-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_13/scaffold_13_6415104-6683877

-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.55572_t
Valid prediction for pasa_asmbl_10930.p1
Valid prediction for snap_scaffold_13-snap.1190-T1
Valid prediction for GeneMark_model.55545_t
Valid prediction for GeneMark_model.55558_t
Valid prediction for snap_scaffold_13-snap.1203-T1
Valid prediction for GlimmerHMM_glimmerT_32489-T1
Valid prediction for snap_scaffold_13-snap.1213-T1
Valid prediction for GeneMark_model.55540_t
Valid prediction for snap_scaffold_13-snap.1215-T1
Couldn't classify 216239, 216301
Couldn't classify 217653, 217711
Sorry, prediction pasa_asmbl_10946.p1 fails validation.
(GGC)	 AG	216239-216301	GT	AGG
(ACA)	 AG	216588-216712	GT	AGG
(CCC)	 AG	216797-216905	GT	CAG
(GAA)	 AG	217006-217113	GT	AAG
(GTC)	 AG	217372-217525	GT	AGG
(GTG)	 AG	217653-217711	AC	GGA
-recovered pasa_asmbl_10946.p1, internal, 216239, 216301
-recovered pasa_asmbl_10946.p1, internal, 216588, 216712
-recovered pasa_asmbl_10946.p1, internal, 216797, 216905
-recovered pasa_asmbl_10946.p1, internal, 217006, 217113
-recovered pasa_asmbl_10946.p1, internal, 217372, 217525
Valid prediction for GlimmerHMM_glimmerT_32490-T1
Valid prediction for HiQ_model.g21758.t1
Valid prediction for snap_scaffold_13-snap.1211-T1
Valid prediction for CodingQuarry_transcript_13044-T1
Couldn't classify 184824, 185314
Sorry, prediction pasa_asmbl_10929.p1 fails validation.
(ATG)	 AG	183779-183803	GT	AGG
(ATG)	 AG	183930-184040	GT	TCG
(GTA)	 AG	184133-184273	GT	TGG
(ATC)	 AG	184389-184507	GT	AGG
(GCT)	 AG	184586-184703	GT	GGG
(GTG)	 AG	184824-185314	GT	GGG
-recovered pasa_asmbl_10929.p1, initial, 183779, 183803
add_exon() Sorry, pasa_asmbl_10929.p1 183930-184040-initial-1 is invalid.
-recovered pasa_asmbl_10929.p1, initial, 183930, 184040
-recovered pasa_asmbl_10929.p1, internal, 183779, 183803
-recovered pasa_asmbl_10929.p1, internal, 183930, 184040
-recovered pasa_asmbl_10929.p1, internal, 184133, 184273
-recovered pasa_asmbl_10929.p1, internal, 184389, 184507
-recovered pasa_asmbl_10929.p1, internal, 184586, 184703
-recovered pasa_asmbl_10929.p1, internal, 184824, 185314
Valid prediction for GeneMark_model.55554_t
Valid prediction for Augustus_model.g21772.t1
Valid prediction for snap_scaffold_13-snap.1196-T1
Valid prediction for snap_scaffold_13-snap.1219-T1
Valid prediction for CodingQuarry_transcript_13036-T1
Valid prediction for snap_scaffold_13-snap.1214-T1
Valid prediction for GeneMark_model.55568_t
Couldn't classify 152855, 152920
Couldn't classify 154107, 154719
Sorry, prediction pasa_asmbl_10925.p1 fails validation.
(TTC)	 AG	152855-152920	GT	GTG
(GGG)	 AG	153794-153987	GT	AGG
(GTA)	 AG	154107-154719	CT	ACC
-recovered pasa_asmbl_10925.p1, internal, 152855, 152920
-recovered pasa_asmbl_10925.p1, internal, 153794, 153987
Valid prediction for GeneMark_model.55556_t
Valid prediction for snap_scaffold_13-snap.1208-T1
Valid prediction for pasa_asmbl_10923.p1
Valid prediction for GlimmerHMM_glimmerT_32511-T1
Valid prediction for Augustus_model.g21773.t1
Valid prediction for GlimmerHMM_glimmerT_32508-T1
Valid prediction for pasa_asmbl_10922.p1
Valid prediction for Augustus_model.g21764.t1
Couldn't classify 154996, 155140
Couldn't classify 156988, 157361
Sorry, prediction pasa_asmbl_10926.p1 fails validation.
(TCC)	 CC	154996-155140	GT	AGG
(ACC)	 AG	155409-155501	GT	AGG
(CAT)	 AG	155838-156007	GT	ACG
(TCC)	 AG	156368-156568	GT	AGG
(GTT)	 AG	156762-156846	GT	GGG
(ATT)	 AG	156988-157361	TT	ACT
-recovered pasa_asmbl_10926.p1, internal, 155409, 155501
-recovered pasa_asmbl_10926.p1, internal, 155838, 156007
-recovered pasa_asmbl_10926.p1, internal, 156368, 156568
-recovered pasa_asmbl_10926.p1, internal, 156762, 156846
Valid prediction for pasa_asmbl_10940.p2
Valid prediction for GeneMark_model.55552_t
Valid prediction for GlimmerHMM_glimmerT_32515-T1
Valid prediction for Augustus_model.g21775.t1
Valid prediction for GeneMark_model.55543_t
Valid prediction for GlimmerHMM_glimmerT_32491-T1
Valid prediction for snap_scaffold_13-snap.1222-T1
Valid prediction for Augustus_model.g21781.t1
Valid prediction for CodingQuarry_transcript_13043-T1
Valid prediction for snap_scaffold_13-snap.1199-T1
Valid prediction for GeneMark_model.55571_t
Valid prediction for Augustus_model.g21765.t1
Valid prediction for snap_scaffold_13-snap.1191-T1
Valid prediction for GlimmerHMM_glimmerT_32504-T1
Valid prediction for GlimmerHMM_glimmerT_32506-T1
Valid prediction for GeneMark_model.55580_t
Valid prediction for GlimmerHMM_glimmerT_32500-T1
Valid prediction for GeneMark_model.55574_t
Valid prediction for GeneMark_model.55549_t
Valid prediction for GlimmerHMM_glimmerT_32512-T1
Valid prediction for GeneMark_model.55578_t
Valid prediction for Augustus_model.g21783.t1
Valid prediction for snap_scaffold_13-snap.1189-T1
Valid prediction for snap_scaffold_13-snap.1221-T1
Valid prediction for CodingQuarry_transcript_13041-T1
Valid prediction for GeneMark_model.55541_t
Valid prediction for snap_scaffold_13-snap.1217-T1
Valid prediction for GeneMark_model.55576_t
Valid prediction for GlimmerHMM_glimmerT_32499-T1
Valid prediction for GlimmerHMM_glimmerT_32517-T1
Valid prediction for GlimmerHMM_glimmerT_32510-T1
Valid prediction for Augustus_model.g21770.t1
Valid prediction for snap_scaffold_13-snap.1220-T1
Valid prediction for Augustus_model.g21777.t1
Valid prediction for snap_scaffold_13-snap.1228-T1
Valid prediction for Augustus_model.g21778.t1
Valid prediction for pasa_asmbl_10928.p1
Valid prediction for snap_scaffold_13-snap.1225-T1
Valid prediction for Augustus_model.g21780.t1
Valid prediction for GlimmerHMM_glimmerT_32514-T1
Valid prediction for GeneMark_model.55564_t
Valid prediction for snap_scaffold_13-snap.1193-T1
Valid prediction for GeneMark_model.55566_t
Valid prediction for snap_scaffold_13-snap.1224-T1
Valid prediction for GeneMark_model.55547_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 pasa_asmbl_10282.p1
Valid prediction for GeneMark_model.55551_t
Valid prediction for GlimmerHMM_glimmerT_32503-T1
Valid prediction for Augustus_model.g21759.t1
Valid prediction for snap_scaffold_13-snap.1201-T1
Valid prediction for GeneMark_model.55557_t
Valid prediction for GlimmerHMM_glimmerT_32507-T1
Valid prediction for snap_scaffold_13-snap.1192-T1
Couldn't classify 166335, 166363
Sorry, prediction pasa_asmbl_9757.p1 fails validation.
(TCA)	 TT	166335-166363	GT	AGG
(ACA)	 AG	166510-166684	GT	TTG
(GGT)	 AG	166799-166917	GT	AGG
(ACC)	 AG	167047-167137	GT	CAG
(GAG)	 AG	167273-167344	GT	GTG
(GTA)	 AG	167467-167589	GT	AGG
(GAC)	 AG	167704-167775	GT	AGG
(GGC)	 AG	167927-168058	GT	AGG
(GCG)	 AG	168165-168227	GT	AGG
(ATT)	 AG	168465-168531	GT	AGG
(CCC)	 AG	168839-169017	TG	GAT
-recovered pasa_asmbl_9757.p1, terminal, 168839, 169017
-recovered pasa_asmbl_9757.p1, internal, 166510, 166684
-recovered pasa_asmbl_9757.p1, internal, 166799, 166917
-recovered pasa_asmbl_9757.p1, internal, 167047, 167137
-recovered pasa_asmbl_9757.p1, internal, 167273, 167344
-recovered pasa_asmbl_9757.p1, internal, 167467, 167589
-recovered pasa_asmbl_9757.p1, internal, 167704, 167775
-recovered pasa_asmbl_9757.p1, internal, 167927, 168058
-recovered pasa_asmbl_9757.p1, internal, 168165, 168227
-recovered pasa_asmbl_9757.p1, internal, 168465, 168531
Valid prediction for GlimmerHMM_glimmerT_32513-T1
Valid prediction for Augustus_model.g21763.t1
Valid prediction for Augustus_model.g21760.t1
Valid prediction for HiQ_model.g21779.t1
Valid prediction for GeneMark_model.55550_t
Valid prediction for snap_scaffold_13-snap.1207-T1
Valid prediction for CodingQuarry_transcript_13038-T1
Valid prediction for GeneMark_model.55563_t
Valid prediction for GeneMark_model.55559_t
Valid prediction for pasa_asmbl_9759.p2
Couldn't classify 208394, 208510
Sorry, prediction pasa_asmbl_10283.p1 fails validation.
(CCC)	 CC	208394-208510	GT	AGG
(GTC)	 AG	209465-209812	CT	GAC
-recovered pasa_asmbl_10283.p1, terminal, 209465, 209812
Valid prediction for GeneMark_model.55562_t
Valid prediction for Augustus_model.g21782.t1
Valid prediction for GeneMark_model.55555_t
Couldn't classify 141100, 141210
Sorry, prediction pasa_asmbl_9760.p1 fails validation.
(GAC)	 CA	141100-141210	GT	AGG
(TGT)	 AG	142282-142411	GT	TGG
(ACA)	 AG	143746-143772	GT	AGG
(AAT)	 AG	146381-146477	GT	TGG
(GTG)	 AG	146754-146902	GT	TGG
(ACA)	 AG	149693-149764	GT	AGG
(ACA)	 AG	150399-150516	GT	AGG
(ATG)	 AG	150875-151036	GT	AGG
(GAA)	 AG	151419-151503	CT	AGC
add_exon() Sorry, pasa_asmbl_9760.p1 150875-151036-initial-1 is invalid.
-recovered pasa_asmbl_9760.p1, initial, 150875, 151036
add_exon() Sorry, pasa_asmbl_9760.p1 149693-149764-terminal-1 is invalid.
-recovered pasa_asmbl_9760.p1, terminal, 149693, 149764
-recovered pasa_asmbl_9760.p1, terminal, 151419, 151503
-recovered pasa_asmbl_9760.p1, internal, 142282, 142411
-recovered pasa_asmbl_9760.p1, internal, 143746, 143772
-recovered pasa_asmbl_9760.p1, internal, 146381, 146477
-recovered pasa_asmbl_9760.p1, internal, 146754, 146902
-recovered pasa_asmbl_9760.p1, internal, 149693, 149764
-recovered pasa_asmbl_9760.p1, internal, 150399, 150516
-recovered pasa_asmbl_9760.p1, internal, 150875, 151036
Valid prediction for CodingQuarry_transcript_13040-T1
Valid prediction for GeneMark_model.55544_t
Valid prediction for GeneMark_model.55542_t
Valid prediction for snap_scaffold_13-snap.1218-T1
Valid prediction for snap_scaffold_13-snap.1194-T1
Valid prediction for snap_scaffold_13-snap.1195-T1
Valid prediction for Augustus_model.g21762.t1
Valid prediction for GlimmerHMM_glimmerT_32505-T1
Valid prediction for snap_scaffold_13-snap.1212-T1
Valid prediction for snap_scaffold_13-snap.1209-T1
Valid prediction for CodingQuarry_transcript_13046-T1
Valid prediction for GlimmerHMM_glimmerT_32496-T1
Valid prediction for pasa_asmbl_9762.p1
Valid prediction for Augustus_model.g21774.t1
Valid prediction for GeneMark_model.55569_t
Valid prediction for snap_scaffold_13-snap.1226-T1
Valid prediction for Augustus_model.g21771.t1
Valid prediction for HiQ_model.g21776.t1
Valid prediction for snap_scaffold_13-snap.1204-T1
Valid prediction for snap_scaffold_13-snap.1200-T1
Valid prediction for snap_scaffold_13-snap.1198-T1
Valid prediction for CodingQuarry_transcript_13037-T1
Valid prediction for snap_scaffold_13-snap.1197-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for HiQ_model.g21766.t1
Valid prediction for snap_scaffold_13-snap.1227-T1
Valid prediction for GlimmerHMM_glimmerT_32502-T1
Valid prediction for GeneMark_model.55570_t
Valid prediction for GlimmerHMM_glimmerT_32493-T1
Valid prediction for GeneMark_model.55579_t
Valid prediction for GlimmerHMM_glimmerT_32497-T1
Valid prediction for GlimmerHMM_glimmerT_32516-T1
Valid prediction for GeneMark_model.55567_t
Valid prediction for GeneMark_model.55560_t
Valid prediction for GeneMark_model.55548_t
Valid prediction for GlimmerHMM_glimmerT_32492-T1
Couldn't classify 240157, 240174
Couldn't classify 243842, 243939
Sorry, prediction pasa_asmbl_10407.p1 fails validation.
(CAG)	 AC	240157-240174	GT	GGG
(GTC)	 AG	241569-241619	GT	AAG
(GTT)	 AG	242820-242912	GT	ACG
(GTC)	 AG	243588-243669	GT	AGG
(GAG)	 AG	243842-243939	GA	GAG
-recovered pasa_asmbl_10407.p1, internal, 241569, 241619
-recovered pasa_asmbl_10407.p1, internal, 242820, 242912
-recovered pasa_asmbl_10407.p1, internal, 243588, 243669
Valid prediction for CodingQuarry_transcript_13042-T1
Valid prediction for pasa_asmbl_9758.p1
Valid prediction for snap_scaffold_13-snap.1216-T1
Valid prediction for snap_scaffold_13-snap.1206-T1
Valid prediction for Augustus_model.g21769.t1
Valid prediction for GeneMark_model.55575_t
Valid prediction for GlimmerHMM_glimmerT_32495-T1
Valid prediction for GeneMark_model.55577_t
Valid prediction for pasa_asmbl_9768.p1
Valid prediction for Augustus_model.g21768.t1
Valid prediction for GeneMark_model.55561_t
Valid prediction for GlimmerHMM_glimmerT_32494-T1
Valid prediction for HiQ_model.g21767.t1
Valid prediction for snap_scaffold_13-snap.1205-T1
Valid prediction for snap_scaffold_13-snap.1223-T1
Valid prediction for GeneMark_model.55546_t
Valid prediction for GlimmerHMM_glimmerT_32501-T1
Valid prediction for GeneMark_model.55553_t
Valid prediction for GeneMark_model.55573_t
Valid prediction for snap_scaffold_13-snap.1202-T1
Valid prediction for snap_scaffold_13-snap.1210-T1
Valid prediction for GlimmerHMM_glimmerT_32509-T1
Valid prediction for Augustus_model.g21761.t1
Valid prediction for GeneMark_model.55565_t
Valid prediction for GlimmerHMM_glimmerT_32498-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 33834, rend_intergenic: 26376  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48706, rend_intergenic: 43437  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56044, rend_intergenic: 48878  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74572, rend_intergenic: 69904  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 211474, rend_intergenic: 208098  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 268774
-exon list size: 655


building trellis

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63.8    
63.9    
64.1    
64.2    
64.4    
64.5    
64.7    
64.8    
65.0    
65.1    
65.3    
65.4    
65.6    
65.8    
65.9    
66.1    
66.2    
66.4    
66.5    
66.7    
66.8    
67.0    
67.1    
67.3    
67.4    
67.6    
67.7    
67.9    
68.0    
68.2    
68.3    
68.5    
68.6    
68.8    
68.9    
69.1    
69.3    
69.4    
69.6    
69.7    
69.9    
70.0    
70.2    
70.3    
70.5    
70.6    
70.8    
70.9    
71.1    
71.2    
71.4    
71.5    
71.7    
71.8    
72.0    
72.1    
72.3    
72.5    
72.6    
72.8    
72.9    
73.1    
73.2    
73.4    
73.5    
73.7    
73.8    
74.0    
74.1    
74.3    
74.4    
74.6    
74.7    
74.9    
75.0    
75.2    
75.3    
75.5    
75.6    
75.8    
76.0    
76.1    
76.3    
76.4    
76.6    
76.7    
76.9    
77.0    
77.2    
77.3    
77.5    
77.6    
77.8    
77.9    
78.1    
78.2    
78.4    
78.5    
78.7    
78.8    
79.0    
79.1    
79.3    
79.5    
79.6    
79.8    
79.9    
80.1    
80.2    
80.4    
80.5    
80.7    
80.8    
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    
83.0    
83.1    
83.3    
83.4    
83.6    
83.7    
83.9    
84.0    
84.2    
84.3    
84.5    
84.6    
84.8    
84.9    
85.1    
85.2    
85.4    
85.5    
85.7    
85.8    
86.0    
86.1    
86.3    
86.5    
86.6    
86.8    
86.9    
87.1    
87.2    
87.4    
87.5    
87.7    
87.8    
88.0    
88.1    
88.3    
88.4    
88.6    
88.7    
88.9    
89.0    
89.2    
89.3    
89.5    
89.6    
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    
92.1    
92.2    
92.4    
92.5    
92.7    
92.8    
93.0    
93.2    
93.3    
93.5    
93.6    
93.8    
93.9    
94.1    
94.2    
94.4    
94.5    
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    
96.7    
96.8    
97.0    
97.1    
97.3    
97.4    
97.6    
97.7    
97.9    
98.0    
98.2    
98.3    
98.5    
98.6    
98.8    
98.9    
99.1    
99.2    
99.4    
99.5    
99.7    
99.8    
-found 35 predictions from path traversal
Error with prediction: snap lend_intergenic: 33834, rend_intergenic: 26376  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48706, rend_intergenic: 43437  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56044, rend_intergenic: 48878  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74572, rend_intergenic: 69904  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 211474, rend_intergenic: 208098  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 28 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 254856 - 268774
-exon list size: 7


building trellis

11.1    
22.2    
33.3    
44.4    
55.6    
66.7    
77.8    
88.9    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 258345 - 268774
-exon list size: 4


building trellis

16.7    
33.3    
50.0    
66.7    
83.3    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support