-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_23/scaffold_23_7617580-7732890

-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_23-snap.1434-T1
Couldn't classify 93061, 93178
Couldn't classify 93619, 93705
Sorry, prediction pasa_asmbl_31023.p1 fails validation.
(AGG)	 TG	93061-93178	GT	AGG
(GCT)	 AG	93377-93528	GT	CTG
(GTC)	 AG	93619-93705	GA	AGG
-recovered pasa_asmbl_31023.p1, internal, 93377, 93528
Valid prediction for GlimmerHMM_glimmerT_52602-T1
Valid prediction for Augustus_model.g35364.t1
Valid prediction for CodingQuarry_transcript_35660-T1
Couldn't classify 84188, 84240
Sorry, prediction pasa_asmbl_31021.p1 fails validation.
(CGC)	 TA	84188-84240	GT	CTG
(GAG)	 AG	84394-84608	GT	AGG
(GTA)	 AG	84838-84934	GT	AGG
(CTT)	 AG	85088-85295	GT	GGG
(TAT)	 AG	85573-85760	GT	TTG
(GTT)	 AG	86172-86272	GT	AGG
(GAA)	 AG	86443-86810	AT	AGA
add_exon() Sorry, pasa_asmbl_31021.p1 86172-86272-terminal-2 is invalid.
-recovered pasa_asmbl_31021.p1, terminal, 86172, 86272
-recovered pasa_asmbl_31021.p1, terminal, 86443, 86810
-recovered pasa_asmbl_31021.p1, internal, 84394, 84608
-recovered pasa_asmbl_31021.p1, internal, 84838, 84934
-recovered pasa_asmbl_31021.p1, internal, 85088, 85295
-recovered pasa_asmbl_31021.p1, internal, 85573, 85760
-recovered pasa_asmbl_31021.p1, internal, 86172, 86272
Valid prediction for GlimmerHMM_glimmerT_52601-T1
Couldn't classify 27452, 27672
Couldn't classify 28109, 28208
Sorry, prediction pasa_asmbl_31240.p2 fails validation.
(GCA)	 CG	27452-27672	GT	AGG
(GTT)	 AG	28109-28208	CA	CAC
Valid prediction for pasa_asmbl_31019.p1
Valid prediction for GeneMark_model.91183_t
Valid prediction for CodingQuarry_transcript_35665-T1
Valid prediction for GlimmerHMM_glimmerT_52590-T1
Valid prediction for GeneMark_model.91177_t
Valid prediction for Augustus_model.g35362.t1
Valid prediction for snap_scaffold_23-snap.1438-T1
Valid prediction for Augustus_model.g35374.t1
Valid prediction for HiQ_model.g35368.t1
Valid prediction for HiQ_model.g35367.t1
Valid prediction for GlimmerHMM_glimmerT_52596-T1
Valid prediction for CodingQuarry_transcript_35661-T1
Valid prediction for pasa_asmbl_31008.p1
Valid prediction for GeneMark_model.91174_t
Valid prediction for GlimmerHMM_glimmerT_52586-T1
Valid prediction for Augustus_model.g35365.t1
Valid prediction for GeneMark_model.91171_t
Valid prediction for GeneMark_model.91185_t
Valid prediction for GlimmerHMM_glimmerT_52595-T1
Valid prediction for GlimmerHMM_glimmerT_52599-T1
Valid prediction for snap_scaffold_23-snap.1441-T1
Valid prediction for CodingQuarry_transcript_35656-T1
Valid prediction for snap_scaffold_23-snap.1428-T1
Valid prediction for GlimmerHMM_glimmerT_52589-T1
Valid prediction for snap_scaffold_23-snap.1424-T1
Valid prediction for CodingQuarry_transcript_35662-T1
Valid prediction for GlimmerHMM_glimmerT_52600-T1
Valid prediction for snap_scaffold_23-snap.1430-T1
Valid prediction for CodingQuarry_transcript_35663-T1
Valid prediction for snap_scaffold_23-snap.1427-T1
Valid prediction for GeneMark_model.91173_t
Valid prediction for Augustus_model.g35373.t1
Valid prediction for GlimmerHMM_glimmerT_52591-T1
Valid prediction for CodingQuarry_transcript_35664-T1
Valid prediction for CodingQuarry_transcript_35659-T1
Couldn't classify 93885, 94038
Sorry, prediction pasa_asmbl_31024.p1 fails validation.
(GAT)	 GA	93885-94038	GT	TGG
(AGC)	 AG	94227-94321	GT	AGG
(GGC)	 AG	94418-94568	GT	AGG
(CCG)	 AG	94662-94813	GT	TGG
(TAT)	 AG	94965-95079	GT	CGG
(GCT)	 AG	95541-95777	GT	AGG
(AGC)	 AG	95896-96022	GT	TGG
(CTC)	 AG	96334-96547	CG	GAC
-recovered pasa_asmbl_31024.p1, terminal, 96334, 96547
-recovered pasa_asmbl_31024.p1, internal, 94227, 94321
-recovered pasa_asmbl_31024.p1, internal, 94418, 94568
-recovered pasa_asmbl_31024.p1, internal, 94662, 94813
-recovered pasa_asmbl_31024.p1, internal, 94965, 95079
-recovered pasa_asmbl_31024.p1, internal, 95541, 95777
-recovered pasa_asmbl_31024.p1, internal, 95896, 96022
Valid prediction for GeneMark_model.91176_t
Valid prediction for GlimmerHMM_glimmerT_52584-T1
Valid prediction for GlimmerHMM_glimmerT_52593-T1
Valid prediction for GeneMark_model.91187_t
Valid prediction for snap_scaffold_23-snap.1440-T1
Valid prediction for snap_scaffold_23-snap.1439-T1
Valid prediction for HiQ_model.g35370.t1
Couldn't classify 56308, 56375
Sorry, prediction pasa_asmbl_31004.p1 fails validation.
(GTG)	 AA	56308-56375	GT	AAG
(ACG)	 AG	56455-56487	GT	AGG
(TAT)	 AG	56577-56644	GT	GGG
(GAT)	 AG	56881-57008	GT	AGG
(CTG)	 AG	57122-57299	GT	GTG
(ACT)	 AG	57545-57753	GT	AGG
-recovered pasa_asmbl_31004.p1, terminal, 56455, 56487
-recovered pasa_asmbl_31004.p1, terminal, 57545, 57753
-recovered pasa_asmbl_31004.p1, internal, 56455, 56487
-recovered pasa_asmbl_31004.p1, internal, 56577, 56644
-recovered pasa_asmbl_31004.p1, internal, 56881, 57008
-recovered pasa_asmbl_31004.p1, internal, 57122, 57299
-recovered pasa_asmbl_31004.p1, internal, 57545, 57753
Valid prediction for GeneMark_model.91168_t
Valid prediction for Augustus_model.g35371.t1
Valid prediction for snap_scaffold_23-snap.1432-T1
Valid prediction for snap_scaffold_23-snap.1431-T1
Couldn't classify 37243, 37287
Couldn't classify 46792, 46830
Sorry, prediction pasa_asmbl_31001.p1 fails validation.
(AAG)	 AG	37243-37287	GT	CCG
(TTC)	 AG	37422-37652	GT	AGG
(GTG)	 AG	37743-37817	GT	AGG
(ATT)	 AG	37970-38011	GT	AGG
(GAG)	 AG	40573-40714	GT	AGG
(ACG)	 AG	40878-41056	GT	AGG
(CTG)	 AG	41202-41328	GT	TGG
(GTG)	 AG	41454-41599	GT	AGG
(GAC)	 AG	41758-41931	GT	AGG
(GAT)	 AG	42199-42435	GT	CGG
(GCG)	 AG	42845-42949	GT	AGG
(GTG)	 AG	44033-44138	GT	GCG
(CCT)	 AG	44708-45046	GT	AGG
(GGC)	 AG	46539-46597	GT	AGG
(GTA)	 AG	46792-46830	CC	CCC
-recovered pasa_asmbl_31001.p1, internal, 37243, 37287
-recovered pasa_asmbl_31001.p1, internal, 37422, 37652
-recovered pasa_asmbl_31001.p1, internal, 37743, 37817
-recovered pasa_asmbl_31001.p1, internal, 37970, 38011
-recovered pasa_asmbl_31001.p1, internal, 40573, 40714
-recovered pasa_asmbl_31001.p1, internal, 40878, 41056
-recovered pasa_asmbl_31001.p1, internal, 41202, 41328
-recovered pasa_asmbl_31001.p1, internal, 41454, 41599
-recovered pasa_asmbl_31001.p1, internal, 41758, 41931
-recovered pasa_asmbl_31001.p1, internal, 42199, 42435
-recovered pasa_asmbl_31001.p1, internal, 42845, 42949
-recovered pasa_asmbl_31001.p1, internal, 44033, 44138
-recovered pasa_asmbl_31001.p1, internal, 44708, 45046
-recovered pasa_asmbl_31001.p1, internal, 46539, 46597
Valid prediction for GeneMark_model.91186_t
Couldn't classify 34549, 34633
Sorry, prediction HiQ_model.g35363.t1 fails validation.
(TTT)	 CA	34549-34633	GT	GGG
(GTA)	 AG	34813-34936	GT	AGG
(ATA)	 AG	35263-35458	GT	AGG
(ACA)	 AG	35571-35666	GT	AGG
(CCT)	 AG	35829-35969	GT	GGG
(ATG)	 AG	36131-36273	GT	AGG
(GGG)	 AG	36599-36698	GT	AGG
(GTT)	 AG	36798-36959	GT	AGG
(ATC)	 AG	37135-37287	GT	CCG
(TTC)	 AG	37422-37652	GT	AGG
(GTG)	 AG	37743-37817	GT	AGG
(ATT)	 AG	37970-38011	GT	AGG
(CCT)	 AG	38707-38802	GT	CTG
(CTT)	 AG	39238-40023	GT	AGG
(GAG)	 AG	40573-40714	GT	AGG
(ACG)	 AG	40878-41056	GT	AGG
(CTG)	 AG	41202-41328	GT	TGG
(GTG)	 AG	41454-41599	GT	AGG
(GAC)	 AG	41758-41931	GT	AGG
(GAT)	 AG	42199-42435	GT	CGG
(GCG)	 AG	42845-42949	GT	AGG
(GTG)	 AG	44033-44138	GT	GCG
(CCT)	 AG	44708-45046	GT	AGG
(GGC)	 AG	46539-46597	GT	AGG
(GTA)	 AG	46792-47040	GT	AGG
(CCC)	 AG	47188-47307	GT	CTG
(CAA)	 AG	47476-47547	GT	CTG
(CTC)	 AG	47943-48122	GA	GAG
-recovered HiQ_model.g35363.t1, initial, 36131, 36273
add_exon() Sorry, HiQ_model.g35363.t1 34813-34936-terminal-3 is invalid.
-recovered HiQ_model.g35363.t1, terminal, 34813, 34936
-recovered HiQ_model.g35363.t1, terminal, 47943, 48122
-recovered HiQ_model.g35363.t1, internal, 34813, 34936
-recovered HiQ_model.g35363.t1, internal, 35263, 35458
-recovered HiQ_model.g35363.t1, internal, 35571, 35666
-recovered HiQ_model.g35363.t1, internal, 35829, 35969
-recovered HiQ_model.g35363.t1, internal, 36131, 36273
-recovered HiQ_model.g35363.t1, internal, 36599, 36698
-recovered HiQ_model.g35363.t1, internal, 36798, 36959
-recovered HiQ_model.g35363.t1, internal, 37135, 37287
-recovered HiQ_model.g35363.t1, internal, 37422, 37652
-recovered HiQ_model.g35363.t1, internal, 37743, 37817
-recovered HiQ_model.g35363.t1, internal, 37970, 38011
-recovered HiQ_model.g35363.t1, internal, 38707, 38802
-recovered HiQ_model.g35363.t1, internal, 39238, 40023
-recovered HiQ_model.g35363.t1, internal, 40573, 40714
-recovered HiQ_model.g35363.t1, internal, 40878, 41056
-recovered HiQ_model.g35363.t1, internal, 41202, 41328
-recovered HiQ_model.g35363.t1, internal, 41454, 41599
-recovered HiQ_model.g35363.t1, internal, 41758, 41931
-recovered HiQ_model.g35363.t1, internal, 42199, 42435
-recovered HiQ_model.g35363.t1, internal, 42845, 42949
-recovered HiQ_model.g35363.t1, internal, 44033, 44138
-recovered HiQ_model.g35363.t1, internal, 44708, 45046
-recovered HiQ_model.g35363.t1, internal, 46539, 46597
-recovered HiQ_model.g35363.t1, internal, 46792, 47040
-recovered HiQ_model.g35363.t1, internal, 47188, 47307
-recovered HiQ_model.g35363.t1, internal, 47476, 47547
Valid prediction for GlimmerHMM_glimmerT_52582-T1
Valid prediction for Augustus_model.g35372.t1
Valid prediction for GlimmerHMM_glimmerT_52588-T1
Valid prediction for snap_scaffold_23-snap.1426-T1
Valid prediction for GeneMark_model.91169_t
Valid prediction for Augustus_model.g35360.t1
Valid prediction for GlimmerHMM_glimmerT_52603-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.91178_t
Valid prediction for GeneMark_model.91188_t
Valid prediction for Augustus_model.g35359.t1
Valid prediction for GeneMark_model.91182_t
Valid prediction for GlimmerHMM_glimmerT_52594-T1
Valid prediction for GeneMark_model.91175_t
Valid prediction for snap_scaffold_23-snap.1425-T1
Valid prediction for Augustus_model.g35369.t1
Valid prediction for snap_scaffold_23-snap.1435-T1
Valid prediction for HiQ_model.g35366.t1
Valid prediction for GeneMark_model.91170_t
Valid prediction for GlimmerHMM_glimmerT_52592-T1
Valid prediction for GlimmerHMM_glimmerT_52585-T1
Valid prediction for GlimmerHMM_glimmerT_52597-T1
Valid prediction for snap_scaffold_23-snap.1422-T1
Valid prediction for GlimmerHMM_glimmerT_52587-T1
Valid prediction for snap_scaffold_23-snap.1421-T1
Valid prediction for snap_scaffold_23-snap.1436-T1
Valid prediction for snap_scaffold_23-snap.1442-T1
Valid prediction for snap_scaffold_23-snap.1429-T1
Valid prediction for snap_scaffold_23-snap.1433-T1
Sorry, intron length (6) is less than minimum required (10)
Valid prediction for GeneMark_model.91180_t
Valid prediction for GeneMark_model.91172_t
Valid prediction for GlimmerHMM_glimmerT_52581-T1
Valid prediction for snap_scaffold_23-snap.1420-T1
Valid prediction for snap_scaffold_23-snap.1437-T1
Valid prediction for CodingQuarry_transcript_35657-T1
Valid prediction for GeneMark_model.91184_t
Valid prediction for HiQ_model.g35361.t1
Valid prediction for snap_scaffold_23-snap.1423-T1
Valid prediction for GeneMark_model.91181_t
Valid prediction for GlimmerHMM_glimmerT_52598-T1
Valid prediction for pasa_asmbl_31762.p1
Valid prediction for GeneMark_model.91167_t
Couldn't classify 96655, 96743
Sorry, prediction pasa_asmbl_31759.p1 fails validation.
(ACT)	 AC	96655-96743	GT	AAG
(ATA)	 AG	97196-97275	GT	AAG
(TGG)	 AG	97371-97522	GT	AAG
(GTG)	 AG	97713-97816	GT	AAG
(GCA)	 AG	98094-98247	GT	AGG
(GTG)	 AG	98327-98477	GT	AGG
(GCC)	 AG	98715-98885	GT	CGG
(GAT)	 AG	99244-99359	GT	AGG
(GAC)	 AG	100076-100120	GT	TGG
(GCT)	 AG	101192-101276	GT	GAG
(CCA)	 AG	101530-101663	AC	AAA
-recovered pasa_asmbl_31759.p1, terminal, 101530, 101663
-recovered pasa_asmbl_31759.p1, internal, 97196, 97275
-recovered pasa_asmbl_31759.p1, internal, 97371, 97522
-recovered pasa_asmbl_31759.p1, internal, 97713, 97816
-recovered pasa_asmbl_31759.p1, internal, 98094, 98247
-recovered pasa_asmbl_31759.p1, internal, 98327, 98477
-recovered pasa_asmbl_31759.p1, internal, 98715, 98885
-recovered pasa_asmbl_31759.p1, internal, 99244, 99359
-recovered pasa_asmbl_31759.p1, internal, 100076, 100120
-recovered pasa_asmbl_31759.p1, internal, 101192, 101276
Valid prediction for CodingQuarry_transcript_35658-T1
Couldn't classify 35630, 35691
Sorry, prediction pasa_asmbl_31957.p2 fails validation.
(ATG)	 CC	34881-34931	GT	CTG
(GTC)	 AG	35022-35142	GT	AGG
(ACC)	 AG	35265-35441	GT	TGG
(AGC)	 AG	35630-35691	CG	AAC
-recovered pasa_asmbl_31957.p2, initial, 34881, 34931
-recovered pasa_asmbl_31957.p2, internal, 35022, 35142
-recovered pasa_asmbl_31957.p2, internal, 35265, 35441
Valid prediction for GlimmerHMM_glimmerT_52583-T1
Valid prediction for GlimmerHMM_glimmerT_52580-T1
Valid prediction for snap_scaffold_23-snap.1443-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 28310, rend_intergenic: 25738  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45150, rend_intergenic: 40868  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107130, rend_intergenic: 104626  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 115311
-exon list size: 469


building trellis

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76.6    
76.9    
77.1    
77.3    
77.5    
77.7    
77.9    
78.1    
78.3    
78.6    
78.8    
79.0    
79.2    
79.4    
79.6    
79.8    
80.0    
80.3    
80.5    
80.7    
80.9    
81.1    
81.3    
81.5    
81.7    
82.0    
82.2    
82.4    
82.6    
82.8    
83.0    
83.2    
83.4    
83.7    
83.9    
84.1    
84.3    
84.5    
84.7    
84.9    
85.1    
85.4    
85.6    
85.8    
86.0    
86.2    
86.4    
86.6    
86.8    
87.0    
87.3    
87.5    
87.7    
87.9    
88.1    
88.3    
88.5    
88.7    
89.0    
89.2    
89.4    
89.6    
89.8    
90.0    
90.2    
90.4    
90.7    
90.9    
91.1    
91.3    
91.5    
91.7    
91.9    
92.1    
92.4    
92.6    
92.8    
93.0    
93.2    
93.4    
93.6    
93.8    
94.1    
94.3    
94.5    
94.7    
94.9    
95.1    
95.3    
95.5    
95.8    
96.0    
96.2    
96.4    
96.6    
96.8    
97.0    
97.2    
97.5    
97.7    
97.9    
98.1    
98.3    
98.5    
98.7    
98.9    
99.2    
99.4    
99.6    
99.8    
-found 22 predictions from path traversal
Error with prediction: snap lend_intergenic: 28310, rend_intergenic: 25738  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45150, rend_intergenic: 40868  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107130, rend_intergenic: 104626  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 22 predictions persist after filtering for low support