-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_22/scaffold_22_6139141-6325383

-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 snap_scaffold_22-snap.1236-T1
Valid prediction for Augustus_model.g34033.t1
Valid prediction for snap_scaffold_22-snap.1217-T1
Valid prediction for GlimmerHMM_glimmerT_50783-T1
Valid prediction for GlimmerHMM_glimmerT_50794-T1
Valid prediction for Augustus_model.g34053.t1
Valid prediction for GeneMark_model.87867_t
Valid prediction for GeneMark_model.87901_t
Valid prediction for GeneMark_model.87919_t
Valid prediction for GeneMark_model.87895_t
Valid prediction for GeneMark_model.87889_t
Valid prediction for GeneMark_model.87903_t
Valid prediction for HiQ_model.g34041.t1
Valid prediction for snap_scaffold_22-snap.1214-T1
Valid prediction for GeneMark_model.87884_t
Valid prediction for GeneMark_model.87909_t
Valid prediction for GlimmerHMM_glimmerT_50802-T1
Valid prediction for GlimmerHMM_glimmerT_50776-T1
Valid prediction for GeneMark_model.87927_t
Valid prediction for Augustus_model.g34051.t1
Valid prediction for GeneMark_model.87917_t
Valid prediction for snap_scaffold_22-snap.1237-T1
Valid prediction for GeneMark_model.87924_t
Valid prediction for snap_scaffold_22-snap.1230-T1
Valid prediction for GeneMark_model.87878_t
Valid prediction for Augustus_model.g34047.t1
Valid prediction for snap_scaffold_22-snap.1216-T1
Valid prediction for snap_scaffold_22-snap.1234-T1
Valid prediction for snap_scaffold_22-snap.1224-T1
Valid prediction for GeneMark_model.87890_t
Valid prediction for GeneMark_model.87925_t
Valid prediction for GeneMark_model.87898_t
Valid prediction for GeneMark_model.87869_t
Valid prediction for GlimmerHMM_glimmerT_50800-T1
Valid prediction for snap_scaffold_22-snap.1198-T1
Valid prediction for snap_scaffold_22-snap.1207-T1
Valid prediction for GeneMark_model.87911_t
Valid prediction for snap_scaffold_22-snap.1225-T1
Valid prediction for snap_scaffold_22-snap.1231-T1
Valid prediction for snap_scaffold_22-snap.1199-T1
Valid prediction for snap_scaffold_22-snap.1206-T1
Valid prediction for GeneMark_model.87922_t
Valid prediction for GeneMark_model.87897_t
Valid prediction for GeneMark_model.87866_t
Valid prediction for GeneMark_model.87882_t
Valid prediction for GlimmerHMM_glimmerT_50797-T1
Valid prediction for snap_scaffold_22-snap.1221-T1
Valid prediction for GeneMark_model.87915_t
Valid prediction for CodingQuarry_transcript_34122-T1
Valid prediction for GeneMark_model.87876_t
Valid prediction for snap_scaffold_22-snap.1219-T1
Valid prediction for snap_scaffold_22-snap.1238-T1
Valid prediction for snap_scaffold_22-snap.1202-T1
Valid prediction for snap_scaffold_22-snap.1212-T1
Valid prediction for GlimmerHMM_glimmerT_50777-T1
Valid prediction for GeneMark_model.87913_t
Valid prediction for snap_scaffold_22-snap.1229-T1
Valid prediction for GeneMark_model.87907_t
Valid prediction for Augustus_model.g34035.t1
Valid prediction for GeneMark_model.87921_t
Valid prediction for GeneMark_model.87905_t
Valid prediction for snap_scaffold_22-snap.1196-T1
Valid prediction for GeneMark_model.87893_t
Valid prediction for GeneMark_model.87870_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.87896_t
Valid prediction for snap_scaffold_22-snap.1208-T1
Valid prediction for snap_scaffold_22-snap.1204-T1
Valid prediction for pasa_asmbl_30086.p1
Valid prediction for GeneMark_model.87868_t
Valid prediction for Augustus_model.g34050.t1
Valid prediction for Augustus_model.g34048.t1
Valid prediction for GeneMark_model.87886_t
Valid prediction for GlimmerHMM_glimmerT_50780-T1
Valid prediction for GeneMark_model.87877_t
Valid prediction for GeneMark_model.87894_t
Valid prediction for GlimmerHMM_glimmerT_50791-T1
Valid prediction for GeneMark_model.87910_t
Valid prediction for GeneMark_model.87892_t
Valid prediction for GeneMark_model.87904_t
Valid prediction for snap_scaffold_22-snap.1197-T1
Valid prediction for GlimmerHMM_glimmerT_50781-T1
Valid prediction for GlimmerHMM_glimmerT_50801-T1
Valid prediction for snap_scaffold_22-snap.1223-T1
Valid prediction for GeneMark_model.87874_t
Valid prediction for snap_scaffold_22-snap.1239-T1
Valid prediction for GeneMark_model.87923_t
Valid prediction for GlimmerHMM_glimmerT_50796-T1
Valid prediction for Augustus_model.g34054.t1
Valid prediction for snap_scaffold_22-snap.1210-T1
Valid prediction for snap_scaffold_22-snap.1200-T1
Valid prediction for Augustus_model.g34032.t1
Valid prediction for snap_scaffold_22-snap.1203-T1
Couldn't classify 13639, 13728
Couldn't classify 14127, 14414
Sorry, prediction pasa_asmbl_30096.p2 fails validation.
(GCC)	 AG	13639-13728	GT	AGG
(GTT)	 AG	14127-14414	AC	TGA
-recovered pasa_asmbl_30096.p2, internal, 13639, 13728
Valid prediction for snap_scaffold_22-snap.1195-T1
Valid prediction for HiQ_model.g34045.t1
Valid prediction for snap_scaffold_22-snap.1211-T1
Valid prediction for snap_scaffold_22-snap.1205-T1
Valid prediction for HiQ_model.g34036.t1
Valid prediction for GlimmerHMM_glimmerT_50798-T1
Couldn't classify 122052, 122193
Couldn't classify 122912, 123034
Sorry, prediction pasa_asmbl_30090.p1 fails validation.
(GTG)	 AC	122052-122193	GT	AGG
(GTG)	 AG	122429-122652	GT	AGG
(ATC)	 AG	122912-123034	GC	TGG
-recovered pasa_asmbl_30090.p1, internal, 122429, 122652
-recovered pasa_asmbl_30090.p1, internal, 122912, 123034
Valid prediction for Augustus_model.g34042.t1
Valid prediction for Augustus_model.g34037.t1
Valid prediction for snap_scaffold_22-snap.1226-T1
Valid prediction for GlimmerHMM_glimmerT_50793-T1
Valid prediction for CodingQuarry_transcript_34124-T1
Valid prediction for GlimmerHMM_glimmerT_50784-T1
Valid prediction for GeneMark_model.87865_t
Valid prediction for GeneMark_model.87872_t
Valid prediction for GeneMark_model.87863_t
Couldn't classify 168652, 168704
Sorry, prediction pasa_asmbl_30079.p1 fails validation.
(GGC)	 AG	168652-168704	GT	AAG
(TTG)	 AG	169732-169825	GT	AGG
(GTG)	 AG	169996-170082	GT	TGG
(TTC)	 AG	171445-171593	GT	ATG
(CTG)	 AG	171859-171952	GT	TGG
(TCA)	 AG	172208-172324	GT	AGG
(ACC)	 AG	172566-172736	GT	AGG
(ACA)	 AG	172886-172964	GT	AGG
(GCA)	 AG	173361-173521	GT	AGG
(GGC)	 AG	174121-174207	GT	AGG
(GAA)	 AG	175870-176092	GT	TGG
(GCA)	 AG	176183-176362	GT	AGG
(TCT)	 AG	176460-176663	GT	GGG
(ACG)	 AG	176820-176927	GT	CGG
(TGA)	 AG	177155-177243	GT	AGG
(GAA)	 AG	177321-177431	AG	AGA
add_exon() Sorry, pasa_asmbl_30079.p1 172886-172964-terminal-3 is invalid.
-recovered pasa_asmbl_30079.p1, terminal, 172886, 172964
-recovered pasa_asmbl_30079.p1, terminal, 177321, 177431
-recovered pasa_asmbl_30079.p1, internal, 168652, 168704
-recovered pasa_asmbl_30079.p1, internal, 169732, 169825
-recovered pasa_asmbl_30079.p1, internal, 169996, 170082
-recovered pasa_asmbl_30079.p1, internal, 171445, 171593
-recovered pasa_asmbl_30079.p1, internal, 171859, 171952
-recovered pasa_asmbl_30079.p1, internal, 172208, 172324
-recovered pasa_asmbl_30079.p1, internal, 172566, 172736
-recovered pasa_asmbl_30079.p1, internal, 172886, 172964
-recovered pasa_asmbl_30079.p1, internal, 173361, 173521
-recovered pasa_asmbl_30079.p1, internal, 174121, 174207
-recovered pasa_asmbl_30079.p1, internal, 175870, 176092
-recovered pasa_asmbl_30079.p1, internal, 176183, 176362
-recovered pasa_asmbl_30079.p1, internal, 176460, 176663
-recovered pasa_asmbl_30079.p1, internal, 176820, 176927
-recovered pasa_asmbl_30079.p1, internal, 177155, 177243
Valid prediction for Augustus_model.g34052.t1
Valid prediction for GeneMark_model.87900_t
Valid prediction for GlimmerHMM_glimmerT_50778-T1
Valid prediction for GlimmerHMM_glimmerT_50786-T1
Valid prediction for GeneMark_model.87928_t
Valid prediction for GlimmerHMM_glimmerT_50789-T1
Valid prediction for snap_scaffold_22-snap.1228-T1
Valid prediction for GeneMark_model.87914_t
Valid prediction for GeneMark_model.87887_t
Valid prediction for GeneMark_model.87888_t
Valid prediction for GeneMark_model.87891_t
Valid prediction for GeneMark_model.87906_t
Valid prediction for Augustus_model.g34043.t1
Valid prediction for GlimmerHMM_glimmerT_50792-T1
Valid prediction for GeneMark_model.87912_t
Valid prediction for pasa_asmbl_30092.p1
Valid prediction for Augustus_model.g34049.t1
Valid prediction for GeneMark_model.87908_t
Valid prediction for GeneMark_model.87899_t
Valid prediction for snap_scaffold_22-snap.1220-T1
Valid prediction for GlimmerHMM_glimmerT_50788-T1
Valid prediction for GeneMark_model.87920_t
Valid prediction for GeneMark_model.87916_t
Valid prediction for snap_scaffold_22-snap.1233-T1
Valid prediction for GeneMark_model.87880_t
Valid prediction for GlimmerHMM_glimmerT_50782-T1
Valid prediction for CodingQuarry_transcript_34121-T1
Valid prediction for GlimmerHMM_glimmerT_50775-T1
Valid prediction for GlimmerHMM_glimmerT_50790-T1
Valid prediction for Augustus_model.g34046.t1
Valid prediction for GeneMark_model.87918_t
Valid prediction for GlimmerHMM_glimmerT_50787-T1
Valid prediction for GlimmerHMM_glimmerT_50799-T1
Valid prediction for GlimmerHMM_glimmerT_50795-T1
Valid prediction for GeneMark_model.87883_t
Valid prediction for GeneMark_model.87875_t
Valid prediction for Augustus_model.g34044.t1
Valid prediction for GeneMark_model.87885_t
Valid prediction for snap_scaffold_22-snap.1227-T1
Valid prediction for Augustus_model.g34034.t1
Valid prediction for snap_scaffold_22-snap.1235-T1
Valid prediction for snap_scaffold_22-snap.1194-T1
Valid prediction for snap_scaffold_22-snap.1209-T1
Valid prediction for CodingQuarry_transcript_34125-T1
Valid prediction for GlimmerHMM_glimmerT_50803-T1
Valid prediction for Augustus_model.g34038.t1
Valid prediction for snap_scaffold_22-snap.1222-T1
Valid prediction for GeneMark_model.87926_t
Valid prediction for snap_scaffold_22-snap.1232-T1
Valid prediction for GlimmerHMM_glimmerT_50779-T1
Valid prediction for Augustus_model.g34040.t1
Valid prediction for Augustus_model.g34039.t1
Valid prediction for snap_scaffold_22-snap.1215-T1
Valid prediction for GeneMark_model.87864_t
Valid prediction for GlimmerHMM_glimmerT_50785-T1
Valid prediction for snap_scaffold_22-snap.1218-T1
Valid prediction for snap_scaffold_22-snap.1201-T1
Valid prediction for snap_scaffold_22-snap.1213-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 7878, rend_intergenic: 6073  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 9076, rend_intergenic: 8813  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19740, rend_intergenic: 11444  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44756, rend_intergenic: 39735  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70727, rend_intergenic: 66325  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74037, rend_intergenic: 70855  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80551, rend_intergenic: 74599  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82879, rend_intergenic: 80913  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90312, rend_intergenic: 86425  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95854, rend_intergenic: 91676  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102095, rend_intergenic: 96292  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108365, rend_intergenic: 102118  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113264, rend_intergenic: 109374  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125565, rend_intergenic: 113849  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141270, rend_intergenic: 126679  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155870, rend_intergenic: 141566  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163347, rend_intergenic: 156778  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167287, rend_intergenic: 163789  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 177664, rend_intergenic: 169279  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 180246, rend_intergenic: 178121  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 186243
-exon list size: 845


building trellis

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58.7    
58.8    
58.9    
59.0    
59.1    
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    
61.2    
61.3    
61.4    
61.5    
61.6    
61.7    
61.9    
62.0    
62.1    
62.2    
62.3    
62.5    
62.6    
62.7    
62.8    
62.9    
63.0    
63.2    
63.3    
63.4    
63.5    
63.6    
63.8    
63.9    
64.0    
64.1    
64.2    
64.3    
64.5    
64.6    
64.7    
64.8    
64.9    
65.1    
65.2    
65.3    
65.4    
65.5    
65.6    
65.8    
65.9    
66.0    
66.1    
66.2    
66.4    
66.5    
66.6    
66.7    
66.8    
66.9    
67.1    
67.2    
67.3    
67.4    
67.5    
67.7    
67.8    
67.9    
68.0    
68.1    
68.2    
68.4    
68.5    
68.6    
68.7    
68.8    
68.9    
69.1    
69.2    
69.3    
69.4    
69.5    
69.7    
69.8    
69.9    
70.0    
70.1    
70.2    
70.4    
70.5    
70.6    
70.7    
70.8    
71.0    
71.1    
71.2    
71.3    
71.4    
71.5    
71.7    
71.8    
71.9    
72.0    
72.1    
72.3    
72.4    
72.5    
72.6    
72.7    
72.8    
73.0    
73.1    
73.2    
73.3    
73.4    
73.6    
73.7    
73.8    
73.9    
74.0    
74.1    
74.3    
74.4    
74.5    
74.6    
74.7    
74.9    
75.0    
75.1    
75.2    
75.3    
75.4    
75.6    
75.7    
75.8    
75.9    
76.0    
76.2    
76.3    
76.4    
76.5    
76.6    
76.7    
76.9    
77.0    
77.1    
77.2    
77.3    
77.4    
77.6    
77.7    
77.8    
77.9    
78.0    
78.2    
78.3    
78.4    
78.5    
78.6    
78.7    
78.9    
79.0    
79.1    
79.2    
79.3    
79.5    
79.6    
79.7    
79.8    
79.9    
80.0    
80.2    
80.3    
80.4    
80.5    
80.6    
80.8    
80.9    
81.0    
81.1    
81.2    
81.3    
81.5    
81.6    
81.7    
81.8    
81.9    
82.1    
82.2    
82.3    
82.4    
82.5    
82.6    
82.8    
82.9    
83.0    
83.1    
83.2    
83.4    
83.5    
83.6    
83.7    
83.8    
83.9    
84.1    
84.2    
84.3    
84.4    
84.5    
84.7    
84.8    
84.9    
85.0    
85.1    
85.2    
85.4    
85.5    
85.6    
85.7    
85.8    
86.0    
86.1    
86.2    
86.3    
86.4    
86.5    
86.7    
86.8    
86.9    
87.0    
87.1    
87.2    
87.4    
87.5    
87.6    
87.7    
87.8    
88.0    
88.1    
88.2    
88.3    
88.4    
88.5    
88.7    
88.8    
88.9    
89.0    
89.1    
89.3    
89.4    
89.5    
89.6    
89.7    
89.8    
90.0    
90.1    
90.2    
90.3    
90.4    
90.6    
90.7    
90.8    
90.9    
91.0    
91.1    
91.3    
91.4    
91.5    
91.6    
91.7    
91.9    
92.0    
92.1    
92.2    
92.3    
92.4    
92.6    
92.7    
92.8    
92.9    
93.0    
93.2    
93.3    
93.4    
93.5    
93.6    
93.7    
93.9    
94.0    
94.1    
94.2    
94.3    
94.5    
94.6    
94.7    
94.8    
94.9    
95.0    
95.2    
95.3    
95.4    
95.5    
95.6    
95.7    
95.9    
96.0    
96.1    
96.2    
96.3    
96.5    
96.6    
96.7    
96.8    
96.9    
97.0    
97.2    
97.3    
97.4    
97.5    
97.6    
97.8    
97.9    
98.0    
98.1    
98.2    
98.3    
98.5    
98.6    
98.7    
98.8    
98.9    
99.1    
99.2    
99.3    
99.4    
99.5    
99.6    
99.8    
99.9    
-found 48 predictions from path traversal
Error with prediction: snap lend_intergenic: 7878, rend_intergenic: 6073  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 9076, rend_intergenic: 8813  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19740, rend_intergenic: 11444  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44756, rend_intergenic: 39735  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70727, rend_intergenic: 66325  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74037, rend_intergenic: 70855  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80551, rend_intergenic: 74599  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82879, rend_intergenic: 80913  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90312, rend_intergenic: 86425  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95854, rend_intergenic: 91676  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102095, rend_intergenic: 96292  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108365, rend_intergenic: 102118  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113264, rend_intergenic: 109374  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125565, rend_intergenic: 113849  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141270, rend_intergenic: 126679  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155870, rend_intergenic: 141566  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163347, rend_intergenic: 156778  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167287, rend_intergenic: 163789  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 177664, rend_intergenic: 169279  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 180246, rend_intergenic: 178121  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 19 predictions persist after filtering for low support