-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_9/scaffold_9_16606937-16870443

-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_24184-T1
Valid prediction for GlimmerHMM_glimmerT_24163-T1
Valid prediction for GeneMark_model.41466_t
Valid prediction for GeneMark_model.41473_t
Valid prediction for Augustus_model.g16170.t1
Valid prediction for GeneMark_model.41482_t
Valid prediction for Augustus_model.g16172.t1
Couldn't classify 41526, 42062
Sorry, prediction pasa_asmbl_54593.p1 fails validation.
(ATA)	 AC	41526-42062	AA	GCA
Valid prediction for GeneMark_model.41492_t
Valid prediction for GlimmerHMM_glimmerT_24157-T1
Valid prediction for GlimmerHMM_glimmerT_24173-T1
Valid prediction for Augustus_model.g16182.t1
Valid prediction for GeneMark_model.41494_t
Valid prediction for GlimmerHMM_glimmerT_24172-T1
Couldn't classify 42240, 43997
Sorry, prediction pasa_asmbl_54594.p1 fails validation.
(TGC)	 TC	42240-43997	TA	AAT
Valid prediction for GlimmerHMM_glimmerT_24160-T1
Valid prediction for snap_scaffold_9-snap.3401-T1
Valid prediction for snap_scaffold_9-snap.3428-T1
Valid prediction for Augustus_model.g16176.t1
Valid prediction for CodingQuarry_transcript_62287-T1
Valid prediction for snap_scaffold_9-snap.3421-T1
Valid prediction for GlimmerHMM_glimmerT_24155-T1
Valid prediction for GeneMark_model.41486_t
Valid prediction for snap_scaffold_9-snap.3405-T1
Valid prediction for GeneMark_model.41461_t
Valid prediction for GeneMark_model.41462_t
Valid prediction for GlimmerHMM_glimmerT_24169-T1
Valid prediction for GeneMark_model.41476_t
Valid prediction for GeneMark_model.41490_t
Valid prediction for GlimmerHMM_glimmerT_24153-T1
Valid prediction for GlimmerHMM_glimmerT_24181-T1
Valid prediction for GlimmerHMM_glimmerT_24166-T1
Valid prediction for GeneMark_model.41471_t
Valid prediction for GeneMark_model.41481_t
Valid prediction for GeneMark_model.41496_t
Valid prediction for GlimmerHMM_glimmerT_24151-T1
Couldn't classify 140233, 140850
Sorry, prediction pasa_asmbl_54600.p1 fails validation.
(AGG)	 GG	140233-140850	TC	GAT
Valid prediction for GlimmerHMM_glimmerT_24176-T1
Valid prediction for GeneMark_model.41478_t
Valid prediction for Augustus_model.g16183.t1
Valid prediction for GeneMark_model.41467_t
Valid prediction for snap_scaffold_9-snap.3402-T1
Valid prediction for GlimmerHMM_glimmerT_24162-T1
Valid prediction for snap_scaffold_9-snap.3409-T1
Valid prediction for snap_scaffold_9-snap.3437-T1
Valid prediction for Augustus_model.g16177.t1
Valid prediction for Augustus_model.g16190.t1
Valid prediction for pasa_asmbl_54597.p1
Valid prediction for snap_scaffold_9-snap.3414-T1
Valid prediction for snap_scaffold_9-snap.3400-T1
Valid prediction for GeneMark_model.41464_t
Valid prediction for snap_scaffold_9-snap.3397-T1
Valid prediction for Augustus_model.g16189.t1
Valid prediction for GeneMark_model.41499_t
Valid prediction for snap_scaffold_9-snap.3407-T1
Valid prediction for CodingQuarry_transcript_62281-T1
Valid prediction for HiQ_model.g16175.t1
Valid prediction for snap_scaffold_9-snap.3433-T1
Valid prediction for snap_scaffold_9-snap.3412-T1
Sorry, intron length (3) is less than minimum required (10)
Couldn't classify 139771, 140115
Sorry, prediction pasa_asmbl_54599.p1 fails validation.
(ATG)	 TC	139771-140115	TG	CCT
Valid prediction for HiQ_model.g16180.t1
Valid prediction for snap_scaffold_9-snap.3408-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GeneMark_model.41489_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 snap_scaffold_9-snap.3417-T1
Valid prediction for Augustus_model.g16201.t1
Valid prediction for GlimmerHMM_glimmerT_24177-T1
Valid prediction for Augustus_model.g16174.t1
Valid prediction for snap_scaffold_9-snap.3413-T1
Valid prediction for GlimmerHMM_glimmerT_24168-T1
Valid prediction for CodingQuarry_transcript_62284-T1
Valid prediction for GlimmerHMM_glimmerT_24159-T1
Valid prediction for snap_scaffold_9-snap.3441-T1
Valid prediction for HiQ_model.g16185.t1
Valid prediction for GlimmerHMM_glimmerT_24167-T1
Valid prediction for snap_scaffold_9-snap.3419-T1
Valid prediction for snap_scaffold_9-snap.3404-T1
Valid prediction for GeneMark_model.41472_t
Couldn't classify 104008, 104058
Couldn't classify 106099, 106238
Sorry, prediction pasa_asmbl_55594.p1 fails validation.
(CCC)	 CG	104008-104058	GT	AGG
(TTC)	 AG	104535-104712	GT	AGG
(CAG)	 AG	106099-106238	TT	GAT
-recovered pasa_asmbl_55594.p1, internal, 104535, 104712
Valid prediction for GeneMark_model.41469_t
Valid prediction for Augustus_model.g16195.t1
Valid prediction for Augustus_model.g16181.t1
Valid prediction for Augustus_model.g16191.t1
Valid prediction for GeneMark_model.41468_t
Valid prediction for pasa_asmbl_55573.p1
Valid prediction for snap_scaffold_9-snap.3436-T1
Valid prediction for CodingQuarry_transcript_62283-T1
Valid prediction for GeneMark_model.41463_t
Valid prediction for snap_scaffold_9-snap.3395-T1
Valid prediction for Augustus_model.g16184.t1
Valid prediction for GlimmerHMM_glimmerT_24161-T1
Valid prediction for snap_scaffold_9-snap.3423-T1
Valid prediction for snap_scaffold_9-snap.3434-T1
Valid prediction for snap_scaffold_9-snap.3435-T1
Valid prediction for GeneMark_model.41474_t
Valid prediction for snap_scaffold_9-snap.3398-T1
Valid prediction for Augustus_model.g16197.t1
Valid prediction for snap_scaffold_9-snap.3415-T1
Valid prediction for snap_scaffold_9-snap.3424-T1
Valid prediction for GeneMark_model.41484_t
Valid prediction for HiQ_model.g16178.t1
Valid prediction for GlimmerHMM_glimmerT_24186-T1
Couldn't classify 171136, 171207
Couldn't classify 172045, 172122
Sorry, prediction pasa_asmbl_55702.p1 fails validation.
(GTC)	 AC	171136-171207	GT	AGG
(GTG)	 AG	171481-171603	GT	AGG
(ATT)	 AG	171743-171880	GT	AGG
(GTA)	 AG	172045-172122	GG	CCG
-recovered pasa_asmbl_55702.p1, internal, 171481, 171603
-recovered pasa_asmbl_55702.p1, internal, 171743, 171880
Valid prediction for GeneMark_model.41497_t
Valid prediction for GlimmerHMM_glimmerT_24152-T1
Valid prediction for GlimmerHMM_glimmerT_24179-T1
Valid prediction for GlimmerHMM_glimmerT_24171-T1
Couldn't classify 253203, 253359
Sorry, prediction pasa_asmbl_55555.p1 fails validation.
(CGT)	 GC	253203-253359	GT	TGG
(CAT)	 AG	253517-253642	GT	TGG
(GTC)	 AG	253832-253934	GT	GGG
(ACA)	 AG	254266-254576	GT	AGG
(GAT)	 AG	255448-255452	CA	GAC
-recovered pasa_asmbl_55555.p1, terminal, 255448, 255452
-recovered pasa_asmbl_55555.p1, internal, 253517, 253642
-recovered pasa_asmbl_55555.p1, internal, 253832, 253934
-recovered pasa_asmbl_55555.p1, internal, 254266, 254576
Valid prediction for snap_scaffold_9-snap.3422-T1
Valid prediction for GeneMark_model.41485_t
Valid prediction for pasa_asmbl_55587.p1
Valid prediction for GeneMark_model.41480_t
Valid prediction for GlimmerHMM_glimmerT_24178-T1
Valid prediction for snap_scaffold_9-snap.3439-T1
Valid prediction for Augustus_model.g16192.t1
Couldn't classify 247371, 247549
Sorry, prediction pasa_asmbl_55556.p1 fails validation.
(GAA)	 AG	247371-247549	GT	GGG
(ATT)	 AG	247702-247825	AA	GAA
-recovered pasa_asmbl_55556.p1, terminal, 247702, 247825
-recovered pasa_asmbl_55556.p1, internal, 247371, 247549
Valid prediction for snap_scaffold_9-snap.3411-T1
Couldn't classify 176268, 176390
Sorry, prediction pasa_asmbl_55577.p1 fails validation.
(AAG)	 CC	176268-176390	GT	AGG
(GTG)	 AG	176485-176592	GC	AGG
(GAC)	 AG	176971-177138	GT	AGG
(GTT)	 AG	177315-177464	GT	AGG
(GTG)	 AG	178307-178438	GT	AGG
(GTC)	 AG	178537-178647	GT	CGG
(GCC)	 AG	178796-178966	GT	AGG
(GAT)	 AG	179560-179781	GT	AGG
(GAA)	 AG	182703-182740	GT	AGG
(GTT)	 AG	182869-182899	GG	AAG
-recovered pasa_asmbl_55577.p1, terminal, 182869, 182899
-recovered pasa_asmbl_55577.p1, internal, 176485, 176592
-recovered pasa_asmbl_55577.p1, internal, 176971, 177138
-recovered pasa_asmbl_55577.p1, internal, 177315, 177464
-recovered pasa_asmbl_55577.p1, internal, 178307, 178438
-recovered pasa_asmbl_55577.p1, internal, 178537, 178647
-recovered pasa_asmbl_55577.p1, internal, 178796, 178966
-recovered pasa_asmbl_55577.p1, internal, 179560, 179781
-recovered pasa_asmbl_55577.p1, internal, 182703, 182740
Valid prediction for Augustus_model.g16194.t1
Valid prediction for pasa_asmbl_55565.p1
Valid prediction for GeneMark_model.41465_t
Valid prediction for GlimmerHMM_glimmerT_24187-T1
Valid prediction for snap_scaffold_9-snap.3425-T1
Valid prediction for snap_scaffold_9-snap.3396-T1
Valid prediction for GeneMark_model.41487_t
Couldn't classify 119455, 119763
Sorry, prediction pasa_asmbl_55589.p1 fails validation.
(TTG)	 CA	119455-119763	GG	GAG
Valid prediction for snap_scaffold_9-snap.3410-T1
Valid prediction for GlimmerHMM_glimmerT_24185-T1
Valid prediction for CodingQuarry_transcript_62288-T1
Valid prediction for snap_scaffold_9-snap.3406-T1
Valid prediction for snap_scaffold_9-snap.3420-T1
Valid prediction for GeneMark_model.41498_t
Valid prediction for Augustus_model.g16188.t1
Valid prediction for GlimmerHMM_glimmerT_24183-T1
Valid prediction for snap_scaffold_9-snap.3416-T1
Valid prediction for snap_scaffold_9-snap.3418-T1
Valid prediction for Augustus_model.g16199.t1
Valid prediction for GlimmerHMM_glimmerT_24154-T1
Valid prediction for Augustus_model.g16171.t1
Valid prediction for Augustus_model.g16196.t1
Valid prediction for snap_scaffold_9-snap.3438-T1
Valid prediction for Augustus_model.g16173.t1
Valid prediction for GlimmerHMM_glimmerT_24165-T1
Valid prediction for Augustus_model.g16200.t1
Valid prediction for snap_scaffold_9-snap.3399-T1
Valid prediction for HiQ_model.g16179.t1
Valid prediction for pasa_asmbl_55581.p1
Valid prediction for GlimmerHMM_glimmerT_24156-T1
Valid prediction for GlimmerHMM_glimmerT_24174-T1
Valid prediction for Augustus_model.g16198.t1
Valid prediction for GeneMark_model.41479_t
Valid prediction for snap_scaffold_9-snap.3403-T1
Valid prediction for Augustus_model.g16193.t1
Valid prediction for GeneMark_model.41493_t
Couldn't classify 141105, 141106
Sorry, prediction CodingQuarry_transcript_62285-T1 fails validation.
(ATG)	 AC	141105-141106	GT	ATG
(GAG)	 AG	141555-141734	GT	AGG
(GCA)	 AG	141908-142082	AC	AAA
-recovered CodingQuarry_transcript_62285-T1, terminal, 141908, 142082
-recovered CodingQuarry_transcript_62285-T1, internal, 141555, 141734
Valid prediction for pasa_asmbl_55570.p1
Couldn't classify 165718, 165847
Couldn't classify 168633, 168779
Sorry, prediction pasa_asmbl_55578.p1 fails validation.
(CGA)	 TT	165718-165847	GT	AGG
(CCG)	 AG	167892-168160	GT	AGG
(CAA)	 AG	168633-168779	CA	GGC
-recovered pasa_asmbl_55578.p1, internal, 167892, 168160
Valid prediction for snap_scaffold_9-snap.3430-T1
Valid prediction for GeneMark_model.41477_t
Valid prediction for GeneMark_model.41475_t
Valid prediction for snap_scaffold_9-snap.3431-T1
Valid prediction for GeneMark_model.41483_t
Valid prediction for GeneMark_model.41491_t
Valid prediction for snap_scaffold_9-snap.3429-T1
Valid prediction for snap_scaffold_9-snap.3440-T1
Valid prediction for GlimmerHMM_glimmerT_24164-T1
Valid prediction for GlimmerHMM_glimmerT_24180-T1
Valid prediction for CodingQuarry_transcript_62282-T1
Valid prediction for snap_scaffold_9-snap.3432-T1
Valid prediction for GeneMark_model.41470_t
Valid prediction for GlimmerHMM_glimmerT_24175-T1
Valid prediction for GeneMark_model.41488_t
Valid prediction for GlimmerHMM_glimmerT_24182-T1
Valid prediction for Augustus_model.g16186.t1
Valid prediction for CodingQuarry_transcript_62286-T1
Couldn't classify 141105, 141106
Sorry, prediction pasa_asmbl_55582.p1 fails validation.
(ATG)	 AC	141105-141106	GT	ATG
(GAG)	 AG	141555-141734	GT	AGG
(GCA)	 AG	141908-142082	AC	AAA
-recovered pasa_asmbl_55582.p1, terminal, 141908, 142082
-recovered pasa_asmbl_55582.p1, internal, 141555, 141734
Valid prediction for GlimmerHMM_glimmerT_24158-T1
Valid prediction for GlimmerHMM_glimmerT_24170-T1
Valid prediction for snap_scaffold_9-snap.3427-T1
Valid prediction for snap_scaffold_9-snap.3426-T1
Valid prediction for Augustus_model.g16187.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 98495, rend_intergenic: 83767  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114185, rend_intergenic: 110621  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138404, rend_intergenic: 136479  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171172, rend_intergenic: 169505  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185713, rend_intergenic: 182517  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 202582, rend_intergenic: 199410  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 263507
-exon list size: 670


building trellis

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70.1    
70.2    
70.4    
70.5    
70.7    
70.8    
71.0    
71.1    
71.3    
71.4    
71.6    
71.7    
71.9    
72.0    
72.2    
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    
75.1    
75.3    
75.4    
75.6    
75.7    
75.9    
76.0    
76.2    
76.3    
76.5    
76.6    
76.8    
76.9    
77.1    
77.2    
77.4    
77.5    
77.7    
77.8    
78.0    
78.1    
78.3    
78.4    
78.6    
78.7    
78.9    
79.0    
79.2    
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    
81.2    
81.4    
81.5    
81.7    
81.8    
82.0    
82.1    
82.3    
82.4    
82.6    
82.7    
82.9    
83.0    
83.2    
83.3    
83.5    
83.6    
83.8    
83.9    
84.1    
84.2    
84.4    
84.5    
84.7    
84.8    
85.0    
85.1    
85.3    
85.4    
85.6    
85.7    
85.9    
86.0    
86.2    
86.3    
86.5    
86.6    
86.8    
86.9    
87.1    
87.2    
87.4    
87.5    
87.6    
87.8    
87.9    
88.1    
88.2    
88.4    
88.5    
88.7    
88.8    
89.0    
89.1    
89.3    
89.4    
89.6    
89.7    
89.9    
90.0    
90.2    
90.3    
90.5    
90.6    
90.8    
90.9    
91.1    
91.2    
91.4    
91.5    
91.7    
91.8    
92.0    
92.1    
92.3    
92.4    
92.6    
92.7    
92.9    
93.0    
93.2    
93.3    
93.5    
93.6    
93.8    
93.9    
94.0    
94.2    
94.3    
94.5    
94.6    
94.8    
94.9    
95.1    
95.2    
95.4    
95.5    
95.7    
95.8    
96.0    
96.1    
96.3    
96.4    
96.6    
96.7    
96.9    
97.0    
97.2    
97.3    
97.5    
97.6    
97.8    
97.9    
98.1    
98.2    
98.4    
98.5    
98.7    
98.8    
99.0    
99.1    
99.3    
99.4    
99.6    
99.7    
99.9    
-found 39 predictions from path traversal
Error with prediction: snap lend_intergenic: 98495, rend_intergenic: 83767  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114185, rend_intergenic: 110621  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138404, rend_intergenic: 136479  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171172, rend_intergenic: 169505  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185713, rend_intergenic: 182517  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 202582, rend_intergenic: 199410  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 31 predictions persist after filtering for low support