728, rend_intergenic: 92561  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102463, rend_intergenic: 99732  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135273, rend_intergenic: 128911  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161452, rend_intergenic: 140238  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170922, rend_intergenic: 166747  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 183337, rend_intergenic: 177853  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 189090, rend_intergenic: 186308  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 191295, rend_intergenic: 191170  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 194092, rend_intergenic: 191298  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 197006, rend_intergenic: 194095  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 206520
-exon list size: 888


building trellis

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60.2    
60.3    
60.4    
60.6    
60.7    
60.8    
60.9    
61.0    
61.1    
61.2    
61.3    
61.5    
61.6    
61.7    
61.8    
61.9    
62.0    
62.1    
62.2    
62.4    
62.5    
62.6    
62.7    
62.8    
62.9    
63.0    
63.1    
63.3    
63.4    
63.5    
63.6    
63.7    
63.8    
63.9    
64.0    
64.2    
64.3    
64.4    
64.5    
64.6    
64.7    
64.8    
64.9    
65.1    
65.2    
65.3    
65.4    
65.5    
65.6    
65.7    
65.8    
66.0    
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    
67.6    
67.8    
67.9    
68.0    
68.1    
68.2    
68.3    
68.4    
68.5    
68.7    
68.8    
68.9    
69.0    
69.1    
69.2    
69.3    
69.4    
69.6    
69.7    
69.8    
69.9    
70.0    
70.1    
70.2    
70.3    
70.4    
70.6    
70.7    
70.8    
70.9    
71.0    
71.1    
71.2    
71.3    
71.5    
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    
73.0    
73.1    
73.3    
73.4    
73.5    
73.6    
73.7    
73.8    
73.9    
74.0    
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    
76.0    
76.1    
76.2    
76.3    
76.4    
76.5    
76.6    
76.7    
76.9    
77.0    
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    
78.5    
78.7    
78.8    
78.9    
79.0    
79.1    
79.2    
79.3    
79.4    
79.6    
79.7    
79.8    
79.9    
80.0    
80.1    
80.2    
80.3    
80.4    
80.6    
80.7    
80.8    
80.9    
81.0    
81.1    
81.2    
81.3    
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    
83.3    
83.4    
83.5    
83.6    
83.7    
83.8    
83.9    
84.0    
84.2    
84.3    
84.4    
84.5    
84.6    
84.7    
84.8    
84.9    
85.1    
85.2    
85.3    
85.4    
85.5    
85.6    
85.7    
85.8    
86.0    
86.1    
86.2    
86.3    
86.4    
86.5    
86.6    
86.7    
86.9    
87.0    
87.1    
87.2    
87.3    
87.4    
87.5    
87.6    
87.8    
87.9    
88.0    
88.1    
88.2    
88.3    
88.4    
88.5    
88.7    
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    
90.2    
90.3    
90.4    
90.6    
90.7    
90.8    
90.9    
91.0    
91.1    
91.2    
91.3    
91.5    
91.6    
91.7    
91.8    
91.9    
92.0    
92.1    
92.2    
92.4    
92.5    
92.6    
92.7    
92.8    
92.9    
93.0    
93.1    
93.3    
93.4    
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    
94.9    
95.1    
95.2    
95.3    
95.4    
95.5    
95.6    
95.7    
95.8    
96.0    
96.1    
96.2    
96.3    
96.4    
96.5    
96.6    
96.7    
96.9    
97.0    
97.1    
97.2    
97.3    
97.4    
97.5    
97.6    
97.8    
97.9    
98.0    
98.1    
98.2    
98.3    
98.4    
98.5    
98.7    
98.8    
98.9    
99.0    
99.1    
99.2    
99.3    
99.4    
99.6    
99.7    
99.8    
99.9    
-found 41 predictions from path traversal
Error with prediction: snap lend_intergenic: 6936, rend_intergenic: 6560  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 13379, rend_intergenic: 8581  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 14063, rend_intergenic: 13451  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 15958, rend_intergenic: 14076  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23441, rend_intergenic: 19200  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48779, rend_intergenic: 23641  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51645, rend_intergenic: 49492  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58863, rend_intergenic: 52409  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65443, rend_intergenic: 60752  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81355, rend_intergenic: 69210  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92205, rend_intergenic: 88653  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94728, rend_intergenic: 92561  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102463, rend_intergenic: 99732  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135273, rend_intergenic: 128911  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161452, rend_intergenic: 140238  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170922, rend_intergenic: 166747  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 183337, rend_intergenic: 177853  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 189090, rend_intergenic: 186308  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 191295, rend_intergenic: 191170  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 194092, rend_intergenic: 191298  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 197006, rend_intergenic: 194095  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 23 predictions persist after filtering for low support