-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_24/scaffold_24_307040-488066

-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 GlimmerHMM_glimmerT_53145-T1
Valid prediction for snap_scaffold_24-snap.67-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for snap_scaffold_24-snap.81-T1
Valid prediction for GlimmerHMM_glimmerT_53133-T1
Valid prediction for GlimmerHMM_glimmerT_53138-T1
Valid prediction for CodingQuarry_transcript_37147-T1
Valid prediction for Augustus_model.g35622.t1
Couldn't classify 29271, 29428
Sorry, prediction pasa_asmbl_32014.p1 fails validation.
(ATG)	 GC	26704-26926	GT	TGG
(GTG)	 AG	27107-27235	GT	AGG
(GCG)	 AG	29271-29428	GG	GGG
-recovered pasa_asmbl_32014.p1, initial, 26704, 26926
-recovered pasa_asmbl_32014.p1, internal, 27107, 27235
Valid prediction for GeneMark_model.92359_t
Valid prediction for GeneMark_model.92353_t
Valid prediction for snap_scaffold_24-snap.85-T1
Valid prediction for Augustus_model.g35621.t1
Valid prediction for snap_scaffold_24-snap.95-T1
Valid prediction for Augustus_model.g35620.t1
Valid prediction for GlimmerHMM_glimmerT_53135-T1
Valid prediction for snap_scaffold_24-snap.97-T1
Valid prediction for snap_scaffold_24-snap.73-T1
Valid prediction for GeneMark_model.92383_t
Valid prediction for GeneMark_model.92351_t
Valid prediction for GeneMark_model.92363_t
Valid prediction for snap_scaffold_24-snap.90-T1
Valid prediction for GlimmerHMM_glimmerT_53142-T1
Valid prediction for GeneMark_model.92390_t
Couldn't classify 133828, 134124
Sorry, prediction pasa_asmbl_32020.p1 fails validation.
(AAC)	 GC	133828-134124	GA	AGG
Valid prediction for pasa_asmbl_32017.p1
Valid prediction for snap_scaffold_24-snap.104-T1
Valid prediction for GeneMark_model.92379_t
Valid prediction for GlimmerHMM_glimmerT_53126-T1
Valid prediction for Augustus_model.g35612.t1
Valid prediction for GlimmerHMM_glimmerT_53143-T1
Valid prediction for snap_scaffold_24-snap.75-T1
Valid prediction for GeneMark_model.92360_t
Valid prediction for snap_scaffold_24-snap.80-T1
Valid prediction for GeneMark_model.92346_t
Couldn't classify 6324, 6410
Couldn't classify 13535, 13671
Sorry, prediction pasa_asmbl_32013.p1 fails validation.
(GGC)	 CT	6324-6410	GT	AGG
(CGT)	 AG	7331-7420	GT	TGG
(TGG)	 AG	7888-8021	GT	TGG
(GGA)	 AG	8274-8355	GT	AGG
(GAG)	 AG	9038-9275	GT	AGG
(AGG)	 AG	9897-10027	GT	GGG
(GAG)	 AG	10179-10247	GT	TGG
(TTC)	 AG	10420-10509	GT	TTG
(GTG)	 AG	11224-11306	GT	AGG
(TTC)	 AG	11491-11606	GT	CAG
(TAT)	 AG	13535-13671	CA	ACC
-recovered pasa_asmbl_32013.p1, internal, 7331, 7420
-recovered pasa_asmbl_32013.p1, internal, 7888, 8021
-recovered pasa_asmbl_32013.p1, internal, 8274, 8355
-recovered pasa_asmbl_32013.p1, internal, 9038, 9275
-recovered pasa_asmbl_32013.p1, internal, 9897, 10027
-recovered pasa_asmbl_32013.p1, internal, 10179, 10247
-recovered pasa_asmbl_32013.p1, internal, 10420, 10509
-recovered pasa_asmbl_32013.p1, internal, 11224, 11306
-recovered pasa_asmbl_32013.p1, internal, 11491, 11606
Valid prediction for GeneMark_model.92377_t
Valid prediction for HiQ_model.g35614.t1
Valid prediction for GeneMark_model.92370_t
Couldn't classify 133549, 133659
Sorry, prediction pasa_asmbl_32019.p1 fails validation.
(ATG)	 TG	132175-132285	GT	AGG
(CTT)	 AG	132362-132520	GT	TCG
(AGC)	 AG	133044-133208	GT	AGG
(GAG)	 AG	133549-133659	AA	AGA
-recovered pasa_asmbl_32019.p1, initial, 132175, 132285
-recovered pasa_asmbl_32019.p1, internal, 132362, 132520
-recovered pasa_asmbl_32019.p1, internal, 133044, 133208
Valid prediction for GlimmerHMM_glimmerT_53136-T1
Valid prediction for GeneMark_model.92344_t
Valid prediction for Augustus_model.g35624.t1
Valid prediction for HiQ_model.g35619.t1
Valid prediction for GeneMark_model.92380_t
Valid prediction for snap_scaffold_24-snap.70-T1
Valid prediction for GeneMark_model.92386_t
Valid prediction for GeneMark_model.92374_t
Valid prediction for GeneMark_model.92357_t
Valid prediction for snap_scaffold_24-snap.79-T1
Valid prediction for GlimmerHMM_glimmerT_53128-T1
Valid prediction for snap_scaffold_24-snap.72-T1
Valid prediction for CodingQuarry_transcript_37146-T1
Valid prediction for GeneMark_model.92373_t
Valid prediction for GlimmerHMM_glimmerT_53140-T1
Valid prediction for GeneMark_model.92382_t
Valid prediction for pasa_asmbl_32024.p1
Valid prediction for snap_scaffold_24-snap.94-T1
Valid prediction for pasa_asmbl_32021.p2
Valid prediction for GeneMark_model.92342_t
Valid prediction for HiQ_model.g35623.t1
Valid prediction for GlimmerHMM_glimmerT_53141-T1
Valid prediction for GlimmerHMM_glimmerT_53144-T1
Valid prediction for GeneMark_model.92355_t
Valid prediction for Augustus_model.g35618.t1
Valid prediction for GeneMark_model.92384_t
Valid prediction for GlimmerHMM_glimmerT_53134-T1
Valid prediction for snap_scaffold_24-snap.84-T1
Valid prediction for snap_scaffold_24-snap.77-T1
Valid prediction for GeneMark_model.92349_t
Valid prediction for GeneMark_model.92365_t
Valid prediction for Augustus_model.g35625.t1
Valid prediction for GlimmerHMM_glimmerT_53139-T1
Valid prediction for snap_scaffold_24-snap.101-T1
Valid prediction for GeneMark_model.92367_t
Valid prediction for GlimmerHMM_glimmerT_53137-T1
Valid prediction for snap_scaffold_24-snap.102-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.92388_t
Valid prediction for GlimmerHMM_glimmerT_53130-T1
Valid prediction for GeneMark_model.92375_t
Valid prediction for snap_scaffold_24-snap.68-T1
Valid prediction for snap_scaffold_24-snap.93-T1
Valid prediction for snap_scaffold_24-snap.74-T1
Valid prediction for GeneMark_model.92348_t
Valid prediction for snap_scaffold_24-snap.109-T1
Valid prediction for snap_scaffold_24-snap.107-T1
Valid prediction for snap_scaffold_24-snap.69-T1
Valid prediction for Augustus_model.g35615.t1
Valid prediction for GeneMark_model.92352_t
Valid prediction for GeneMark_model.92364_t
Valid prediction for GeneMark_model.92389_t
Valid prediction for snap_scaffold_24-snap.91-T1
Valid prediction for GeneMark_model.92343_t
Valid prediction for GeneMark_model.92347_t
Valid prediction for GeneMark_model.92387_t
Valid prediction for GeneMark_model.92356_t
Valid prediction for snap_scaffold_24-snap.82-T1
Valid prediction for snap_scaffold_24-snap.76-T1
Valid prediction for snap_scaffold_24-snap.86-T1
Valid prediction for snap_scaffold_24-snap.87-T1
Valid prediction for snap_scaffold_24-snap.78-T1
Valid prediction for GeneMark_model.92376_t
Valid prediction for GeneMark_model.92371_t
Valid prediction for snap_scaffold_24-snap.99-T1
Valid prediction for GeneMark_model.92385_t
Valid prediction for Augustus_model.g35616.t1
Couldn't classify 140048, 140246
Couldn't classify 140352, 140461
Sorry, prediction CodingQuarry_transcript_37145-T1 fails validation.
(ATG)	 CA	138965-138999	GT	TGG
(GCC)	 AG	139466-139556	GT	CCG
(GGC)	 AG	140048-140246	AA	GGA
(TGG)	 GG	140352-140461	GC	AAG
-recovered CodingQuarry_transcript_37145-T1, initial, 138965, 138999
-recovered CodingQuarry_transcript_37145-T1, internal, 139466, 139556
Valid prediction for Augustus_model.g35613.t1
Valid prediction for snap_scaffold_24-snap.92-T1
Valid prediction for GeneMark_model.92361_t
Valid prediction for snap_scaffold_24-snap.105-T1
Valid prediction for snap_scaffold_24-snap.83-T1
Valid prediction for snap_scaffold_24-snap.100-T1
Valid prediction for snap_scaffold_24-snap.89-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_53127-T1
Valid prediction for GlimmerHMM_glimmerT_53132-T1
Valid prediction for GlimmerHMM_glimmerT_53129-T1
Couldn't classify 127031, 127107
Sorry, prediction pasa_asmbl_32697.p1 fails validation.
(ACC)	 CC	127031-127107	GT	CAG
(GGT)	 AG	127308-127494	GT	AGG
(GAG)	 AG	127823-127961	GT	TGG
(GTC)	 AG	129600-129772	GT	AGG
(ATA)	 AG	129953-129985	GT	AGG
(CTG)	 AG	130529-130687	GT	GAG
-recovered pasa_asmbl_32697.p1, terminal, 130529, 130687
-recovered pasa_asmbl_32697.p1, internal, 127308, 127494
-recovered pasa_asmbl_32697.p1, internal, 127823, 127961
-recovered pasa_asmbl_32697.p1, internal, 129600, 129772
-recovered pasa_asmbl_32697.p1, internal, 129953, 129985
-recovered pasa_asmbl_32697.p1, internal, 130529, 130687
Valid prediction for snap_scaffold_24-snap.108-T1
Valid prediction for GeneMark_model.92378_t
Valid prediction for snap_scaffold_24-snap.98-T1
Valid prediction for snap_scaffold_24-snap.106-T1
Valid prediction for GeneMark_model.92372_t
Valid prediction for GeneMark_model.92341_t
Valid prediction for GeneMark_model.92362_t
Valid prediction for GeneMark_model.92369_t
Valid prediction for GeneMark_model.92345_t
Valid prediction for GlimmerHMM_glimmerT_53131-T1
Valid prediction for snap_scaffold_24-snap.103-T1
Valid prediction for Augustus_model.g35617.t1
Valid prediction for snap_scaffold_24-snap.88-T1
Valid prediction for snap_scaffold_24-snap.71-T1
Valid prediction for GeneMark_model.92358_t
Valid prediction for GeneMark_model.92350_t
Valid prediction for snap_scaffold_24-snap.96-T1
Valid prediction for GeneMark_model.92366_t
Valid prediction for snap_scaffold_24-snap.110-T1
Valid prediction for GeneMark_model.92354_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 16123, rend_intergenic: 6248  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21581, rend_intergenic: 17187  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24566, rend_intergenic: 22118  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46043, rend_intergenic: 45268  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49431, rend_intergenic: 48005  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58342, rend_intergenic: 50454  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60908, rend_intergenic: 58955  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68732, rend_intergenic: 66519  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86831, rend_intergenic: 70721  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92200, rend_intergenic: 86853  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104637, rend_intergenic: 92608  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106408, rend_intergenic: 105067  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117786, rend_intergenic: 114584  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132715, rend_intergenic: 119935  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133607, rend_intergenic: 133050  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140791, rend_intergenic: 136739  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175076, rend_intergenic: 143306  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 181027
-exon list size: 881


building trellis

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64.8    
64.9    
65.0    
65.1    
65.2    
65.3    
65.5    
65.6    
65.7    
65.8    
65.9    
66.0    
66.1    
66.3    
66.4    
66.5    
66.6    
66.7    
66.8    
66.9    
67.0    
67.2    
67.3    
67.4    
67.5    
67.6    
67.7    
67.8    
68.0    
68.1    
68.2    
68.3    
68.4    
68.5    
68.6    
68.7    
68.9    
69.0    
69.1    
69.2    
69.3    
69.4    
69.5    
69.6    
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    
72.3    
72.4    
72.5    
72.6    
72.7    
72.8    
72.9    
73.0    
73.2    
73.3    
73.4    
73.5    
73.6    
73.7    
73.8    
74.0    
74.1    
74.2    
74.3    
74.4    
74.5    
74.6    
74.7    
74.9    
75.0    
75.1    
75.2    
75.3    
75.4    
75.5    
75.7    
75.8    
75.9    
76.0    
76.1    
76.2    
76.3    
76.4    
76.6    
76.7    
76.8    
76.9    
77.0    
77.1    
77.2    
77.3    
77.5    
77.6    
77.7    
77.8    
77.9    
78.0    
78.1    
78.3    
78.4    
78.5    
78.6    
78.7    
78.8    
78.9    
79.0    
79.2    
79.3    
79.4    
79.5    
79.6    
79.7    
79.8    
80.0    
80.1    
80.2    
80.3    
80.4    
80.5    
80.6    
80.7    
80.9    
81.0    
81.1    
81.2    
81.3    
81.4    
81.5    
81.7    
81.8    
81.9    
82.0    
82.1    
82.2    
82.3    
82.4    
82.6    
82.7    
82.8    
82.9    
83.0    
83.1    
83.2    
83.4    
83.5    
83.6    
83.7    
83.8    
83.9    
84.0    
84.1    
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    
87.7    
87.8    
87.9    
88.0    
88.1    
88.2    
88.3    
88.4    
88.6    
88.7    
88.8    
88.9    
89.0    
89.1    
89.2    
89.4    
89.5    
89.6    
89.7    
89.8    
89.9    
90.0    
90.1    
90.3    
90.4    
90.5    
90.6    
90.7    
90.8    
90.9    
91.1    
91.2    
91.3    
91.4    
91.5    
91.6    
91.7    
91.8    
92.0    
92.1    
92.2    
92.3    
92.4    
92.5    
92.6    
92.8    
92.9    
93.0    
93.1    
93.2    
93.3    
93.4    
93.5    
93.7    
93.8    
93.9    
94.0    
94.1    
94.2    
94.3    
94.5    
94.6    
94.7    
94.8    
94.9    
95.0    
95.1    
95.2    
95.4    
95.5    
95.6    
95.7    
95.8    
95.9    
96.0    
96.1    
96.3    
96.4    
96.5    
96.6    
96.7    
96.8    
96.9    
97.1    
97.2    
97.3    
97.4    
97.5    
97.6    
97.7    
97.8    
98.0    
98.1    
98.2    
98.3    
98.4    
98.5    
98.6    
98.8    
98.9    
99.0    
99.1    
99.2    
99.3    
99.4    
99.5    
99.7    
99.8    
99.9    
-found 24 predictions from path traversal
Error with prediction: snap lend_intergenic: 16123, rend_intergenic: 6248  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21581, rend_intergenic: 17187  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24566, rend_intergenic: 22118  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46043, rend_intergenic: 45268  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49431, rend_intergenic: 48005  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58342, rend_intergenic: 50454  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60908, rend_intergenic: 58955  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68732, rend_intergenic: 66519  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86831, rend_intergenic: 70721  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92200, rend_intergenic: 86853  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104637, rend_intergenic: 92608  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106408, rend_intergenic: 105067  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117786, rend_intergenic: 114584  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132715, rend_intergenic: 119935  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133607, rend_intergenic: 133050  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140791, rend_intergenic: 136739  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175076, rend_intergenic: 143306  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